[{"language":[{"iso":"eng"}],"article_number":"jcs.204198","ddc":["581"],"intvolume":" 131","month":"01","publication_identifier":{"issn":["0021-9533"]},"_id":"913","department":[{"_id":"JiFr"}],"isi":1,"has_accepted_license":"1","volume":131,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publication":"Journal of Cell Science","citation":{"mla":"Tejos, Ricardo, et al. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” Journal of Cell Science, vol. 131, no. 2, jcs. 204198, Company of Biologists, 2018, doi:10.1242/jcs.204198.","apa":"Tejos, R., Rodríguez Furlán, C., Adamowski, M., Sauer, M., Norambuena, L., & Friml, J. (2018). PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.204198","chicago":"Tejos, Ricardo, Cecilia Rodríguez Furlán, Maciek Adamowski, Michael Sauer, Lorena Norambuena, and Jiří Friml. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” Journal of Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.204198.","ieee":"R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, and J. Friml, “PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana,” Journal of Cell Science, vol. 131, no. 2. Company of Biologists, 2018.","short":"R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, J. Friml, Journal of Cell Science 131 (2018).","ama":"Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. Journal of Cell Science. 2018;131(2). doi:10.1242/jcs.204198","ista":"Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. 2018. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. Journal of Cell Science. 131(2), jcs. 204198."},"date_created":"2018-12-11T11:49:10Z","file_date_updated":"2020-07-14T12:48:15Z","date_updated":"2025-07-10T12:01:38Z","quality_controlled":"1","ec_funded":1,"issue":"2","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000424842400019"]},"doi":"10.1242/jcs.204198","title":"PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana","publist_id":"6530","oa_version":"Published Version","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-04-12T08:46:32Z","file_size":14925985,"file_id":"6299","checksum":"bf156c20a4f117b4b932370d54cbac8c","access_level":"open_access","creator":"dernst","relation":"main_file","file_name":"2017_adamowski_PATELLINS_are.pdf"}],"day":"29","article_processing_charge":"No","pubrep_id":"988","publisher":"Company of Biologists","author":[{"last_name":"Tejos","first_name":"Ricardo","full_name":"Tejos, Ricardo"},{"first_name":"Cecilia","full_name":"Rodríguez Furlán, Cecilia","last_name":"Rodríguez Furlán"},{"first_name":"Maciek","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski"},{"first_name":"Michael","full_name":"Sauer, Michael","last_name":"Sauer"},{"first_name":"Lorena","full_name":"Norambuena, Lorena","last_name":"Norambuena"},{"full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"date_published":"2018-01-29T00:00:00Z","corr_author":"1","status":"public","abstract":[{"lang":"eng","text":"Coordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We performed a microarray-based approach to find regulators of the auxin-induced PIN relocation in the Arabidopsis thaliana root. We identified a subset of a family of phosphatidylinositol transfer proteins (PITP), the PATELLINs (PATL). Here, we show that PATLs are expressed in partially overlapping cells types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia, and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests PATLs redundantly play a crucial role in polarity and patterning in Arabidopsis."}],"publication_status":"published","year":"2018","scopus_import":"1"},{"status":"public","abstract":[{"lang":"eng","text":"AtNHX5 and AtNHX6 are endosomal Na+,K+/H+ antiporters that are critical for growth and development in Arabidopsis, but the mechanism behind their action remains unknown. Here, we report that AtNHX5 and AtNHX6, functioning as H+ leak, control auxin homeostasis and auxin-mediated development. We found that nhx5 nhx6 exhibited growth variations of auxin-related defects. We further showed that nhx5 nhx6 was affected in auxin homeostasis. Genetic analysis showed that AtNHX5 and AtNHX6 were required for the function of the ER-localized auxin transporter PIN5. Although AtNHX5 and AtNHX6 were co-localized with PIN5 at ER, they did not interact directly. Instead, the conserved acidic residues in AtNHX5 and AtNHX6, which are essential for exchange activity, were required for PIN5 function. AtNHX5 and AtNHX6 regulated the pH in ER. Overall, AtNHX5 and AtNHX6 may regulate auxin transport across the ER via the pH gradient created by their transport activity. H+-leak pathway provides a fine-tuning mechanism that controls cellular auxin fluxes. "}],"publication_status":"published","scopus_import":"1","year":"2018","file":[{"file_name":"2018_PlantCellEnv_Fan.pdf","creator":"dernst","relation":"main_file","file_id":"7042","file_size":1937976,"access_level":"open_access","checksum":"6a20f843565f962cb20281cdf5e40914","content_type":"application/pdf","date_updated":"2020-07-14T12:46:32Z","date_created":"2019-11-18T16:22:22Z"}],"article_processing_charge":"No","day":"01","publisher":"Wiley-Blackwell","author":[{"last_name":"Fan","full_name":"Fan, Ligang","first_name":"Ligang"},{"last_name":"Zhao","first_name":"Lei","full_name":"Zhao, Lei"},{"first_name":"Wei","full_name":"Hu, Wei","last_name":"Hu"},{"last_name":"Li","first_name":"Weina","full_name":"Li, Weina"},{"first_name":"Ondřej","full_name":"Novák, Ondřej","last_name":"Novák"},{"last_name":"Strnad","first_name":"Miroslav","full_name":"Strnad, Miroslav"},{"orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu","full_name":"Simon, Sibu","last_name":"Simon"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml"},{"last_name":"Shen","full_name":"Shen, Jinbo","first_name":"Jinbo"},{"first_name":"Liwen","full_name":"Jiang, Liwen","last_name":"Jiang"},{"first_name":"Quan","full_name":"Qiu, Quan","last_name":"Qiu"}],"pmid":1,"date_published":"2018-05-01T00:00:00Z","title":"NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development","doi":"10.1111/pce.13153","publist_id":"7359","acknowledgement":"This work was supported by the National Natural Science Foundation of China (31571464, 31371438 and 31070222 to Q.S.Q.), the National Basic Research Program of China (973 project, 2013CB429904 to Q.S.Q.), the Research Fund for the Doctoral Program of Higher Education of China (20130211110001 to Q.S.Q.), the Ministry of Education, Youth and Sports of the Czech Republic (the National Program for Sustainability I, LO1204), and The Czech Science Foundation GAČR (GA13–40637S) to JF. We thank Dr. Tom J. Guilfoyle for DR5::GUS line and Dr. Jia Li for pBIB‐RFP vector and DR5::GFP line. We thank Liping Guan and Yang Zhao for their help with the confocal microscope assay. ","oa_version":"Submitted Version","external_id":{"isi":["000426870500012"],"pmid":["29360148"]},"publication":"Plant, Cell and Environment","type":"journal_article","citation":{"chicago":"Fan, Ligang, Lei Zhao, Wei Hu, Weina Li, Ondřej Novák, Miroslav Strnad, Sibu Simon, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment. Wiley-Blackwell, 2018. https://doi.org/10.1111/pce.13153.","apa":"Fan, L., Zhao, L., Hu, W., Li, W., Novák, O., Strnad, M., … Qiu, Q. (2018). NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. Wiley-Blackwell. https://doi.org/10.1111/pce.13153","mla":"Fan, Ligang, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment, vol. 41, Wiley-Blackwell, 2018, pp. 850–64, doi:10.1111/pce.13153.","ista":"Fan L, Zhao L, Hu W, Li W, Novák O, Strnad M, Simon S, Friml J, Shen J, Jiang L, Qiu Q. 2018. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 41, 850–864.","ama":"Fan L, Zhao L, Hu W, et al. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 2018;41:850-864. doi:10.1111/pce.13153","short":"L. Fan, L. Zhao, W. Hu, W. Li, O. Novák, M. Strnad, S. Simon, J. Friml, J. Shen, L. Jiang, Q. Qiu, Plant, Cell and Environment 41 (2018) 850–864.","ieee":"L. Fan et al., “NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development,” Plant, Cell and Environment, vol. 41. Wiley-Blackwell, pp. 850–864, 2018."},"date_created":"2018-12-11T11:46:36Z","quality_controlled":"1","date_updated":"2023-09-13T09:03:18Z","file_date_updated":"2020-07-14T12:46:32Z","oa":1,"volume":41,"article_type":"original","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"JiFr"}],"_id":"462","isi":1,"page":"850 - 864","has_accepted_license":"1","language":[{"iso":"eng"}],"tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"intvolume":" 41","ddc":["580"],"month":"05"},{"status":"public","year":"2018","scopus_import":"1","abstract":[{"text":"Cell polarity, manifested by the localization of proteins to distinct polar plasma membrane domains, is a key prerequisite of multicellular life. In plants, PIN auxin transporters are prominent polarity markers crucial for a plethora of developmental processes. Cell polarity mechanisms in plants are distinct from other eukaryotes and still largely elusive. In particular, how the cell polarities are propagated and maintained following cell division remains unknown. Plant cytokinesis is orchestrated by the cell plate—a transient centrifugally growing endomembrane compartment ultimately forming the cross wall1. Trafficking of polar membrane proteins is typically redirected to the cell plate, and these will consequently have opposite polarity in at least one of the daughter cells2–5. Here, we provide mechanistic insights into post-cytokinetic re-establishment of cell polarity as manifested by the apical, polar localization of PIN2. We show that the apical domain is defined in a cell-intrinsic manner and that re-establishment of PIN2 localization to this domain requires de novo protein secretion and endocytosis, but not basal-to-apical transcytosis. Furthermore, we identify a PINOID-related kinase WAG1, which phosphorylates PIN2 in vitro6 and is transcriptionally upregulated specifically in dividing cells, as a crucial regulator of post-cytokinetic PIN2 polarity re-establishment.","lang":"eng"}],"publication_status":"published","day":"03","article_processing_charge":"No","date_published":"2018-12-03T00:00:00Z","pmid":1,"publisher":"Nature Research","author":[{"last_name":"Glanc","full_name":"Glanc, Matous","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","first_name":"Matyas","last_name":"Fendrych"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml"}],"title":"Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division","doi":"10.1038/s41477-018-0318-3","oa_version":"Submitted Version","issue":"12","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30518833"}],"ec_funded":1,"external_id":{"pmid":["30518833"],"isi":["000454576600017"]},"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"citation":{"ama":"Glanc M, Fendrych M, Friml J. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. 2018;4(12):1082-1088. doi:10.1038/s41477-018-0318-3","short":"M. Glanc, M. Fendrych, J. Friml, Nature Plants 4 (2018) 1082–1088.","ista":"Glanc M, Fendrych M, Friml J. 2018. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. 4(12), 1082–1088.","ieee":"M. Glanc, M. Fendrych, and J. Friml, “Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division,” Nature Plants, vol. 4, no. 12. Nature Research, pp. 1082–1088, 2018.","apa":"Glanc, M., Fendrych, M., & Friml, J. (2018). Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. Nature Research. https://doi.org/10.1038/s41477-018-0318-3","chicago":"Glanc, Matous, Matyas Fendrych, and Jiří Friml. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” Nature Plants. Nature Research, 2018. https://doi.org/10.1038/s41477-018-0318-3.","mla":"Glanc, Matous, et al. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” Nature Plants, vol. 4, no. 12, Nature Research, 2018, pp. 1082–88, doi:10.1038/s41477-018-0318-3."},"type":"journal_article","publication":"Nature Plants","quality_controlled":"1","date_updated":"2025-04-14T07:45:02Z","date_created":"2018-12-16T22:59:18Z","volume":4,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2055-0278"]},"page":"1082-1088","isi":1,"_id":"5673","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"month":"12","intvolume":" 4"},{"date_created":"2018-12-11T11:44:17Z","quality_controlled":"1","date_updated":"2023-09-19T10:00:46Z","file_date_updated":"2020-07-14T12:46:13Z","publication":"Journal of Experimental Botany","type":"journal_article","citation":{"mla":"Vu, Lam, et al. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany, vol. 69, no. 19, Oxford University Press, 2018, pp. 4609–24, doi:10.1093/jxb/ery204.","apa":"Vu, L., Zhu, T., Verstraeten, I., Van De Cotte, B., Gevaert, K., & De Smet, I. (2018). Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery204","chicago":"Vu, Lam, Tingting Zhu, Inge Verstraeten, Brigitte Van De Cotte, Kris Gevaert, and Ive De Smet. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery204.","ieee":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, and I. De Smet, “Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms,” Journal of Experimental Botany, vol. 69, no. 19. Oxford University Press, pp. 4609–4624, 2018.","short":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, I. De Smet, Journal of Experimental Botany 69 (2018) 4609–4624.","ama":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 2018;69(19):4609-4624. doi:10.1093/jxb/ery204","ista":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. 2018. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 69(19), 4609–4624."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"volume":69,"department":[{"_id":"JiFr"}],"_id":"36","isi":1,"has_accepted_license":"1","page":"4609 - 4624","intvolume":" 69","ddc":["581"],"month":"08","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by.png","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)"},"publication_status":"published","abstract":[{"lang":"eng","text":"Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity."}],"scopus_import":"1","year":"2018","status":"public","publisher":"Oxford University Press","author":[{"last_name":"Vu","first_name":"Lam","full_name":"Vu, Lam"},{"last_name":"Zhu","full_name":"Zhu, Tingting","first_name":"Tingting"},{"last_name":"Verstraeten","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","full_name":"Verstraeten, Inge"},{"last_name":"Van De Cotte","full_name":"Van De Cotte, Brigitte","first_name":"Brigitte"},{"first_name":"Kris","full_name":"Gevaert, Kris","last_name":"Gevaert"},{"full_name":"De Smet, Ive","first_name":"Ive","last_name":"De Smet"}],"date_published":"2018-08-31T00:00:00Z","file":[{"file_name":"2018_JournalExperimBotany_Vu.pdf","creator":"dernst","relation":"main_file","file_id":"5741","file_size":3359316,"access_level":"open_access","checksum":"34cb0a1611588b75bd6f4913fb4e30f1","date_updated":"2020-07-14T12:46:13Z","content_type":"application/pdf","date_created":"2018-12-18T09:47:51Z"}],"article_processing_charge":"No","day":"31","publist_id":"8019","acknowledgement":"TZ is supported by a grant from the Chinese Scholarship Council.","oa_version":"Published Version","doi":"10.1093/jxb/ery204","title":"Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms","external_id":{"isi":["000443568700010"]},"issue":"19"},{"citation":{"chicago":"Trinh, Hoang, Inge Verstraeten, and Danny Geelen. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” In Root Development , 1761:95–102. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-7747-5_7.","apa":"Trinh, H., Verstraeten, I., & Geelen, D. (2018). In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In Root Development (Vol. 1761, pp. 95–102). Springer Nature. https://doi.org/10.1007/978-1-4939-7747-5_7","mla":"Trinh, Hoang, et al. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102, doi:10.1007/978-1-4939-7747-5_7.","ista":"Trinh H, Verstraeten I, Geelen D. 2018.In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . MIMB, vol. 1761, 95–102.","short":"H. Trinh, I. Verstraeten, D. Geelen, in:, Root Development , Springer Nature, 2018, pp. 95–102.","ama":"Trinh H, Verstraeten I, Geelen D. In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . Vol 1761. Springer Nature; 2018:95-102. doi:10.1007/978-1-4939-7747-5_7","ieee":"H. Trinh, I. Verstraeten, and D. Geelen, “In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls,” in Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102."},"type":"book_chapter","publication":"Root Development ","date_created":"2018-12-11T11:46:18Z","quality_controlled":"1","date_updated":"2021-01-12T07:54:21Z","volume":1761,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1064-3745"]},"department":[{"_id":"JiFr"}],"_id":"408","alternative_title":["MIMB"],"page":"95 - 102","language":[{"iso":"eng"}],"intvolume":" 1761","month":"03","status":"public","abstract":[{"lang":"eng","text":"Adventitious roots (AR) are de novo formed roots that emerge from any part of the plant or from callus in tissue culture, except root tissue. The plant tissue origin and the method by which they are induced determine the physiological properties of emerged ARs. Hence, a standard method encompassing all types of AR does not exist. Here we describe a method for the induction and analysis of AR that emerge from the etiolated hypocotyl of dicot plants. The hypocotyl is formed during embryogenesis and shows a determined developmental pattern which usually does not involve AR formation. However, the hypocotyl shows propensity to form de novo roots under specific circumstances such as removal of the root system, high humidity or flooding, or during de-etiolation. The hypocotyl AR emerge from a pericycle-like cell layer surrounding the vascular tissue of the central cylinder, which is reminiscent to the developmental program of lateral roots. Here we propose an easy protocol for in vitro hypocotyl AR induction from etiolated Arabidopsis seedlings."}],"publication_status":"published","scopus_import":"1","year":"2018","article_processing_charge":"No","day":"01","author":[{"last_name":"Trinh","full_name":"Trinh, Hoang","first_name":"Hoang"},{"last_name":"Verstraeten","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","full_name":"Verstraeten, Inge"},{"last_name":"Geelen","first_name":"Danny","full_name":"Geelen, Danny"}],"publisher":"Springer Nature","pmid":1,"date_published":"2018-03-01T00:00:00Z","title":"In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls","doi":"10.1007/978-1-4939-7747-5_7","publist_id":"7421","oa_version":"None","external_id":{"pmid":["29525951"]}},{"year":"2018","scopus_import":1,"quality_controlled":"1","date_updated":"2021-01-12T07:54:34Z","abstract":[{"lang":"eng","text":"Immunolocalization is a valuable tool for cell biology research that allows to rapidly determine the localization and expression levels of endogenous proteins. In plants, whole-mount in situ immunolocalization remains a challenging method, especially in tissues protected by waxy layers and complex cell wall carbohydrates. Here, we present a robust method for whole-mount in situ immunolocalization in primary root meristems and lateral root primordia in Arabidopsis thaliana. For good epitope preservation, fixation is done in an alkaline paraformaldehyde/glutaraldehyde mixture. This fixative is suitable for detecting a wide range of proteins, including integral transmembrane proteins and proteins peripherally attached to the plasma membrane. From initiation until emergence from the primary root, lateral root primordia are surrounded by several layers of differentiated tissues with a complex cell wall composition that interferes with the efficient penetration of all buffers. Therefore, immunolocalization in early lateral root primordia requires a modified method, including a strong solvent treatment for removal of hydrophobic barriers and a specific cocktail of cell wall-degrading enzymes. The presented method allows for easy, reliable, and high-quality in situ detection of the subcellular localization of endogenous proteins in primary and lateral root meristems without the need of time-consuming crosses or making translational fusions to fluorescent proteins."}],"publication_status":"published","date_created":"2018-12-11T11:46:20Z","status":"public","type":"book_chapter","publication":"Root Development. Methods and Protocols","citation":{"ista":"Karampelias M, Tejos R, Friml J, Vanneste S. 2018.Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In: Root Development. Methods and Protocols. Methods in Molecular Biology, vol. 1761, 131–143.","ama":"Karampelias M, Tejos R, Friml J, Vanneste S. Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In: Ristova D, Barbez E, eds. Root Development. Methods and Protocols. Vol 1761. MIMB. Springer; 2018:131-143. doi:10.1007/978-1-4939-7747-5_10","short":"M. Karampelias, R. Tejos, J. Friml, S. Vanneste, in:, D. Ristova, E. Barbez (Eds.), Root Development. Methods and Protocols, Springer, 2018, pp. 131–143.","ieee":"M. Karampelias, R. Tejos, J. Friml, and S. Vanneste, “Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia,” in Root Development. Methods and Protocols, vol. 1761, D. Ristova and E. Barbez, Eds. Springer, 2018, pp. 131–143.","chicago":"Karampelias, Michael, Ricardo Tejos, Jiří Friml, and Steffen Vanneste. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana Root Meristems and Lateral Root Primordia.” In Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, 1761:131–43. MIMB. Springer, 2018. https://doi.org/10.1007/978-1-4939-7747-5_10.","apa":"Karampelias, M., Tejos, R., Friml, J., & Vanneste, S. (2018). Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In D. Ristova & E. Barbez (Eds.), Root Development. Methods and Protocols (Vol. 1761, pp. 131–143). Springer. https://doi.org/10.1007/978-1-4939-7747-5_10","mla":"Karampelias, Michael, et al. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana Root Meristems and Lateral Root Primordia.” Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, vol. 1761, Springer, 2018, pp. 131–43, doi:10.1007/978-1-4939-7747-5_10."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_published":"2018-03-11T00:00:00Z","publisher":"Springer","author":[{"full_name":"Karampelias, Michael","first_name":"Michael","last_name":"Karampelias"},{"last_name":"Tejos","first_name":"Ricardo","full_name":"Tejos, Ricardo"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"}],"day":"11","volume":1761,"oa_version":"None","page":"131 - 143","alternative_title":["Methods in Molecular Biology"],"publist_id":"7418","department":[{"_id":"JiFr"}],"_id":"411","doi":"10.1007/978-1-4939-7747-5_10","title":"Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia","month":"03","editor":[{"last_name":"Ristova","first_name":"Daniela","full_name":"Ristova, Daniela"},{"first_name":"Elke","full_name":"Barbez, Elke","last_name":"Barbez"}],"intvolume":" 1761","language":[{"iso":"eng"}],"series_title":"MIMB"},{"file":[{"file_name":"2018_PNAS_Salanenka.pdf","relation":"main_file","creator":"dernst","checksum":"1fcf7223fb8f99559cfa80bd6f24ce44","access_level":"open_access","file_size":1924101,"file_id":"5700","date_created":"2018-12-17T12:30:14Z","content_type":"application/pdf","date_updated":"2020-07-14T12:46:26Z"}],"article_processing_charge":"No","day":"03","publisher":"National Academy of Sciences","author":[{"id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87","full_name":"Salanenka, Yuliya","first_name":"Yuliya","last_name":"Salanenka"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","first_name":"Inge","last_name":"Verstraeten"},{"last_name":"Löfke","first_name":"Christian","full_name":"Löfke, Christian"},{"id":"7DAAEDA4-02D0-11E9-B11A-A5A4D7DFFFD0","first_name":"Kaori","full_name":"Tabata, Kaori","last_name":"Tabata"},{"last_name":"Naramoto","first_name":"Satoshi","full_name":"Naramoto, Satoshi"},{"last_name":"Glanc","orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","full_name":"Glanc, Matous"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí"}],"date_published":"2018-04-03T00:00:00Z","status":"public","corr_author":"1","publication_status":"published","abstract":[{"lang":"eng","text":"The plant hormone gibberellic acid (GA) is a crucial regulator of growth and development. The main paradigm of GA signaling puts forward transcriptional regulation via the degradation of DELLA transcriptional repressors. GA has also been shown to regulate tropic responses by modulation of the plasma membrane incidence of PIN auxin transporters by an unclear mechanism. Here we uncovered the cellular and molecular mechanisms by which GA redirects protein trafficking and thus regulates cell surface functionality. Photoconvertible reporters revealed that GA balances the protein traffic between the vacuole degradation route and recycling back to the cell surface. Low GA levels promote vacuolar delivery and degradation of multiple cargos, including PIN proteins, whereas high GA levels promote their recycling to the plasma membrane. This GA effect requires components of the retromer complex, such as Sorting Nexin 1 (SNX1) and its interacting, microtubule (MT)-associated protein, the Cytoplasmic Linker-Associated Protein (CLASP1). Accordingly, GA regulates the subcellular distribution of SNX1 and CLASP1, and the intact MT cytoskeleton is essential for the GA effect on trafficking. This GA cellular action occurs through DELLA proteins that regulate the MT and retromer presumably via their interaction partners Prefoldins (PFDs). Our study identified a branching of the GA signaling pathway at the level of DELLA proteins, which, in parallel to regulating transcription, also target by a nontranscriptional mechanism the retromer complex acting at the intersection of the degradation and recycling trafficking routes. By this mechanism, GA can redirect receptors and transporters to the cell surface, thus coregulating multiple processes, including PIN-dependent auxin fluxes during tropic responses."}],"scopus_import":"1","year":"2018","ec_funded":1,"issue":"14","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"external_id":{"isi":["000429012500073"]},"doi":"10.1073/pnas.1721760115","title":"Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane","publist_id":"7395","acknowledgement":"We gratefully acknowledge M. Blázquez (Instituto de Biología Molecular y Celular de Plantas), M. Fendrych, C. Cuesta Moliner (Institute of Science and Technology Austria), M. Vanstraelen, M. Nowack (Center for Plant Systems Biology, Ghent), C. Luschnig (Universitat fur Bodenkultur Wien, Vienna), S. Simon (Central European Institute of Technology, Brno), C. Sommerville (Carnegie Institution for Science), and Y. Gu (Penn State University) for making available the materials used in this study;\r\n...funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement 282300.\r\nCC BY NC ND","oa_version":"Published Version","oa":1,"volume":115,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"ieee":"Y. Salanenka et al., “Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 14. National Academy of Sciences, pp. 3716–3721, 2018.","ista":"Salanenka Y, Verstraeten I, Löfke C, Tabata K, Naramoto S, Glanc M, Friml J. 2018. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. Proceedings of the National Academy of Sciences of the United States of America. 115(14), 3716–3721.","short":"Y. Salanenka, I. Verstraeten, C. Löfke, K. Tabata, S. Naramoto, M. Glanc, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 3716–3721.","ama":"Salanenka Y, Verstraeten I, Löfke C, et al. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(14):3716-3721. doi:10.1073/pnas.1721760115","mla":"Salanenka, Yuliya, et al. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 14, National Academy of Sciences, 2018, pp. 3716–21, doi:10.1073/pnas.1721760115.","chicago":"Salanenka, Yuliya, Inge Verstraeten, Christian Löfke, Kaori Tabata, Satoshi Naramoto, Matous Glanc, and Jiří Friml. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1721760115.","apa":"Salanenka, Y., Verstraeten, I., Löfke, C., Tabata, K., Naramoto, S., Glanc, M., & Friml, J. (2018). Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1721760115"},"type":"journal_article","date_created":"2018-12-11T11:46:25Z","quality_controlled":"1","date_updated":"2025-06-03T11:21:29Z","file_date_updated":"2020-07-14T12:46:26Z","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by_nc_nd.png","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)"},"intvolume":" 115","ddc":["580"],"month":"04","department":[{"_id":"JiFr"}],"_id":"428","isi":1,"page":" 3716 - 3721","has_accepted_license":"1"},{"day":"26","article_processing_charge":"No","date_published":"2018-06-26T00:00:00Z","author":[{"last_name":"Abbas","first_name":"Mohamad","full_name":"Abbas, Mohamad","id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"García J","full_name":"Hernández, García J","last_name":"Hernández"},{"first_name":"Stephan","full_name":"Pollmann, Stephan","last_name":"Pollmann"},{"last_name":"Samodelov","full_name":"Samodelov, Sophia L","first_name":"Sophia L"},{"last_name":"Kolb","first_name":"Martina","full_name":"Kolb, Martina"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí"},{"last_name":"Hammes","full_name":"Hammes, Ulrich Z","first_name":"Ulrich Z"},{"first_name":"Matias D","full_name":"Zurbriggen, Matias D","last_name":"Zurbriggen"},{"full_name":"Blázquez, Miguel","first_name":"Miguel","last_name":"Blázquez"},{"last_name":"Alabadí","full_name":"Alabadí, David","first_name":"David"}],"publisher":"National Academy of Sciences","status":"public","year":"2018","scopus_import":"1","publication_status":"published","abstract":[{"text":"Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses.","lang":"eng"}],"OA_place":"repository","issue":"26","main_file_link":[{"open_access":"1","url":"http://eprints.nottingham.ac.uk/52388/"}],"ec_funded":1,"external_id":{"isi":["000436245000096"]},"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"OA_type":"green","doi":"10.1073/pnas.1806565115","title":"Auxin methylation is required for differential growth in Arabidopsis","oa_version":"Submitted Version","publist_id":"7710","article_type":"original","volume":115,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Abbas, Mohamad, et al. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS, vol. 115, no. 26, National Academy of Sciences, 2018, pp. 6864–69, doi:10.1073/pnas.1806565115.","chicago":"Abbas, Mohamad, García J Hernández, Stephan Pollmann, Sophia L Samodelov, Martina Kolb, Jiří Friml, Ulrich Z Hammes, Matias D Zurbriggen, Miguel Blázquez, and David Alabadí. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1806565115.","apa":"Abbas, M., Hernández, G. J., Pollmann, S., Samodelov, S. L., Kolb, M., Friml, J., … Alabadí, D. (2018). Auxin methylation is required for differential growth in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1806565115","ieee":"M. Abbas et al., “Auxin methylation is required for differential growth in Arabidopsis,” PNAS, vol. 115, no. 26. National Academy of Sciences, pp. 6864–6869, 2018.","ista":"Abbas M, Hernández GJ, Pollmann S, Samodelov SL, Kolb M, Friml J, Hammes UZ, Zurbriggen MD, Blázquez M, Alabadí D. 2018. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 115(26), 6864–6869.","ama":"Abbas M, Hernández GJ, Pollmann S, et al. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 2018;115(26):6864-6869. doi:10.1073/pnas.1806565115","short":"M. Abbas, G.J. Hernández, S. Pollmann, S.L. Samodelov, M. Kolb, J. Friml, U.Z. Hammes, M.D. Zurbriggen, M. Blázquez, D. Alabadí, PNAS 115 (2018) 6864–6869."},"publication":"PNAS","type":"journal_article","quality_controlled":"1","date_updated":"2026-04-28T08:29:26Z","date_created":"2018-12-11T11:45:11Z","language":[{"iso":"eng"}],"month":"06","intvolume":" 115","page":"6864-6869","department":[{"_id":"JiFr"}],"_id":"203","isi":1},{"year":"2018","scopus_import":"1","abstract":[{"lang":"eng","text":"Auxin is unique among plant hormones due to its directional transport that is mediated by the polarly distributed PIN auxin transporters at the plasma membrane. The canalization hypothesis proposes that the auxin feedback on its polar flow is a crucial, plant-specific mechanism mediating multiple self-organizing developmental processes. Here, we used the auxin effect on the PIN polar localization in Arabidopsis thaliana roots as a proxy for the auxin feedback on the PIN polarity during canalization. We performed microarray experiments to find regulators of this process that act downstream of auxin. We identified genes that were transcriptionally regulated by auxin in an AXR3/IAA17- and ARF7/ARF19-dependent manner. Besides the known components of the PIN polarity, such as PID and PIP5K kinases, a number of potential new regulators were detected, among which the WRKY23 transcription factor, which was characterized in more detail. Gain- and loss-of-function mutants confirmed a role for WRKY23 in mediating the auxin effect on the PIN polarity. Accordingly, processes requiring auxin-mediated PIN polarity rearrangements, such as vascular tissue development during leaf venation, showed a higher WRKY23 expression and required the WRKY23 activity. Our results provide initial insights into the auxin transcriptional network acting upstream of PIN polarization and, potentially, canalization-mediated plant development."}],"publication_status":"published","corr_author":"1","status":"public","date_published":"2018-01-29T00:00:00Z","pubrep_id":"967","author":[{"last_name":"Prat","first_name":"Tomas","full_name":"Prat, Tomas","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hajny","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","first_name":"Jakub","full_name":"Hajny, Jakub"},{"last_name":"Grunewald","first_name":"Wim","full_name":"Grunewald, Wim"},{"first_name":"Mina K","full_name":"Vasileva, Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","last_name":"Vasileva"},{"last_name":"Molnar","first_name":"Gergely","full_name":"Molnar, Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tejos","first_name":"Ricardo","full_name":"Tejos, Ricardo"},{"last_name":"Schmid","full_name":"Schmid, Markus","first_name":"Markus"},{"last_name":"Sauer","full_name":"Sauer, Michael","first_name":"Michael"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí"}],"publisher":"Public Library of Science","day":"29","article_processing_charge":"Yes","file":[{"file_name":"IST-2018-967-v1+1_journal.pgen.1007177.pdf","relation":"main_file","creator":"system","access_level":"open_access","checksum":"0276d66788ec076f4924164a39e6a712","file_id":"4843","file_size":24709062,"date_created":"2018-12-12T10:10:52Z","content_type":"application/pdf","date_updated":"2020-07-14T12:46:30Z"}],"oa_version":"Published Version","publist_id":"7373","doi":"10.1371/journal.pgen.1007177","title":"WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity","external_id":{"isi":["000423718600034"]},"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300"}],"issue":"1","ec_funded":1,"file_date_updated":"2020-07-14T12:46:30Z","date_updated":"2026-05-18T22:30:56Z","quality_controlled":"1","date_created":"2018-12-11T11:46:32Z","citation":{"apa":"Prat, T., Hajny, J., Grunewald, W., Vasileva, M. K., Molnar, G., Tejos, R., … Friml, J. (2018). WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007177","chicago":"Prat, Tomas, Jakub Hajny, Wim Grunewald, Mina K Vasileva, Gergely Molnar, Ricardo Tejos, Markus Schmid, Michael Sauer, and Jiří Friml. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” PLoS Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007177.","mla":"Prat, Tomas, et al. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” PLoS Genetics, vol. 14, no. 1, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007177.","short":"T. Prat, J. Hajny, W. Grunewald, M.K. Vasileva, G. Molnar, R. Tejos, M. Schmid, M. Sauer, J. Friml, PLoS Genetics 14 (2018).","ama":"Prat T, Hajny J, Grunewald W, et al. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. 2018;14(1). doi:10.1371/journal.pgen.1007177","ista":"Prat T, Hajny J, Grunewald W, Vasileva MK, Molnar G, Tejos R, Schmid M, Sauer M, Friml J. 2018. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. 14(1).","ieee":"T. Prat et al., “WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity,” PLoS Genetics, vol. 14, no. 1. Public Library of Science, 2018."},"publication":"PLoS Genetics","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"status":"public","id":"7172","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"1127"},{"relation":"dissertation_contains","id":"8822","status":"public"}]},"volume":14,"oa":1,"has_accepted_license":"1","_id":"449","isi":1,"department":[{"_id":"JiFr"}],"month":"01","ddc":["581"],"intvolume":" 14","tmp":{"image":"/images/cc_by.png","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)"},"language":[{"iso":"eng"}]},{"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8822"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"volume":8,"date_created":"2018-12-11T11:45:06Z","date_updated":"2026-05-18T22:30:56Z","quality_controlled":"1","file_date_updated":"2020-07-14T12:45:20Z","citation":{"chicago":"Grones, Peter, Melinda F Abas, Jakub Hajny, Angharad Jones, Sascha Waidmann, Jürgen Kleine Vehn, and Jiří Friml. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” Scientific Reports. Springer, 2018. https://doi.org/10.1038/s41598-018-28188-1.","apa":"Grones, P., Abas, M. F., Hajny, J., Jones, A., Waidmann, S., Kleine Vehn, J., & Friml, J. (2018). PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. Springer. https://doi.org/10.1038/s41598-018-28188-1","mla":"Grones, Peter, et al. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” Scientific Reports, vol. 8, no. 1, 10279, Springer, 2018, doi:10.1038/s41598-018-28188-1.","ista":"Grones P, Abas MF, Hajny J, Jones A, Waidmann S, Kleine Vehn J, Friml J. 2018. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. 8(1), 10279.","ama":"Grones P, Abas MF, Hajny J, et al. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-28188-1","short":"P. Grones, M.F. Abas, J. Hajny, A. Jones, S. Waidmann, J. Kleine Vehn, J. Friml, Scientific Reports 8 (2018).","ieee":"P. Grones et al., “PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism,” Scientific Reports, vol. 8, no. 1. Springer, 2018."},"type":"journal_article","publication":"Scientific Reports","intvolume":" 8","ddc":["581"],"month":"07","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by.png","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)"},"article_number":"10279","isi":1,"_id":"191","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"has_accepted_license":"1","author":[{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Grones, Peter","last_name":"Grones"},{"full_name":"Abas, Melinda F","first_name":"Melinda F","id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","last_name":"Abas"},{"first_name":"Jakub","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny"},{"last_name":"Jones","full_name":"Jones, Angharad","first_name":"Angharad"},{"last_name":"Waidmann","first_name":"Sascha","full_name":"Waidmann, Sascha"},{"last_name":"Kleine Vehn","full_name":"Kleine Vehn, Jürgen","first_name":"Jürgen"},{"last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"publisher":"Springer","date_published":"2018-07-06T00:00:00Z","file":[{"date_created":"2018-12-17T15:38:56Z","content_type":"application/pdf","date_updated":"2020-07-14T12:45:20Z","checksum":"266b03f4fb8198e83141617aaa99dcab","access_level":"open_access","file_size":2413876,"file_id":"5714","relation":"main_file","creator":"dernst","file_name":"2018_ScientificReports_Grones.pdf"}],"article_processing_charge":"No","day":"06","publication_status":"published","abstract":[{"lang":"eng","text":"Intercellular distribution of the plant hormone auxin largely depends on the polar subcellular distribution of the plasma membrane PIN-FORMED (PIN) auxin transporters. PIN polarity switches in response to different developmental and environmental signals have been shown to redirect auxin fluxes mediating certain developmental responses. PIN phosphorylation at different sites and by different kinases is crucial for PIN function. Here we investigate the role of PIN phosphorylation during gravitropic response. Loss- and gain-of-function mutants in PINOID and related kinases but not in D6PK kinase as well as mutations mimicking constitutive dephosphorylated or phosphorylated status of two clusters of predicted phosphorylation sites partially disrupted PIN3 phosphorylation and caused defects in gravitropic bending in roots and hypocotyls. In particular, they impacted PIN3 polarity rearrangements in response to gravity and during feed-back regulation by auxin itself. Thus PIN phosphorylation, besides regulating transport activity and apical-basal targeting, is also important for the rapid polarity switches in response to environmental and endogenous signals."}],"scopus_import":"1","year":"2018","status":"public","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"},{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985"}],"external_id":{"isi":["000437673200053"]},"ec_funded":1,"issue":"1","publist_id":"7729","oa_version":"Published Version","title":"PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism","doi":"10.1038/s41598-018-28188-1"},{"intvolume":" 30","ddc":["580"],"month":"04","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by.png","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)"},"_id":"412","isi":1,"department":[{"_id":"JiFr"}],"page":"700 - 716","has_accepted_license":"1","publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6269"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"volume":30,"article_type":"original","date_created":"2018-12-11T11:46:20Z","date_updated":"2026-05-18T22:31:00Z","quality_controlled":"1","file_date_updated":"2022-05-23T09:12:38Z","type":"journal_article","publication":"The Plant Cell","citation":{"mla":"Adamowski, Maciek, et al. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell, vol. 30, no. 3, American Society of Plant Biologists, 2018, pp. 700–16, doi:10.1105/tpc.17.00785.","chicago":"Adamowski, Maciek, Madhumitha Narasimhan, Urszula Kania, Matous Glanc, Geert De Jaeger, and Jiří Friml. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell. American Society of Plant Biologists, 2018. https://doi.org/10.1105/tpc.17.00785.","apa":"Adamowski, M., Narasimhan, M., Kania, U., Glanc, M., De Jaeger, G., & Friml, J. (2018). A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.17.00785","ieee":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, and J. Friml, “A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis,” The Plant Cell, vol. 30, no. 3. American Society of Plant Biologists, pp. 700–716, 2018.","ista":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. 2018. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 30(3), 700–716.","short":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, J. Friml, The Plant Cell 30 (2018) 700–716.","ama":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 2018;30(3):700-716. doi:10.1105/tpc.17.00785"},"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"external_id":{"pmid":["29511054"],"isi":["000429441400018"]},"ec_funded":1,"issue":"3","publist_id":"7417","acknowledgement":"We thank James Matthew Watson, Monika Borowska, and Peggy Stolt-Bergner at ProTech Facility of the Vienna Biocenter Core Facilities for the CRISPR/CAS9 construct; Anna Müller for assistance with molecular cloning; Sebastian Bednarek, Liwen Jiang, and Daniël Van Damme for sharing published material; Matyáš Fendrych, Daniël Van Damme, and Lindy Abas for valuable discussions; and Martine De Cock for help with correcting the manuscript. This work was supported by the European Research Council under the European Union Seventh Framework Programme (FP7/2007-2013)/ERC Grant 282300 and by the Ministry of Education of the Czech Republic/MŠMT project NPUI-LO1417.","oa_version":"Published Version","title":"A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis","doi":"10.1105/tpc.17.00785","author":[{"last_name":"Adamowski","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","full_name":"Adamowski, Maciek"},{"last_name":"Narasimhan","orcid":"0000-0002-8600-0671","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha","full_name":"Narasimhan, Madhumitha"},{"last_name":"Kania","full_name":"Kania, Urszula","first_name":"Urszula","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matous","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc"},{"last_name":"De Jaeger","first_name":"Geert","full_name":"De Jaeger, Geert"},{"full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"publisher":"American Society of Plant Biologists","date_published":"2018-04-09T00:00:00Z","pmid":1,"file":[{"file_size":4407538,"file_id":"11406","checksum":"4e165e653b67d3f0684697f21aace5a1","success":1,"access_level":"open_access","date_updated":"2022-05-23T09:12:38Z","content_type":"application/pdf","date_created":"2022-05-23T09:12:38Z","file_name":"2018_PlantCell_Adamowski.pdf","creator":"dernst","relation":"main_file"}],"article_processing_charge":"No","day":"09","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is a cellular trafficking process in which cargoes and lipids are internalized from the plasma membrane into vesicles coated with clathrin and adaptor proteins. CME is essential for many developmental and physiological processes in plants, but its underlying mechanism is not well characterised compared to that in yeast and animal systems. Here, we searched for new factors involved in CME in Arabidopsis thaliana by performing Tandem Affinity Purification of proteins that interact with clathrin light chain, a principal component of the clathrin coat. Among the confirmed interactors, we found two putative homologues of the clathrin-coat uncoating factor auxilin previously described in non-plant systems. Overexpression of AUXILIN-LIKE1 and AUXILIN-LIKE2 in A. thaliana caused an arrest of seedling growth and development. This was concomitant with inhibited endocytosis due to blocking of clathrin recruitment after the initial step of adaptor protein binding to the plasma membrane. By contrast, auxilin-like(1/2) loss-of-function lines did not present endocytosis-related developmental or cellular phenotypes under normal growth conditions. This work contributes to the on-going characterization of the endocytotic machinery in plants and provides a robust tool for conditionally and specifically interfering with CME in A. thaliana.","lang":"eng"}],"publication_status":"published","scopus_import":"1","year":"2018","status":"public","corr_author":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"10083","relation":"dissertation_contains"}]},"article_type":"original","volume":8,"oa":1,"file_date_updated":"2020-07-14T12:46:29Z","date_updated":"2026-05-18T22:31:19Z","quality_controlled":"1","date_created":"2018-12-11T11:46:30Z","citation":{"ieee":"L. Li, G. Krens, M. Fendrych, and J. Friml, “Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls,” Bio-protocol, vol. 8, no. 1. Bio-protocol, 2018.","short":"L. Li, G. Krens, M. Fendrych, J. Friml, Bio-Protocol 8 (2018).","ama":"Li L, Krens G, Fendrych M, Friml J. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol. 2018;8(1). doi:10.21769/BioProtoc.2685","ista":"Li L, Krens G, Fendrych M, Friml J. 2018. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol. 8(1).","mla":"Li, Lanxin, et al. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” Bio-Protocol, vol. 8, no. 1, Bio-protocol, 2018, doi:10.21769/BioProtoc.2685.","apa":"Li, L., Krens, G., Fendrych, M., & Friml, J. (2018). Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-Protocol. Bio-protocol. https://doi.org/10.21769/BioProtoc.2685","chicago":"Li, Lanxin, Gabriel Krens, Matyas Fendrych, and Jiří Friml. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” Bio-Protocol. Bio-protocol, 2018. https://doi.org/10.21769/BioProtoc.2685."},"type":"journal_article","publication":"Bio-protocol","month":"01","ddc":["576","581"],"intvolume":" 8","tmp":{"image":"/images/cc_by.png","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)"},"language":[{"iso":"eng"}],"has_accepted_license":"1","_id":"442","department":[{"_id":"JiFr"},{"_id":"Bio"}],"publication_identifier":{"eissn":["2331-8325"]},"date_published":"2018-01-05T00:00:00Z","pubrep_id":"970","author":[{"last_name":"Li","full_name":"Li, Lanxin","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X"},{"last_name":"Krens","first_name":"Gabriel","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fendrych","full_name":"Fendrych, Matyas","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699"},{"first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"publisher":"Bio-protocol","day":"05","article_processing_charge":"No","file":[{"file_name":"IST-2018-970-v1+1_2018_Lanxin_Real-time_analysis.pdf","creator":"system","relation":"main_file","file_id":"5299","file_size":11352389,"access_level":"open_access","checksum":"6644ba698206eda32b0abf09128e63e3","content_type":"application/pdf","date_updated":"2020-07-14T12:46:29Z","date_created":"2018-12-12T10:17:43Z"}],"year":"2018","abstract":[{"lang":"eng","text":"The rapid auxin-triggered growth of the Arabidopsis hypocotyls involves the nuclear TIR1/AFB-Aux/IAA signaling and is accompanied by acidification of the apoplast and cell walls (Fendrych et al., 2016). Here, we describe in detail the method for analysis of the elongation and the TIR1/AFB-Aux/IAA-dependent auxin response in hypocotyl segments as well as the determination of relative values of the cell wall pH."}],"publication_status":"published","corr_author":"1","status":"public","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"issue":"1","ec_funded":1,"oa_version":"Published Version","acknowledgement":"This protocol was adapted from Fendrych et al., 2016. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385, and Austrian Science Fund (FWF) [M 2128-B21]. ","publist_id":"7381","title":"Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls","doi":"10.21769/BioProtoc.2685"},{"issue":"1","ec_funded":1,"external_id":{"pmid":["27837086"],"isi":["000394135800041"]},"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300"}],"title":"Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation","doi":"10.1104/pp.16.00943","oa_version":"Submitted Version","publist_id":"6199","day":"01","article_processing_charge":"No","file":[{"relation":"main_file","creator":"dernst","file_name":"2016_PlantPhysi_Steenackers.pdf","date_created":"2019-11-18T16:12:25Z","date_updated":"2020-07-14T12:44:36Z","content_type":"application/pdf","access_level":"open_access","checksum":"fd4d1cfe7ed70e54bb12ae3881f3fb91","file_id":"7040","file_size":4109142}],"pmid":1,"date_published":"2017-01-01T00:00:00Z","author":[{"full_name":"Steenackers, Ward","first_name":"Ward","last_name":"Steenackers"},{"first_name":"Petr","full_name":"Klíma, Petr","last_name":"Klíma"},{"full_name":"Quareshy, Mussa","first_name":"Mussa","last_name":"Quareshy"},{"first_name":"Igor","full_name":"Cesarino, Igor","last_name":"Cesarino"},{"last_name":"Kumpf","full_name":"Kumpf, Robert","first_name":"Robert"},{"full_name":"Corneillie, Sander","first_name":"Sander","last_name":"Corneillie"},{"first_name":"Pedro","full_name":"Araújo, Pedro","last_name":"Araújo"},{"first_name":"Tom","full_name":"Viaene, Tom","last_name":"Viaene"},{"last_name":"Goeminne","full_name":"Goeminne, Geert","first_name":"Geert"},{"last_name":"Nowack","full_name":"Nowack, Moritz","first_name":"Moritz"},{"full_name":"Ljung, Karin","first_name":"Karin","last_name":"Ljung"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí"},{"last_name":"Blakeslee","full_name":"Blakeslee, Joshua","first_name":"Joshua"},{"last_name":"Novák","first_name":"Ondřej","full_name":"Novák, Ondřej"},{"first_name":"Eva","full_name":"Zažímalová, Eva","last_name":"Zažímalová"},{"first_name":"Richard","full_name":"Napier, Richard","last_name":"Napier"},{"full_name":"Boerjan, Wout","first_name":"Wout","last_name":"Boerjan"},{"full_name":"Vanholme, Bartel","first_name":"Bartel","last_name":"Vanholme"}],"publisher":"American Society of Plant Biologists","status":"public","year":"2017","scopus_import":"1","publication_status":"published","abstract":[{"lang":"eng","text":"Auxin steers numerous physiological processes in plants, making the tight control of its endogenous levels and spatiotemporal distribution a necessity. This regulation is achieved by different mechanisms, including auxin biosynthesis, metabolic conversions, degradation, and transport. Here, we introduce cis-cinnamic acid (c-CA) as a novel and unique addition to a small group of endogenous molecules affecting in planta auxin concentrations. c-CA is the photo-isomerization product of the phenylpropanoid pathway intermediate trans-CA (t-CA). When grown on c-CA-containing medium, an evolutionary diverse set of plant species were shown to exhibit phenotypes characteristic for high auxin levels, including inhibition of primary root growth, induction of root hairs, and promotion of adventitious and lateral rooting. By molecular docking and receptor binding assays, we showed that c-CA itself is neither an auxin nor an anti-auxin, and auxin profiling data revealed that c-CA does not significantly interfere with auxin biosynthesis. Single cell-based auxin accumulation assays showed that c-CA, and not t-CA, is a potent inhibitor of auxin efflux. Auxin signaling reporters detected changes in spatiotemporal distribution of the auxin response along the root of c-CA-treated plants, and long-distance auxin transport assays showed no inhibition of rootward auxin transport. Overall, these results suggest that the phenotypes of c-CA-treated plants are the consequence of a local change in auxin accumulation, induced by the inhibition of auxin efflux. This work reveals a novel mechanism how plants may regulate auxin levels and adds a novel, naturally occurring molecule to the chemical toolbox for the studies of auxin homeostasis."}],"language":[{"iso":"eng"}],"month":"01","ddc":["580"],"intvolume":" 173","publication_identifier":{"issn":["0032-0889"]},"page":"552 - 565","has_accepted_license":"1","department":[{"_id":"JiFr"}],"_id":"1159","isi":1,"article_type":"original","volume":173,"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Plant Physiology","citation":{"mla":"Steenackers, Ward, et al. “Cis-Cinnamic Acid Is a Novel Natural Auxin Efflux Inhibitor That Promotes Lateral Root Formation.” Plant Physiology, vol. 173, no. 1, American Society of Plant Biologists, 2017, pp. 552–65, doi:10.1104/pp.16.00943.","apa":"Steenackers, W., Klíma, P., Quareshy, M., Cesarino, I., Kumpf, R., Corneillie, S., … Vanholme, B. (2017). Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.00943","chicago":"Steenackers, Ward, Petr Klíma, Mussa Quareshy, Igor Cesarino, Robert Kumpf, Sander Corneillie, Pedro Araújo, et al. “Cis-Cinnamic Acid Is a Novel Natural Auxin Efflux Inhibitor That Promotes Lateral Root Formation.” Plant Physiology. American Society of Plant Biologists, 2017. https://doi.org/10.1104/pp.16.00943.","ieee":"W. Steenackers et al., “Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation,” Plant Physiology, vol. 173, no. 1. American Society of Plant Biologists, pp. 552–565, 2017.","short":"W. Steenackers, P. Klíma, M. Quareshy, I. Cesarino, R. Kumpf, S. Corneillie, P. Araújo, T. Viaene, G. Goeminne, M. Nowack, K. Ljung, J. Friml, J. Blakeslee, O. Novák, E. Zažímalová, R. Napier, W. Boerjan, B. Vanholme, Plant Physiology 173 (2017) 552–565.","ama":"Steenackers W, Klíma P, Quareshy M, et al. Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation. Plant Physiology. 2017;173(1):552-565. doi:10.1104/pp.16.00943","ista":"Steenackers W, Klíma P, Quareshy M, Cesarino I, Kumpf R, Corneillie S, Araújo P, Viaene T, Goeminne G, Nowack M, Ljung K, Friml J, Blakeslee J, Novák O, Zažímalová E, Napier R, Boerjan W, Vanholme B. 2017. Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation. Plant Physiology. 173(1), 552–565."},"type":"journal_article","file_date_updated":"2020-07-14T12:44:36Z","date_updated":"2025-04-15T07:48:02Z","quality_controlled":"1","date_created":"2018-12-11T11:50:28Z"},{"type":"journal_article","publication":"Journal of visualized experiments JoVE","citation":{"ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light sheet fluorescence microscopy of plant roots growing on the surface of a gel,” Journal of visualized experiments JoVE, vol. 2017, no. 119. Journal of Visualized Experiments, 2017.","ista":"von Wangenheim D, Hauschild R, Friml J. 2017. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of visualized experiments JoVE. 2017(119), e55044.","short":"D. von Wangenheim, R. Hauschild, J. Friml, Journal of Visualized Experiments JoVE 2017 (2017).","ama":"von Wangenheim D, Hauschild R, Friml J. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of visualized experiments JoVE. 2017;2017(119). doi:10.3791/55044","mla":"von Wangenheim, Daniel, et al. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Journal of Visualized Experiments JoVE, vol. 2017, no. 119, e55044, Journal of Visualized Experiments, 2017, doi:10.3791/55044.","chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Journal of Visualized Experiments JoVE. Journal of Visualized Experiments, 2017. https://doi.org/10.3791/55044.","apa":"von Wangenheim, D., Hauschild, R., & Friml, J. (2017). Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of Visualized Experiments JoVE. Journal of Visualized Experiments. https://doi.org/10.3791/55044"},"date_updated":"2025-04-15T06:50:23Z","file_date_updated":"2018-12-12T10:16:32Z","date_created":"2018-12-11T11:50:01Z","oa":1,"volume":2017,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"relation":"popular_science","id":"5565","status":"public"}]},"has_accepted_license":"1","_id":"1078","isi":1,"department":[{"_id":"JiFr"},{"_id":"Bio"}],"article_number":"e55044","language":[{"iso":"eng"}],"month":"01","intvolume":" 2017","ddc":["580"],"status":"public","scopus_import":"1","year":"2017","publication_status":"published","abstract":[{"lang":"eng","text":"One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. "}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"article_processing_charge":"No","day":"18","file":[{"file_name":"IST-2017-808-v1+1_2017_VWangenheim_list.pdf","creator":"system","relation":"main_file","file_size":57678,"file_id":"5219","access_level":"open_access","date_updated":"2018-12-12T10:16:31Z","content_type":"application/pdf","date_created":"2018-12-12T10:16:31Z"},{"content_type":"application/pdf","date_updated":"2018-12-12T10:16:32Z","date_created":"2018-12-12T10:16:32Z","file_size":1317820,"file_id":"5220","access_level":"open_access","creator":"system","relation":"main_file","file_name":"IST-2017-808-v1+2_2017_VWangenheim_article.pdf"}],"date_published":"2017-01-18T00:00:00Z","author":[{"last_name":"Von Wangenheim","orcid":"0000-0002-6862-1247","id":"49E91952-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","full_name":"Von Wangenheim, Daniel"},{"last_name":"Hauschild","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Hauschild, Robert"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí"}],"publisher":"Journal of Visualized Experiments","pubrep_id":"808","title":"Light sheet fluorescence microscopy of plant roots growing on the surface of a gel","doi":"10.3791/55044","oa_version":"Published Version","publist_id":"6302","issue":"119","ec_funded":1,"external_id":{"isi":["000397847200041"]},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"},{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}]},{"citation":{"short":"B. Kuhn, T. Nodzyński, S. Errafi, R. Bucher, S. Gupta, B. Aryal, P. Dobrev, L. Bigler, M. Geisler, E. Zažímalová, J. Friml, C. Ringli, Scientific Reports 7 (2017).","ama":"Kuhn B, Nodzyński T, Errafi S, et al. Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific Reports. 2017;7. doi:10.1038/srep41906","ista":"Kuhn B, Nodzyński T, Errafi S, Bucher R, Gupta S, Aryal B, Dobrev P, Bigler L, Geisler M, Zažímalová E, Friml J, Ringli C. 2017. Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific Reports. 7, 41906.","ieee":"B. Kuhn et al., “Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity,” Scientific Reports, vol. 7. Nature Publishing Group, 2017.","apa":"Kuhn, B., Nodzyński, T., Errafi, S., Bucher, R., Gupta, S., Aryal, B., … Ringli, C. (2017). Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep41906","chicago":"Kuhn, Benjamin, Tomasz Nodzyński, Sanae Errafi, Rahel Bucher, Shibu Gupta, Bibek Aryal, Petre Dobrev, et al. “Flavonol-Induced Changes in PIN2 Polarity and Auxin Transport in the Arabidopsis Thaliana Rol1-2 Mutant Require Phosphatase Activity.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep41906.","mla":"Kuhn, Benjamin, et al. “Flavonol-Induced Changes in PIN2 Polarity and Auxin Transport in the Arabidopsis Thaliana Rol1-2 Mutant Require Phosphatase Activity.” Scientific Reports, vol. 7, 41906, Nature Publishing Group, 2017, doi:10.1038/srep41906."},"type":"journal_article","publication":"Scientific Reports","date_created":"2018-12-11T11:50:12Z","file_date_updated":"2018-12-12T10:18:09Z","quality_controlled":"1","date_updated":"2025-07-10T11:50:06Z","volume":7,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2045-2322"]},"department":[{"_id":"JiFr"}],"_id":"1110","isi":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"article_number":"41906","tmp":{"image":"/images/cc_by.png","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)"},"ddc":["581"],"intvolume":" 7","month":"02","status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"The phytohormone auxin is a major determinant and regulatory component important for plant development. Auxin transport between cells is mediated by a complex system of transporters such as AUX1/LAX, PIN, and ABCB proteins, and their localization and activity is thought to be influenced by phosphatases and kinases. Flavonols have been shown to alter auxin transport activity and changes in flavonol accumulation in the Arabidopsis thaliana rol1-2 mutant cause defects in auxin transport and seedling development. A new mutation in ROOTS CURL IN NPA 1 (RCN1), encoding a regulatory subunit of the phosphatase PP2A, was found to suppress the growth defects of rol1-2 without changing the flavonol content. rol1-2 rcn1-3 double mutants show wild type-like auxin transport activity while levels of free auxin are not affected by rcn1-3. In the rol1-2 mutant, PIN2 shows a flavonol-induced basal-to-apical shift in polar localization which is reversed in the rol1-2 rcn1-3 to basal localization. In vivo analysis of PINOID action, a kinase known to influence PIN protein localization in a PP2A-antagonistic manner, revealed a negative impact of flavonols on PINOID activity. Together, these data suggest that flavonols affect auxin transport by modifying the antagonistic kinase/phosphatase equilibrium."}],"year":"2017","scopus_import":"1","file":[{"date_updated":"2018-12-12T10:18:09Z","content_type":"application/pdf","date_created":"2018-12-12T10:18:09Z","file_id":"5328","file_size":1654496,"access_level":"open_access","creator":"system","relation":"main_file","file_name":"IST-2017-803-v1+1_srep41906.pdf"}],"day":"06","article_processing_charge":"No","pubrep_id":"803","author":[{"last_name":"Kuhn","full_name":"Kuhn, Benjamin","first_name":"Benjamin"},{"full_name":"Nodzyński, Tomasz","first_name":"Tomasz","last_name":"Nodzyński"},{"full_name":"Errafi, Sanae","first_name":"Sanae","last_name":"Errafi"},{"first_name":"Rahel","full_name":"Bucher, Rahel","last_name":"Bucher"},{"first_name":"Shibu","full_name":"Gupta, Shibu","last_name":"Gupta"},{"first_name":"Bibek","full_name":"Aryal, Bibek","last_name":"Aryal"},{"full_name":"Dobrev, Petre","first_name":"Petre","last_name":"Dobrev"},{"last_name":"Bigler","full_name":"Bigler, Laurent","first_name":"Laurent"},{"first_name":"Markus","full_name":"Geisler, Markus","last_name":"Geisler"},{"full_name":"Zažímalová, Eva","first_name":"Eva","last_name":"Zažímalová"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml"},{"first_name":"Christoph","full_name":"Ringli, Christoph","last_name":"Ringli"}],"publisher":"Nature Publishing Group","date_published":"2017-02-06T00:00:00Z","title":"Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity","doi":"10.1038/srep41906","publist_id":"6258","oa_version":"Published Version","acknowledgement":"European Research Council (project ERC-2011-StG-20101109-PSDP), European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation (GA13-40637S) [JF].","ec_funded":1,"project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"external_id":{"isi":["000393367600001"]}},{"type":"journal_article","citation":{"ista":"Kitakura S, Adamowski M, Matsuura Y, Santuari L, Kouno H, Arima K, Hardtke C, Friml J, Kakimoto T, Tanaka H. 2017. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. 58(10), 1801–1811.","ama":"Kitakura S, Adamowski M, Matsuura Y, et al. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. 2017;58(10). doi:10.1093/pcp/pcx118","short":"S. Kitakura, M. Adamowski, Y. Matsuura, L. Santuari, H. Kouno, K. Arima, C. Hardtke, J. Friml, T. Kakimoto, H. Tanaka, Plant and Cell Physiology 58 (2017).","ieee":"S. Kitakura et al., “BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana,” Plant and Cell Physiology, vol. 58, no. 10. Oxford University Press, 2017.","chicago":"Kitakura, Saeko, Maciek Adamowski, Yuki Matsuura, Luca Santuari, Hirotaka Kouno, Kohei Arima, Christian Hardtke, Jiří Friml, Tatsuo Kakimoto, and Hirokazu Tanaka. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” Plant and Cell Physiology. Oxford University Press, 2017. https://doi.org/10.1093/pcp/pcx118.","apa":"Kitakura, S., Adamowski, M., Matsuura, Y., Santuari, L., Kouno, H., Arima, K., … Tanaka, H. (2017). BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcx118","mla":"Kitakura, Saeko, et al. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” Plant and Cell Physiology, vol. 58, no. 10, 1801–1811, Oxford University Press, 2017, doi:10.1093/pcp/pcx118."},"publication":"Plant and Cell Physiology","file_date_updated":"2020-07-14T12:48:06Z","quality_controlled":"1","date_updated":"2025-07-10T11:54:55Z","date_created":"2018-12-11T11:48:34Z","volume":58,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0032-0781"]},"has_accepted_license":"1","_id":"799","department":[{"_id":"JiFr"}],"isi":1,"article_number":"1801-1811","language":[{"iso":"eng"}],"month":"08","ddc":["581"],"intvolume":" 58","status":"public","year":"2017","scopus_import":"1","publication_status":"published","abstract":[{"lang":"eng","text":"Membrane traffic at the trans-Golgi network (TGN) is crucial for correctly distributing various membrane proteins to their destination. Polarly localized auxin efflux proteins, including PIN-FORMED1 (PIN1), are dynamically transported between the endosomes and the plasma membrane (PM) in the plant cells. The intracellular trafficking of PIN1 protein is sensitive to a fungal toxin brefeldin A (BFA), which is known to inhibit guanine-nucleotide exchange factors for ADP ribosylation factors (ARF GEFs) such as GNOM. However, the molecular details of the BFA-sensitive trafficking pathway have not been revealed fully. In a previous study, we have identified an Arabidopsis mutant BFA-visualized endocytic trafficking defective 3 (ben3) which exhibited reduced sensitivity to BFA in terms of BFA-induced intracellular PIN1 agglomeration. Here, we show that BEN3 encodes a member of BIG family ARF GEFs, BIG2. Fluorescent proteins tagged BEN3/BIG2 co-localized with markers for TGN / early endosome (EE). Inspection of conditionally induced de novo synthesized PIN1 confirmed that its secretion to the PM is BFA-sensitive and established BEN3/BIG2 as a crucial component of this BFA action at the level of TGN/EE. Furthermore, ben3 mutation alleviated BFA-induced agglomeration of another TGN-localized ARF GEF BEN1/MIN7. Taken together our results suggest that BEN3/BIG2 is an ARF GEF component, which confers BFA sensitivity to the TGN/EE in Arabidopsis."}],"day":"21","article_processing_charge":"No","file":[{"file_id":"6333","file_size":1352913,"access_level":"open_access","checksum":"bd3e3a94d55416739cbb19624bb977f8","content_type":"application/pdf","date_updated":"2020-07-14T12:48:06Z","date_created":"2019-04-17T07:52:34Z","file_name":"2017_PlantCellPhysio_Kitakura.pdf","creator":"dernst","relation":"main_file"}],"date_published":"2017-08-21T00:00:00Z","pmid":1,"pubrep_id":"1009","author":[{"full_name":"Kitakura, Saeko","first_name":"Saeko","last_name":"Kitakura"},{"orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","full_name":"Adamowski, Maciek","last_name":"Adamowski"},{"full_name":"Matsuura, Yuki","first_name":"Yuki","last_name":"Matsuura"},{"first_name":"Luca","full_name":"Santuari, Luca","last_name":"Santuari"},{"full_name":"Kouno, Hirotaka","first_name":"Hirotaka","last_name":"Kouno"},{"last_name":"Arima","full_name":"Arima, Kohei","first_name":"Kohei"},{"first_name":"Christian","full_name":"Hardtke, Christian","last_name":"Hardtke"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí"},{"last_name":"Kakimoto","full_name":"Kakimoto, Tatsuo","first_name":"Tatsuo"},{"last_name":"Tanaka","first_name":"Hirokazu","full_name":"Tanaka, Hirokazu"}],"publisher":"Oxford University Press","title":"BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana","doi":"10.1093/pcp/pcx118","oa_version":"Submitted Version","publist_id":"6854","issue":"10","external_id":{"pmid":["29016942"],"isi":["000413220400019"]}},{"intvolume":" 6","ddc":["570"],"month":"06","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by.png","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)"},"article_number":"e26792","department":[{"_id":"JiFr"},{"_id":"Bio"},{"_id":"CaHe"},{"_id":"EvBe"}],"_id":"946","isi":1,"has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5566"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"volume":6,"date_created":"2018-12-11T11:49:21Z","date_updated":"2025-04-15T06:37:26Z","quality_controlled":"1","file_date_updated":"2020-07-14T12:48:15Z","publication":"eLife","type":"journal_article","citation":{"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.","short":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, J. Friml, ELife 6 (2017).","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","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.","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.","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","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."},"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"name":"Molecular basis of root growth inhibition by auxin","call_identifier":"FWF","_id":"2572ED28-B435-11E9-9278-68D0E5697425","grant_number":"M02128"},{"grant_number":"I 1774-B16","call_identifier":"FWF","name":"Hormone cross-talk drives nutrient dependent plant development","_id":"2542D156-B435-11E9-9278-68D0E5697425"},{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"external_id":{"isi":["000404728300001"]},"ec_funded":1,"publist_id":"6471","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","oa_version":"Published Version","doi":"10.7554/eLife.26792","title":"Live tracking of moving samples in confocal microscopy for vertically grown roots","author":[{"first_name":"Daniel","full_name":"Von Wangenheim, Daniel","orcid":"0000-0002-6862-1247","id":"49E91952-F248-11E8-B48F-1D18A9856A87","last_name":"Von Wangenheim"},{"last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","first_name":"Robert"},{"orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","full_name":"Fendrych, Matyas","last_name":"Fendrych"},{"first_name":"Vanessa","full_name":"Barone, Vanessa","orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","last_name":"Barone"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková"},{"last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publisher":"eLife Sciences Publications","pubrep_id":"847","date_published":"2017-06-19T00:00:00Z","file":[{"file_name":"IST-2017-847-v1+1_elife-26792-v2.pdf","relation":"main_file","creator":"system","checksum":"9af3398cb0d81f99d79016a616df22e9","access_level":"open_access","file_size":19581847,"file_id":"5315","date_created":"2018-12-12T10:17:57Z","date_updated":"2020-07-14T12:48:15Z","content_type":"application/pdf"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"article_processing_charge":"Yes","day":"19","abstract":[{"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.","lang":"eng"}],"publication_status":"published","scopus_import":"1","year":"2017","status":"public"},{"article_processing_charge":"No","day":"17","file":[{"access_level":"open_access","checksum":"e1f05e5850dfd9f9434d2d373ca61941","file_id":"4969","file_size":7443683,"date_created":"2018-12-12T10:12:49Z","date_updated":"2020-07-14T12:46:58Z","content_type":"application/pdf","file_name":"IST-2018-929-v1+1_56106.pdf","relation":"main_file","creator":"system"}],"date_published":"2017-11-17T00:00:00Z","author":[{"first_name":"Ewa","full_name":"Mazur, Ewa","last_name":"Mazur"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí"}],"publisher":"IntechOpen","pubrep_id":"929","status":"public","year":"2017","abstract":[{"text":"Development of vascular tissue is a remarkable example of intercellular communication and coordinated development involving hormonal signaling and tissue polarity. Thus far, studies on vascular patterning and regeneration have been conducted mainly in trees—woody plants—with a well-developed layer of vascular cambium and secondary tissues. Trees are difficult to use as genetic models, i.e., due to long generation time, unstable environmental conditions, and lack of available mutants and transgenic lines. Therefore, the use of the main genetic model plant Arabidopsis thaliana (L.) Heynh., with a wealth of available marker and transgenic lines, provides a unique opportunity to address molecular mechanism of vascular tissue formation and regeneration. With specific treatments, the tiny weed Arabidopsis can serve as a model to understand the growth of mighty trees and interconnect a tree physiology with molecular genetics and cell biology of Arabidopsis.","lang":"eng"}],"publication_status":"published","ec_funded":1,"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"doi":"10.5772/intechopen.69712","title":"Vascular tissue development and regeneration in the model plant arabidopsis","oa_version":"Published Version","publist_id":"7269","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"earlier_version","id":"1274","status":"public"}]},"type":"book_chapter","citation":{"chicago":"Mazur, Ewa, and Jiří Friml. “Vascular Tissue Development and Regeneration in the Model Plant Arabidopsis.” In Plant Engineering, edited by Snježana Jurić, 113–40. Plant Engineering. IntechOpen, 2017. https://doi.org/10.5772/intechopen.69712.","apa":"Mazur, E., & Friml, J. (2017). Vascular tissue development and regeneration in the model plant arabidopsis. In S. Jurić (Ed.), Plant Engineering (pp. 113–140). IntechOpen. https://doi.org/10.5772/intechopen.69712","mla":"Mazur, Ewa, and Jiří Friml. “Vascular Tissue Development and Regeneration in the Model Plant Arabidopsis.” Plant Engineering, edited by Snježana Jurić, IntechOpen, 2017, pp. 113–40, doi:10.5772/intechopen.69712.","ista":"Mazur E, Friml J. 2017.Vascular tissue development and regeneration in the model plant arabidopsis. In: Plant Engineering. Agricultural and Biological Sciences, , 113–140.","short":"E. Mazur, J. Friml, in:, S. Jurić (Ed.), Plant Engineering, IntechOpen, 2017, pp. 113–140.","ama":"Mazur E, Friml J. Vascular tissue development and regeneration in the model plant arabidopsis. In: Jurić S, ed. Plant Engineering. Plant Engineering. IntechOpen; 2017:113-140. doi:10.5772/intechopen.69712","ieee":"E. Mazur and J. Friml, “Vascular tissue development and regeneration in the model plant arabidopsis,” in Plant Engineering, S. Jurić, Ed. IntechOpen, 2017, pp. 113–140."},"publication":"Plant Engineering","date_updated":"2025-09-22T08:43:49Z","quality_controlled":"1","file_date_updated":"2020-07-14T12:46:58Z","date_created":"2018-12-11T11:47:05Z","tmp":{"image":"/images/cc_by.png","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)"},"series_title":"Plant Engineering","language":[{"iso":"eng"}],"editor":[{"last_name":"Jurić","first_name":"Snježana","full_name":"Jurić, Snježana"}],"month":"11","ddc":["581"],"alternative_title":["Agricultural and Biological Sciences"],"has_accepted_license":"1","page":"113 - 140","_id":"545","department":[{"_id":"JiFr"}]},{"ec_funded":1,"month":"04","ddc":["580"],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"title":"Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel","doi":"10.15479/AT:ISTA:66","has_accepted_license":"1","oa_version":"Published Version","acknowledgement":"fund: FP7-ERC 0101109","publist_id":"6302","department":[{"_id":"JiFr"},{"_id":"Bio"}],"_id":"5565","day":"10","article_processing_charge":"No","file":[{"file_name":"IST-2017-66-v1+1_WangenheimHighResolution55044-NEW_1.mp4","relation":"main_file","creator":"system","checksum":"b7552fc23540a85dc5a22fd4484eae71","access_level":"open_access","file_size":101497758,"file_id":"5599","date_created":"2018-12-12T13:02:33Z","content_type":"video/mp4","date_updated":"2020-07-14T12:47:03Z"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2017-04-10T00:00:00Z","related_material":{"record":[{"relation":"research_paper","id":"1078","status":"public"}]},"author":[{"last_name":"Von Wangenheim","full_name":"Von Wangenheim, Daniel","first_name":"Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247"},{"last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","first_name":"Robert"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml"}],"publisher":"Institute of Science and Technology Austria","datarep_id":"66","status":"public","type":"research_data","citation":{"ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel.” Institute of Science and Technology Austria, 2017.","ista":"von Wangenheim D, Hauschild R, Friml J. 2017. Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel, Institute of Science and Technology Austria, 10.15479/AT:ISTA:66.","short":"D. von Wangenheim, R. Hauschild, J. Friml, (2017).","ama":"von Wangenheim D, Hauschild R, Friml J. Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel. 2017. doi:10.15479/AT:ISTA:66","mla":"von Wangenheim, Daniel, et al. Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:66.","chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:66.","apa":"von Wangenheim, D., Hauschild, R., & Friml, J. (2017). Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:66"},"year":"2017","file_date_updated":"2020-07-14T12:47:03Z","date_updated":"2025-04-15T07:48:04Z","abstract":[{"lang":"eng","text":"One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. \r\nThe Video is licensed under a CC BY NC ND license. "}],"date_created":"2018-12-12T12:31:34Z"},{"external_id":{"isi":["000418896700091"]},"issue":"12","publist_id":"7242","oa_version":"Published Version","title":"Control of endogenous auxin levels in plant root development","doi":"10.3390/ijms18122587","publisher":"MDPI","author":[{"first_name":"Damilola","full_name":"Olatunji, Damilola","last_name":"Olatunji"},{"full_name":"Geelen, Danny","first_name":"Danny","last_name":"Geelen"},{"full_name":"Verstraeten, Inge","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","last_name":"Verstraeten"}],"pubrep_id":"917","date_published":"2017-12-01T00:00:00Z","file":[{"creator":"system","relation":"main_file","file_name":"IST-2017-917-v1+1_ijms-18-02587.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-12T10:08:55Z","file_id":"4718","file_size":920962,"access_level":"open_access","checksum":"82d51f11e493f7eec02976d9a9a9805e"}],"article_processing_charge":"No","day":"01","abstract":[{"text":"In this review, we summarize the different biosynthesis-related pathways that contribute to the regulation of endogenous auxin in plants. We demonstrate that all known genes involved in auxin biosynthesis also have a role in root formation, from the initiation of a root meristem during embryogenesis to the generation of a functional root system with a primary root, secondary lateral root branches and adventitious roots. Furthermore, the versatile adaptation of root development in response to environmental challenges is mediated by both local and distant control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial and temporal regulation of auxin biosynthesis plays a central role in determining root architecture.","lang":"eng"}],"publication_status":"published","scopus_import":"1","year":"2017","status":"public","corr_author":"1","intvolume":" 18","ddc":["580"],"month":"12","language":[{"iso":"eng"}],"tmp":{"image":"/images/cc_by.png","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)"},"article_number":"2587","department":[{"_id":"JiFr"}],"_id":"572","isi":1,"has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"volume":18,"date_created":"2018-12-11T11:47:15Z","date_updated":"2025-09-11T07:38:50Z","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:10Z","citation":{"mla":"Olatunji, Damilola, et al. “Control of Endogenous Auxin Levels in Plant Root Development.” International Journal of Molecular Sciences, vol. 18, no. 12, 2587, MDPI, 2017, doi:10.3390/ijms18122587.","apa":"Olatunji, D., Geelen, D., & Verstraeten, I. (2017). Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms18122587","chicago":"Olatunji, Damilola, Danny Geelen, and Inge Verstraeten. “Control of Endogenous Auxin Levels in Plant Root Development.” International Journal of Molecular Sciences. MDPI, 2017. https://doi.org/10.3390/ijms18122587.","ieee":"D. Olatunji, D. Geelen, and I. Verstraeten, “Control of endogenous auxin levels in plant root development,” International Journal of Molecular Sciences, vol. 18, no. 12. MDPI, 2017.","short":"D. Olatunji, D. Geelen, I. Verstraeten, International Journal of Molecular Sciences 18 (2017).","ama":"Olatunji D, Geelen D, Verstraeten I. Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. 2017;18(12). doi:10.3390/ijms18122587","ista":"Olatunji D, Geelen D, Verstraeten I. 2017. Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. 18(12), 2587."},"publication":"International Journal of Molecular Sciences","type":"journal_article"}]