[{"publication_identifier":{"issn":["0959437X"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1016/j.gde.2017.03.010","project":[{"_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16","call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000404880400013"],"pmid":["28391060"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publist_id":"6394","file_date_updated":"2019-04-17T08:00:36Z","volume":45,"date_created":"2018-12-11T11:49:38Z","date_updated":"2023-09-22T09:48:15Z","author":[{"last_name":"Ötvös","first_name":"Krisztina","orcid":"0000-0002-5503-4983","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","full_name":"Ötvös, Krisztina"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"}],"department":[{"_id":"EvBe"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2017","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2017-08-01T00:00:00Z","page":"82 - 89","citation":{"ieee":"K. Ötvös and E. Benková, “Spatiotemporal mechanisms of root branching,” Current Opinion in Genetics & Development, vol. 45. Elsevier, pp. 82–89, 2017.","apa":"Ötvös, K., & Benková, E. (2017). Spatiotemporal mechanisms of root branching. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2017.03.010","ista":"Ötvös K, Benková E. 2017. Spatiotemporal mechanisms of root branching. Current Opinion in Genetics & Development. 45, 82–89.","ama":"Ötvös K, Benková E. Spatiotemporal mechanisms of root branching. Current Opinion in Genetics & Development. 2017;45:82-89. doi:10.1016/j.gde.2017.03.010","chicago":"Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.” Current Opinion in Genetics & Development. Elsevier, 2017. https://doi.org/10.1016/j.gde.2017.03.010.","short":"K. Ötvös, E. Benková, Current Opinion in Genetics & Development 45 (2017) 82–89.","mla":"Ötvös, Krisztina, and Eva Benková. “Spatiotemporal Mechanisms of Root Branching.” Current Opinion in Genetics & Development, vol. 45, Elsevier, 2017, pp. 82–89, doi:10.1016/j.gde.2017.03.010."},"publication":"Current Opinion in Genetics & Development","abstract":[{"text":"The fundamental tasks of the root system are, besides anchoring, mediating interactions between plant and soil and providing the plant with water and nutrients. The architecture of the root system is controlled by endogenous mechanisms that constantly integrate environmental signals, such as availability of nutrients and water. Extremely important for efficient soil exploitation and survival under less favorable conditions is the developmental flexibility of the root system that is largely determined by its postembryonic branching capacity. Modulation of initiation and outgrowth of lateral roots provides roots with an exceptional plasticity, allows optimal adjustment to underground heterogeneity, and enables effective soil exploitation and use of resources. Here we discuss recent advances in understanding the molecular mechanisms that shape the plant root system and integrate external cues to adapt to the changing environment.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","file":[{"file_name":"Otvos_Benkova_CurOpDevBiol_2017.pdf","access_level":"open_access","file_size":364133,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6336","date_updated":"2019-04-17T08:00:36Z","date_created":"2019-04-17T08:00:36Z","success":1}],"pubrep_id":"1017","intvolume":" 45","title":"Spatiotemporal mechanisms of root branching","ddc":["575"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1004"},{"scopus_import":"1","day":"19","has_accepted_license":"1","article_processing_charge":"Yes","publication":"eLife","citation":{"mla":"von Wangenheim, Daniel, et al. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” ELife, vol. 6, e26792, eLife Sciences Publications, 2017, doi:10.7554/eLife.26792.","short":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, J. Friml, ELife 6 (2017).","chicago":"Wangenheim, Daniel von, Robert Hauschild, Matyas Fendrych, Vanessa Barone, Eva Benková, and Jiří Friml. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.26792.","ama":"von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. Live tracking of moving samples in confocal microscopy for vertically grown roots. eLife. 2017;6. doi:10.7554/eLife.26792","ista":"von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. 2017. Live tracking of moving samples in confocal microscopy for vertically grown roots. eLife. 6, e26792.","apa":"von Wangenheim, D., Hauschild, R., Fendrych, M., Barone, V., Benková, E., & Friml, J. (2017). Live tracking of moving samples in confocal microscopy for vertically grown roots. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.26792","ieee":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, and J. Friml, “Live tracking of moving samples in confocal microscopy for vertically grown roots,” eLife, vol. 6. eLife Sciences Publications, 2017."},"date_published":"2017-06-19T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Roots navigate through soil integrating environmental signals to orient their growth. The Arabidopsis root is a widely used model for developmental, physiological and cell biological studies. Live imaging greatly aids these efforts, but the horizontal sample position and continuous root tip displacement present significant difficulties. Here, we develop a confocal microscope setup for vertical sample mounting and integrated directional illumination. We present TipTracker – a custom software for automatic tracking of diverse moving objects usable on various microscope setups. Combined, this enables observation of root tips growing along the natural gravity vector over prolonged periods of time, as well as the ability to induce rapid gravity or light stimulation. We also track migrating cells in the developing zebrafish embryo, demonstrating the utility of this system in the acquisition of high-resolution data sets of dynamic samples. We provide detailed descriptions of the tools enabling the easy implementation on other microscopes."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"946","title":"Live tracking of moving samples in confocal microscopy for vertically grown roots","status":"public","ddc":["570"],"intvolume":" 6","pubrep_id":"847","file":[{"date_created":"2018-12-12T10:17:57Z","date_updated":"2020-07-14T12:48:15Z","checksum":"9af3398cb0d81f99d79016a616df22e9","file_id":"5315","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":19581847,"file_name":"IST-2017-847-v1+1_elife-26792-v2.pdf","access_level":"open_access"}],"oa_version":"Published Version","month":"06","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000404728300001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Molecular basis of root growth inhibition by auxin","call_identifier":"FWF","grant_number":"M02128","_id":"2572ED28-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"doi":"10.7554/eLife.26792","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"article_number":"e26792","file_date_updated":"2020-07-14T12:48:15Z","ec_funded":1,"publist_id":"6471","license":"https://creativecommons.org/licenses/by/4.0/","year":"2017","acknowledgement":"Funding: Marie Curie Actions (FP7/2007-2013 no 291734) to Daniel von Wangenheim; Austrian Science Fund (M 2128-B21) to Matyáš Fendrych; Austrian Science Fund (FWF01_I1774S) to Eva Benková; European Research Council (FP7/2007-2013 no 282300) to Jiří Friml. \r\nThe authors are grateful to the Miba Machine Shop at IST Austria for their contribution to the microscope setup and to Yvonne Kemper for reading, understanding and correcting the manuscript.\r\n#BioimagingFacility","publication_status":"published","department":[{"_id":"JiFr"},{"_id":"Bio"},{"_id":"CaHe"},{"_id":"EvBe"}],"publisher":"eLife Sciences Publications","author":[{"last_name":"Von Wangenheim","first_name":"Daniel","orcid":"0000-0002-6862-1247","id":"49E91952-F248-11E8-B48F-1D18A9856A87","full_name":"Von Wangenheim, Daniel"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","first_name":"Matyas","last_name":"Fendrych","full_name":"Fendrych, Matyas"},{"id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","first_name":"Vanessa","last_name":"Barone","full_name":"Barone, Vanessa"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"related_material":{"record":[{"id":"5566","status":"public","relation":"popular_science"}]},"date_updated":"2024-02-21T13:49:34Z","date_created":"2018-12-11T11:49:21Z","volume":6},{"publication":"Auxins and Cytokinins in Plant Biology","citation":{"short":"A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017) 1–29.","mla":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology, vol. 1569, Springer, 2017, pp. 1–29, doi:10.1007/978-1-4939-6831-2_1.","chicago":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology. Springer, 2017. https://doi.org/10.1007/978-1-4939-6831-2_1.","ama":"Hurny A, Benková E. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 2017;1569:1-29. doi:10.1007/978-1-4939-6831-2_1","apa":"Hurny, A., & Benková, E. (2017). Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. Springer. https://doi.org/10.1007/978-1-4939-6831-2_1","ieee":"A. Hurny and E. Benková, “Methodological advances in auxin and cytokinin biology,” Auxins and Cytokinins in Plant Biology, vol. 1569. Springer, pp. 1–29, 2017.","ista":"Hurny A, Benková E. 2017. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 1569, 1–29."},"page":"1 - 29","date_published":"2017-03-17T00:00:00Z","scopus_import":1,"day":"17","has_accepted_license":"1","_id":"1024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["575"],"status":"public","title":"Methodological advances in auxin and cytokinin biology","intvolume":" 1569","pubrep_id":"1019","file":[{"file_name":"IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf","access_level":"open_access","file_size":840646,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5068","date_created":"2018-12-12T10:14:18Z","date_updated":"2019-10-15T07:47:05Z"}],"oa_version":"Submitted Version","type":"journal_article","alternative_title":["Methods in Molecular Biology"],"abstract":[{"lang":"eng","text":"The history of auxin and cytokinin biology including the initial discoveries by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt (1919) is a beautiful demonstration of unceasing continuity of research. Novel findings are integrated into existing hypotheses and models and deepen our understanding of biological principles. At the same time new questions are triggered and hand to hand with this new methodologies are developed to address these new challenges."}],"oa":1,"quality_controlled":"1","project":[{"_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF"}],"doi":"10.1007/978-1-4939-6831-2_1","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["10643745"]},"year":"2017","publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"Springer","author":[{"full_name":"Hurny, Andrej","orcid":"0000-0003-3638-1426","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","last_name":"Hurny","first_name":"Andrej"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva"}],"related_material":{"record":[{"id":"539","relation":"dissertation_contains","status":"public"}]},"date_created":"2018-12-11T11:49:45Z","date_updated":"2024-03-27T23:30:17Z","volume":1569,"file_date_updated":"2019-10-15T07:47:05Z","publist_id":"6369"},{"month":"07","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"quality_controlled":"1","doi":"10.1038/celldisc.2016.18","language":[{"iso":"eng"}],"article_number":"16018","publist_id":"6299","ec_funded":1,"file_date_updated":"2018-12-12T10:13:33Z","year":"2016","acknowledgement":"We thank Bonnie Bartel, Jenny Russinova and Niko Geldner\r\nfor sharing published material, Martine de Cock and Annick\r\nBleys for help in preparing the manuscript. This work was\r\nsupported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP); Czech Science Foundation\r\nGAČR (GA13-40637S); project CEITEC—Central European\r\nInstitute of Technology (CZ.1.05/1.1.00/02.0068). SV is a\r\npostdoctoral fellow of the Research Foundation-Flanders.\r\nSN is a Project Assistant Professor supported by the Japanese\r\nSociety for the Promotion of Science (JSPS; 30612022 to SN),\r\nthe NC-CARP project of the Ministry of Education, Culture,\r\nSports, Science and Technology in Japan to SN.","publisher":"Nature Publishing Group","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"publication_status":"published","author":[{"full_name":"Łangowski, Łukasz","last_name":"Łangowski","first_name":"Łukasz"},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560","first_name":"Krzysztof T","last_name":"Wabnik","full_name":"Wabnik, Krzysztof T"},{"orcid":"0000-0001-5039-9660","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Hongjiang","full_name":"Li, Hongjiang"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"last_name":"Naramoto","first_name":"Satoshi","full_name":"Naramoto, Satoshi"},{"first_name":"Hirokazu","last_name":"Tanaka","full_name":"Tanaka, Hirokazu"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"volume":2,"date_updated":"2021-01-12T06:48:08Z","date_created":"2018-12-11T11:50:02Z","scopus_import":1,"has_accepted_license":"1","day":"19","citation":{"ista":"Łangowski Ł, Wabnik KT, Li H, Vanneste S, Naramoto S, Tanaka H, Friml J. 2016. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery. 2, 16018.","ieee":"Ł. Łangowski et al., “Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells,” Cell Discovery, vol. 2. Nature Publishing Group, 2016.","apa":"Łangowski, Ł., Wabnik, K. T., Li, H., Vanneste, S., Naramoto, S., Tanaka, H., & Friml, J. (2016). Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery. Nature Publishing Group. https://doi.org/10.1038/celldisc.2016.18","ama":"Łangowski Ł, Wabnik KT, Li H, et al. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery. 2016;2. doi:10.1038/celldisc.2016.18","chicago":"Łangowski, Łukasz, Krzysztof T Wabnik, Hongjiang Li, Steffen Vanneste, Satoshi Naramoto, Hirokazu Tanaka, and Jiří Friml. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” Cell Discovery. Nature Publishing Group, 2016. https://doi.org/10.1038/celldisc.2016.18.","mla":"Łangowski, Łukasz, et al. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” Cell Discovery, vol. 2, 16018, Nature Publishing Group, 2016, doi:10.1038/celldisc.2016.18.","short":"Ł. Łangowski, K.T. Wabnik, H. Li, S. Vanneste, S. Naramoto, H. Tanaka, J. Friml, Cell Discovery 2 (2016)."},"publication":"Cell Discovery","date_published":"2016-07-19T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The asymmetric localization of proteins in the plasma membrane domains of eukaryotic cells is a fundamental manifestation of cell polarity that is central to multicellular organization and developmental patterning. In plants, the mechanisms underlying the polar localization of cargo proteins are still largely unknown and appear to be fundamentally distinct from those operating in mammals. Here, we present a systematic, quantitative comparative analysis of the polar delivery and subcellular localization of proteins that characterize distinct polar plasma membrane domains in plant cells. The combination of microscopic analyses and computational modeling revealed a mechanistic framework common to diverse polar cargos and underlying the establishment and maintenance of apical, basal, and lateral polar domains in plant cells. This mechanism depends on the polar secretion, constitutive endocytic recycling, and restricted lateral diffusion of cargos within the plasma membrane. Moreover, our observations suggest that polar cargo distribution involves the individual protein potential to form clusters within the plasma membrane and interact with the extracellular matrix. Our observations provide insights into the shared cellular mechanisms of polar cargo delivery and polarity maintenance in plant cells."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1081","intvolume":" 2","title":"Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells","ddc":["580"],"status":"public","pubrep_id":"757","file":[{"content_type":"application/pdf","file_size":5261671,"creator":"system","file_name":"IST-2017-757-v1+1_celldisc201618.pdf","access_level":"open_access","date_updated":"2018-12-12T10:13:33Z","date_created":"2018-12-12T10:13:33Z","relation":"main_file","file_id":"5017"}],"oa_version":"Published Version"},{"intvolume":" 28","title":"A model of differential growth guided apical hook formation in plants","status":"public","_id":"1153","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","issue":"10","abstract":[{"text":"Differential cell growth enables flexible organ bending in the presence of environmental signals such as light or gravity. A prominent example of the developmental processes based on differential cell growth is the formation of the apical hook that protects the fragile shoot apical meristem when it breaks through the soil during germination. Here, we combined in silico and in vivo approaches to identify a minimal mechanism producing auxin gradient-guided differential growth during the establishment of the apical hook in the model plant Arabidopsis thaliana. Computer simulation models based on experimental data demonstrate that asymmetric expression of the PIN-FORMED auxin efflux carrier at the concave (inner) versus convex (outer) side of the hook suffices to establish an auxin maximum in the epidermis at the concave side of the apical hook. Furthermore, we propose a mechanism that translates this maximum into differential growth, and thus curvature, of the apical hook. Through a combination of experimental and in silico computational approaches, we have identified the individual contributions of differential cell elongation and proliferation to defining the apical hook and reveal the role of auxin-ethylene crosstalk in balancing these two processes. © 2016 American Society of Plant Biologists. All rights reserved.","lang":"eng"}],"page":"2464 - 2477","citation":{"chicago":"Žádníková, Petra, Krzysztof T Wabnik, Anas Abuzeineh, Marçal Gallemí, Dominique Van Der Straeten, Richard Smith, Dirk Inze, Jiří Friml, Przemysław Prusinkiewicz, and Eva Benková. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” Plant Cell. American Society of Plant Biologists, 2016. https://doi.org/10.1105/tpc.15.00569.","mla":"Žádníková, Petra, et al. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” Plant Cell, vol. 28, no. 10, American Society of Plant Biologists, 2016, pp. 2464–77, doi:10.1105/tpc.15.00569.","short":"P. Žádníková, K.T. Wabnik, A. Abuzeineh, M. Gallemí, D. Van Der Straeten, R. Smith, D. Inze, J. Friml, P. Prusinkiewicz, E. Benková, Plant Cell 28 (2016) 2464–2477.","ista":"Žádníková P, Wabnik KT, Abuzeineh A, Gallemí M, Van Der Straeten D, Smith R, Inze D, Friml J, Prusinkiewicz P, Benková E. 2016. A model of differential growth guided apical hook formation in plants. Plant Cell. 28(10), 2464–2477.","apa":"Žádníková, P., Wabnik, K. T., Abuzeineh, A., Gallemí, M., Van Der Straeten, D., Smith, R., … Benková, E. (2016). A model of differential growth guided apical hook formation in plants. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.15.00569","ieee":"P. Žádníková et al., “A model of differential growth guided apical hook formation in plants,” Plant Cell, vol. 28, no. 10. American Society of Plant Biologists, pp. 2464–2477, 2016.","ama":"Žádníková P, Wabnik KT, Abuzeineh A, et al. A model of differential growth guided apical hook formation in plants. Plant Cell. 2016;28(10):2464-2477. doi:10.1105/tpc.15.00569"},"publication":"Plant Cell","date_published":"2016-10-01T00:00:00Z","scopus_import":1,"day":"01","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"publisher":"American Society of Plant Biologists","publication_status":"published","acknowledgement":"We thank Martine De Cock and Annick Bleys for help in preparing the manuscript, Daniel Van Damme for sharing material and stimulating discussion, and Rudiger Simon for support during revision of the manuscript.\r\nThis work was supported by grants from the European Research Council (StartingIndependentResearchGrantERC-2007-Stg-207362-HCPO)and the Czech Science Foundation (GACR CZ.1.07/2.3.00/20.0043) to E.B.\r\nand Natural Sciences and Engineering Research Council of Canada Discovery Grant 2014-05325 to P.P. K.W. acknowledges funding from a Human Frontier Science Program Long-Term Fellowship (LT-000209-2014).","year":"2016","volume":28,"date_updated":"2021-01-12T06:48:40Z","date_created":"2018-12-11T11:50:26Z","author":[{"full_name":"Žádníková, Petra","first_name":"Petra","last_name":"Žádníková"},{"full_name":"Wabnik, Krzysztof T","first_name":"Krzysztof T","last_name":"Wabnik","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560"},{"full_name":"Abuzeineh, Anas","last_name":"Abuzeineh","first_name":"Anas"},{"full_name":"Gallemí, Marçal","last_name":"Gallemí","first_name":"Marçal"},{"first_name":"Dominique","last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique"},{"full_name":"Smith, Richard","last_name":"Smith","first_name":"Richard"},{"full_name":"Inze, Dirk","first_name":"Dirk","last_name":"Inze"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"full_name":"Prusinkiewicz, Przemysław","first_name":"Przemysław","last_name":"Prusinkiewicz"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"}],"publist_id":"6205","ec_funded":1,"project":[{"grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis","call_identifier":"FP7"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134968/","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1105/tpc.15.00569","month":"10"},{"scopus_import":1,"day":"01","month":"12","page":"4419 - 4424","quality_controlled":"1","citation":{"chicago":"Cucinotta, Mara, Silvia Manrique, Andrea Guazzotti, Nadia Quadrelli, Marta Mendes, Eva Benková, and Lucia Colombo. “Cytokinin Response Factors Integrate Auxin and Cytokinin Pathways for Female Reproductive Organ Development.” Development. Company of Biologists, 2016. https://doi.org/10.1242/dev.143545.","mla":"Cucinotta, Mara, et al. “Cytokinin Response Factors Integrate Auxin and Cytokinin Pathways for Female Reproductive Organ Development.” Development, vol. 143, no. 23, Company of Biologists, 2016, pp. 4419–24, doi:10.1242/dev.143545.","short":"M. Cucinotta, S. Manrique, A. Guazzotti, N. Quadrelli, M. Mendes, E. Benková, L. Colombo, Development 143 (2016) 4419–4424.","ista":"Cucinotta M, Manrique S, Guazzotti A, Quadrelli N, Mendes M, Benková E, Colombo L. 2016. Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development. Development. 143(23), 4419–4424.","apa":"Cucinotta, M., Manrique, S., Guazzotti, A., Quadrelli, N., Mendes, M., Benková, E., & Colombo, L. (2016). Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development. Development. Company of Biologists. https://doi.org/10.1242/dev.143545","ieee":"M. Cucinotta et al., “Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development,” Development, vol. 143, no. 23. Company of Biologists, pp. 4419–4424, 2016.","ama":"Cucinotta M, Manrique S, Guazzotti A, et al. Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development. Development. 2016;143(23):4419-4424. doi:10.1242/dev.143545"},"publication":"Development","language":[{"iso":"eng"}],"doi":"10.1242/dev.143545","date_published":"2016-12-01T00:00:00Z","type":"journal_article","issue":"23","publist_id":"6168","abstract":[{"lang":"eng","text":"The developmental programme of the pistil is under the control of both auxin and cytokinin. Crosstalk between these factors converges on regulation of the auxin carrier PIN-FORMED 1 (PIN1). Here, we show that in the triple transcription factor mutant cytokinin response factor 2 (crf2) crf3 crf6 both pistil length and ovule number were reduced. PIN1 expression was also lower in the triple mutant and the phenotypes could not be rescued by exogenous cytokinin application. pin1 complementation studies using genomic PIN1 constructs showed that the pistil phenotypes were only rescued when the PCRE1 domain, to which CRFs bind, was present. Without this domain, pin mutants resemble the crf2 crf3 crf6 triple mutant, indicating the pivotal role of CRFs in auxin-cytokinin crosstalk."}],"publisher":"Company of Biologists","department":[{"_id":"EvBe"}],"intvolume":" 143","title":"Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development","status":"public","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1185","year":"2016","acknowledgement":"M.C. was funded by a PhD fellowship from the Università degli Studi di Milano-Bicocca and from Ministero dell'Istruzione, dell'Università e della Ricerca (MIUR) [MIUR-PRIN 2012]. L.C. is also supported by MIUR [MIUR-PRIN 2012]. We would like to thank Andrew MacCabe and Edward Kiegle for editing the paper.","oa_version":"None","volume":143,"date_updated":"2021-01-12T06:48:56Z","date_created":"2018-12-11T11:50:36Z","author":[{"full_name":"Cucinotta, Mara","first_name":"Mara","last_name":"Cucinotta"},{"last_name":"Manrique","first_name":"Silvia","full_name":"Manrique, Silvia"},{"last_name":"Guazzotti","first_name":"Andrea","full_name":"Guazzotti, Andrea"},{"last_name":"Quadrelli","first_name":"Nadia","full_name":"Quadrelli, Nadia"},{"full_name":"Mendes, Marta","first_name":"Marta","last_name":"Mendes"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"},{"full_name":"Colombo, Lucia","last_name":"Colombo","first_name":"Lucia"}]},{"alternative_title":["Methods in Molecular Biology"],"type":"book_chapter","abstract":[{"lang":"eng","text":"Mechanisms for cell protection are essential for survival of multicellular organisms. In plants, the apical hook, which is transiently formed in darkness when the germinating seedling penetrates towards the soil surface, plays such protective role and shields the vitally important shoot apical meristem and cotyledons from damage. The apical hook is formed by bending of the upper hypocotyl soon after germination, and it is maintained in a closed stage while the hypocotyl continues to penetrate through the soil and rapidly opens when exposed to light in proximity of the soil surface. To uncover the complex molecular network orchestrating this spatiotemporally tightly coordinated process, monitoring of the apical hook development in real time is indispensable. Here we describe an imaging platform that enables high-resolution kinetic analysis of this dynamic developmental process. © Springer Science+Business Media New York 2017."}],"publist_id":"6135","status":"public","title":"Real time analysis of the apical hook development","publication_status":"published","intvolume":" 1497","publisher":"Humana Press","department":[{"_id":"EvBe"}],"_id":"1210","acknowledgement":"We thank Herman \r\nHöfte \r\n, Todor Asenov, Robert Hauschield, and \r\nMarcal Gallemi for help with the establishment of the real-time \r\nimaging platform and technical support. This work was supported \r\nby the Czech Science Foundation (GA13-39982S) to Eva Benková. \r\nDominique Van Der Straeten acknowledges the Research \r\nFoundation Flanders for fi\r\n nancial support (G.0656.13N). Dajo \r\nSmet holds a PhD fellowship of the Research Foundation Flanders. ","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","date_updated":"2021-01-12T06:49:07Z","date_created":"2018-12-11T11:50:44Z","oa_version":"None","volume":1497,"author":[{"id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87","last_name":"Zhu","first_name":"Qiang","full_name":"Zhu, Qiang"},{"first_name":"Petra","last_name":"Žádníková","full_name":"Žádníková, Petra"},{"first_name":"Dajo","last_name":"Smet","full_name":"Smet, Dajo"},{"last_name":"Van Der Straeten","first_name":"Dominique","full_name":"Van Der Straeten, Dominique"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"}],"scopus_import":1,"month":"11","day":"19","quality_controlled":"1","page":"1 - 8","publication":"Plant Hormones","citation":{"mla":"Zhu, Qiang, et al. “Real Time Analysis of the Apical Hook Development.” Plant Hormones, vol. 1497, Humana Press, 2016, pp. 1–8, doi:10.1007/978-1-4939-6469-7_1.","short":"Q. Zhu, P. Žádníková, D. Smet, D. Van Der Straeten, E. Benková, in:, Plant Hormones, Humana Press, 2016, pp. 1–8.","chicago":"Zhu, Qiang, Petra Žádníková, Dajo Smet, Dominique Van Der Straeten, and Eva Benková. “Real Time Analysis of the Apical Hook Development.” In Plant Hormones, 1497:1–8. Humana Press, 2016. https://doi.org/10.1007/978-1-4939-6469-7_1.","ama":"Zhu Q, Žádníková P, Smet D, Van Der Straeten D, Benková E. Real time analysis of the apical hook development. In: Plant Hormones. Vol 1497. Humana Press; 2016:1-8. doi:10.1007/978-1-4939-6469-7_1","ista":"Zhu Q, Žádníková P, Smet D, Van Der Straeten D, Benková E. 2016.Real time analysis of the apical hook development. In: Plant Hormones. Methods in Molecular Biology, vol. 1497, 1–8.","apa":"Zhu, Q., Žádníková, P., Smet, D., Van Der Straeten, D., & Benková, E. (2016). Real time analysis of the apical hook development. In Plant Hormones (Vol. 1497, pp. 1–8). Humana Press. https://doi.org/10.1007/978-1-4939-6469-7_1","ieee":"Q. Zhu, P. Žádníková, D. Smet, D. Van Der Straeten, and E. Benková, “Real time analysis of the apical hook development,” in Plant Hormones, vol. 1497, Humana Press, 2016, pp. 1–8."},"language":[{"iso":"eng"}],"doi":"10.1007/978-1-4939-6469-7_1","date_published":"2016-11-19T00:00:00Z"},{"doi":"10.1242/dev.130211","date_published":"2016-05-03T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ieee":"M. Gallemi et al., “DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis,” Development, vol. 143, no. 9. Company of Biologists, pp. 1623–1631, 2016.","apa":"Gallemi, M., Galstyan, A., Paulišić, S., Then, C., Ferrández Ayela, A., Lorenzo Orts, L., … Martínez García, J. (2016). DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis. Development. Company of Biologists. https://doi.org/10.1242/dev.130211","ista":"Gallemi M, Galstyan A, Paulišić S, Then C, Ferrández Ayela A, Lorenzo Orts L, Roig Villanova I, Wang X, Micol J, Ponce M, Devlin P, Martínez García J. 2016. DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis. Development. 143(9), 1623–1631.","ama":"Gallemi M, Galstyan A, Paulišić S, et al. DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis. Development. 2016;143(9):1623-1631. doi:10.1242/dev.130211","chicago":"Gallemi, Marçal, Anahit Galstyan, Sandi Paulišić, Christiane Then, Almudena Ferrández Ayela, Laura Lorenzo Orts, Irma Roig Villanova, et al. “DRACULA2 Is a Dynamic Nucleoporin with a Role in Regulating the Shade Avoidance Syndrome in Arabidopsis.” Development. Company of Biologists, 2016. https://doi.org/10.1242/dev.130211.","short":"M. Gallemi, A. Galstyan, S. Paulišić, C. Then, A. Ferrández Ayela, L. Lorenzo Orts, I. Roig Villanova, X. Wang, J. Micol, M. Ponce, P. Devlin, J. Martínez García, Development 143 (2016) 1623–1631.","mla":"Gallemi, Marçal, et al. “DRACULA2 Is a Dynamic Nucleoporin with a Role in Regulating the Shade Avoidance Syndrome in Arabidopsis.” Development, vol. 143, no. 9, Company of Biologists, 2016, pp. 1623–31, doi:10.1242/dev.130211."},"publication":"Development","page":"1623 - 1631","quality_controlled":"1","day":"03","month":"05","scopus_import":1,"author":[{"first_name":"Marcal","last_name":"Gallemi Rovira","id":"460C6802-F248-11E8-B48F-1D18A9856A87","full_name":"Gallemi Rovira, Marcal"},{"last_name":"Galstyan","first_name":"Anahit","full_name":"Galstyan, Anahit"},{"last_name":"Paulišić","first_name":"Sandi","full_name":"Paulišić, Sandi"},{"last_name":"Then","first_name":"Christiane","full_name":"Then, Christiane"},{"first_name":"Almudena","last_name":"Ferrández Ayela","full_name":"Ferrández Ayela, Almudena"},{"first_name":"Laura","last_name":"Lorenzo Orts","full_name":"Lorenzo Orts, Laura"},{"last_name":"Roig Villanova","first_name":"Irma","full_name":"Roig Villanova, Irma"},{"full_name":"Wang, Xuewen","first_name":"Xuewen","last_name":"Wang"},{"full_name":"Micol, José","first_name":"José","last_name":"Micol"},{"full_name":"Ponce, Maria","first_name":"Maria","last_name":"Ponce"},{"last_name":"Devlin","first_name":"Paul","full_name":"Devlin, Paul"},{"full_name":"Martínez García, Jaime","first_name":"Jaime","last_name":"Martínez García"}],"volume":143,"oa_version":"None","date_updated":"2021-01-12T06:49:27Z","date_created":"2018-12-11T11:50:59Z","_id":"1258","acknowledgement":"M.G. received an FPI fellowship from the Spanish Ministerio de Economía y Competitividad (MINECO). A.G. and A.F.-A. received FPU fellowships from the Spanish Ministerio de Educación. S.P. received an FI fellowship from the Agència de Gestió D'ajuts Universitaris i de Recerca (AGAUR - Generalitat de Catalunya). C.T. received a Marie Curie IEF postdoctoral contract funded by the European Commission. I.R.-V. received initially an FPI fellowship from the Spanish MINECO and later a Beatriu de Pinós contract from AGAUR. Our research is supported by grants from the Spanish MINECO-FEDER [BIO2008-00169, BIO2011-23489 and BIO2014-59895-P] and Generalitat de Catalunya [2011-SGR447 and Xarba] to J.F.M.-G., and Generalitat Valenciana [PROMETEO/2009/112, PROMETEOII/2014/006] to M.R.P. and J.L.M. We acknowledge the support of the Spanish MINECO for the ‘Centro de Excelencia Severo Ochoa 2016-2019’ [award SEV-2015-0533]. We thank the CRAG greenhouse service for plant care; Chus Burillo for technical help; Sergi Portolés and Carles Rentero for assistance with mutagenesis; Mark Estelle (UCSD, USA) for providing sar1-4, sar3-1 and sar3-3 seeds; Juanjo López-Moya (CRAG, Barcelona; 35S:HcPro plasmid) and Dolors Ludevid (CRAG; C307 plasmid) for providing DNA plasmids; and Manuel Rodríguez-Concepción (CRAG) and Miguel Blázquez (IBMCP, Valencia, Spain) for comments on the manuscript.","year":"2016","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Company of Biologists","intvolume":" 143","department":[{"_id":"EvBe"}],"title":"DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis","status":"public","publication_status":"published","publist_id":"6068","issue":"9","abstract":[{"text":"When plants grow in close proximity basic resources such as light can become limiting. Under such conditions plants respond to anticipate and/or adapt to the light shortage, a process known as the shade avoidance syndrome (SAS). Following genetic screening using a shade-responsive luciferase reporter line (PHYB:LUC), we identified DRACULA2 (DRA2), which encodes an Arabidopsis homolog of mammalian nucleoporin 98, a component of the nuclear pore complex (NPC). DRA2, together with other nucleoporins, participates positively in the control of the hypocotyl elongation response to plant proximity, a role that can be considered dependent on the nucleocytoplasmic transport of macromolecules (i.e. is transport dependent). In addition, our results reveal a specific role for DRA2 in controlling shade-induced gene expression. We suggest that this novel regulatory role of DRA2 is transport independent and that it might rely on its dynamic localization within and outside of the NPC. These results provide mechanistic insights in to how SAS responses are rapidly established by light conditions. They also indicate that nucleoporins have an active role in plant signaling.","lang":"eng"}],"type":"journal_article"},{"_id":"1264","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 171","status":"public","title":"Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier","oa_version":"Submitted Version","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"n contrast with the wealth of recent reports about the function of μ-adaptins and clathrin adaptor protein (AP) complexes, there is very little information about the motifs that determine the sorting of membrane proteins within clathrin-coated vesicles in plants. Here, we investigated putative sorting signals in the large cytosolic loop of the Arabidopsis (Arabidopsis thaliana) PIN-FORMED1 (PIN1) auxin transporter, which are involved in binding μ-adaptins and thus in PIN1 trafficking and localization. We found that Phe-165 and Tyr-280, Tyr-328, and Tyr-394 are involved in the binding of different μ-adaptins in vitro. However, only Phe-165, which binds μA(μ2)- and μD(μ3)-adaptin, was found to be essential for PIN1 trafficking and localization in vivo. The PIN1:GFP-F165A mutant showed reduced endocytosis but also localized to intracellular structures containing several layers of membranes and endoplasmic reticulum (ER) markers, suggesting that they correspond to ER or ER-derived membranes. While PIN1:GFP localized normally in a μA (μ2)-adaptin mutant, it accumulated in big intracellular structures containing LysoTracker in a μD (μ3)-adaptin mutant, consistent with previous results obtained with mutants of other subunits of the AP-3 complex. Our data suggest that Phe-165, through the binding of μA (μ2)- and μD (μ3)-adaptin, is important for PIN1 endocytosis and for PIN1 trafficking along the secretory pathway, respectively."}],"citation":{"mla":"Sancho Andrés, Gloria, et al. “Sorting Motifs Involved in the Trafficking and Localization of the PIN1 Auxin Efflux Carrier.” Plant Physiology, vol. 171, no. 3, American Society of Plant Biologists, 2016, pp. 1965–82, doi:10.1104/pp.16.00373.","short":"G. Sancho Andrés, E. Soriano Ortega, C. Gao, J. Bernabé Orts, M. Narasimhan, A. Müller, R. Tejos, L. Jiang, J. Friml, F. Aniento, M. Marcote, Plant Physiology 171 (2016) 1965–1982.","chicago":"Sancho Andrés, Gloria, Esther Soriano Ortega, Caiji Gao, Joan Bernabé Orts, Madhumitha Narasimhan, Anna Müller, Ricardo Tejos, et al. “Sorting Motifs Involved in the Trafficking and Localization of the PIN1 Auxin Efflux Carrier.” Plant Physiology. American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.00373.","ama":"Sancho Andrés G, Soriano Ortega E, Gao C, et al. Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology. 2016;171(3):1965-1982. doi:10.1104/pp.16.00373","ista":"Sancho Andrés G, Soriano Ortega E, Gao C, Bernabé Orts J, Narasimhan M, Müller A, Tejos R, Jiang L, Friml J, Aniento F, Marcote M. 2016. Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology. 171(3), 1965–1982.","ieee":"G. Sancho Andrés et al., “Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier,” Plant Physiology, vol. 171, no. 3. American Society of Plant Biologists, pp. 1965–1982, 2016.","apa":"Sancho Andrés, G., Soriano Ortega, E., Gao, C., Bernabé Orts, J., Narasimhan, M., Müller, A., … Marcote, M. (2016). Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.00373"},"publication":"Plant Physiology","page":"1965 - 1982","date_published":"2016-07-01T00:00:00Z","scopus_import":1,"day":"01","year":"2016","acknowledgement":"We thank Dr. R. Offringa (Leiden University) for providing the GST-\r\nPIN-CL construct; Sandra Richter and Gerd Jurgens (University of Tübin-\r\ngen) for providing the estradiol-inducible PIN1-RFP construct and the\r\ngnl1 mutant expressing BFA-sensitive GNL1; F.J. Santonja (University of Valencia)\r\nfor help with the statistical analysis; Jurgen Kleine-Vehn, Elke Barbez, and\r\nEva Benkova for helpful discussions; the Salk Institute Genomic Analysis\r\nLaboratory for providing the sequence-indexed Arabidopsis T-DNA in-\r\nsertion mutants; and the greenhouse section and the microscopy section\r\nof SCSIE (University of Valencia) and Pilar Selvi for excellent technical\r\nassistance.","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publication_status":"published","author":[{"full_name":"Sancho Andrés, Gloria","first_name":"Gloria","last_name":"Sancho Andrés"},{"first_name":"Esther","last_name":"Soriano Ortega","full_name":"Soriano Ortega, Esther"},{"full_name":"Gao, Caiji","last_name":"Gao","first_name":"Caiji"},{"first_name":"Joan","last_name":"Bernabé Orts","full_name":"Bernabé Orts, Joan"},{"full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","last_name":"Narasimhan","first_name":"Madhumitha"},{"last_name":"Müller","first_name":"Anna","id":"420AB15A-F248-11E8-B48F-1D18A9856A87","full_name":"Müller, Anna"},{"full_name":"Tejos, Ricardo","first_name":"Ricardo","last_name":"Tejos"},{"full_name":"Jiang, Liwen","last_name":"Jiang","first_name":"Liwen"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Fernando","last_name":"Aniento","full_name":"Aniento, Fernando"},{"full_name":"Marcote, Maria","last_name":"Marcote","first_name":"Maria"}],"volume":171,"date_updated":"2021-01-12T06:49:29Z","date_created":"2018-12-11T11:51:01Z","ec_funded":1,"publist_id":"6059","oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936568/","open_access":"1"}],"project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"quality_controlled":"1","doi":"10.1104/pp.16.00373","language":[{"iso":"eng"}],"month":"07"},{"abstract":[{"lang":"eng","text":"Extracellular matrices (ECMs) are central to the advent of multicellular life, and their mechanical propertiesare modulated by and impinge on intracellular signaling pathways that regulate vital cellular functions. High spatial-resolution mapping of mechanical properties in live cells is, however, extremely challenging. Thus, our understanding of how signaling pathways process physiological signals to generate appropriate mechanical responses is limited. We introduce fluorescence emission-Brillouin scattering imaging (FBi), a method for the parallel and all-optical measurements of mechanical properties and fluorescence at the submicrometer scale in living organisms. Using FBi, we showed thatchanges in cellular hydrostatic pressure and cytoplasm viscoelasticity modulate the mechanical signatures of plant ECMs. We further established that the measured "stiffness" of plant ECMs is symmetrically patternedin hypocotyl cells undergoing directional growth. Finally, application of this method to Arabidopsis thaliana with photoreceptor mutants revealed that red and far-red light signals are essential modulators of ECM viscoelasticity. By mapping the viscoelastic signatures of a complex ECM, we provide proof of principlefor the organism-wide applicability of FBi for measuring the mechanical outputs of intracellular signaling pathways. As such, our work has implications for investigations of mechanosignaling pathways and developmental biology."}],"publist_id":"6057","issue":"435","article_number":"rs5","type":"journal_article","author":[{"full_name":"Elsayad, Kareem","last_name":"Elsayad","first_name":"Kareem"},{"last_name":"Werner","first_name":"Stephanie","full_name":"Werner, Stephanie"},{"id":"460C6802-F248-11E8-B48F-1D18A9856A87","last_name":"Gallemi Rovira","first_name":"Marcal","full_name":"Gallemi Rovira, Marcal"},{"first_name":"Jixiang","last_name":"Kong","full_name":"Kong, Jixiang"},{"full_name":"Guajardo, Edmundo","first_name":"Edmundo","last_name":"Guajardo"},{"full_name":"Zhang, Lijuan","first_name":"Lijuan","last_name":"Zhang"},{"last_name":"Jaillais","first_name":"Yvon","full_name":"Jaillais, Yvon"},{"last_name":"Greb","first_name":"Thomas","full_name":"Greb, Thomas"},{"full_name":"Belkhadir, Youssef","first_name":"Youssef","last_name":"Belkhadir"}],"date_updated":"2021-01-12T06:49:29Z","date_created":"2018-12-11T11:51:02Z","oa_version":"None","volume":9,"year":"2016","_id":"1265","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging","publication_status":"published","intvolume":" 9","department":[{"_id":"EvBe"}],"publisher":"American Association for the Advancement of Science","day":"05","month":"07","scopus_import":1,"doi":"10.1126/scisignal.aaf6326","date_published":"2016-07-05T00:00:00Z","language":[{"iso":"eng"}],"publication":"Science Signaling","citation":{"apa":"Elsayad, K., Werner, S., Gallemi, M., Kong, J., Guajardo, E., Zhang, L., … Belkhadir, Y. (2016). Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging. Science Signaling. American Association for the Advancement of Science. https://doi.org/10.1126/scisignal.aaf6326","ieee":"K. Elsayad et al., “Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging,” Science Signaling, vol. 9, no. 435. American Association for the Advancement of Science, 2016.","ista":"Elsayad K, Werner S, Gallemi M, Kong J, Guajardo E, Zhang L, Jaillais Y, Greb T, Belkhadir Y. 2016. Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging. Science Signaling. 9(435), rs5.","ama":"Elsayad K, Werner S, Gallemi M, et al. Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging. Science Signaling. 2016;9(435). doi:10.1126/scisignal.aaf6326","chicago":"Elsayad, Kareem, Stephanie Werner, Marçal Gallemi, Jixiang Kong, Edmundo Guajardo, Lijuan Zhang, Yvon Jaillais, Thomas Greb, and Youssef Belkhadir. “Mapping the Subcellular Mechanical Properties of Live Cells in Tissues with Fluorescence Emission-Brillouin Imaging.” Science Signaling. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/scisignal.aaf6326.","short":"K. Elsayad, S. Werner, M. Gallemi, J. Kong, E. Guajardo, L. Zhang, Y. Jaillais, T. Greb, Y. Belkhadir, Science Signaling 9 (2016).","mla":"Elsayad, Kareem, et al. “Mapping the Subcellular Mechanical Properties of Live Cells in Tissues with Fluorescence Emission-Brillouin Imaging.” Science Signaling, vol. 9, no. 435, rs5, American Association for the Advancement of Science, 2016, doi:10.1126/scisignal.aaf6326."},"quality_controlled":"1"},{"date_updated":"2021-01-12T06:49:31Z","date_created":"2018-12-11T11:51:03Z","volume":91,"author":[{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"Springer","year":"2016","file_date_updated":"2020-07-14T12:44:42Z","publist_id":"6052","language":[{"iso":"eng"}],"doi":"10.1007/s11103-016-0501-8","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"08","file":[{"file_name":"IST-2016-697-v1+1_s11103-016-0501-8.pdf","access_level":"open_access","creator":"system","file_size":297282,"content_type":"application/pdf","file_id":"5349","relation":"main_file","date_created":"2018-12-12T10:18:28Z","date_updated":"2020-07-14T12:44:42Z","checksum":"0ffb7a15c5336b3a55248cc67021a825"}],"oa_version":"Published Version","pubrep_id":"697","title":"Plant hormones in interactions with the environment","status":"public","ddc":["581"],"intvolume":" 91","_id":"1269","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Plants are continuously exposed to a myriad of external signals such as fluctuating nutrients availability, drought, heat, cold, high salinity, or pathogen/pest attacks that can severely affect their development, growth, and fertility. As sessile organisms, plants must therefore be able to sense and rapidly react to these external inputs, activate efficient responses, and adjust development to changing conditions. In recent years, significant progress has been made towards understanding the molecular mechanisms underlying the intricate and complex communication between plants and the environment. It is now becoming increasingly evident that hormones have an important regulatory role in plant adaptation and defense mechanisms.","lang":"eng"}],"issue":"6","type":"journal_article","date_published":"2016-08-01T00:00:00Z","page":"597","publication":"Plant Molecular Biology","citation":{"ista":"Benková E. 2016. Plant hormones in interactions with the environment. Plant Molecular Biology. 91(6), 597.","ieee":"E. Benková, “Plant hormones in interactions with the environment,” Plant Molecular Biology, vol. 91, no. 6. Springer, p. 597, 2016.","apa":"Benková, E. (2016). Plant hormones in interactions with the environment. Plant Molecular Biology. Springer. https://doi.org/10.1007/s11103-016-0501-8","ama":"Benková E. Plant hormones in interactions with the environment. Plant Molecular Biology. 2016;91(6):597. doi:10.1007/s11103-016-0501-8","chicago":"Benková, Eva. “Plant Hormones in Interactions with the Environment.” Plant Molecular Biology. Springer, 2016. https://doi.org/10.1007/s11103-016-0501-8.","mla":"Benková, Eva. “Plant Hormones in Interactions with the Environment.” Plant Molecular Biology, vol. 91, no. 6, Springer, 2016, p. 597, doi:10.1007/s11103-016-0501-8.","short":"E. Benková, Plant Molecular Biology 91 (2016) 597."},"day":"01","has_accepted_license":"1","scopus_import":1},{"publist_id":"6044","volume":143,"date_created":"2018-12-11T11:51:04Z","date_updated":"2021-01-12T06:49:32Z","author":[{"full_name":"Porco, Silvana","last_name":"Porco","first_name":"Silvana"},{"first_name":"Antoine","last_name":"Larrieu","full_name":"Larrieu, Antoine"},{"full_name":"Du, Yujuan","last_name":"Du","first_name":"Yujuan"},{"full_name":"Gaudinier, Allison","last_name":"Gaudinier","first_name":"Allison"},{"full_name":"Goh, Tatsuaki","last_name":"Goh","first_name":"Tatsuaki"},{"full_name":"Swarup, Kamal","first_name":"Kamal","last_name":"Swarup"},{"first_name":"Ranjan","last_name":"Swarup","full_name":"Swarup, Ranjan"},{"full_name":"Kuempers, Britta","last_name":"Kuempers","first_name":"Britta"},{"first_name":"Anthony","last_name":"Bishopp","full_name":"Bishopp, Anthony"},{"full_name":"Lavenus, Julien","first_name":"Julien","last_name":"Lavenus"},{"full_name":"Casimiro, Ilda","last_name":"Casimiro","first_name":"Ilda"},{"full_name":"Hill, Kristine","last_name":"Hill","first_name":"Kristine"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"first_name":"Hidehiro","last_name":"Fukaki","full_name":"Fukaki, Hidehiro"},{"last_name":"Brady","first_name":"Siobhan","full_name":"Brady, Siobhan"},{"full_name":"Scheres, Ben","first_name":"Ben","last_name":"Scheres"},{"full_name":"Peéet, Benjamin","first_name":"Benjamin","last_name":"Peéet"},{"full_name":"Bennett, Malcolm","last_name":"Bennett","first_name":"Malcolm"}],"publisher":"Company of Biologists","department":[{"_id":"EvBe"}],"publication_status":"published","year":"2016","acknowledgement":"We acknowledge the support of glasshouse technicians at the University of\r\nNottingham for help with plant growth and the Nottingham\r\nArabidopsis\r\nStock Centre\r\n(NASC) for providing\r\nArabidopsis\r\nlines. This research was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (to A.B. and M.J.B.); the European Research Council (ERC) Advanced Grant SysArc (to B.S.) and FUTUREROOTS (to M.J.B.); The Royal Society for University and Wolfson Research Fellowship awards (to A.B. and M.J.B.); a Federation of European Biochemical Societies (FEBS) Long-Term Fellowship (to B.P.); an Intra-European Fellowship for Career Development under the 7th framework of the European Commission [IEF-2008-220506 to B.P.]; a European Molecular Biology Organization (EMBO) Long-Term Fellowship (to B.P.); and a European Reintegration Grant under the 7th framework of the European Commission [ERG-2010-276662 to B.P.]; Interuniversity Attraction Poles Programme [initiated by the Belgian Science Policy Office (Federaal Wetenschapsbeleid)] (to M.J.B.); The Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan: Grants-in-Aid for Scientific Research on Innovative Areas [25110330 to H.F.] and a JSPS Research Fellowship for Young Scientists [12J02079 to T.G.]; funds for research performed by S.M.B. and A.G. were provided by University of California, Davis startup funds.","month":"09","language":[{"iso":"eng"}],"doi":"10.1242/dev.136283","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01595056/"}],"issue":"18","abstract":[{"lang":"eng","text":"Lateral root primordia (LRP) originate from pericycle stem cells located deep within parental root tissues. LRP emerge through overlying root tissues by inducing auxin-dependent cell separation and hydraulic changes in adjacent cells. The auxin-inducible auxin influx carrier LAX3 plays a key role concentrating this signal in cells overlying LRP. Delimiting LAX3 expression to two adjacent cell files overlying new LRP is crucial to ensure that auxin-regulated cell separation occurs solely along their shared walls. Multiscale modeling has predicted that this highly focused pattern of expression requires auxin to sequentially induce auxin efflux and influx carriers PIN3 and LAX3, respectively. Consistent with model predictions, we report that auxin-inducible LAX3 expression is regulated indirectly by AUXIN RESPONSE FACTOR 7 (ARF7). Yeast one-hybrid screens revealed that the LAX3 promoter is bound by the transcription factor LBD29, which is a direct target for regulation by ARF7. Disrupting auxin-inducible LBD29 expression or expressing an LBD29-SRDX transcriptional repressor phenocopied the lax3 mutant, resulting in delayed lateral root emergence. We conclude that sequential LBD29 and LAX3 induction by auxin is required to coordinate cell separation and organ emergence."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 143","title":"Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1273","day":"13","scopus_import":1,"date_published":"2016-09-13T00:00:00Z","page":"3340 - 3349","citation":{"mla":"Porco, Silvana, et al. “Lateral Root Emergence in Arabidopsis Is Dependent on Transcription Factor LBD29 Regulation of Auxin Influx Carrier LAX3.” Development, vol. 143, no. 18, Company of Biologists, 2016, pp. 3340–49, doi:10.1242/dev.136283.","short":"S. Porco, A. Larrieu, Y. Du, A. Gaudinier, T. Goh, K. Swarup, R. Swarup, B. Kuempers, A. Bishopp, J. Lavenus, I. Casimiro, K. Hill, E. Benková, H. Fukaki, S. Brady, B. Scheres, B. Peéet, M. Bennett, Development 143 (2016) 3340–3349.","chicago":"Porco, Silvana, Antoine Larrieu, Yujuan Du, Allison Gaudinier, Tatsuaki Goh, Kamal Swarup, Ranjan Swarup, et al. “Lateral Root Emergence in Arabidopsis Is Dependent on Transcription Factor LBD29 Regulation of Auxin Influx Carrier LAX3.” Development. Company of Biologists, 2016. https://doi.org/10.1242/dev.136283.","ama":"Porco S, Larrieu A, Du Y, et al. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development. 2016;143(18):3340-3349. doi:10.1242/dev.136283","ista":"Porco S, Larrieu A, Du Y, Gaudinier A, Goh T, Swarup K, Swarup R, Kuempers B, Bishopp A, Lavenus J, Casimiro I, Hill K, Benková E, Fukaki H, Brady S, Scheres B, Peéet B, Bennett M. 2016. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development. 143(18), 3340–3349.","apa":"Porco, S., Larrieu, A., Du, Y., Gaudinier, A., Goh, T., Swarup, K., … Bennett, M. (2016). Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development. Company of Biologists. https://doi.org/10.1242/dev.136283","ieee":"S. Porco et al., “Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3,” Development, vol. 143, no. 18. Company of Biologists, pp. 3340–3349, 2016."},"publication":"Development"},{"day":"01","scopus_import":1,"date_published":"2016-10-01T00:00:00Z","citation":{"ama":"Bouguyon E, Perrine Walker F, Pervent M, et al. Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. 2016;172(2):1237-1248. doi:10.1104/pp.16.01047","ieee":"E. Bouguyon et al., “Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor,” Plant Physiology, vol. 172, no. 2. American Society of Plant Biologists, pp. 1237–1248, 2016.","apa":"Bouguyon, E., Perrine Walker, F., Pervent, M., Rochette, J., Cuesta, C., Benková, E., … Nacry, P. (2016). Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.01047","ista":"Bouguyon E, Perrine Walker F, Pervent M, Rochette J, Cuesta C, Benková E, Martinière A, Bach L, Krouk G, Gojon A, Nacry P. 2016. Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. 172(2), 1237–1248.","short":"E. Bouguyon, F. Perrine Walker, M. Pervent, J. Rochette, C. Cuesta, E. Benková, A. Martinière, L. Bach, G. Krouk, A. Gojon, P. Nacry, Plant Physiology 172 (2016) 1237–1248.","mla":"Bouguyon, Eléonore, et al. “Nitrate Controls Root Development through Posttranscriptional Regulation of the NRT1.1/NPF6.3 Transporter Sensor.” Plant Physiology, vol. 172, no. 2, American Society of Plant Biologists, 2016, pp. 1237–48, doi:10.1104/pp.16.01047.","chicago":"Bouguyon, Eléonore, Francine Perrine Walker, Marjorie Pervent, Juliette Rochette, Candela Cuesta, Eva Benková, Alexandre Martinière, et al. “Nitrate Controls Root Development through Posttranscriptional Regulation of the NRT1.1/NPF6.3 Transporter Sensor.” Plant Physiology. American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.01047."},"publication":"Plant Physiology","page":"1237 - 1248","issue":"2","abstract":[{"lang":"eng","text":"Plants are able to modulate root growth and development to optimize their nitrogen nutrition. In Arabidopsis (Arabidopsis thaliana), the adaptive root response to nitrate (NO3 -) depends on the NRT1.1/NPF6.3 transporter/sensor. NRT1.1 represses emergence of lateral root primordia (LRPs) at low concentration or absence of NO3 - through its auxin transport activity that lowers auxin accumulation in LR. However, these functional data strongly contrast with the known transcriptional regulation of NRT1.1, which is markedly repressed in LRPs in the absence of NO3 -. To explain this discrepancy, we investigated in detail the spatiotemporal expression pattern of the NRT1.1 protein during LRP development and combined local transcript analysis with the use of transgenic lines expressing tagged NRT1.1 proteins. Our results show that although NO3 - stimulates NRT1.1 transcription and probably mRNA stability both in primary root tissues and in LRPs, it acts differentially on protein accumulation, depending on the tissues considered with stimulation in cortex and epidermis of the primary root and a strong repression in LRPs and to a lower extent at the primary root tip. This demonstrates that NRT1.1 is strongly regulated at the posttranscriptional level by tissue-specific mechanisms. These mechanisms are crucial for controlling the large palette of adaptive responses to NO3 - mediated by NRT1.1 as they ensure that the protein is present in the proper tissue under the specific conditions where it plays a signaling role in this particular tissue."}],"type":"journal_article","oa_version":"Preprint","_id":"1281","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 172","status":"public","title":"Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor","month":"10","doi":"10.1104/pp.16.01047","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047109/"}],"oa":1,"quality_controlled":"1","publist_id":"6035","author":[{"last_name":"Bouguyon","first_name":"Eléonore","full_name":"Bouguyon, Eléonore"},{"full_name":"Perrine Walker, Francine","first_name":"Francine","last_name":"Perrine Walker"},{"last_name":"Pervent","first_name":"Marjorie","full_name":"Pervent, Marjorie"},{"full_name":"Rochette, Juliette","first_name":"Juliette","last_name":"Rochette"},{"id":"33A3C818-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1923-2410","first_name":"Candela","last_name":"Cuesta","full_name":"Cuesta, Candela"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"},{"last_name":"Martinière","first_name":"Alexandre","full_name":"Martinière, Alexandre"},{"full_name":"Bach, Lien","last_name":"Bach","first_name":"Lien"},{"last_name":"Krouk","first_name":"Gabriel","full_name":"Krouk, Gabriel"},{"last_name":"Gojon","first_name":"Alain","full_name":"Gojon, Alain"},{"full_name":"Nacry, Philippe","last_name":"Nacry","first_name":"Philippe"}],"volume":172,"date_created":"2018-12-11T11:51:07Z","date_updated":"2021-01-12T06:49:36Z","acknowledgement":"This work was supported by the Agropolis Foundation (RHIZOPOLIS project to A.G. and P.N., and RTRA 2009-2011 project to F.P.-W.), the Knowledge Biobase Economy European project (KBBE-005-002 Root enhancement for crop improvement to M.P. and P.N.), and the European EURoot project (FP7-KBBE-2011-5 to J.R., A.G., and P.N.). We thank Carine Alcon for the help with analysis of confocal images, Xavier\r\nDumont for assistance with Arabidopsis transformations, staff members of the\r\nInstitut de Biologie Intégrative des Plantes for technical assistance with biological\r\nmaterial culture, and students and trainees for assistance with laboratory work.\r\nConfocal observations were made at the Montpellier RIO Imaging facility.","year":"2016","publisher":"American Society of Plant Biologists","department":[{"_id":"EvBe"}],"publication_status":"published"},{"file_date_updated":"2020-07-14T12:44:42Z","publist_id":"6033","author":[{"full_name":"Zhu, Qiang","id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87","last_name":"Zhu","first_name":"Qiang"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"}],"date_created":"2018-12-11T11:51:08Z","date_updated":"2021-01-12T06:49:36Z","volume":21,"year":"2016","acknowledgement":"This work was supported by the Austrian Science Fund (FWF01_I1774S) to E.B., the Natural Science Foundation of Fujian Province (2016J01099), and the Fujian–Taiwan Joint Innovative Center for Germplasm Resources and Cultivation of Crops (FJ 2011 Program, No 2015-75) to Q.Z. The\r\nauthors\r\nthank\r\nIsrael\r\nAusin\r\nand\r\nXu\r\nChen\r\nfor\r\ncritical\r\nreading\r\nof\r\nthe\r\nmanuscript.","publication_status":"published","department":[{"_id":"EvBe"}],"publisher":"Cell Press","month":"10","doi":"10.1016/j.tplants.2016.08.003","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"quality_controlled":"1","project":[{"grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development"}],"abstract":[{"lang":"eng","text":"The impact of the plant hormone ethylene on seedling development has long been recognized; however, its ecophysiological relevance is unexplored. Three recent studies demonstrate that ethylene is a critical endogenous integrator of various environmental signals including mechanical stress, light, and oxygen availability during seedling germination and growth through the soil."}],"issue":"10","type":"journal_article","pubrep_id":"1018","oa_version":"Submitted Version","file":[{"creator":"system","content_type":"application/pdf","file_size":229094,"file_name":"IST-2018-1018-v1+1_Zhu_and_Benkova_TIPS_2016.pdf","access_level":"local","date_created":"2018-12-12T10:08:19Z","date_updated":"2020-07-14T12:44:42Z","checksum":"4d569977fad7a7f22b7e3424003d2ab1","file_id":"4679","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1283","status":"public","title":"Seedlings’ strategy to overcome a soil barrier","ddc":["575"],"intvolume":" 21","day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2016-10-01T00:00:00Z","publication":"Trends in Plant Science","citation":{"ama":"Zhu Q, Benková E. Seedlings’ strategy to overcome a soil barrier. Trends in Plant Science. 2016;21(10):809-811. doi:10.1016/j.tplants.2016.08.003","ieee":"Q. Zhu and E. Benková, “Seedlings’ strategy to overcome a soil barrier,” Trends in Plant Science, vol. 21, no. 10. Cell Press, pp. 809–811, 2016.","apa":"Zhu, Q., & Benková, E. (2016). Seedlings’ strategy to overcome a soil barrier. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2016.08.003","ista":"Zhu Q, Benková E. 2016. Seedlings’ strategy to overcome a soil barrier. Trends in Plant Science. 21(10), 809–811.","short":"Q. Zhu, E. Benková, Trends in Plant Science 21 (2016) 809–811.","mla":"Zhu, Qiang, and Eva Benková. “Seedlings’ Strategy to Overcome a Soil Barrier.” Trends in Plant Science, vol. 21, no. 10, Cell Press, 2016, pp. 809–11, doi:10.1016/j.tplants.2016.08.003.","chicago":"Zhu, Qiang, and Eva Benková. “Seedlings’ Strategy to Overcome a Soil Barrier.” Trends in Plant Science. Cell Press, 2016. https://doi.org/10.1016/j.tplants.2016.08.003."},"article_type":"original","page":"809 - 811"},{"publication":"Plant Physiology","citation":{"ama":"Zwack P, De Clercq I, Howton T, et al. Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. Plant Physiology. 2016;172(2):1249-1258. doi:10.1104/pp.16.00415","apa":"Zwack, P., De Clercq, I., Howton, T., Hallmark, H. T., Hurny, A., Keshishian, E., … Rashotte, A. (2016). Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.00415","ieee":"P. Zwack et al., “Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress,” Plant Physiology, vol. 172, no. 2. American Society of Plant Biologists, pp. 1249–1258, 2016.","ista":"Zwack P, De Clercq I, Howton T, Hallmark HT, Hurny A, Keshishian E, Parish A, Benková E, Mukhtar MS, Van Breusegem F, Rashotte A. 2016. Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. Plant Physiology. 172(2), 1249–1258.","short":"P. Zwack, I. De Clercq, T. Howton, H.T. Hallmark, A. Hurny, E. Keshishian, A. Parish, E. Benková, M.S. Mukhtar, F. Van Breusegem, A. Rashotte, Plant Physiology 172 (2016) 1249–1258.","mla":"Zwack, Paul, et al. “Cytokinin Response Factor 6 Represses Cytokinin-Associated Genes during Oxidative Stress.” Plant Physiology, vol. 172, no. 2, American Society of Plant Biologists, 2016, pp. 1249–58, doi:10.1104/pp.16.00415.","chicago":"Zwack, Paul, Inge De Clercq, Timothy Howton, H Tucker Hallmark, Andrej Hurny, Erika Keshishian, Alyssa Parish, et al. “Cytokinin Response Factor 6 Represses Cytokinin-Associated Genes during Oxidative Stress.” Plant Physiology. American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.00415."},"article_type":"original","page":"1249 - 1258","date_published":"2016-10-02T00:00:00Z","scopus_import":"1","day":"02","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1331","title":"Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress","status":"public","intvolume":" 172","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Cytokinin is a phytohormone that is well known for its roles in numerous plant growth and developmental processes, yet it has also been linked to abiotic stress response in a less defined manner. Arabidopsis (Arabidopsis thaliana) Cytokinin Response Factor 6 (CRF6) is a cytokinin-responsive AP2/ERF-family transcription factor that, through the cytokinin signaling pathway, plays a key role in the inhibition of dark-induced senescence. CRF6 expression is also induced by oxidative stress, and here we show a novel function for CRF6 in relation to oxidative stress and identify downstream transcriptional targets of CRF6 that are repressed in response to oxidative stress. Analysis of transcriptomic changes in wild-type and crf6 mutant plants treated with H2O2 identified CRF6-dependent differentially expressed transcripts, many of which were repressed rather than induced. Moreover, many repressed genes also show decreased expression in 35S:CRF6 overexpressing plants. Together, these findings suggest that CRF6 functions largely as a transcriptional repressor. Interestingly, among the H2O2 repressed CRF6-dependent transcripts was a set of five genes associated with cytokinin processes: (signaling) ARR6, ARR9, ARR11, (biosynthesis) LOG7, and (transport) ABCG14. We have examined mutants of these cytokinin-associated target genes to reveal novel connections to oxidative stress. Further examination of CRF6-DNA interactions indicated that CRF6 may regulate its targets both directly and indirectly. Together, this shows that CRF6 functions during oxidative stress as a negative regulator to control this cytokinin-associated module of CRF6- dependent genes and establishes a novel connection between cytokinin and oxidative stress response."}],"issue":"2","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.16.00415"}],"oa":1,"quality_controlled":"1","doi":"10.1104/pp.16.00415","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"acknowledgement":"This work was financially supported by the following: The Alabama Agricultural Experiment Station HATCH grants 370222-310010-2055 and 370225-310006-2055 for funding to P.J.Z., E.A.K, A.M.P., and A.M.R. P.J.Z. and E.A.K were supported by an Auburn University Cellular and Molecular Biosciences Research Fellowship. I.D.C. is a postdoctoral fellow of the Research Foundation Flanders (FWO) (FWO/PDO14/043) and is also supported by FWO travel\r\ngrant 12N2415N. F.V.B. was supported by grants from the Interuniversity Attraction Poles Programme (IUAP P7/29 MARS) initiated by the Belgian Science Policy Office and Ghent University (Multidisciplinary Research Partnership Biotechnology for a Sustainable Economy, grant 01MRB510W).","year":"2016","publication_status":"published","publisher":"American Society of Plant Biologists","department":[{"_id":"EvBe"}],"author":[{"full_name":"Zwack, Paul","first_name":"Paul","last_name":"Zwack"},{"first_name":"Inge","last_name":"De Clercq","full_name":"De Clercq, Inge"},{"full_name":"Howton, Timothy","last_name":"Howton","first_name":"Timothy"},{"full_name":"Hallmark, H Tucker","first_name":"H Tucker","last_name":"Hallmark"},{"last_name":"Hurny","first_name":"Andrej","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","full_name":"Hurny, Andrej"},{"first_name":"Erika","last_name":"Keshishian","full_name":"Keshishian, Erika"},{"full_name":"Parish, Alyssa","first_name":"Alyssa","last_name":"Parish"},{"full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"},{"last_name":"Mukhtar","first_name":"M Shahid","full_name":"Mukhtar, M Shahid"},{"last_name":"Van Breusegem","first_name":"Frank","full_name":"Van Breusegem, Frank"},{"full_name":"Rashotte, Aaron","last_name":"Rashotte","first_name":"Aaron"}],"date_updated":"2022-05-24T09:26:03Z","date_created":"2018-12-11T11:51:25Z","volume":172,"publist_id":"5937"},{"quality_controlled":"1","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","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"pmid":[" 26883363"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"doi":"10.1101/gad.276964.115","month":"03","department":[{"_id":"EvBe"}],"publisher":"Cold Spring Harbor Laboratory Press","publication_status":"published","pmid":1,"year":"2016","acknowledgement":"This work was supported by a European Research Council Starting Inde-pendent Research grant (ERC-2007-Stg-207362-HCPO to J.D.), Research Foundation-Flanders (G033711N to A.A.), and the Austrian Science Fund (FWF01_I1774S to E.B.). P.M. is indebted to the Federation of European Biochemical Sciences for a Long-Term Fellowship. ","volume":30,"date_created":"2018-12-11T11:52:20Z","date_updated":"2021-01-12T06:51:08Z","author":[{"first_name":"Peter","last_name":"Marhavy","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741","full_name":"Marhavy, Peter"},{"last_name":"Montesinos López","first_name":"Juan C","orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","full_name":"Montesinos López, Juan C"},{"full_name":"Abuzeineh, Anas","first_name":"Anas","last_name":"Abuzeineh"},{"full_name":"Van Damme, Daniël","last_name":"Van Damme","first_name":"Daniël"},{"last_name":"Vermeer","first_name":"Joop","full_name":"Vermeer, Joop"},{"last_name":"Duclercq","first_name":"Jérôme","full_name":"Duclercq, Jérôme"},{"full_name":"Rakusova, Hana","first_name":"Hana","last_name":"Rakusova"},{"first_name":"Petra","last_name":"Marhavá","id":"44E59624-F248-11E8-B48F-1D18A9856A87","full_name":"Marhavá, Petra"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"first_name":"Niko","last_name":"Geldner","full_name":"Geldner, Niko"},{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","publist_id":"5691","file_date_updated":"2020-07-14T12:44:58Z","page":"471 - 483","citation":{"apa":"Marhavý, P., Montesinos López, J. C., Abuzeineh, A., Van Damme, D., Vermeer, J., Duclercq, J., … Benková, E. (2016). Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.276964.115","ieee":"P. Marhavý et al., “Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation,” Genes and Development, vol. 30, no. 4. Cold Spring Harbor Laboratory Press, pp. 471–483, 2016.","ista":"Marhavý P, Montesinos López JC, Abuzeineh A, Van Damme D, Vermeer J, Duclercq J, Rakusova H, Marhavá P, Friml J, Geldner N, Benková E. 2016. Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation. Genes and Development. 30(4), 471–483.","ama":"Marhavý P, Montesinos López JC, Abuzeineh A, et al. Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation. Genes and Development. 2016;30(4):471-483. doi:10.1101/gad.276964.115","chicago":"Marhavý, Peter, Juan C Montesinos López, Anas Abuzeineh, Daniël Van Damme, Joop Vermeer, Jérôme Duclercq, Hana Rakusova, et al. “Targeted Cell Elimination Reveals an Auxin-Guided Biphasic Mode of Lateral Root Initiation.” Genes and Development. Cold Spring Harbor Laboratory Press, 2016. https://doi.org/10.1101/gad.276964.115.","short":"P. Marhavý, J.C. Montesinos López, A. Abuzeineh, D. Van Damme, J. Vermeer, J. Duclercq, H. Rakusova, P. Marhavá, J. Friml, N. Geldner, E. Benková, Genes and Development 30 (2016) 471–483.","mla":"Marhavý, Peter, et al. “Targeted Cell Elimination Reveals an Auxin-Guided Biphasic Mode of Lateral Root Initiation.” Genes and Development, vol. 30, no. 4, Cold Spring Harbor Laboratory Press, 2016, pp. 471–83, doi:10.1101/gad.276964.115."},"publication":"Genes and Development","date_published":"2016-03-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","intvolume":" 30","ddc":["570"],"title":"Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation","status":"public","_id":"1492","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"checksum":"ea394498ee56270e021d1028a29358a0","date_updated":"2020-07-14T12:44:58Z","date_created":"2019-01-25T09:56:11Z","relation":"main_file","file_id":"5883","content_type":"application/pdf","file_size":2757636,"creator":"kschuh","access_level":"open_access","file_name":"2016_GeneDev_Marhavy.pdf"}],"type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"To sustain a lifelong ability to initiate organs, plants retain pools of undifferentiated cells with a preserved prolif eration capacity. The root pericycle represents a unique tissue with conditional meristematic activity, and its tight control determines initiation of lateral organs. Here we show that the meristematic activity of the pericycle is constrained by the interaction with the adjacent endodermis. Release of these restraints by elimination of endo dermal cells by single-cell ablation triggers the pericycle to re-enter the cell cycle. We found that endodermis removal substitutes for the phytohormone auxin-dependent initiation of the pericycle meristematic activity. However, auxin is indispensable to steer the cell division plane orientation of new organ-defining divisions. We propose a dual, spatiotemporally distinct role for auxin during lateral root initiation. In the endodermis, auxin releases constraints arising from cell-to-cell interactions that compromise the pericycle meristematic activity, whereas, in the pericycle, auxin defines the orientation of the cell division plane to initiate lateral roots."}]},{"publication":"Scientific Reports","citation":{"ista":"Mazur E, Benková E, Friml J. 2016. Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. Scientific Reports. 6, 33754.","ieee":"E. Mazur, E. Benková, and J. Friml, “Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","apa":"Mazur, E., Benková, E., & Friml, J. (2016). Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep33754","ama":"Mazur E, Benková E, Friml J. Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. Scientific Reports. 2016;6. doi:10.1038/srep33754","chicago":"Mazur, Ewa, Eva Benková, and Jiří Friml. “Vascular Cambium Regeneration and Vessel Formation in Wounded Inflorescence Stems of Arabidopsis.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep33754.","mla":"Mazur, Ewa, et al. “Vascular Cambium Regeneration and Vessel Formation in Wounded Inflorescence Stems of Arabidopsis.” Scientific Reports, vol. 6, 33754, Nature Publishing Group, 2016, doi:10.1038/srep33754.","short":"E. Mazur, E. Benková, J. Friml, Scientific Reports 6 (2016)."},"date_published":"2016-09-21T00:00:00Z","scopus_import":"1","day":"21","has_accepted_license":"1","article_processing_charge":"No","_id":"1274","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["581"],"title":"Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis","status":"public","intvolume":" 6","pubrep_id":"692","oa_version":"Published Version","file":[{"file_size":2895147,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-692-v1+1_srep33754.pdf","checksum":"ee371fbc9124ad93157a95829264e4fe","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:13:25Z","relation":"main_file","file_id":"5008"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Synchronized tissue polarization during regeneration or de novo vascular tissue formation is a plant-specific example of intercellular communication and coordinated development. According to the canalization hypothesis, the plant hormone auxin serves as polarizing signal that mediates directional channel formation underlying the spatio-temporal vasculature patterning. A necessary part of canalization is a positive feedback between auxin signaling and polarity of the intercellular auxin flow. The cellular and molecular mechanisms of this process are still poorly understood, not the least, because of a lack of a suitable model system. We show that the main genetic model plant, Arabidopsis (Arabidopsis thaliana) can be used to study the canalization during vascular cambium regeneration and new vasculature formation. We monitored localized auxin responses, directional auxin-transport channels formation, and establishment of new vascular cambium polarity during regenerative processes after stem wounding. The increased auxin response above and around the wound preceded the formation of PIN1 auxin transporter-marked channels from the primarily homogenous tissue and the transient, gradual changes in PIN1 localization preceded the polarity of newly formed vascular tissue. Thus, Arabidopsis is a useful model for studies of coordinated tissue polarization and vasculature formation after wounding allowing for genetic and mechanistic dissection of the canalization hypothesis."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["27649687"]},"oa":1,"quality_controlled":"1","doi":"10.1038/srep33754","language":[{"iso":"eng"}],"month":"09","acknowledgement":"We wish to thank Prof. Ewa U. Kurczyńska for initiation of this work and valuable advices. We thank Martine De Cock for help in preparing the manuscript. This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP), the European Social Fund (CZ.1.07/2.3.00/20.0043), and the Czech Science Foundation GAČR (GA13-40637 S) to J.F., (GA 13-39982S) to E.B. and E.M. and in part by the European Regional Development Fund (project “CEITEC, Central European Institute of Technology”, CZ.1.05/1.1.00/02.0068).","year":"2016","pmid":1,"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"author":[{"full_name":"Mazur, Ewa","first_name":"Ewa","last_name":"Mazur"},{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"545"}]},"date_updated":"2024-02-12T12:03:42Z","date_created":"2018-12-11T11:51:05Z","volume":6,"article_number":"33754","file_date_updated":"2020-07-14T12:44:42Z","publist_id":"6042"},{"scopus_import":1,"month":"05","day":"05","publication":"Journal of Experimental Botany","citation":{"chicago":"Robert, Hélène, Lucie Crhák Khaitová, Souad Mroue, and Eva Benková. “The Importance of Localized Auxin Production for Morphogenesis of Reproductive Organs and Embryos in Arabidopsis.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv256.","short":"H. Robert, L. Crhák Khaitová, S. Mroue, E. Benková, Journal of Experimental Botany 66 (2015) 5029–5042.","mla":"Robert, Hélène, et al. “The Importance of Localized Auxin Production for Morphogenesis of Reproductive Organs and Embryos in Arabidopsis.” Journal of Experimental Botany, vol. 66, no. 16, Oxford University Press, 2015, pp. 5029–42, doi:10.1093/jxb/erv256.","apa":"Robert, H., Crhák Khaitová, L., Mroue, S., & Benková, E. (2015). The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv256","ieee":"H. Robert, L. Crhák Khaitová, S. Mroue, and E. Benková, “The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis,” Journal of Experimental Botany, vol. 66, no. 16. Oxford University Press, pp. 5029–5042, 2015.","ista":"Robert H, Crhák Khaitová L, Mroue S, Benková E. 2015. The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. Journal of Experimental Botany. 66(16), 5029–5042.","ama":"Robert H, Crhák Khaitová L, Mroue S, Benková E. The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. Journal of Experimental Botany. 2015;66(16):5029-5042. doi:10.1093/jxb/erv256"},"quality_controlled":"1","page":"5029 - 5042","date_published":"2015-05-05T00:00:00Z","doi":"10.1093/jxb/erv256","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Plant sexual reproduction involves highly structured and specialized organs: stamens (male) and gynoecia (female, containing ovules). These organs synchronously develop within protective flower buds, until anthesis, via tightly coordinated mechanisms that are essential for effective fertilization and production of viable seeds. The phytohormone auxin is one of the key endogenous signalling molecules controlling initiation and development of these, and other, plant organs. In particular, its uneven distribution, resulting from tightly controlled production, metabolism and directional transport, is an important morphogenic factor. In this review we discuss how developmentally controlled and localized auxin biosynthesis and transport contribute to the coordinated development of plants' reproductive organs, and their fertilized derivatives (embryos) via the regulation of auxin levels and distribution within and around them. Current understanding of the links between de novo local auxin biosynthesis, auxin transport and/or signalling is presented to highlight the importance of the non-cell autonomous action of auxin production on development and morphogenesis of reproductive organs and embryos. An overview of transcription factor families, which spatiotemporally define local auxin production by controlling key auxin biosynthetic enzymes, is also presented."}],"issue":"16","publist_id":"5631","_id":"1540","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The work was supported by grants from: the Employment of Best Young Scientists for International Cooperation Empowerment/OPVKII programme (CZ.1.07/2.3.00/30.0037) to HSR and LCK; the Czech Science Foundation (GA13-39982S) to EB, LCK and SM; and the SoMoPro II programme (3SGA5602), cofinanced by the South-Moravian Region and the EU (FP7/2007–2013 People Programme), to HSR.","year":"2015","status":"public","title":"The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"EvBe"}],"intvolume":" 66","author":[{"full_name":"Robert, Hélène","first_name":"Hélène","last_name":"Robert"},{"first_name":"Lucie","last_name":"Crhák Khaitová","full_name":"Crhák Khaitová, Lucie"},{"first_name":"Souad","last_name":"Mroue","full_name":"Mroue, Souad"},{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"date_updated":"2021-01-12T06:51:29Z","date_created":"2018-12-11T11:52:36Z","volume":66,"oa_version":"None"},{"year":"2015","acknowledgement":"of the European Research Council (project ERC-2011-StG-20101109-PSDP) (to J.F.), a FEBS long-term fellowship (to P.M.) ","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"publisher":"Nature Publishing Group","publication_status":"published","author":[{"first_name":"Qian","last_name":"Chen","full_name":"Chen, Qian"},{"first_name":"Yang","last_name":"Liu","full_name":"Liu, Yang"},{"full_name":"Maere, Steven","last_name":"Maere","first_name":"Steven"},{"first_name":"Eunkyoung","last_name":"Lee","full_name":"Lee, Eunkyoung"},{"last_name":"Van Isterdael","first_name":"Gert","full_name":"Van Isterdael, Gert"},{"full_name":"Xie, Zidian","first_name":"Zidian","last_name":"Xie"},{"full_name":"Xuan, Wei","first_name":"Wei","last_name":"Xuan"},{"full_name":"Lucas, Jessica","last_name":"Lucas","first_name":"Jessica"},{"last_name":"Vassileva","first_name":"Valya","full_name":"Vassileva, Valya"},{"full_name":"Kitakura, Saeko","first_name":"Saeko","last_name":"Kitakura"},{"first_name":"Peter","last_name":"Marhavy","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741","full_name":"Marhavy, Peter"},{"full_name":"Wabnik, Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560","first_name":"Krzysztof T","last_name":"Wabnik"},{"last_name":"Geldner","first_name":"Niko","full_name":"Geldner, Niko"},{"full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Le, Jie","first_name":"Jie","last_name":"Le"},{"full_name":"Fukaki, Hidehiro","last_name":"Fukaki","first_name":"Hidehiro"},{"full_name":"Grotewold, Erich","last_name":"Grotewold","first_name":"Erich"},{"full_name":"Li, Chuanyou","first_name":"Chuanyou","last_name":"Li"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"last_name":"Sack","first_name":"Fred","full_name":"Sack, Fred"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"}],"volume":6,"date_created":"2018-12-11T11:52:48Z","date_updated":"2021-01-12T06:51:42Z","article_number":"8821","publist_id":"5597","file_date_updated":"2020-07-14T12:45:02Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1038/ncomms9821","language":[{"iso":"eng"}],"month":"11","_id":"1574","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 6","ddc":["580"],"status":"public","title":"A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development","pubrep_id":"477","oa_version":"Published Version","file":[{"file_id":"5085","relation":"main_file","date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-12T10:14:32Z","checksum":"8ff5c108899b548806e1cb7a302fe76d","file_name":"IST-2016-477-v1+1_ncomms9821.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1701815}],"type":"journal_article","abstract":[{"lang":"eng","text":"Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level."}],"citation":{"short":"Q. Chen, Y. Liu, S. Maere, E. Lee, G. Van Isterdael, Z. Xie, W. Xuan, J. Lucas, V. Vassileva, S. Kitakura, P. Marhavý, K.T. Wabnik, N. Geldner, E. Benková, J. Le, H. Fukaki, E. Grotewold, C. Li, J. Friml, F. Sack, T. Beeckman, S. Vanneste, Nature Communications 6 (2015).","mla":"Chen, Qian, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications, vol. 6, 8821, Nature Publishing Group, 2015, doi:10.1038/ncomms9821.","chicago":"Chen, Qian, Yang Liu, Steven Maere, Eunkyoung Lee, Gert Van Isterdael, Zidian Xie, Wei Xuan, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9821.","ama":"Chen Q, Liu Y, Maere S, et al. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 2015;6. doi:10.1038/ncomms9821","ieee":"Q. Chen et al., “A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","apa":"Chen, Q., Liu, Y., Maere, S., Lee, E., Van Isterdael, G., Xie, Z., … Vanneste, S. (2015). A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9821","ista":"Chen Q, Liu Y, Maere S, Lee E, Van Isterdael G, Xie Z, Xuan W, Lucas J, Vassileva V, Kitakura S, Marhavý P, Wabnik KT, Geldner N, Benková E, Le J, Fukaki H, Grotewold E, Li C, Friml J, Sack F, Beeckman T, Vanneste S. 2015. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 6, 8821."},"publication":"Nature Communications","date_published":"2015-11-18T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"18"},{"month":"04","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis","call_identifier":"FP7"}],"quality_controlled":"1","doi":"10.3389/fpls.2015.00218","language":[{"iso":"eng"}],"publist_id":"5578","ec_funded":1,"file_date_updated":"2020-07-14T12:45:03Z","year":"2015","department":[{"_id":"EvBe"}],"publisher":"Frontiers Research Foundation","publication_status":"published","author":[{"full_name":"Žádníková, Petra","last_name":"Žádníková","first_name":"Petra"},{"last_name":"Smet","first_name":"Dajo","full_name":"Smet, Dajo"},{"full_name":"Zhu, Qiang","first_name":"Qiang","last_name":"Zhu","id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dominique","last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique"},{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"volume":6,"date_updated":"2021-01-12T06:51:50Z","date_created":"2018-12-11T11:52:55Z","scopus_import":1,"has_accepted_license":"1","day":"14","citation":{"ista":"Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. 2015. Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. 6(4).","apa":"Žádníková, P., Smet, D., Zhu, Q., Van Der Straeten, D., & Benková, E. (2015). Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2015.00218","ieee":"P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, and E. Benková, “Strategies of seedlings to overcome their sessile nature: Auxin in mobility control,” Frontiers in Plant Science, vol. 6, no. 4. Frontiers Research Foundation, 2015.","ama":"Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. 2015;6(4). doi:10.3389/fpls.2015.00218","chicago":"Žádníková, Petra, Dajo Smet, Qiang Zhu, Dominique Van Der Straeten, and Eva Benková. “Strategies of Seedlings to Overcome Their Sessile Nature: Auxin in Mobility Control.” Frontiers in Plant Science. Frontiers Research Foundation, 2015. https://doi.org/10.3389/fpls.2015.00218.","mla":"Žádníková, Petra, et al. “Strategies of Seedlings to Overcome Their Sessile Nature: Auxin in Mobility Control.” Frontiers in Plant Science, vol. 6, no. 4, Frontiers Research Foundation, 2015, doi:10.3389/fpls.2015.00218.","short":"P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, E. Benková, Frontiers in Plant Science 6 (2015)."},"publication":"Frontiers in Plant Science","date_published":"2015-04-14T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"text":"Plants are sessile organisms that are permanently restricted to their site of germination. To compensate for their lack of mobility, plants evolved unique mechanisms enabling them to rapidly react to ever changing environmental conditions and flexibly adapt their postembryonic developmental program. A prominent demonstration of this developmental plasticity is their ability to bend organs in order to reach the position most optimal for growth and utilization of light, nutrients, and other resources. Shortly after germination, dicotyledonous seedlings form a bended structure, the so-called apical hook, to protect the delicate shoot meristem and cotyledons from damage when penetrating through the soil. Upon perception of a light stimulus, the apical hook rapidly opens and the photomorphogenic developmental program is activated. After germination, plant organs are able to align their growth with the light source and adopt the most favorable orientation through bending, in a process named phototropism. On the other hand, when roots and shoots are diverted from their upright orientation, they immediately detect a change in the gravity vector and bend to maintain a vertical growth direction. Noteworthy, despite the diversity of external stimuli perceived by different plant organs, all plant tropic movements share a common mechanistic basis: differential cell growth. In our review, we will discuss the molecular principles underlying various tropic responses with the focus on mechanisms mediating the perception of external signals, transduction cascades and downstream responses that regulate differential cell growth and consequently, organ bending. In particular, we highlight common and specific features of regulatory pathways in control of the bending of organs and a role for the plant hormone auxin as a key regulatory component.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1593","intvolume":" 6","ddc":["570"],"title":"Strategies of seedlings to overcome their sessile nature: Auxin in mobility control","status":"public","pubrep_id":"471","oa_version":"Published Version","file":[{"file_name":"IST-2016-471-v1+1_fpls-06-00218.pdf","access_level":"open_access","creator":"system","file_size":965690,"content_type":"application/pdf","file_id":"5142","relation":"main_file","date_created":"2018-12-12T10:15:23Z","date_updated":"2020-07-14T12:45:03Z","checksum":"c454d642e18dfa86820b97a86cd6d3cc"}]}]