[{"publication_identifier":{"issn":["0960-9822"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"22286","title":"Auxin and the control of plant growth and development","quality_controlled":"1","department":[{"_id":"EvBe"},{"_id":"GradSch"}],"date_created":"2026-07-13T09:39:40Z","researchdata_availability":"no","pmid":1,"citation":{"apa":"Leitner, V., &#38; Benková, E. (2026). Auxin and the control of plant growth and development. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2026.04.047\">https://doi.org/10.1016/j.cub.2026.04.047</a>","ama":"Leitner V, Benková E. Auxin and the control of plant growth and development. <i>Current Biology</i>. 2026;36(13):R739-R744. doi:<a href=\"https://doi.org/10.1016/j.cub.2026.04.047\">10.1016/j.cub.2026.04.047</a>","ista":"Leitner V, Benková E. 2026. Auxin and the control of plant growth and development. Current Biology. 36(13), R739–R744.","short":"V. Leitner, E. Benková, Current Biology 36 (2026) R739–R744.","mla":"Leitner, Valentin, and Eva Benková. “Auxin and the Control of Plant Growth and Development.” <i>Current Biology</i>, vol. 36, no. 13, Elsevier, 2026, pp. R739–44, doi:<a href=\"https://doi.org/10.1016/j.cub.2026.04.047\">10.1016/j.cub.2026.04.047</a>.","chicago":"Leitner, Valentin, and Eva Benková. “Auxin and the Control of Plant Growth and Development.” <i>Current Biology</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.cub.2026.04.047\">https://doi.org/10.1016/j.cub.2026.04.047</a>.","ieee":"V. Leitner and E. Benková, “Auxin and the control of plant growth and development,” <i>Current Biology</i>, vol. 36, no. 13. Elsevier, pp. R739–R744, 2026."},"scopus_import":"1","article_type":"original","publication_status":"published","month":"07","intvolume":"        36","das_tickbox":"0","external_id":{"pmid":["42407441"]},"year":"2026","day":"06","date_updated":"2026-07-13T11:11:56Z","type":"journal_article","author":[{"first_name":"Valentin","id":"4c665ce3-0016-11ec-bea0-e44de7a4fa3d","last_name":"Leitner","full_name":"Leitner, Valentin"},{"orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","last_name":"Benková"}],"publisher":"Elsevier","issue":"13","supplementarymaterial":"no","publication":"Current Biology","abstract":[{"lang":"eng","text":"Plants are remarkable organisms. Unlike animals, they cannot flee and, rooted in one place, they must cope with whatever challenges arise — nutrient scarcity, drought, shade, wind or obstacles in the soil. Their extraordinary ability to survive in such unstable environmental conditions lies in their capacity to adapt. In response to environmental signals, plants can rapidly adjust the rate of organ growth, change the direction of growth, bend toward resources, or remodel their body architecture by promoting or suppressing the formation of new organs such as lateral roots, branches, leaves, or flowers. This unique developmental plasticity depends on chemical signals, plant hormones that serve as regulators and coordinators of endogenous molecular and cellular processes. Chief among these signals is auxin, a plant hormone central to nearly every aspect of plant life."}],"corr_author":"1","status":"public","oa_version":"None","volume":36,"page":"R739-R744","article_processing_charge":"No","doi":"10.1016/j.cub.2026.04.047","date_published":"2026-07-06T00:00:00Z","language":[{"iso":"eng"}],"OA_type":"closed access"},{"year":"2026","related_material":{"record":[{"id":"21363","relation":"research_data","status":"public"}]},"das_tickbox":"1","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"month":"02","license":"https://creativecommons.org/licenses/by-sa/4.0/","alternative_title":["ISTA Thesis"],"publication_status":"published","acknowledgement":"I would like to acknowledge the Austrian Academy of Sciences (ÖAW) and European\r\nResearch Executive Agency (REA) for funding my research (DOC ÖAW Fellowship\r\n26130, Horizon Europe BOLERO Project 101060393). ","ddc":["570","575","583"],"citation":{"ieee":"S. Riegler, “Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea  species,” Institute of Science and Technology Austria, 2026.","chicago":"Riegler, Stefan. “Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21360\">https://doi.org/10.15479/AT-ISTA-21360</a>.","mla":"Riegler, Stefan. <i>Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21360\">10.15479/AT-ISTA-21360</a>.","short":"S. Riegler, Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species, Institute of Science and Technology Austria, 2026.","ista":"Riegler S. 2026. Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea  species. Institute of Science and Technology Austria.","apa":"Riegler, S. (2026). <i>Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea  species</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21360\">https://doi.org/10.15479/AT-ISTA-21360</a>","ama":"Riegler S. Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea  species. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21360\">10.15479/AT-ISTA-21360</a>"},"has_accepted_license":"1","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"doi_confirm":"1","title":"Root system plasticity under nutrient limitation: Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea  species","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"date_created":"2026-02-27T09:08:14Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"21360","publication_identifier":{"issn":["2663-337X"]},"OA_place":"repository","language":[{"iso":"eng"}],"date_published":"2026-02-26T00:00:00Z","file_date_updated":"2026-03-02T10:59:50Z","page":"185","article_processing_charge":"No","doi":"10.15479/AT-ISTA-21360","oa_version":"Published Version","file":[{"date_created":"2026-03-02T10:59:50Z","checksum":"2f1f44e8536c2538f94a440217452c9f","relation":"source_file","content_type":"application/x-zip-compressed","creator":"sriegler","file_size":31430022,"access_level":"closed","file_name":"2026_Riegler_Stefan_Thesis.zip","file_id":"21386","date_updated":"2026-03-02T10:59:50Z"},{"access_level":"closed","file_id":"21387","file_name":"2026_Riegler_Stefan_Thesis.pdf","date_updated":"2026-03-02T10:59:49Z","file_size":11635090,"creator":"sriegler","content_type":"application/pdf","embargo":"2027-02-27","embargo_to":"open_access","checksum":"2e8dc39640bc26ae5684c944c619719b","date_created":"2026-03-02T10:59:49Z","relation":"main_file"}],"corr_author":"1","status":"public","publisher":"Institute of Science and Technology Austria","author":[{"id":"FF6018E0-D806-11E9-8E43-0B14E6697425","first_name":"Stefan","orcid":"0000-0003-3413-1343","full_name":"Riegler, Stefan","last_name":"Riegler"}],"supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková"}],"type":"dissertation","degree_awarded":"PhD","date_updated":"2026-07-27T14:30:08Z","day":"26","project":[{"_id":"34afa094-11ca-11ed-8bc3-a375845a59fb","name":"Breeding for coffee and cocoa root resilience in low input farming systems based on improved rootstocks","grant_number":"101060393"}]},{"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","_id":"21363","date_updated":"2026-07-27T14:30:07Z","day":"27","citation":{"mla":"Riegler, Stefan. <i>Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species</i>. Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21363\">10.15479/AT-ISTA-21363</a>.","chicago":"Riegler, Stefan. “Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis Thaliana and Coffea  Species.” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21363\">https://doi.org/10.15479/AT-ISTA-21363</a>.","ieee":"S. Riegler, “Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea  species.” Institute of Science and Technology Austria, 2026.","ama":"Riegler S. Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea  species. 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21363\">10.15479/AT-ISTA-21363</a>","apa":"Riegler, S. (2026). Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea  species. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21363\">https://doi.org/10.15479/AT-ISTA-21363</a>","ista":"Riegler S. 2026. Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea  species, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-21363\">10.15479/AT-ISTA-21363</a>.","short":"S. Riegler, (2026)."},"publisher":"Institute of Science and Technology Austria","author":[{"orcid":"0000-0003-3413-1343","first_name":"Stefan","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","last_name":"Riegler","full_name":"Riegler, Stefan"}],"has_accepted_license":"1","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"title":"Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea  species","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"date_created":"2026-02-27T09:18:41Z","type":"research_data","oa_version":"Published Version","contributor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","contributor_type":"supervisor","last_name":"Benková"}],"month":"02","file":[{"content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_id":"21364","file_name":"SupplementaryTables.xlsx","date_updated":"2026-02-27T09:11:33Z","access_level":"closed","file_size":63749444,"creator":"sriegler","relation":"main_file","checksum":"de9145fa166a28c588b5184a2d3d4fee","embargo_to":"open_access","date_created":"2026-02-27T09:11:33Z","embargo":"2027-02-27"},{"embargo":"2027-02-27","relation":"main_file","embargo_to":"open_access","date_created":"2026-02-27T09:13:11Z","checksum":"ce1f163551c96cee45943a8ea29720b6","creator":"sriegler","file_size":124,"file_name":"ReadMe.txt","date_updated":"2026-02-27T09:13:11Z","file_id":"21365","access_level":"closed","content_type":"text/plain"}],"abstract":[{"text":"The data contains information on coffee differential gene expression as well as co-expression and trait correlations in two separate experiments. First, contrasting nitrogen supply, second, intra- and interspecific grafting.","lang":"eng"}],"corr_author":"1","ddc":["575"],"status":"public","date_published":"2026-02-27T00:00:00Z","file_date_updated":"2026-02-27T09:13:11Z","year":"2026","related_material":{"record":[{"id":"21360","relation":"used_in_publication","status":"public"}]},"article_processing_charge":"No","doi":"10.15479/AT-ISTA-21363"},{"article_processing_charge":"Yes","doi":"10.1038/s41467-026-74881-5","volume":17,"file_date_updated":"2026-08-20T06:44:33Z","language":[{"iso":"eng"}],"OA_type":"gold","date_published":"2026-08-07T00:00:00Z","status":"public","abstract":[{"text":"Ginseng (Panax ginseng) derives its renowned therapeutic properties from ginsenoside metabolites. However, the long cultivation cycle and susceptibility to diseases hinder the advancement of the ginseng industry. Here, we demonstrate that the embryonic protoderm of ginseng can efficiently produce ginsenosides. Single-cell transcriptome and mass spectrometry imaging analyses reveal that ginsenosides accumulate in the protoderm of ginseng embryonic callus (EC) at levels comparable to those in forest ginseng. Epigenetic analyses indicate that elevated histone acetylation and enhanced chromatin accessibility at regeneration- and ginsenoside metabolism-related gene loci are associated with the ginsenoside-producing capacity of EC. Increasing histone acetylation levels or overexpressing the regeneration-related WUSCHEL-RELATED HOMEOBOX11 (WOX11) gene further enhances ginsenoside production in EC. Our findings suggest that the protoderm of EC could serve as an in situ biological compartment for high-efficiency ginsenoside producion, offering a complementary approach to traditional ginseng cultivation.","lang":"eng"}],"file":[{"relation":"main_file","checksum":"0b4ff29f0d0168b11be32a5f22ded9e4","date_created":"2026-08-20T06:44:33Z","success":1,"content_type":"application/pdf","date_updated":"2026-08-20T06:44:33Z","file_id":"22742","file_name":"2026_NatureComm_Liu.pdf","access_level":"open_access","creator":"dernst","file_size":2429551}],"publication":"Nature Communications","supplementarymaterial":"yes","oa_version":"Published Version","type":"journal_article","publisher":"Springer Nature","author":[{"full_name":"Liu, Juan","last_name":"Liu","first_name":"Juan"},{"full_name":"Zhai, Ning","last_name":"Zhai","first_name":"Ning"},{"full_name":"Zhang, Shiyi","last_name":"Zhang","first_name":"Shiyi"},{"first_name":"Yosuke","full_name":"Tamada, Yosuke","last_name":"Tamada"},{"first_name":"Tonghui","last_name":"Li","full_name":"Li, Tonghui"},{"last_name":"Zhang","full_name":"Zhang, Linfan","first_name":"Linfan"},{"last_name":"Chen","full_name":"Chen, Tong","first_name":"Tong"},{"full_name":"Wang, Chenglin","last_name":"Wang","first_name":"Chenglin"},{"last_name":"Yang","full_name":"Yang, Jian","first_name":"Jian"},{"last_name":"Gao","full_name":"Gao, Jiaqi","first_name":"Jiaqi"},{"last_name":"Li","full_name":"Li, Xiang","first_name":"Xiang","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Junhui","last_name":"Zhou","full_name":"Zhou, Junhui"},{"first_name":"Yonghong","full_name":"Zhang, Yonghong","last_name":"Zhang"},{"orcid":"0000-0001-7313-6740","first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu","last_name":"Liu"},{"full_name":"Wang, Yuan","last_name":"Wang","first_name":"Yuan"},{"full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"},{"first_name":"Chen","full_name":"Li, Chen","last_name":"Li"},{"full_name":"Xu, Lin","last_name":"Xu","first_name":"Lin"},{"last_name":"Huang","full_name":"Huang, Luqi","first_name":"Luqi"}],"day":"07","date_updated":"2026-08-20T06:45:46Z","das_tickbox":"1","intvolume":"        17","year":"2026","external_id":{"pmid":["42350386"]},"ddc":["580"],"publication_status":"published","acknowledgement":"The authors are grateful to Professor Linfeng Li from the School of Life Science, Fudan University, for his assistance during the ginseng genome annotation. This work was supported by Key project at central government level: The ability establishment of sustainable use for valuable Chinese medicine resources (2060302-2401-08 to L.X. and J.L.), the National Natural Science Foundation of China (82373987 to J.L., 31701294 to L.X., 32225007 to L.X., and 32300285 to N.Z.), the Fundamental Research Funds for the Central public welfare research institutes (ZZ13-YQ-093, ZZXT202508 to J.L.), the CACMS Innovation Fund (CI2025G00-06 to J.L.), the Principle Investigator Program (HBMUPI202104 to Y.Z.), the Key R&D Program of Shandong Province, China (2024LZGC025 to L.X.), the National Key R&D Program of China (2024YFF1000700/2023YFE0101100 to L.X.), Strategic Priority Research Program of Chinese Academy of Sciences (XDB0630000 to L.X.), and China Postdoctoral Science Foundation (2023M733490 to N.Z.).","dataavailabilitystatement":"The RNA-seq data generated in this study have been deposited in the GSA database under accession code CRA008967. The scRNA-seq data generated in this study have been deposited in the GSA database under accession code CRA026200. The ATAC-seq data generated in this study have been deposited in the GSA database under accession code CRA008969. The ChIP-seq data generated in this study have been deposited in the GSA database under accession code CRA008968. Single-cell RNA-seq data and scripts are publicly available on Zenodo (https://zenodo.org/records/20392012). Primers are in Supplemental Table 5. Source data are provided with this paper.","scopus_import":"1","article_type":"original","oa":1,"month":"08","DOAJ_listed":"1","researchdata_availability":"yes","date_created":"2026-08-16T22:01:42Z","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"quality_controlled":"1","title":"Single-cell analyses identify the ginseng embryonic protoderm as a native compartment for high-efficiency ginsenoside production","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","citation":{"mla":"Liu, Juan, et al. “Single-Cell Analyses Identify the Ginseng Embryonic Protoderm as a Native Compartment for High-Efficiency Ginsenoside Production.” <i>Nature Communications</i>, vol. 17, 7994, Springer Nature, 2026, doi:<a href=\"https://doi.org/10.1038/s41467-026-74881-5\">10.1038/s41467-026-74881-5</a>.","chicago":"Liu, Juan, Ning Zhai, Shiyi Zhang, Yosuke Tamada, Tonghui Li, Linfan Zhang, Tong Chen, et al. “Single-Cell Analyses Identify the Ginseng Embryonic Protoderm as a Native Compartment for High-Efficiency Ginsenoside Production.” <i>Nature Communications</i>. Springer Nature, 2026. <a href=\"https://doi.org/10.1038/s41467-026-74881-5\">https://doi.org/10.1038/s41467-026-74881-5</a>.","ieee":"J. Liu <i>et al.</i>, “Single-cell analyses identify the ginseng embryonic protoderm as a native compartment for high-efficiency ginsenoside production,” <i>Nature Communications</i>, vol. 17. Springer Nature, 2026.","apa":"Liu, J., Zhai, N., Zhang, S., Tamada, Y., Li, T., Zhang, L., … Huang, L. (2026). Single-cell analyses identify the ginseng embryonic protoderm as a native compartment for high-efficiency ginsenoside production. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-026-74881-5\">https://doi.org/10.1038/s41467-026-74881-5</a>","ama":"Liu J, Zhai N, Zhang S, et al. Single-cell analyses identify the ginseng embryonic protoderm as a native compartment for high-efficiency ginsenoside production. <i>Nature Communications</i>. 2026;17. doi:<a href=\"https://doi.org/10.1038/s41467-026-74881-5\">10.1038/s41467-026-74881-5</a>","ista":"Liu J, Zhai N, Zhang S, Tamada Y, Li T, Zhang L, Chen T, Wang C, Yang J, Gao J, Li X, Zhou J, Zhang Y, Liu Y, Wang Y, Friml J, Benková E, Li C, Xu L, Huang L. 2026. Single-cell analyses identify the ginseng embryonic protoderm as a native compartment for high-efficiency ginsenoside production. Nature Communications. 17, 7994.","short":"J. Liu, N. Zhai, S. Zhang, Y. Tamada, T. Li, L. Zhang, T. Chen, C. Wang, J. Yang, J. Gao, X. Li, J. Zhou, Y. Zhang, Y. Liu, Y. Wang, J. Friml, E. Benková, C. Li, L. Xu, L. Huang, Nature Communications 17 (2026)."},"pmid":1,"OA_place":"publisher","publication_identifier":{"eissn":["2041-1723"]},"article_number":"7994","_id":"22712","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"19003","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"ec_funded":1,"article_number":"koaf006","PlanS_conform":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"ama":"Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion microscopy in plant roots. <i>The Plant Cell</i>. 2025;37(4). doi:<a href=\"https://doi.org/10.1093/plcell/koaf006\">10.1093/plcell/koaf006</a>","apa":"Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou, V., Sommer, C. M., … Danzl, J. G. (2025). Super-resolution expansion microscopy in plant roots. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koaf006\">https://doi.org/10.1093/plcell/koaf006</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, The Plant Cell 37 (2025).","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. 2025. Super-resolution expansion microscopy in plant roots. The Plant Cell. 37(4), koaf006.","mla":"Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>The Plant Cell</i>, vol. 37, no. 4, koaf006, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/plcell/koaf006\">10.1093/plcell/koaf006</a>.","ieee":"M. C. Gallei <i>et al.</i>, “Super-resolution expansion microscopy in plant roots,” <i>The Plant Cell</i>, vol. 37, no. 4. Oxford University Press, 2025.","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>The Plant Cell</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/plcell/koaf006\">https://doi.org/10.1093/plcell/koaf006</a>."},"pmid":1,"has_accepted_license":"1","date_created":"2025-02-05T06:52:06Z","title":"Super-resolution expansion microscopy in plant roots","quality_controlled":"1","department":[{"_id":"EvBe"},{"_id":"JoDa"},{"_id":"JiFr"}],"month":"04","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"},{"_id":"M-Shop"}],"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\nThis project has received funding from the European Research Council under the Horizon 2020 Framework Programme (grant agreement No 742985, J.F.). It has also received funding from the Horizon 2020 Framework Programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 (M.G.). S.T. has received funding as an ISTplus Fellow from the Horizon 2020 Framework Programme under Marie Skłodowska-Curie grant agreement no. 754411 and from EMBO via a Long-Term Fellowship (grant number ALTF 679-2018). M.R.T. received funding from the Austrian Academy of Sciences with DOC fellowship no. 26137. The project has further received funding from the Austrian Science Fund, via grant DK W1232 (M.R.T., N.A.D., and J.G.D). W.J. received a postdoctoral fellowship from the Human Frontier Science Program (LT000557/2018). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","publication_status":"published","ddc":["580"],"oa":1,"article_type":"original","scopus_import":"1","external_id":{"pmid":["39792900"],"isi":["001462763100001"]},"year":"2025","intvolume":"        37","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"18689"},{"status":"public","relation":"research_data","id":"18837"}]},"date_updated":"2026-06-10T08:30:19Z","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"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"},{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","grant_number":"26137","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5"},{"_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1232-B24","name":"Molecular Drug Targets"}],"isi":1,"day":"01","publisher":"Oxford University Press","author":[{"last_name":"Gallei","full_name":"Gallei, Michelle C","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368"},{"full_name":"Truckenbrodt, Sven M","last_name":"Truckenbrodt","first_name":"Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87"},{"id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","full_name":"Kreuzinger, Caroline","last_name":"Kreuzinger"},{"first_name":"Syamala","id":"F8660870-D756-11E9-98C5-34DFE5697425","orcid":"0009-0002-5890-120X","last_name":"Inumella","full_name":"Inumella, Syamala"},{"first_name":"Vitali","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","full_name":"Vistunou, Vitali","last_name":"Vistunou"},{"first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","last_name":"Sommer"},{"full_name":"Tavakoli, Mojtaba","last_name":"Tavakoli","orcid":"0000-0002-7667-6854","first_name":"Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","last_name":"Agudelo Duenas","full_name":"Agudelo Duenas, Nathalie"},{"full_name":"Vorlaufer, Jakob","last_name":"Vorlaufer","orcid":"0009-0000-7590-3501","id":"937696FA-C996-11E9-8C7C-CF13E6697425","first_name":"Jakob"},{"first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0201-2315","last_name":"Jahr","full_name":"Jahr, Wiebke"},{"last_name":"Randuch","full_name":"Randuch, Marek","first_name":"Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae"},{"last_name":"Johnson","full_name":"Johnson, Alexander J","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková"},{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"orcid":"0000-0001-8559-3973","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","full_name":"Danzl, Johann G"}],"type":"journal_article","oa_version":"Published Version","corr_author":"1","abstract":[{"lang":"eng","text":"Super-resolution methods provide far better spatial resolution than the optical diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless, they have yet to attain widespread use in plants, largely due to plants’ challenging optical properties. Expansion microscopy improves effective resolution by isotropically increasing the physical distances between sample structures while preserving relative spatial arrangements and clearing the sample. However, its application to plants has been hindered by the rigid, mechanically cohesive structure of plant tissues. Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over conventional microscopy. Our results highlight the microtubule cytoskeleton organization and interaction between molecularly defined cellular constituents. Combining PlantEx with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution and visualize the complex organization of subcellular organelles from intact tissues by example of the densely packed COPI-coated vesicles associated with the Golgi apparatus and put these into a cellular structural context. Our results show that expansion microscopy can be applied to increase effective imaging resolution in Arabidopsis root specimens. "}],"status":"public","issue":"4","file":[{"content_type":"application/pdf","file_size":53904111,"creator":"dernst","access_level":"open_access","file_id":"20092","date_updated":"2025-07-31T07:03:43Z","file_name":"2025_PlantCell_Gallei.pdf","checksum":"9d3f8218ff37a29f29c48a7bbe831bd3","date_created":"2025-07-31T07:03:43Z","relation":"main_file","success":1}],"publication":"The Plant Cell","language":[{"iso":"eng"}],"OA_type":"hybrid","date_published":"2025-04-01T00:00:00Z","file_date_updated":"2025-07-31T07:03:43Z","article_processing_charge":"Yes (via OA deal)","doi":"10.1093/plcell/koaf006","volume":37},{"external_id":{"pmid":["40262524"],"isi":["001477400800001"]},"year":"2025","intvolume":"        60","month":"04","scopus_import":"1","article_type":"letter_note","publication_status":"published","citation":{"chicago":"Benková, Eva. “Unlocking Plant Regeneration: The Role for Glutathione.” <i>Developmental Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2025.03.012\">https://doi.org/10.1016/j.devcel.2025.03.012</a>.","ieee":"E. Benková, “Unlocking plant regeneration: The role for glutathione,” <i>Developmental Cell</i>, vol. 60, no. 8. Elsevier, pp. 1137–1139, 2025.","mla":"Benková, Eva. “Unlocking Plant Regeneration: The Role for Glutathione.” <i>Developmental Cell</i>, vol. 60, no. 8, Elsevier, 2025, pp. 1137–39, doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.03.012\">10.1016/j.devcel.2025.03.012</a>.","ista":"Benková E. 2025. Unlocking plant regeneration: The role for glutathione. Developmental Cell. 60(8), 1137–1139.","short":"E. Benková, Developmental Cell 60 (2025) 1137–1139.","ama":"Benková E. Unlocking plant regeneration: The role for glutathione. <i>Developmental Cell</i>. 2025;60(8):1137-1139. doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.03.012\">10.1016/j.devcel.2025.03.012</a>","apa":"Benková, E. (2025). Unlocking plant regeneration: The role for glutathione. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2025.03.012\">https://doi.org/10.1016/j.devcel.2025.03.012</a>"},"pmid":1,"title":"Unlocking plant regeneration: The role for glutathione","department":[{"_id":"EvBe"}],"quality_controlled":"1","date_created":"2025-04-20T22:01:28Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"19594","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"date_published":"2025-04-21T00:00:00Z","OA_type":"closed access","language":[{"iso":"eng"}],"volume":60,"page":"1137-1139","doi":"10.1016/j.devcel.2025.03.012","article_processing_charge":"No","oa_version":"None","issue":"8","publication":"Developmental Cell","abstract":[{"lang":"eng","text":"In this issue of Developmental Cell, Lee et al. identify a pivotal role for glutathione (GSH) in plant regeneration, a vital biological process enabling plants to regrow tissues and organs after injury. Applying single-cell RNA sequencing (scRNA-seq) and live imaging, the authors demonstrate that GSH, released upon tissue damage, accelerates cell-cycle transitions, particularly shortening the G1 phase, thereby facilitating efficient organ regeneration."}],"corr_author":"1","status":"public","author":[{"orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","full_name":"Benková, Eva"}],"publisher":"Elsevier","type":"journal_article","date_updated":"2025-09-30T12:07:36Z","day":"21","isi":1},{"date_updated":"2026-05-20T07:53:03Z","APC_amount":"3642,79 EUR","isi":1,"project":[{"call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"day":"04","publisher":"Frontiers Media","author":[{"last_name":"Gallemi","full_name":"Gallemi, Marçal","first_name":"Marçal","id":"460C6802-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4675-6893"},{"last_name":"Montesinos López","full_name":"Montesinos López, Juan C","orcid":"0000-0001-9179-6099","first_name":"Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zarevski","full_name":"Zarevski, Nikola","first_name":"Nikola","id":"18e95355-e05a-11ea-a9c0-8fba1b89e83a"},{"first_name":"Jan","last_name":"Pribyl","full_name":"Pribyl, Jan"},{"full_name":"Skládal, Petr","last_name":"Skládal","first_name":"Petr"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739"}],"type":"journal_article","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"corr_author":"1","status":"public","publication":"Frontiers in Plant Science","file":[{"date_created":"2025-07-31T07:28:54Z","checksum":"9e6b8b53ba56d4a24a9bd91cf6d2dc58","relation":"main_file","success":1,"content_type":"application/pdf","file_size":3665187,"creator":"dernst","access_level":"open_access","date_updated":"2025-07-31T07:28:54Z","file_name":"2025_FrontiersPlantSc_Gallemi.pdf","file_id":"20093"}],"language":[{"iso":"eng"}],"OA_type":"gold","date_published":"2025-07-04T00:00:00Z","file_date_updated":"2025-07-31T07:28:54Z","article_processing_charge":"Yes","doi":"10.3389/fpls.2025.1612366","volume":16,"_id":"20080","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","publication_identifier":{"eissn":["1664-462X"]},"ec_funded":1,"article_number":"1612366","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"PlanS_conform":"1","citation":{"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>.","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.","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>.","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>","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>","short":"M. Gallemi, J.C. Montesinos López, N. Zarevski, J. Pribyl, P. Skládal, E.B. Hannezo, E. Benková, Frontiers in Plant Science 16 (2025).","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."},"pmid":1,"has_accepted_license":"1","date_created":"2025-07-27T22:01:26Z","title":"Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties","quality_controlled":"1","department":[{"_id":"EdHa"},{"_id":"EvBe"},{"_id":"CaGu"}],"month":"07","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"}],"DOAJ_listed":"1","ddc":["580"],"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.","article_type":"original","oa":1,"scopus_import":"1","external_id":{"pmid":["40688689"],"isi":["001530690900001"]},"year":"2025","intvolume":"        16"},{"publication_status":"published","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.","ddc":["580"],"alternative_title":["ISTA Thesis"],"month":"08","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"related_material":{"record":[{"id":"18063","status":"public","relation":"part_of_dissertation"}]},"year":"2025","OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"_id":"20117","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2025-08-04T15:24:21Z","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"title":"The role of dynamin related protein 2A in cytokinin regulated plant growth and development","has_accepted_license":"1","citation":{"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>","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>","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.","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>.","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>.","ieee":"Y. Wang, “The role of dynamin related protein 2A in cytokinin regulated plant growth and development,” Institute of Science and Technology Austria, 2025."},"status":"public","corr_author":"1","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":25798848,"creator":"yiqwang","access_level":"closed","file_id":"20209","file_name":"2025_Wang_Yiqun_Thesis.docx","date_updated":"2025-08-22T08:53:46Z","date_created":"2025-08-22T08:22:10Z","checksum":"36b87c17d12c7bf5955d6d812acb8d77","relation":"source_file"},{"file_size":12628313,"creator":"yiqwang","access_level":"closed","file_name":"2025_Wang_Yiqun_Thesis.pdf","file_id":"20211","date_updated":"2025-09-03T09:36:52Z","content_type":"application/pdf","embargo":"2026-09-03","date_created":"2025-08-22T10:32:30Z","embargo_to":"open_access","checksum":"8d7a2383f66377da675d379ec30ea0fe","relation":"main_file"}],"oa_version":"Published Version","article_processing_charge":"No","doi":"10.15479/AT-ISTA-20117","page":"108","file_date_updated":"2025-09-03T09:36:52Z","date_published":"2025-08-04T00:00:00Z","language":[{"iso":"eng"}],"day":"04","date_updated":"2026-04-07T11:49:34Z","degree_awarded":"PhD","type":"dissertation","supervisor":[{"last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Wang, Yiqun","last_name":"Wang","id":"82F537F2-B517-11E9-84D7-6433E6697425","first_name":"Yiqun"}]},{"intvolume":"       123","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"20362"}]},"year":"2025","external_id":{"pmid":["40782342"],"isi":["001547884300001"]},"publication_status":"published","ddc":["580"],"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).","scopus_import":"1","article_type":"original","oa":1,"month":"08","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"date_created":"2025-08-17T22:01:36Z","department":[{"_id":"EvBe"},{"_id":"JiFr"},{"_id":"GradSch"}],"quality_controlled":"1","title":"Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development","PlanS_conform":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"has_accepted_license":"1","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>.","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>.","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).","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>"},"pmid":1,"publication_identifier":{"eissn":["1365-313X"],"issn":["0960-7412"]},"OA_place":"publisher","article_number":"e70396","_id":"20187","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"Yes (via OA deal)","doi":"10.1111/tpj.70396","volume":123,"file_date_updated":"2025-09-01T14:09:31Z","language":[{"iso":"eng"}],"OA_type":"hybrid","date_published":"2025-08-01T00:00:00Z","status":"public","abstract":[{"lang":"eng","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."}],"corr_author":"1","publication":"Plant Journal","file":[{"success":1,"relation":"main_file","checksum":"1cdc3341d2d23101abca72521f1f23cb","date_created":"2025-09-01T14:09:31Z","file_id":"20264","date_updated":"2025-09-01T14:09:31Z","file_name":"2025_PlantJournal_Babic.pdf","access_level":"open_access","file_size":5791111,"creator":"dernst","content_type":"application/pdf"}],"issue":"3","oa_version":"Published Version","type":"journal_article","author":[{"full_name":"Babic, David","last_name":"Babic","first_name":"David","id":"db566d23-f6e0-11ea-865d-e6f270e968e7"},{"orcid":"0000-0002-9357-9415","id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed","full_name":"Abualia, Rashed","last_name":"Abualia"},{"last_name":"Fiedler","full_name":"Fiedler, Lukas","first_name":"Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986"},{"orcid":"0000-0001-5187-8401","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","first_name":"Linlin","full_name":"Qi, Linlin","last_name":"Qi"},{"first_name":"Frédérique","last_name":"Tellier","full_name":"Tellier, Frédérique"},{"last_name":"Smoljan","full_name":"Smoljan, Adrijana","id":"cced8a85-223e-11ed-af04-b0596c55053b","first_name":"Adrijana"},{"full_name":"Rakusova, Hana","last_name":"Rakusova","id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","first_name":"Hana"},{"id":"3CDB6F94-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Valošek","full_name":"Valošek, Petr"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin","full_name":"Han, Huibin","last_name":"Han"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková"},{"first_name":"Jean Denis","last_name":"Faure","full_name":"Faure, Jean Denis"},{"full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"publisher":"Wiley","isi":1,"project":[{"grant_number":"I06123","name":"Peptide receptors for auxin canalization in Arabidopsis","_id":"bd76d395-d553-11ed-ba76-f678c14f9033"}],"day":"01","date_updated":"2026-04-07T11:52:02Z"},{"file":[{"file_size":7501548,"creator":"dbabic","file_id":"20388","date_updated":"2025-09-26T07:29:11Z","file_name":"2025_David_Babic_Thesis.pdf","access_level":"closed","content_type":"application/pdf","embargo":"2026-09-25","relation":"main_file","date_created":"2025-09-24T13:43:14Z","embargo_to":"open_access","checksum":"5ecf274281a54a41e0288bc79edf7492"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-09-26T07:29:11Z","file_id":"20389","file_name":"Thesis_Babic_draft.docx","access_level":"closed","file_size":23206052,"creator":"dbabic","relation":"source_file","checksum":"2703e548390de0a1af7a707137e8ab3b","date_created":"2025-09-24T13:43:14Z"}],"corr_author":"1","status":"public","oa_version":"Published Version","page":"116","article_processing_charge":"No","doi":"10.15479/AT-ISTA-20362","date_published":"2025-09-18T00:00:00Z","language":[{"iso":"eng"}],"file_date_updated":"2025-09-26T07:29:11Z","day":"18","date_updated":"2026-04-07T11:52:02Z","type":"dissertation","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Babic","full_name":"Babic, David","id":"db566d23-f6e0-11ea-865d-e6f270e968e7","first_name":"David"}],"supervisor":[{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Benková, Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"alternative_title":["ISTA Thesis"],"ddc":["580"],"publication_status":"published","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"month":"09","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"20187"}]},"year":"2025","OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"20362","title":"Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"EvBe"}],"date_created":"2025-09-17T13:28:01Z","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>","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>","ista":"Babic D. 2025. Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana. Institute of Science and Technology Austria.","short":"D. Babic, Mechanisms of Auxin-Mediated Early Embryogenesis in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2025.","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>.","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>.","ieee":"D. Babic, “Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2025."},"has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"ddc":["000"],"publication_status":"published","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).","oa":1,"scopus_import":"1","article_type":"original","month":"11","DOAJ_listed":"1","intvolume":"         6","related_material":{"link":[{"url":"https://ista.ac.at/en/news/carbon-footprint-of-conference-travel/","relation":"research_data","description":"News on ISTA website"}],"record":[{"status":"public","relation":"research_data","id":"20242"}]},"year":"2025","publication_identifier":{"eissn":["2699-0016"]},"OA_place":"publisher","_id":"20664","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-11-23T23:01:39Z","title":"Quantifying the carbon footprint of conference travel: The case of NMR meetings","quality_controlled":"1","department":[{"_id":"JoFi"},{"_id":"GaTk"},{"_id":"JoCs"},{"_id":"EvBe"},{"_id":"TaHa"},{"_id":"GradSch"},{"_id":"GeKa"},{"_id":"PaSc"}],"PlanS_conform":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"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.","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>.","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>.","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.","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.","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>","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>"},"has_accepted_license":"1","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."}],"corr_author":"1","status":"public","issue":"2","publication":"Magnetic Resonance","file":[{"success":1,"checksum":"c63dd47b0e77f9451821436bb77d27c9","date_created":"2025-11-24T08:25:19Z","relation":"main_file","file_size":3081399,"creator":"dernst","access_level":"open_access","file_name":"2025_MagneticResonance_Kapoor.pdf","file_id":"20672","date_updated":"2025-11-24T08:25:19Z","content_type":"application/pdf"}],"oa_version":"Published Version","page":"243-256","article_processing_charge":"Yes","doi":"10.5194/mr-6-243-2025","volume":6,"language":[{"iso":"eng"}],"OA_type":"gold","date_published":"2025-11-10T00:00:00Z","file_date_updated":"2025-11-24T08:25:19Z","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"day":"10","APC_amount":"1260 EUR","date_updated":"2026-06-10T08:45:11Z","type":"journal_article","publisher":"Copernicus Publications","author":[{"last_name":"Kapoor","full_name":"Kapoor, Lucky","orcid":"0000-0001-8319-2148","id":"84b9700b-15b2-11ec-abd3-831089e67615","first_name":"Lucky"},{"full_name":"Ruzickova, Natalia","last_name":"Ruzickova","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","first_name":"Natalia"},{"id":"68AA0E5A-AFDA-11E9-9994-141DE6697425","first_name":"Predrag","full_name":"Zivadinovic, Predrag","last_name":"Zivadinovic"},{"full_name":"Leitner, Valentin","last_name":"Leitner","id":"4c665ce3-0016-11ec-bea0-e44de7a4fa3d","first_name":"Valentin"},{"id":"44A03D04-AEA4-11E9-B225-EA2DE6697425","first_name":"Maria A","full_name":"Sisak, Maria A","last_name":"Sisak"},{"id":"2a69ab4b-896a-11ed-bdf8-cb8641cf2b21","first_name":"Cecelia N","full_name":"Mweka, Cecelia N","last_name":"Mweka"},{"id":"c15a5412-de82-11ed-b809-8dc1aa996e40","first_name":"Jeroen A","full_name":"Dobbelaere, Jeroen A","last_name":"Dobbelaere"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","full_name":"Katsaros, Georgios"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda"}]},{"oa_version":"Published Version","publication":"bioRxiv","abstract":[{"lang":"eng","text":"Receptor-like kinases (RLKs), particularly the Transmembrane Kinase (TMK) family, play essential roles in signaling and development, with TMKs being key components of auxin perception and downstream phosphorylation events. While TMKs’ involvement in auxin canalization, a process essential for vasculature formation and regeneration, has been established, nonetheless, the additional signaling and regulatory partners remain poorly understood. In this study, we identify and characterize seven leucine-rich repeat RLKs (TINT1–TINT7) as novel interactors of TMK1, revealing their diverse evolutionary, structural, and functional characteristics. Our results show that TINTs interact with TMK1 and highlight their roles in regulating various developmental processes. Majority of TINTs contributes, together with TMK1, to auxin canalization, with TINT5 linking TMK1 to other canalization component CAMEL. Beyond canalization, we also establish the role of TINT-TMK1 interactions in processes such as stomatal movement and the hypocotyl’s gravitropic response. These findings suggest that TINTs, through their interaction with TMK1, are integral components of various signaling networks, contributing to both auxin canalization and broader plant development."}],"corr_author":"1","status":"public","date_published":"2025-03-02T00:00:00Z","language":[{"iso":"eng"}],"OA_type":"green","doi":"10.1101/2025.02.28.640727","article_processing_charge":"No","date_updated":"2026-08-14T09:33:45Z","day":"02","author":[{"first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","last_name":"Monzer","full_name":"Monzer, Aline"},{"first_name":"Ewa","last_name":"Mazur","full_name":"Mazur, Ewa"},{"full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237"},{"last_name":"Gallei","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","last_name":"Zou","full_name":"Zou, Minxia"},{"id":"79a5a1be-04a3-11f0-ba18-a1730e0b58e9","first_name":"Michael","full_name":"Smejkal, Michael","last_name":"Smejkal"},{"last_name":"Cervenova","full_name":"Cervenova, Ema","id":"9f185b95-04a3-11f0-8245-f5e32eeb470f","first_name":"Ema"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"type":"preprint","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"month":"03","oa":1,"publication_status":"draft","acknowledgement":"We deeply appreciate M. Wrzaczek’s constructive input and insightful discussions, which significantly enriched this work. We thank L. Fiedler for helping with the heat map and for the discussions. We also thank the facilities at ISTA, the imaging and optics (IOF) and Lab Support (LSF) facilities for their service and assistance.","ddc":["580"],"year":"2025","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19395"}]},"das_tickbox":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"19398","OA_place":"repository","citation":{"chicago":"Monzer, Aline, Ewa Mazur, Lesia Rodriguez Solovey, Michelle C Gallei, Minxia Zou, Michael Smejkal, Ema Cervenova, and Jiří Friml. “TMK Interacting Network of Receptor like Kinases for Auxin Canalization and Beyond.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.02.28.640727\">https://doi.org/10.1101/2025.02.28.640727</a>.","ieee":"A. Monzer <i>et al.</i>, “TMK interacting network of receptor like kinases for auxin canalization and beyond,” <i>bioRxiv</i>. .","mla":"Monzer, Aline, et al. “TMK Interacting Network of Receptor like Kinases for Auxin Canalization and Beyond.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.02.28.640727\">10.1101/2025.02.28.640727</a>.","ista":"Monzer A, Mazur E, Rodriguez Solovey L, Gallei MC, Zou M, Smejkal M, Cervenova E, Friml J. TMK interacting network of receptor like kinases for auxin canalization and beyond. bioRxiv, <a href=\"https://doi.org/10.1101/2025.02.28.640727\">10.1101/2025.02.28.640727</a>.","short":"A. Monzer, E. Mazur, L. Rodriguez Solovey, M.C. Gallei, M. Zou, M. Smejkal, E. Cervenova, J. Friml, BioRxiv (n.d.).","ama":"Monzer A, Mazur E, Rodriguez Solovey L, et al. TMK interacting network of receptor like kinases for auxin canalization and beyond. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.02.28.640727\">10.1101/2025.02.28.640727</a>","apa":"Monzer, A., Mazur, E., Rodriguez Solovey, L., Gallei, M. C., Zou, M., Smejkal, M., … Friml, J. (n.d.). TMK interacting network of receptor like kinases for auxin canalization and beyond. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.02.28.640727\">https://doi.org/10.1101/2025.02.28.640727</a>"},"has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"TMK interacting network of receptor like kinases for auxin canalization and beyond","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"EvBe"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.02.28.640727"}],"date_created":"2025-03-12T14:28:53Z"},{"supervisor":[{"last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739"}],"publisher":"Institute of Science and Technology Austria","author":[{"id":"F8660870-D756-11E9-98C5-34DFE5697425","first_name":"Syamala","orcid":"0009-0002-5890-120X","last_name":"Inumella","full_name":"Inumella, Syamala"}],"degree_awarded":"PhD","type":"dissertation","date_updated":"2026-06-12T08:34:29Z","day":"23","file_date_updated":"2026-05-23T22:30:02Z","date_published":"2025-05-23T00:00:00Z","language":[{"iso":"eng"}],"article_processing_charge":"No","doi":"10.15479/AT-ISTA-19722","page":"113","oa_version":"Published Version","status":"public","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"}],"corr_author":"1","file":[{"relation":"main_file","date_created":"2025-05-28T11:59:11Z","checksum":"847ec70b2e40f50e0ddc7b8da201d52c","embargo":"2026-05-23","content_type":"application/pdf","file_size":8292363,"creator":"sinumell","file_id":"19757","date_updated":"2026-05-23T22:30:02Z","file_name":"Final Thesis_Syamala Inumella.pdf","access_level":"open_access"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_updated":"2026-05-23T22:30:02Z","file_id":"19758","file_name":"Final Thesis_Syamala Inumella.docx","file_size":7145703,"creator":"sinumell","checksum":"17cdffdae13a5f65bdad9c84e9e0e3bd","date_created":"2025-05-28T11:59:11Z","embargo_to":"open_access","relation":"source_file"}],"has_accepted_license":"1","citation":{"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>.","ieee":"S. Inumella, “Molecular mechanisms of microtubule reorganization in elongating root epidermal cells,” Institute of Science and Technology Austria, 2025.","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>.","ista":"Inumella S. 2025. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. Institute of Science and Technology Austria.","short":"S. Inumella, Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells, Institute of Science and Technology Austria, 2025.","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>","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>"},"date_created":"2025-05-23T15:21:29Z","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"title":"Molecular mechanisms of microtubule reorganization in elongating root epidermal cells","_id":"19722","OA_embargo":"12","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","OA_place":"publisher","publication_identifier":{"isbn":["978-3-99078-059-6"],"issn":["2663-337X"]},"year":"2025","month":"05","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"acknowledgement":"Special thanks to the Plant Facility.","ddc":["580"],"publication_status":"published","oa":1,"alternative_title":["ISTA Thesis"]},{"oa":1,"publication_status":"published","ddc":["580"],"month":"01","intvolume":"        34","external_id":{"pmid":["38194926"]},"year":"2024","publication_identifier":{"eissn":["1879-0445"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14842","title":"Eva Benkova","quality_controlled":"1","department":[{"_id":"EvBe"}],"date_created":"2024-01-21T23:00:56Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2023.11.039"}],"pmid":1,"citation":{"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>","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>","short":"E. Benková, Eva Benkova, Elsevier, 2024.","ista":"Benková E. 2024. Eva Benkova, Elsevier,p.","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>.","ieee":"E. Benková, <i>Eva Benkova</i>, vol. 34, no. 1. Elsevier, 2024, pp. R3–R5.","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>."},"issue":"1","publication":"Current Biology","corr_author":"1","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"}],"status":"public","oa_version":"Published Version","volume":34,"page":"R3-R5","article_processing_charge":"No","doi":"10.1016/j.cub.2023.11.039","language":[{"iso":"eng"}],"date_published":"2024-01-08T00:00:00Z","day":"08","date_updated":"2026-06-18T17:40:39Z","type":"other_academic_publication","publisher":"Elsevier","author":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková"}]},{"external_id":{"pmid":["38579717"],"isi":["001301584600001"]},"year":"2024","related_material":{"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/how-plants-heal-wounds/"}]},"intvolume":"        59","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"month":"05","article_type":"original","oa":1,"scopus_import":"1","ddc":["570"],"publication_status":"published","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).","citation":{"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.","short":"L. Hörmayer, J.C. Montesinos López, N. Trozzi, L. Spona, S. Yoshida, P. Marhavá, S. Caballero Mancebo, E. Benková, C.-P.J. Heisenberg, Y. Dagdas, M. Majda, J. Friml, Developmental Cell 59 (2024) 1333–1344.e4.","apa":"Hörmayer, L., Montesinos López, J. C., Trozzi, N., Spona, L., Yoshida, S., Marhavá, P., … Friml, J. (2024). Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.03.009\">https://doi.org/10.1016/j.devcel.2024.03.009</a>","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>","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>.","ieee":"L. Hörmayer <i>et al.</i>, “Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization,” <i>Developmental Cell</i>, vol. 59, no. 10. Elsevier, p. 1333–1344.e4, 2024.","mla":"Hörmayer, Lukas, et al. “Mechanical Forces in Plant Tissue Matrix Orient Cell Divisions via Microtubule Stabilization.” <i>Developmental Cell</i>, vol. 59, no. 10, Elsevier, 2024, p. 1333–1344.e4, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.03.009\">10.1016/j.devcel.2024.03.009</a>."},"pmid":1,"has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"title":"Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization","department":[{"_id":"JiFr"},{"_id":"EvBe"},{"_id":"CaHe"}],"quality_controlled":"1","date_created":"2024-04-08T12:07:57Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"15301","ec_funded":1,"publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"date_published":"2024-05-20T00:00:00Z","language":[{"iso":"eng"}],"file_date_updated":"2024-08-20T11:22:16Z","volume":59,"page":"1333-1344.e4","doi":"10.1016/j.devcel.2024.03.009","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","issue":"10","publication":"Developmental Cell","file":[{"content_type":"application/pdf","file_id":"17452","file_name":"2024_DevelopmentalCell_Hoermayer.pdf","date_updated":"2024-08-20T11:22:16Z","access_level":"open_access","file_size":5195262,"creator":"dernst","relation":"main_file","date_created":"2024-08-20T11:22:16Z","checksum":"22b374fb50a40d380b7686c84258d271","success":1}],"corr_author":"1","abstract":[{"text":"Plant morphogenesis relies exclusively on oriented cell expansion and division. Nonetheless, the mechanism(s) determining division plane orientation remain elusive. Here, we studied tissue healing after laser-assisted wounding in roots of Arabidopsis thaliana and uncovered how mechanical forces stabilize and reorient the microtubule cytoskeleton for the orientation of cell division. We identified that root tissue functions as an interconnected cell matrix, with a radial gradient of tissue extendibility causing predictable tissue deformation after wounding. This deformation causes instant redirection of expansion in the surrounding cells and reorientation of microtubule arrays, ultimately predicting cell division orientation. Microtubules are destabilized under low tension, whereas stretching of cells, either through wounding or external aspiration, immediately induces their polymerization. The higher microtubule abundance in the stretched cell parts leads to the reorientation of microtubule arrays and, ultimately, informs cell division planes. This provides a long-sought mechanism for flexible re-arrangement of cell divisions by mechanical forces for tissue reconstruction and plant architecture.","lang":"eng"}],"status":"public","publisher":"Elsevier","author":[{"first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926","last_name":"Hörmayer","full_name":"Hörmayer, Lukas"},{"orcid":"0000-0001-9179-6099","first_name":"Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","full_name":"Montesinos López, Juan C","last_name":"Montesinos López"},{"first_name":"N","full_name":"Trozzi, N","last_name":"Trozzi"},{"full_name":"Spona, Leonhard","last_name":"Spona","first_name":"Leonhard","id":"b52391fb-f636-11ee-939c-8a8c47552e8a"},{"full_name":"Yoshida, Saiko","last_name":"Yoshida","first_name":"Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87"},{"id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra","full_name":"Marhavá, Petra","last_name":"Marhavá"},{"full_name":"Caballero Mancebo, Silvia","last_name":"Caballero Mancebo","orcid":"0000-0002-5223-3346","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","first_name":"Silvia"},{"orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","last_name":"Benková"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"},{"last_name":"Dagdas","full_name":"Dagdas, Y","first_name":"Y"},{"last_name":"Majda","full_name":"Majda, M","first_name":"M"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"}],"type":"journal_article","date_updated":"2025-09-04T13:32:08Z","day":"20","isi":1,"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988"}]},{"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","pmid":1,"citation":{"ieee":"M. Králová <i>et al.</i>, “A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis,” <i>Molecular Plant</i>, vol. 17, no. 12. Elsevier, pp. 1850–1865, 2024.","chicago":"Králová, Michaela, Ivona Kubalová, Jakub Hajný, Karolina Kubiasova, Karolína Vagaská, Zengxiang Ge, Michelle C Gallei, et al. “A Decoy Receptor Derived from Alternative Splicing Fine-Tunes Cytokinin Signaling in Arabidopsis.” <i>Molecular Plant</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.molp.2024.11.001\">https://doi.org/10.1016/j.molp.2024.11.001</a>.","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.","ista":"Králová M, Kubalová I, Hajný J, Kubiasova K, Vagaská K, Ge Z, Gallei MC, Semerádová H, Kuchařová A, Hönig M, Monzer A, Kovačik M, Friml J, Novák O, Benková E, Ikeda Y, Zalabák D. 2024. A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis. Molecular Plant. 17(12), 1850–1865.","apa":"Králová, M., Kubalová, I., Hajný, J., Kubiasova, K., Vagaská, K., Ge, Z., … Zalabák, D. (2024). A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2024.11.001\">https://doi.org/10.1016/j.molp.2024.11.001</a>","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>"},"date_created":"2024-11-28T11:13:35Z","quality_controlled":"1","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"title":"A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis","_id":"18596","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"publisher","publication_identifier":{"issn":["1674-2052"]},"year":"2024","external_id":{"pmid":["39501563"],"isi":["001373778300001"]},"intvolume":"        17","month":"12","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"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.","publication_status":"published","ddc":["580"],"article_type":"original","oa":1,"scopus_import":"1","author":[{"last_name":"Králová","full_name":"Králová, Michaela","first_name":"Michaela"},{"last_name":"Kubalová","full_name":"Kubalová, Ivona","first_name":"Ivona"},{"full_name":"Hajný, Jakub","last_name":"Hajný","first_name":"Jakub"},{"first_name":"Karolina","id":"946011F4-3E71-11EA-860B-C7A73DDC885E","orcid":"0000-0001-5630-9419","last_name":"Kubiasova","full_name":"Kubiasova, Karolina"},{"first_name":"Karolína","last_name":"Vagaská","full_name":"Vagaská, Karolína"},{"full_name":"Ge, Zengxiang","last_name":"Ge","orcid":"0000-0001-9381-3577","first_name":"Zengxiang","id":"f43371a3-09ff-11eb-8013-bd0c6a2f6de8"},{"first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","last_name":"Gallei"},{"last_name":"Semerádová","full_name":"Semerádová, Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","first_name":"Hana"},{"full_name":"Kuchařová, Anna","last_name":"Kuchařová","first_name":"Anna"},{"last_name":"Hönig","full_name":"Hönig, Martin","first_name":"Martin"},{"last_name":"Monzer","full_name":"Monzer, Aline","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425"},{"first_name":"Martin","full_name":"Kovačik, Martin","last_name":"Kovačik"},{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739"},{"full_name":"Ikeda, Yoshihisa","last_name":"Ikeda","first_name":"Yoshihisa"},{"first_name":"David","last_name":"Zalabák","full_name":"Zalabák, David"}],"publisher":"Elsevier","type":"journal_article","date_updated":"2025-09-08T14:46:45Z","isi":1,"day":"02","file_date_updated":"2024-12-03T11:08:09Z","date_published":"2024-12-02T00:00:00Z","language":[{"iso":"eng"}],"OA_type":"hybrid","article_processing_charge":"Yes (in subscription journal)","doi":"10.1016/j.molp.2024.11.001","page":"1850-1865","volume":17,"oa_version":"Published Version","status":"public","abstract":[{"text":"Hormone perception and signaling pathways have a fundamental regulatory function in the physiological processes of plants. Cytokinins, a class of plant hormones, regulate cell division and meristem maintenance. The cytokinin signaling pathway is well established in the model plant Arabidopsis thaliana. Several negative feedback mechanisms, tightly controlling cytokinin signaling output, have been described previously. In this study, we identified a new feedback mechanism executed through alternative splicing of the cytokinin receptor AHK4/CRE1. A novel splicing variant named CRE1int7 results from seventh intron retention, introducing a premature termination codon in the transcript. We showed that CRE1int7 is translated in planta into a truncated receptor lacking the C-terminal receiver domain essential for signal transduction. CRE1int7 can bind cytokinin but cannot activate the downstream cascade. We present a novel negative feedback mechanism of the cytokinin signaling pathway, facilitated by a decoy receptor that can inactivate canonical cytokinin receptors via dimerization and compete with them for ligand binding. Ensuring proper plant growth and development requires precise control of the cytokinin signaling pathway at several levels. CRE1int7 represents a so-far unknown mechanism for fine-tuning the cytokinin signaling pathway in Arabidopsis.","lang":"eng"}],"file":[{"relation":"main_file","checksum":"a11feea4b1677df76b632eca04bfc1dd","date_created":"2024-12-03T11:08:09Z","success":1,"content_type":"application/pdf","file_id":"18612","file_name":"2024_MolecularPlant_Kralova.pdf","date_updated":"2024-12-03T11:08:09Z","access_level":"open_access","creator":"dernst","file_size":3308945}],"publication":"Molecular Plant","issue":"12"},{"type":"journal_article","author":[{"first_name":"Yakun","last_name":"Peng","full_name":"Peng, Yakun"},{"first_name":"Kangkang","last_name":"Ji","full_name":"Ji, Kangkang"},{"first_name":"Yanbo","full_name":"Mao, Yanbo","last_name":"Mao"},{"last_name":"Wang","full_name":"Wang, Yiqun","first_name":"Yiqun","id":"82F537F2-B517-11E9-84D7-6433E6697425"},{"full_name":"Korbei, Barbara","last_name":"Korbei","first_name":"Barbara"},{"full_name":"Luschnig, Christian","last_name":"Luschnig","first_name":"Christian"},{"last_name":"Shen","full_name":"Shen, Jinbo","first_name":"Jinbo"},{"last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tan","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","orcid":"0000-0002-0471-8285"}],"publisher":"Springer Nature","day":"04","project":[{"_id":"bd76d395-d553-11ed-ba76-f678c14f9033","name":"Peptide receptors for auxin canalization in Arabidopsis","grant_number":"I06123"},{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","grant_number":"P37051","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors"}],"isi":1,"date_updated":"2026-04-07T11:49:33Z","volume":7,"article_processing_charge":"Yes","doi":"10.1038/s42003-024-06747-9","date_published":"2024-09-04T00:00:00Z","language":[{"iso":"eng"}],"file_date_updated":"2024-09-17T09:44:29Z","file":[{"success":1,"checksum":"7d66af41c90e73d1b8a375eb652a9561","date_created":"2024-09-17T09:44:29Z","relation":"main_file","creator":"dernst","file_size":7718758,"access_level":"open_access","date_updated":"2024-09-17T09:44:29Z","file_id":"18084","file_name":"2024_CommBiology_Peng.pdf","content_type":"application/pdf"}],"publication":"Communications Biology","abstract":[{"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.","lang":"eng"}],"status":"public","oa_version":"Published Version","title":"Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis","quality_controlled":"1","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"date_created":"2024-09-15T22:01:38Z","citation":{"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.","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>.","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>.","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).","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.","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>","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>"},"pmid":1,"has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_number":"1085","publication_identifier":{"eissn":["2399-3642"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"18063","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"20117"}]},"intvolume":"         7","external_id":{"isi":["001306499600002"],"pmid":["39232040"]},"year":"2024","article_type":"original","oa":1,"scopus_import":"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).","ddc":["570"],"publication_status":"published","month":"09"},{"type":"preprint","author":[{"last_name":"Gallei","full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","orcid":"0000-0003-1286-7368"},{"id":"45812BD4-F248-11E8-B48F-1D18A9856A87","first_name":"Sven M","last_name":"Truckenbrodt","full_name":"Truckenbrodt, Sven M"},{"id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","last_name":"Kreuzinger","full_name":"Kreuzinger, Caroline"},{"full_name":"Inumella, Syamala","last_name":"Inumella","id":"F8660870-D756-11E9-98C5-34DFE5697425","first_name":"Syamala","orcid":"0009-0002-5890-120X"},{"id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","first_name":"Vitali","last_name":"Vistunou","full_name":"Vistunou, Vitali"},{"last_name":"Sommer","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","orcid":"0000-0003-1216-9105"},{"full_name":"Tavakoli, Mojtaba","last_name":"Tavakoli","orcid":"0000-0002-7667-6854","first_name":"Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Agudelo Duenas","full_name":"Agudelo Duenas, Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","first_name":"Nathalie"},{"first_name":"Jakob","id":"937696FA-C996-11E9-8C7C-CF13E6697425","orcid":"0009-0000-7590-3501","full_name":"Vorlaufer, Jakob","last_name":"Vorlaufer"},{"last_name":"Jahr","full_name":"Jahr, Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke","orcid":"0000-0003-0201-2315"},{"full_name":"Randuch, Marek","last_name":"Randuch","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","first_name":"Marek"},{"orcid":"0000-0002-2739-8843","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","full_name":"Johnson, Alexander J"},{"last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739"},{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl"}],"project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"UltraX - achieving sub-nanometer resolution in light microscopy using iterative X10 microscopy in combination with nanobodies and STED","grant_number":"ALTF 679-2018","_id":"269B5B22-B435-11E9-9278-68D0E5697425"}],"day":"21","date_updated":"2026-07-28T08:33:52Z","article_processing_charge":"No","doi":"10.1101/2024.02.21.581330","date_published":"2024-02-21T00:00:00Z","language":[{"iso":"eng"}],"corr_author":"1","abstract":[{"lang":"eng","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."}],"status":"public","publication":"bioRxiv","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.02.21.581330"}],"date_created":"2024-12-19T12:28:00Z","title":"Super-resolution expansion microscopy in plant roots","department":[{"_id":"EvBe"},{"_id":"JoDa"},{"_id":"JiFr"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"citation":{"ieee":"M. C. Gallei <i>et al.</i>, “Super-resolution expansion microscopy in plant roots,” <i>bioRxiv</i>. .","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>.","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.).","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>.","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>","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>"},"OA_place":"repository","ec_funded":1,"_id":"18689","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"later_version","id":"19003"},{"id":"18681","status":"public","relation":"dissertation_contains"}]},"year":"2024","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.","publication_status":"draft","oa":1,"month":"02","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}]},{"publisher":"MDPI","author":[{"last_name":"Abualia","full_name":"Abualia, R","first_name":"R"},{"id":"FF6018E0-D806-11E9-8E43-0B14E6697425","first_name":"Stefan","orcid":"0000-0003-3413-1343","last_name":"Riegler","full_name":"Riegler, Stefan"},{"full_name":"Benková, Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"type":"journal_article","date_updated":"2025-04-15T06:27:18Z","project":[{"grant_number":"26130","name":"Functional asymmetry of medial habenula outputs in mice","_id":"62883ed7-2b32-11ec-9570-93580204e56b"}],"isi":1,"day":"13","file_date_updated":"2023-07-12T10:01:54Z","date_published":"2023-06-13T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.3390/cells12121613","article_processing_charge":"Yes","volume":12,"oa_version":"Published Version","status":"public","corr_author":"1","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"}],"publication":"Cells","file":[{"content_type":"application/pdf","access_level":"open_access","file_id":"13218","date_updated":"2023-07-12T10:01:54Z","file_name":"2023_cells_Abualia.pdf","creator":"alisjak","file_size":1066802,"date_created":"2023-07-12T10:01:54Z","checksum":"6dc9df5f4f59fc27c509c275060354a5","relation":"main_file","success":1}],"issue":"12","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"has_accepted_license":"1","pmid":1,"citation":{"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>.","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>.","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.","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>","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>","ista":"Abualia R, Riegler S, Benková E. 2023. Nitrate, auxin and cytokinin - a trio to tango. Cells. 12(12), 1613.","short":"R. Abualia, S. Riegler, E. Benková, Cells 12 (2023)."},"date_created":"2023-07-12T07:41:25Z","department":[{"_id":"EvBe"}],"quality_controlled":"1","title":"Nitrate, auxin and cytokinin - a trio to tango","_id":"13214","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2073-4409"]},"article_number":"1613","year":"2023","external_id":{"pmid":["37371083"],"isi":["001017033600001"]},"intvolume":"        12","month":"06","acknowledgement":"This work was supported by the Austrian Academy of Sciences ÖAW: Doc fellowship (26130) to Stefan Riegler.","publication_status":"published","ddc":["570"],"article_type":"review","oa":1,"scopus_import":"1"},{"publication":"Journal of Cell Science","issue":"15","status":"public","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."}],"oa_version":"None","volume":136,"article_processing_charge":"No","doi":"10.1242/jcs.260668","language":[{"iso":"eng"}],"date_published":"2023-08-01T00:00:00Z","OA_type":"free access","day":"01","isi":1,"project":[{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_updated":"2025-06-25T06:28:45Z","type":"journal_article","publisher":"The Company of Biologists","author":[{"first_name":"Tomohito","last_name":"Higashi","full_name":"Higashi, Tomohito"},{"first_name":"Rachel E.","last_name":"Stephenson","full_name":"Stephenson, Rachel E."},{"full_name":"Schwayer, Cornelia","last_name":"Schwayer","orcid":"0000-0001-5130-2226","first_name":"Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87"},{"id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","first_name":"Karla","last_name":"Huljev","full_name":"Huljev, Karla"},{"first_name":"Atsuko Y.","last_name":"Higashi","full_name":"Higashi, Atsuko Y."},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"},{"first_name":"Hideki","full_name":"Chiba, Hideki","last_name":"Chiba"},{"first_name":"Ann L.","last_name":"Miller","full_name":"Miller, Ann L."}],"oa":1,"scopus_import":"1","article_type":"original","ddc":["570"],"publication_status":"published","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.]. ","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"month":"08","intvolume":"       136","year":"2023","external_id":{"pmid":["37461809"],"isi":["001070149000001"]},"article_number":"jcs260668","ec_funded":1,"OA_place":"publisher","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14082","quality_controlled":"1","department":[{"_id":"CaHe"},{"_id":"EvBe"}],"title":"ZnUMBA - a live imaging method to detect local barrier breaches","main_file_link":[{"url":"https://doi.org/10.1242/jcs.260668","open_access":"1"}],"date_created":"2023-08-20T22:01:13Z","has_accepted_license":"1","pmid":1,"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>.","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.","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>.","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>","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>","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).","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."}}]