[{"type":"journal_article","status":"public","_id":"3005","publist_id":"3697","author":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"full_name":"Benfey, Philip","last_name":"Benfey","first_name":"Philip"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"full_name":"Bennett, Malcolm","last_name":"Bennett","first_name":"Malcolm"},{"full_name":"Berleth, Thomas","last_name":"Berleth","first_name":"Thomas"},{"full_name":"Geldner, Niko","last_name":"Geldner","first_name":"Niko"},{"first_name":"Markus","last_name":"Grebe","full_name":"Grebe, Markus"},{"last_name":"Heisler","full_name":"Heisler, Marcus","first_name":"Marcus"},{"last_name":"Hejátko","full_name":"Hejátko, Jan","first_name":"Jan"},{"first_name":"Gerd","full_name":"Jürgens, Gerd","last_name":"Jürgens"},{"first_name":"Thomas","last_name":"Laux","full_name":"Laux, Thomas"},{"first_name":"Keith","full_name":"Lindsey, Keith","last_name":"Lindsey"},{"first_name":"Wolfgang","full_name":"Lukowitz, Wolfgang","last_name":"Lukowitz"},{"last_name":"Luschnig","full_name":"Luschnig, Christian","first_name":"Christian"},{"first_name":"Remko","full_name":"Offringa, Remko","last_name":"Offringa"},{"first_name":"Ben","full_name":"Scheres, Ben","last_name":"Scheres"},{"first_name":"Ranjan","last_name":"Swarup","full_name":"Swarup, Ranjan"},{"first_name":"Ramón","last_name":"Torres Ruiz","full_name":"Torres Ruiz, Ramón"},{"last_name":"Weijers","full_name":"Weijers, Dolf","first_name":"Dolf"},{"last_name":"Zažímalová","full_name":"Zažímalová, Eva","first_name":"Eva"}],"title":"Apical-basal polarity: Why plant cells don't stand on their heads","date_updated":"2021-01-12T07:40:24Z","citation":{"mla":"Friml, Jiří, et al. “Apical-Basal Polarity: Why Plant Cells Don’t Stand on Their Heads.” Trends in Plant Science, vol. 11, no. 1, Cell Press, 2006, pp. 12–14, doi:10.1016/j.tplants.2005.11.010.","short":"J. Friml, P. Benfey, E. Benková, M. Bennett, T. Berleth, N. Geldner, M. Grebe, M. Heisler, J. Hejátko, G. Jürgens, T. Laux, K. Lindsey, W. Lukowitz, C. Luschnig, R. Offringa, B. Scheres, R. Swarup, R. Torres Ruiz, D. Weijers, E. Zažímalová, Trends in Plant Science 11 (2006) 12–14.","ieee":"J. Friml et al., “Apical-basal polarity: Why plant cells don’t stand on their heads,” Trends in Plant Science, vol. 11, no. 1. Cell Press, pp. 12–14, 2006.","ama":"Friml J, Benfey P, Benková E, et al. Apical-basal polarity: Why plant cells don’t stand on their heads. Trends in Plant Science. 2006;11(1):12-14. doi:10.1016/j.tplants.2005.11.010","apa":"Friml, J., Benfey, P., Benková, E., Bennett, M., Berleth, T., Geldner, N., … Zažímalová, E. (2006). Apical-basal polarity: Why plant cells don’t stand on their heads. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2005.11.010","chicago":"Friml, Jiří, Philip Benfey, Eva Benková, Malcolm Bennett, Thomas Berleth, Niko Geldner, Markus Grebe, et al. “Apical-Basal Polarity: Why Plant Cells Don’t Stand on Their Heads.” Trends in Plant Science. Cell Press, 2006. https://doi.org/10.1016/j.tplants.2005.11.010.","ista":"Friml J, Benfey P, Benková E, Bennett M, Berleth T, Geldner N, Grebe M, Heisler M, Hejátko J, Jürgens G, Laux T, Lindsey K, Lukowitz W, Luschnig C, Offringa R, Scheres B, Swarup R, Torres Ruiz R, Weijers D, Zažímalová E. 2006. Apical-basal polarity: Why plant cells don’t stand on their heads. Trends in Plant Science. 11(1), 12–14."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","publisher":"Cell Press","intvolume":" 11","month":"01","oa_version":"None","page":"12 - 14","date_created":"2018-12-11T12:00:49Z","date_published":"2006-01-01T00:00:00Z","doi":"10.1016/j.tplants.2005.11.010","issue":"1","volume":11,"year":"2006","publication_status":"published","language":[{"iso":"eng"}],"publication":"Trends in Plant Science","day":"01"},{"abstract":[{"lang":"eng","text":"Plants and some animals have a profound capacity to regenerate organs from adult tissues. Molecular mechanisms for regeneration have, however, been largely unexplored. Here we investigate a local regeneration response in Arabidopsis roots. Laser-induced wounding disrupts the flow of auxin-a cell-fate-instructive plant hormone-in root tips, and we demonstrate that resulting cell-fate changes require the PLETHORA, SHORTROOT, and SCARECROW transcription factors. These transcription factors regulate the expression and polar position of PIN auxin efflux-facilitating membrane proteins to reconstitute auxin transport in renewed root tips. Thus, a regeneration mechanism using embryonic root stem-cell patterning factors first responds to and subsequently stabilizes a new hormone distribution."}],"quality_controlled":0,"publisher":"American Association for the Advancement of Science","month":"01","intvolume":" 311","year":"2006","publication_status":"published","day":"20","publication":"Science","page":"385 - 388","issue":"5759","date_published":"2006-01-20T00:00:00Z","doi":"10.1126/science.1121790","volume":311,"date_created":"2018-12-11T12:00:50Z","_id":"3008","type":"journal_article","status":"public","citation":{"ista":"Xu J, Hofhuis H, Heidstra R, Sauer M, Friml J, Scheres B. 2006. A molecular framework for plant regeneration. Science. 311(5759), 385–388.","chicago":"Xu, Jian, Hugo Hofhuis, Renze Heidstra, Michael Sauer, Jiří Friml, and Ben Scheres. “A Molecular Framework for Plant Regeneration.” Science. American Association for the Advancement of Science, 2006. https://doi.org/10.1126/science.1121790.","short":"J. Xu, H. Hofhuis, R. Heidstra, M. Sauer, J. Friml, B. Scheres, Science 311 (2006) 385–388.","ieee":"J. Xu, H. Hofhuis, R. Heidstra, M. Sauer, J. Friml, and B. Scheres, “A molecular framework for plant regeneration,” Science, vol. 311, no. 5759. American Association for the Advancement of Science, pp. 385–388, 2006.","ama":"Xu J, Hofhuis H, Heidstra R, Sauer M, Friml J, Scheres B. A molecular framework for plant regeneration. Science. 2006;311(5759):385-388. doi:10.1126/science.1121790","apa":"Xu, J., Hofhuis, H., Heidstra, R., Sauer, M., Friml, J., & Scheres, B. (2006). A molecular framework for plant regeneration. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1121790","mla":"Xu, Jian, et al. “A Molecular Framework for Plant Regeneration.” Science, vol. 311, no. 5759, American Association for the Advancement of Science, 2006, pp. 385–88, doi:10.1126/science.1121790."},"date_updated":"2021-01-12T07:40:25Z","extern":1,"publist_id":"3695","author":[{"first_name":"Jian","full_name":"Xu, Jian","last_name":"Xu"},{"first_name":"Hugo","last_name":"Hofhuis","full_name":"Hofhuis, Hugo"},{"first_name":"Renze","last_name":"Heidstra","full_name":"Heidstra, Renze"},{"full_name":"Sauer, Michael","last_name":"Sauer","first_name":"Michael"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596"},{"first_name":"Ben","full_name":"Scheres, Ben","last_name":"Scheres"}],"title":"A molecular framework for plant regeneration"},{"page":"1199 - 1202","date_created":"2018-12-11T12:00:50Z","date_published":"2006-01-01T00:00:00Z","issue":"7","doi":"10.1242/jcs.02910","volume":119,"publication_status":"published","year":"2006","language":[{"iso":"eng"}],"publication":"Journal of Cell Science","day":"01","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/16554435"}],"oa":1,"quality_controlled":"1","publisher":"Company of Biologists","intvolume":" 119","month":"01","oa_version":"Published Version","pmid":1,"external_id":{"pmid":[" 16554435"]},"author":[{"full_name":"Paciorek, Tomasz","last_name":"Paciorek","first_name":"Tomasz"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"publist_id":"3693","title":"Auxin signaling","date_updated":"2021-01-12T07:40:25Z","citation":{"chicago":"Paciorek, Tomasz, and Jiří Friml. “Auxin Signaling.” Journal of Cell Science. Company of Biologists, 2006. https://doi.org/10.1242/jcs.02910.","ista":"Paciorek T, Friml J. 2006. Auxin signaling. Journal of Cell Science. 119(7), 1199–1202.","mla":"Paciorek, Tomasz, and Jiří Friml. “Auxin Signaling.” Journal of Cell Science, vol. 119, no. 7, Company of Biologists, 2006, pp. 1199–202, doi:10.1242/jcs.02910.","apa":"Paciorek, T., & Friml, J. (2006). Auxin signaling. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.02910","ama":"Paciorek T, Friml J. Auxin signaling. Journal of Cell Science. 2006;119(7):1199-1202. doi:10.1242/jcs.02910","short":"T. Paciorek, J. Friml, Journal of Cell Science 119 (2006) 1199–1202.","ieee":"T. Paciorek and J. Friml, “Auxin signaling,” Journal of Cell Science, vol. 119, no. 7. Company of Biologists, pp. 1199–1202, 2006."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","type":"journal_article","status":"public","_id":"3009"},{"oa_version":"None","abstract":[{"lang":"eng","text":"Plant development is characterized by a profound ability to regenerate and form tissues with new axes of polarity. An unsolved question concerns how the position within a tissue and cues from neighboring cells are integrated to specify the polarity of individual cells. The canalization hypothesis proposes a feedback effect of the phytohormone auxin on the directionality of intercellular auxin flow as a means to polarize tissues. Here we identify a cellular and molecular mechanism for canalization. Local auxin application, wounding, or auxin accumulation during de novo organ formation lead to rearrangements in the subcellular polar localization of PIN auxin transport components. This auxin effect on PIN polarity is cell-specific, does not depend on PIN transcription, and involves the Aux/IAA-ARF (indole-3-acetic acid-auxin response factor) signaling pathway. Our data suggest that auxin acts as polarizing cue, which links individual cell polarity with tissue and organ polarity through control of PIN polar targeting. This feedback regulation provides a conceptual framework for polarization during multiple regenerative and patterning processes in plants."}],"intvolume":" 20","month":"10","publisher":"Cold Spring Harbor Laboratory Press","publication":"Genes and Development","language":[{"iso":"eng"}],"day":"15","publication_status":"published","year":"2006","date_created":"2018-12-11T12:00:53Z","related_material":{"link":[{"relation":"erratum","url":"http://genesdev.cshlp.org/content/21/11/1431.short"}]},"issue":"20","doi":"10.1101/gad.390806","volume":20,"date_published":"2006-10-15T00:00:00Z","page":"2902 - 2911","_id":"3016","status":"public","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","date_updated":"2021-11-16T07:53:09Z","citation":{"ista":"Sauer M, Balla J, Luschnig C, Wiśniewska J, Reinöhl V, Friml J, Benková E. 2006. Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity. Genes and Development. 20(20), 2902–2911.","chicago":"Sauer, Michael, Jozef Balla, Christian Luschnig, Justyna Wiśniewska, Vilém Reinöhl, Jiří Friml, and Eva Benková. “Canalization of Auxin Flow by Aux/IAA-ARF-Dependent Feedback Regulation of PIN Polarity.” Genes and Development. Cold Spring Harbor Laboratory Press, 2006. https://doi.org/10.1101/gad.390806.","ama":"Sauer M, Balla J, Luschnig C, et al. Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity. Genes and Development. 2006;20(20):2902-2911. doi:10.1101/gad.390806","apa":"Sauer, M., Balla, J., Luschnig, C., Wiśniewska, J., Reinöhl, V., Friml, J., & Benková, E. (2006). Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.390806","ieee":"M. Sauer et al., “Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity,” Genes and Development, vol. 20, no. 20. Cold Spring Harbor Laboratory Press, pp. 2902–2911, 2006.","short":"M. Sauer, J. Balla, C. Luschnig, J. Wiśniewska, V. Reinöhl, J. Friml, E. Benková, Genes and Development 20 (2006) 2902–2911.","mla":"Sauer, Michael, et al. “Canalization of Auxin Flow by Aux/IAA-ARF-Dependent Feedback Regulation of PIN Polarity.” Genes and Development, vol. 20, no. 20, Cold Spring Harbor Laboratory Press, 2006, pp. 2902–11, doi:10.1101/gad.390806."},"title":"Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity","article_processing_charge":"No","publist_id":"3686","author":[{"full_name":"Sauer, Michael","last_name":"Sauer","first_name":"Michael"},{"first_name":"Jozef","last_name":"Balla","full_name":"Balla, Jozef"},{"full_name":"Luschnig, Christian","last_name":"Luschnig","first_name":"Christian"},{"first_name":"Justyna","last_name":"Wiśniewska","full_name":"Wiśniewska, Justyna"},{"last_name":"Reinöhl","full_name":"Reinöhl, Vilém","first_name":"Vilém"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}]},{"date_created":"2018-12-11T12:00:53Z","doi":"10.1007/s00018-006-6116-5","date_published":"2006-12-01T00:00:00Z","volume":63,"issue":"23","page":"2738 - 2754","publication":"Cellular and Molecular Life Sciences","language":[{"iso":"eng"}],"day":"01","year":"2006","publication_status":"published","intvolume":" 63","month":"12","quality_controlled":"1","publisher":"Birkhäuser","oa_version":"None","abstract":[{"text":"The plant hormone auxin plays crucial roles in regulating plant growth development, including embryo and root patterning, organ formation, vascular tissue differentiation and growth responses to environmental stimuli. Asymmetric auxin distribution patterns have been observed within tissues, and these so-called auxin gradients change dynamically during different developmental processes. Most auxin is synthesized in the shoot and distributed directionally throughout the plant. This polar auxin transport is mediated by auxin influx and efflux facilitators, whose subcellular polar localizations guide the direction of auxin flow. The polar localization of PIN auxin efflux carriers changes in response to developmental and external cues in order to channel auxin flow in a regulated manner for organized growth. Auxin itself modulates the expression and subcellular localization of PIN proteins, contributing to a complex pattern of feedback regulation. Here we review the available information mainly from studies of a model plant, Arabidopsis thaliana, on the generation of auxin gradients, the regulation of polar auxin transport and further downstream cellular events.","lang":"eng"}],"title":"Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development","publist_id":"3685","author":[{"last_name":"Tanaka","full_name":"Tanaka, Hirokazu","first_name":"Hirokazu"},{"full_name":"Dhonukshe, Pankaj","last_name":"Dhonukshe","first_name":"Pankaj"},{"first_name":"Philip","full_name":"Brewer, Philip","last_name":"Brewer"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"ista":"Tanaka H, Dhonukshe P, Brewer P, Friml J. 2006. Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development. Cellular and Molecular Life Sciences. 63(23), 2738–2754.","chicago":"Tanaka, Hirokazu, Pankaj Dhonukshe, Philip Brewer, and Jiří Friml. “Spatiotemporal Asymmetric Auxin Distribution: A Means to Coordinate Plant Development.” Cellular and Molecular Life Sciences. Birkhäuser, 2006. https://doi.org/10.1007/s00018-006-6116-5.","apa":"Tanaka, H., Dhonukshe, P., Brewer, P., & Friml, J. (2006). Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development. Cellular and Molecular Life Sciences. Birkhäuser. https://doi.org/10.1007/s00018-006-6116-5","ama":"Tanaka H, Dhonukshe P, Brewer P, Friml J. Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development. Cellular and Molecular Life Sciences. 2006;63(23):2738-2754. doi:10.1007/s00018-006-6116-5","short":"H. Tanaka, P. Dhonukshe, P. Brewer, J. Friml, Cellular and Molecular Life Sciences 63 (2006) 2738–2754.","ieee":"H. Tanaka, P. Dhonukshe, P. Brewer, and J. Friml, “Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development,” Cellular and Molecular Life Sciences, vol. 63, no. 23. Birkhäuser, pp. 2738–2754, 2006.","mla":"Tanaka, Hirokazu, et al. “Spatiotemporal Asymmetric Auxin Distribution: A Means to Coordinate Plant Development.” Cellular and Molecular Life Sciences, vol. 63, no. 23, Birkhäuser, 2006, pp. 2738–54, doi:10.1007/s00018-006-6116-5."},"date_updated":"2021-01-12T07:40:29Z","status":"public","type":"journal_article","_id":"3017"},{"status":"public","type":"journal_article","_id":"3018","title":"Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1","author":[{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"first_name":"Pankaj","last_name":"Dhonukshe","full_name":"Dhonukshe, Pankaj"},{"first_name":"Ranjan","last_name":"Swarup","full_name":"Swarup, Ranjan"},{"first_name":"Malcolm","full_name":"Bennett, Malcolm","last_name":"Bennett"},{"full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"publist_id":"3684","extern":1,"date_updated":"2021-01-12T07:40:29Z","citation":{"mla":"Kleine Vehn, Jürgen, et al. “Subcellular Trafficking of the Arabidopsis Auxin Influx Carrier AUX1 Uses a Novel Pathway Distinct from PIN1.” Plant Cell, vol. 18, no. 11, American Society of Plant Biologists, 2006, pp. 3171–81, doi:10.1105/tpc.106.042770.","ieee":"J. Kleine Vehn, P. Dhonukshe, R. Swarup, M. Bennett, and J. Friml, “Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1,” Plant Cell, vol. 18, no. 11. American Society of Plant Biologists, pp. 3171–3181, 2006.","short":"J. Kleine Vehn, P. Dhonukshe, R. Swarup, M. Bennett, J. Friml, Plant Cell 18 (2006) 3171–3181.","apa":"Kleine Vehn, J., Dhonukshe, P., Swarup, R., Bennett, M., & Friml, J. (2006). Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.106.042770","ama":"Kleine Vehn J, Dhonukshe P, Swarup R, Bennett M, Friml J. Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1. Plant Cell. 2006;18(11):3171-3181. doi:10.1105/tpc.106.042770","chicago":"Kleine Vehn, Jürgen, Pankaj Dhonukshe, Ranjan Swarup, Malcolm Bennett, and Jiří Friml. “Subcellular Trafficking of the Arabidopsis Auxin Influx Carrier AUX1 Uses a Novel Pathway Distinct from PIN1.” Plant Cell. American Society of Plant Biologists, 2006. https://doi.org/10.1105/tpc.106.042770.","ista":"Kleine Vehn J, Dhonukshe P, Swarup R, Bennett M, Friml J. 2006. Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1. Plant Cell. 18(11), 3171–3181."},"intvolume":" 18","month":"11","publisher":"American Society of Plant Biologists","quality_controlled":0,"abstract":[{"lang":"eng","text":"The directional flow of the plant hormone auxin mediates multiple developmental processes, including patterning and tropisms. Apical and basal plasma membrane localization of AUXIN-RESISTANT1 (AUX1) and PIN-FORMED1 (PIN1) auxin transport components underpins the directionality of intercellular auxin flow in Arabidopsis thaliana roots. Here, we examined the mechanism of polar trafficking of AUX1. Real-time live cell analysis along with subcellular markers revealed that AUX1 resides at the apical plasma membrane of protophloem cells and at highly dynamic subpopulations of Golgi apparatus and endosomes in all cell types. Plasma membrane and intracellular pools of AUX1 are interconnected by actin-dependent constitutive trafficking, which is not sensitive to the vesicle trafficking inhibitor brefeldin A. AUX1 subcellular dynamics are not influenced by the auxin influx inhibitor NOA but are blocked by the auxin efflux inhibitors TIBA and PBA. Furthermore, auxin transport inhibitors and interference with the sterol composition of membranes disrupt polar AUX1 distribution at the plasma membrane. Compared with PIN1 trafficking, AUX1 dynamics display different sensitivities to trafficking inhibitors and are independent of the endosomal trafficking regulator ARF GEF GNOM. Hence, AUX1 uses a novel trafficking pathway in plants that is distinct from PIN trafficking, providing an additional mechanism for the fine regulation of auxin transport."}],"date_created":"2018-12-11T12:00:53Z","volume":18,"date_published":"2006-11-01T00:00:00Z","doi":"10.1105/tpc.106.042770","issue":"11","page":"3171 - 3181","publication":"Plant Cell","day":"01","year":"2006","publication_status":"published"},{"doi":"10.1038/nprot.2006.333","date_published":"2006-11-01T00:00:00Z","issue":"4","volume":1,"date_created":"2018-12-11T12:00:54Z","page":"1939 - 1946","day":"01","publication":"Nature Protocols","publication_status":"published","year":"2006","month":"11","intvolume":" 1","publisher":"Nature Publishing Group","quality_controlled":0,"abstract":[{"lang":"eng","text":"High throughput microarray transcription analyses provide us with the expression profiles for large amounts of plant genes. However, their tissue and cellular resolution is limited. Thus, for detailed functional analysis, it is still necessary to examine the expression pattern of selected candidate genes at a cellular level. Here, we present an in situ mRNA hybridization method that is routinely used for the analysis of plant gene expression patterns. The protocol is optimized for whole mount mRNA localizations in Arabidopsis seedling tissues including embryos, roots, hypocotyls and young primary leaves. It can also be used for comparable tissues in other species. Part of the protocol can also be automated and performed by a liquid handling robot. Here we present a detailed protocol, recommended controls and troubleshooting, along with examples of several applications. The total time to carry out the entire procedure is ∼7 d, depending on the tissue used."}],"title":"In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples","publist_id":"3683","author":[{"full_name":"Hejátko, Jan","last_name":"Hejátko","first_name":"Jan"},{"last_name":"Blilou","full_name":"Blilou, Ikram","first_name":"Ikram"},{"full_name":"Brewer, Philip B","last_name":"Brewer","first_name":"Philip"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596"},{"last_name":"Scheres","full_name":"Scheres, Ben","first_name":"Ben"},{"orcid":"0000-0002-8510-9739","full_name":"Eva Benková","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"extern":1,"citation":{"chicago":"Hejátko, Jan, Ikram Blilou, Philip Brewer, Jiří Friml, Ben Scheres, and Eva Benková. “In Situ Hybridization Technique for MRNA Detection in Whole Mount Arabidopsis Samples.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.333.","ista":"Hejátko J, Blilou I, Brewer P, Friml J, Scheres B, Benková E. 2006. In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples. Nature Protocols. 1(4), 1939–1946.","mla":"Hejátko, Jan, et al. “In Situ Hybridization Technique for MRNA Detection in Whole Mount Arabidopsis Samples.” Nature Protocols, vol. 1, no. 4, Nature Publishing Group, 2006, pp. 1939–46, doi:10.1038/nprot.2006.333.","ama":"Hejátko J, Blilou I, Brewer P, Friml J, Scheres B, Benková E. In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples. Nature Protocols. 2006;1(4):1939-1946. doi:10.1038/nprot.2006.333","apa":"Hejátko, J., Blilou, I., Brewer, P., Friml, J., Scheres, B., & Benková, E. (2006). In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.333","short":"J. Hejátko, I. Blilou, P. Brewer, J. Friml, B. Scheres, E. Benková, Nature Protocols 1 (2006) 1939–1946.","ieee":"J. Hejátko, I. Blilou, P. Brewer, J. Friml, B. Scheres, and E. Benková, “In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples,” Nature Protocols, vol. 1, no. 4. Nature Publishing Group, pp. 1939–1946, 2006."},"date_updated":"2021-01-12T07:40:30Z","status":"public","type":"journal_article","_id":"3020"},{"publication_status":"published","year":"2006","publication":"Nature Protocols","day":"01","page":"98 - 103","date_created":"2018-12-11T12:00:52Z","issue":"1","date_published":"2006-06-01T00:00:00Z","doi":"10.1038/nprot.2006.15","volume":1,"abstract":[{"text":"As the field of plant molecular biology is swiftly advancing, a need has been created for methods that allow rapid and reliable in situ localization of proteins in plant cells. Here we describe a whole-mount 'immunolocalization' technique for various plant tissues, including roots, hypocotyls, cotyledons, young primary leaves and embryos of Arabidopsis thaliana and other species. The detailed protocol, recommended controls and troubleshooting are presented, along with examples of applications. The protocol consists of five main procedures: tissue fixation, tissue permeation, blocking, primary and secondary antibody incubation. Notably, the first procedure (tissue fixation) includes several steps (4-12) that are absolutely necessary for protein localization in hypocotyls, cotyledons and young primary leaves but should be omitted for other tissues. The protocol is usually done in 3 days, but could also be completed in 2 days.","lang":"eng"}],"quality_controlled":0,"publisher":"Nature Publishing Group","intvolume":" 1","month":"06","citation":{"apa":"Sauer, M., Paciorek, T., Benková, E., & Friml, J. (2006). Immunocytochemical techniques for whole mount in situ protein localization in plants. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.15","ama":"Sauer M, Paciorek T, Benková E, Friml J. Immunocytochemical techniques for whole mount in situ protein localization in plants. Nature Protocols. 2006;1(1):98-103. doi:10.1038/nprot.2006.15","ieee":"M. Sauer, T. Paciorek, E. Benková, and J. Friml, “Immunocytochemical techniques for whole mount in situ protein localization in plants,” Nature Protocols, vol. 1, no. 1. Nature Publishing Group, pp. 98–103, 2006.","short":"M. Sauer, T. Paciorek, E. Benková, J. Friml, Nature Protocols 1 (2006) 98–103.","mla":"Sauer, Michael, et al. “Immunocytochemical Techniques for Whole Mount in Situ Protein Localization in Plants.” Nature Protocols, vol. 1, no. 1, Nature Publishing Group, 2006, pp. 98–103, doi:10.1038/nprot.2006.15.","ista":"Sauer M, Paciorek T, Benková E, Friml J. 2006. Immunocytochemical techniques for whole mount in situ protein localization in plants. Nature Protocols. 1(1), 98–103.","chicago":"Sauer, Michael, Tomasz Paciorek, Eva Benková, and Jiří Friml. “Immunocytochemical Techniques for Whole Mount in Situ Protein Localization in Plants.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.15."},"date_updated":"2021-01-12T07:40:28Z","extern":1,"publist_id":"3688","author":[{"first_name":"Michael","full_name":"Sauer, Michael","last_name":"Sauer"},{"first_name":"Tomasz","last_name":"Paciorek","full_name":"Paciorek, Tomasz"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Eva Benková","orcid":"0000-0002-8510-9739","last_name":"Benková"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"title":"Immunocytochemical techniques for whole mount in situ protein localization in plants","_id":"3015","type":"journal_article","status":"public"},{"status":"public","type":"journal_article","_id":"3013","title":"Immunocytochemical technique for protein localization in sections of plant tissues","author":[{"full_name":"Paciorek, Tomasz","last_name":"Paciorek","first_name":"Tomasz"},{"first_name":"Michael","full_name":"Sauer, Michael","last_name":"Sauer"},{"first_name":"Jozef","last_name":"Balla","full_name":"Balla, Jozef"},{"last_name":"Wiśniewska","full_name":"Wiśniewska, Justyna","first_name":"Justyna"},{"last_name":"Friml","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"3689","extern":1,"citation":{"ama":"Paciorek T, Sauer M, Balla J, Wiśniewska J, Friml J. Immunocytochemical technique for protein localization in sections of plant tissues. Nature Protocols. 2006;1(1):104-107. doi:10.1038/nprot.2006.16","apa":"Paciorek, T., Sauer, M., Balla, J., Wiśniewska, J., & Friml, J. (2006). Immunocytochemical technique for protein localization in sections of plant tissues. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.16","short":"T. Paciorek, M. Sauer, J. Balla, J. Wiśniewska, J. Friml, Nature Protocols 1 (2006) 104–107.","ieee":"T. Paciorek, M. Sauer, J. Balla, J. Wiśniewska, and J. Friml, “Immunocytochemical technique for protein localization in sections of plant tissues,” Nature Protocols, vol. 1, no. 1. Nature Publishing Group, pp. 104–107, 2006.","mla":"Paciorek, Tomasz, et al. “Immunocytochemical Technique for Protein Localization in Sections of Plant Tissues.” Nature Protocols, vol. 1, no. 1, Nature Publishing Group, 2006, pp. 104–07, doi:10.1038/nprot.2006.16.","ista":"Paciorek T, Sauer M, Balla J, Wiśniewska J, Friml J. 2006. Immunocytochemical technique for protein localization in sections of plant tissues. Nature Protocols. 1(1), 104–107.","chicago":"Paciorek, Tomasz, Michael Sauer, Jozef Balla, Justyna Wiśniewska, and Jiří Friml. “Immunocytochemical Technique for Protein Localization in Sections of Plant Tissues.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.16."},"date_updated":"2021-01-12T07:40:27Z","intvolume":" 1","month":"06","quality_controlled":0,"publisher":"Nature Publishing Group","abstract":[{"lang":"eng","text":"There is a growing demand for methods that allow rapid and reliable in situ localization of proteins in plant cells. The immunocytochemistry protocol presented here can be used routinely to observe protein localization patterns in tissue sections of various plant species. This protocol is especially suitable for plant species with more-complex tissue architecture (such as maize, Zea mays), which makes it difficult to use an easier whole-mount procedure for protein localization. To facilitate the antibody-antigen reaction, it is necessary to include a wax-embedding and tissue-sectioning step. The protocol consists of the following procedures: chemical fixation of tissue, dehydration, wax embedding, sectioning, dewaxing, rehydration, blocking and antibody incubation. The detailed protocol, recommended controls and troubleshooting are presented here, along with examples of applications."}],"date_created":"2018-12-11T12:00:52Z","volume":1,"date_published":"2006-06-01T00:00:00Z","doi":"10.1038/nprot.2006.16","issue":"1","page":"104 - 107","publication":"Nature Protocols","day":"01","publication_status":"published","year":"2006"},{"date_created":"2018-12-11T12:00:52Z","volume":1,"doi":"10.1038/nprot.2006.226","issue":"3","date_published":"2006-08-01T00:00:00Z","page":"1462 - 1467","publication":"Nature Protocols","day":"01","year":"2006","publication_status":"published","intvolume":" 1","month":"08","publisher":"Nature Publishing Group","quality_controlled":0,"abstract":[{"lang":"eng","text":"Plant biology is currently confronted with an overflow of expression profile data provided by high-throughput microarray transcription analyses. However, the tissue and cellular resolution of these techniques is limited. Thus, it is still necessary to examine the expression pattern of selected candidate genes at a cellular level. Here we present an in situ mRNA hybridization method that is routinely used in the analysis of gene expression patterns. The protocol is optimized for mRNA localizations in sectioned tissue of Arabidopsis seedlings including embryos, roots, hypocotyls, young primary leaves and flowers. The detailed protocol, recommended controls and troubleshooting are presented along with examples of application. The total time for the process is 10 days."}],"title":"In situ hybridization for mRNA detection in Arabidopsis tissue sections","author":[{"full_name":"Brewer, Philip B","last_name":"Brewer","first_name":"Philip"},{"full_name":"Heisler, Marcus G","last_name":"Heisler","first_name":"Marcus"},{"full_name":"Hejátko, Jan","last_name":"Hejátko","first_name":"Jan"},{"full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Eva Benková","orcid":"0000-0002-8510-9739","last_name":"Benková"}],"publist_id":"3687","extern":1,"citation":{"ista":"Brewer P, Heisler M, Hejátko J, Friml J, Benková E. 2006. In situ hybridization for mRNA detection in Arabidopsis tissue sections. Nature Protocols. 1(3), 1462–1467.","chicago":"Brewer, Philip, Marcus Heisler, Jan Hejátko, Jiří Friml, and Eva Benková. “In Situ Hybridization for MRNA Detection in Arabidopsis Tissue Sections.” Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.226.","ieee":"P. Brewer, M. Heisler, J. Hejátko, J. Friml, and E. Benková, “In situ hybridization for mRNA detection in Arabidopsis tissue sections,” Nature Protocols, vol. 1, no. 3. Nature Publishing Group, pp. 1462–1467, 2006.","short":"P. Brewer, M. Heisler, J. Hejátko, J. Friml, E. Benková, Nature Protocols 1 (2006) 1462–1467.","apa":"Brewer, P., Heisler, M., Hejátko, J., Friml, J., & Benková, E. (2006). In situ hybridization for mRNA detection in Arabidopsis tissue sections. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.226","ama":"Brewer P, Heisler M, Hejátko J, Friml J, Benková E. In situ hybridization for mRNA detection in Arabidopsis tissue sections. Nature Protocols. 2006;1(3):1462-1467. doi:10.1038/nprot.2006.226","mla":"Brewer, Philip, et al. “In Situ Hybridization for MRNA Detection in Arabidopsis Tissue Sections.” Nature Protocols, vol. 1, no. 3, Nature Publishing Group, 2006, pp. 1462–67, doi:10.1038/nprot.2006.226."},"date_updated":"2021-01-12T07:40:28Z","status":"public","type":"journal_article","_id":"3014"}]