[{"date_updated":"2021-01-12T07:40:34Z","publication_status":"published","year":"2008","publist_id":"3672","day":"18","month":"03","publication":"PNAS","date_published":"2008-03-18T00:00:00Z","volume":105,"abstract":[{"lang":"eng","text":"Many aspects of plant development, including patterning and tropisms, are largely dependent on the asymmetric distribution of the plant signaling molecule auxin. Auxin transport inhibitors (ATIs), which interfere with directional auxin transport, have been essential tools in formulating this concept. However, despite the use of ATIs in plant research for many decades, the mechanism of ATI action has remained largely elusive. Using real-time live-cell microscopy, we show here that prominent ATIs such as 2,3,5-triiodobenzoic acid (TIBA) and 2-(1-pyrenoyl) benzoic acid (PBA) inhibit vesicle trafficking in plant, yeast, and mammalian cells. Effects on micropinocytosis, rab5-labeled endosomal motility at the periphery of HeLa cells and on fibroblast mobility indicate that ATIs influence actin cytoskeleton. Visualization of actin cytoskeleton dynamics in plants, yeast, and mammalian cells show that ATIs stabilize actin. Conversely, stabilizing actin by chemical or genetic means interferes with endocytosis, vesicle motility, auxin transport, and plant development, including auxin transport-dependent processes. Our results show that a class of ATIs act as actin stabilizers and advocate that actin-dependent trafficking of auxin transport components participates in the mechanism of auxin transport. These studies also provide an example of how the common eukaryotic process of actin-based vesicle motility can fulfill a plant-specific physiological role."}],"author":[{"full_name":"Dhonukshe, Pankaj","first_name":"Pankaj","last_name":"Dhonukshe"},{"first_name":"Ilya","last_name":"Grigoriev","full_name":"Grigoriev, Ilya S"},{"full_name":"Fischer, Rainer","last_name":"Fischer","first_name":"Rainer"},{"full_name":"Tominaga, Motoki","first_name":"Motoki","last_name":"Tominaga"},{"first_name":"David","last_name":"Robinson","full_name":"Robinson, David G"},{"last_name":"Hašek","first_name":"Jiří","full_name":"Hašek, Jiří"},{"full_name":"Paciorek, Tomasz","first_name":"Tomasz","last_name":"Paciorek"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"full_name":"Seifertová, Daniela","first_name":"Daniela","last_name":"Seifertová"},{"first_name":"Ricardo","last_name":"Tejos","full_name":"Tejos, Ricardo"},{"full_name":"Meisel, Lee A","last_name":"Meisel","first_name":"Lee"},{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"},{"last_name":"Gadella","first_name":"Theodorus","full_name":"Gadella, Theodorus W"},{"last_name":"Stierhof","first_name":"York","full_name":"Stierhof, York-Dieter"},{"last_name":"Ueda","first_name":"Takashi","full_name":"Ueda, Takashi"},{"last_name":"Oiwa","first_name":"Kazuhiro","full_name":"Oiwa, Kazuhiro"},{"last_name":"Akhmanova","first_name":"Anna","full_name":"Akhmanova, Anna"},{"full_name":"Brock, Roland","last_name":"Brock","first_name":"Roland"},{"first_name":"Anne","last_name":"Spang","full_name":"Spang, Anne"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"issue":"11","quality_controlled":0,"intvolume":"       105","_id":"3031","page":"4489 - 4494","doi":"10.1073/pnas.0711414105","date_created":"2018-12-11T12:00:58Z","status":"public","type":"journal_article","title":"Auxin transport inhibitors impair vesicle motility and actin cytoskeleton dynamics in diverse eukaryotes","extern":1,"citation":{"ieee":"P. Dhonukshe <i>et al.</i>, “Auxin transport inhibitors impair vesicle motility and actin cytoskeleton dynamics in diverse eukaryotes,” <i>PNAS</i>, vol. 105, no. 11. National Academy of Sciences, pp. 4489–4494, 2008.","ista":"Dhonukshe P, Grigoriev I, Fischer R, Tominaga M, Robinson D, Hašek J, Paciorek T, Petrášek J, Seifertová D, Tejos R, Meisel L, Zažímalová E, Gadella T, Stierhof Y, Ueda T, Oiwa K, Akhmanova A, Brock R, Spang A, Friml J. 2008. Auxin transport inhibitors impair vesicle motility and actin cytoskeleton dynamics in diverse eukaryotes. PNAS. 105(11), 4489–4494.","ama":"Dhonukshe P, Grigoriev I, Fischer R, et al. Auxin transport inhibitors impair vesicle motility and actin cytoskeleton dynamics in diverse eukaryotes. <i>PNAS</i>. 2008;105(11):4489-4494. doi:<a href=\"https://doi.org/10.1073/pnas.0711414105\">10.1073/pnas.0711414105</a>","chicago":"Dhonukshe, Pankaj, Ilya Grigoriev, Rainer Fischer, Motoki Tominaga, David Robinson, Jiří Hašek, Tomasz Paciorek, et al. “Auxin Transport Inhibitors Impair Vesicle Motility and Actin Cytoskeleton Dynamics in Diverse Eukaryotes.” <i>PNAS</i>. National Academy of Sciences, 2008. <a href=\"https://doi.org/10.1073/pnas.0711414105\">https://doi.org/10.1073/pnas.0711414105</a>.","short":"P. Dhonukshe, I. Grigoriev, R. Fischer, M. Tominaga, D. Robinson, J. Hašek, T. Paciorek, J. Petrášek, D. Seifertová, R. Tejos, L. Meisel, E. Zažímalová, T. Gadella, Y. Stierhof, T. Ueda, K. Oiwa, A. Akhmanova, R. Brock, A. Spang, J. Friml, PNAS 105 (2008) 4489–4494.","apa":"Dhonukshe, P., Grigoriev, I., Fischer, R., Tominaga, M., Robinson, D., Hašek, J., … Friml, J. (2008). Auxin transport inhibitors impair vesicle motility and actin cytoskeleton dynamics in diverse eukaryotes. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0711414105\">https://doi.org/10.1073/pnas.0711414105</a>","mla":"Dhonukshe, Pankaj, et al. “Auxin Transport Inhibitors Impair Vesicle Motility and Actin Cytoskeleton Dynamics in Diverse Eukaryotes.” <i>PNAS</i>, vol. 105, no. 11, National Academy of Sciences, 2008, pp. 4489–94, doi:<a href=\"https://doi.org/10.1073/pnas.0711414105\">10.1073/pnas.0711414105</a>."},"publisher":"National Academy of Sciences"},{"page":"526 - 531","_id":"3032","intvolume":"        18","date_created":"2018-12-11T12:00:58Z","doi":"10.1016/j.cub.2008.03.021","quality_controlled":0,"publisher":"Cell Press","extern":1,"citation":{"mla":"Kleine Vehn, Jürgen, et al. “ARF GEF Dependent Transcytosis and Polar Delivery of PIN Auxin Carriers in Arabidopsis.” <i>Current Biology</i>, vol. 18, no. 7, Cell Press, 2008, pp. 526–31, doi:<a href=\"https://doi.org/10.1016/j.cub.2008.03.021\">10.1016/j.cub.2008.03.021</a>.","apa":"Kleine Vehn, J., Dhonukshe, P., Sauer, M., Brewer, P., Wiśniewska, J., Paciorek, T., … Friml, J. (2008). ARF GEF dependent transcytosis and polar delivery of PIN auxin carriers in Arabidopsis. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2008.03.021\">https://doi.org/10.1016/j.cub.2008.03.021</a>","chicago":"Kleine Vehn, Jürgen, Pankaj Dhonukshe, Michael Sauer, Philip Brewer, Justyna Wiśniewska, Tomasz Paciorek, Eva Benková, and Jiří Friml. “ARF GEF Dependent Transcytosis and Polar Delivery of PIN Auxin Carriers in Arabidopsis.” <i>Current Biology</i>. Cell Press, 2008. <a href=\"https://doi.org/10.1016/j.cub.2008.03.021\">https://doi.org/10.1016/j.cub.2008.03.021</a>.","ama":"Kleine Vehn J, Dhonukshe P, Sauer M, et al. ARF GEF dependent transcytosis and polar delivery of PIN auxin carriers in Arabidopsis. <i>Current Biology</i>. 2008;18(7):526-531. doi:<a href=\"https://doi.org/10.1016/j.cub.2008.03.021\">10.1016/j.cub.2008.03.021</a>","short":"J. Kleine Vehn, P. Dhonukshe, M. Sauer, P. Brewer, J. Wiśniewska, T. Paciorek, E. Benková, J. Friml, Current Biology 18 (2008) 526–531.","ieee":"J. Kleine Vehn <i>et al.</i>, “ARF GEF dependent transcytosis and polar delivery of PIN auxin carriers in Arabidopsis,” <i>Current Biology</i>, vol. 18, no. 7. Cell Press, pp. 526–531, 2008.","ista":"Kleine Vehn J, Dhonukshe P, Sauer M, Brewer P, Wiśniewska J, Paciorek T, Benková E, Friml J. 2008. ARF GEF dependent transcytosis and polar delivery of PIN auxin carriers in Arabidopsis. Current Biology. 18(7), 526–531."},"type":"journal_article","status":"public","title":"ARF GEF dependent transcytosis and polar delivery of PIN auxin carriers in Arabidopsis","publist_id":"3670","day":"08","year":"2008","month":"04","publication":"Current Biology","date_updated":"2021-01-12T07:40:34Z","publication_status":"published","issue":"7","abstract":[{"text":"\n\nCell polarity manifested by the polar cargo delivery to different plasma-membrane domains is a fundamental feature of multicellular organisms. Pathways for polar delivery have been identified in animals; prominent among them is transcytosis, which involves cargo movement between different sides of the cell [1]. PIN transporters are prominent polar cargoes in plants, whose polar subcellular localization determines the directional flow of the signaling molecule auxin [2, 3]. In this study, we address the cellular mechanisms of PIN polar targeting and dynamic polarity changes. We show that apical and basal PIN targeting pathways are interconnected but molecularly distinct by means of ARF GEF vesicle-trafficking regulators. Pharmacological or genetic interference with the Arabidopsis ARF GEF GNOM leads specifically to apicalization of basal cargoes such as PIN1. We visualize the translocation of PIN proteins between the opposite sides of polarized cells in vivo and show that this PIN transcytosis occurs by endocytic recycling and alternative recruitment of the same cargo molecules by apical and basal targeting machineries. Our data suggest that an ARF GEF-dependent transcytosis-like mechanism is operational in plants and provides a plausible mechanism to trigger changes in PIN polarity and hence auxin fluxes during embryogenesis and organogenesis.","lang":"eng"}],"volume":18,"date_published":"2008-04-08T00:00:00Z","author":[{"last_name":"Kleine Vehn","first_name":"Jürgen","full_name":"Kleine-Vehn, Jürgen"},{"last_name":"Dhonukshe","first_name":"Pankaj","full_name":"Dhonukshe, Pankaj"},{"full_name":"Sauer, Michael","first_name":"Michael","last_name":"Sauer"},{"last_name":"Brewer","first_name":"Philip","full_name":"Brewer, Philip B"},{"last_name":"Wiśniewska","first_name":"Justyna","full_name":"Wiśniewska, Justyna"},{"last_name":"Paciorek","first_name":"Tomasz","full_name":"Paciorek, Tomasz"},{"first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Eva Benková"},{"full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"}]},{"alternative_title":["Methods In Molecular Biology"],"date_published":"2008-01-01T00:00:00Z","abstract":[{"text":"\nEmbryogenesis in Arabidopsis thaliana depends on the proper establishment and maintenance of local auxin accumulation. In the course of elucidating the connections between developmental progress and auxin distribution, several techniques have been developed to investigate spatial and temporal distribution of auxin response or accumulation in Arabidopsis embryos. This chapter reviews and describes two independent methods, the detection of the activity of auxin responsive transgenes and immunolocalization of auxin itself.","lang":"eng"}],"volume":427,"author":[{"full_name":"Sauer, Michael","first_name":"Michael","last_name":"Sauer"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"year":"2008","day":"01","publist_id":"3668","month":"01","publication":"Plant Embryogenesis","date_updated":"2021-01-12T07:40:35Z","publication_status":"published","citation":{"ieee":"M. Sauer and J. Friml, “Visualization of auxin gradients in embryogenesis ,” in <i>Plant Embryogenesis</i>, vol. 427, M. Suárez and P. Bozhkov, Eds. Humana Press, 2008, pp. 137–144.","ista":"Sauer M, Friml J. 2008.Visualization of auxin gradients in embryogenesis . In: Plant Embryogenesis. Methods In Molecular Biology, vol. 427, 137–144.","mla":"Sauer, Michael, and Jiří Friml. “Visualization of Auxin Gradients in Embryogenesis .” <i>Plant Embryogenesis</i>, edited by María Suárez and Peter Bozhkov, vol. 427, Humana Press, 2008, pp. 137–44, doi:<a href=\"https://doi.org/10.1007/978-1-59745-273-1_11\">10.1007/978-1-59745-273-1_11</a>.","apa":"Sauer, M., &#38; Friml, J. (2008). Visualization of auxin gradients in embryogenesis . In M. Suárez &#38; P. Bozhkov (Eds.), <i>Plant Embryogenesis</i> (Vol. 427, pp. 137–144). Humana Press. <a href=\"https://doi.org/10.1007/978-1-59745-273-1_11\">https://doi.org/10.1007/978-1-59745-273-1_11</a>","chicago":"Sauer, Michael, and Jiří Friml. “Visualization of Auxin Gradients in Embryogenesis .” In <i>Plant Embryogenesis</i>, edited by María Suárez and Peter Bozhkov, 427:137–44. Humana Press, 2008. <a href=\"https://doi.org/10.1007/978-1-59745-273-1_11\">https://doi.org/10.1007/978-1-59745-273-1_11</a>.","short":"M. Sauer, J. Friml, in:, M. Suárez, P. Bozhkov (Eds.), Plant Embryogenesis, Humana Press, 2008, pp. 137–144.","ama":"Sauer M, Friml J. Visualization of auxin gradients in embryogenesis . In: Suárez M, Bozhkov P, eds. <i>Plant Embryogenesis</i>. Vol 427. Humana Press; 2008:137-144. doi:<a href=\"https://doi.org/10.1007/978-1-59745-273-1_11\">10.1007/978-1-59745-273-1_11</a>"},"extern":1,"publisher":"Humana Press","status":"public","type":"book_chapter","title":"Visualization of auxin gradients in embryogenesis ","intvolume":"       427","_id":"3033","page":"137 - 144","date_created":"2018-12-11T12:00:58Z","doi":"10.1007/978-1-59745-273-1_11","editor":[{"first_name":"María","last_name":"Suárez","full_name":"Suárez, María F"},{"full_name":"Bozhkov,  Peter V","last_name":"Bozhkov","first_name":"Peter"}],"quality_controlled":0},{"author":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"last_name":"Sauer","first_name":"Michael","full_name":"Sauer, Michael"}],"date_published":"2008-05-15T00:00:00Z","abstract":[{"text":"They can't move away from shade, so plants resort to a molecular solution to find a place in the sun. The action they take is quite radical, and involves a reprogramming of their development. ","lang":"eng"}],"volume":453,"issue":"7193","publication_status":"published","date_updated":"2021-01-12T07:40:35Z","month":"05","oa_version":"None","publication":"Nature","year":"2008","language":[{"iso":"eng"}],"day":"15","publist_id":"3669","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Plant biology: In their neighbour's shadow","status":"public","type":"journal_article","extern":"1","citation":{"short":"J. Friml, M. Sauer, Nature 453 (2008) 298–299.","ama":"Friml J, Sauer M. Plant biology: In their neighbour’s shadow. <i>Nature</i>. 2008;453(7193):298-299. doi:<a href=\"https://doi.org/10.1038/453298a\">10.1038/453298a</a>","chicago":"Friml, Jiří, and Michael Sauer. “Plant Biology: In Their Neighbour’s Shadow.” <i>Nature</i>. Nature Publishing Group, 2008. <a href=\"https://doi.org/10.1038/453298a\">https://doi.org/10.1038/453298a</a>.","apa":"Friml, J., &#38; Sauer, M. (2008). Plant biology: In their neighbour’s shadow. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/453298a\">https://doi.org/10.1038/453298a</a>","mla":"Friml, Jiří, and Michael Sauer. “Plant Biology: In Their Neighbour’s Shadow.” <i>Nature</i>, vol. 453, no. 7193, Nature Publishing Group, 2008, pp. 298–99, doi:<a href=\"https://doi.org/10.1038/453298a\">10.1038/453298a</a>.","ista":"Friml J, Sauer M. 2008. Plant biology: In their neighbour’s shadow. Nature. 453(7193), 298–299.","ieee":"J. Friml and M. Sauer, “Plant biology: In their neighbour’s shadow,” <i>Nature</i>, vol. 453, no. 7193. Nature Publishing Group, pp. 298–299, 2008."},"publisher":"Nature Publishing Group","quality_controlled":"1","article_type":"letter_note","date_created":"2018-12-11T12:00:59Z","doi":"10.1038/453298a","intvolume":"       453","page":"298 - 299","_id":"3034"},{"alternative_title":["Methods In Molecular Biology"],"author":[{"full_name":"Sauer, Michael","first_name":"Michael","last_name":"Sauer"},{"first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"volume":427,"abstract":[{"text":"Embryogenesis of Arabidopsis thaliana follows a nearly invariant cell division pattern and provides an ideal system for studies of early plant development. However, experimental manipulation with embryogenesis is difficult, as the embryo develops deeply inside maternal tissues. Here, we present a method to culture zygotic Arabidopsis embryos in vitro. It enables culturing for prolonged periods of time from the first developmental stages on. The technique omits excision of the embryo by culturing the entire ovule, which facilitates the manual procedure. It allows pharmacological manipulation of embryo development and does not interfere with standard techniques for localizing gene expression and protein localization in the cultivated embryos.","lang":"eng"}],"date_published":"2008-03-07T00:00:00Z","publication":"Plant Embryogenesis","month":"03","publist_id":"3667","day":"07","year":"2008","publication_status":"published","date_updated":"2021-01-12T07:40:35Z","publisher":"Humana Press","citation":{"ama":"Sauer M, Friml J. In vitro culture of Arabidopsis embryos . In: Suárez M, Bozhkov P, eds. <i>Plant Embryogenesis</i>. Vol 427. Humana Press; 2008:71-76. doi:<a href=\"https://doi.org/10.1007/978-1-59745-273-1_5\">10.1007/978-1-59745-273-1_5</a>","chicago":"Sauer, Michael, and Jiří Friml. “In Vitro Culture of Arabidopsis Embryos .” In <i>Plant Embryogenesis</i>, edited by María Suárez and Peter Bozhkov, 427:71–76. Humana Press, 2008. <a href=\"https://doi.org/10.1007/978-1-59745-273-1_5\">https://doi.org/10.1007/978-1-59745-273-1_5</a>.","short":"M. Sauer, J. Friml, in:, M. Suárez, P. Bozhkov (Eds.), Plant Embryogenesis, Humana Press, 2008, pp. 71–76.","apa":"Sauer, M., &#38; Friml, J. (2008). In vitro culture of Arabidopsis embryos . In M. Suárez &#38; P. Bozhkov (Eds.), <i>Plant Embryogenesis</i> (Vol. 427, pp. 71–76). Humana Press. <a href=\"https://doi.org/10.1007/978-1-59745-273-1_5\">https://doi.org/10.1007/978-1-59745-273-1_5</a>","mla":"Sauer, Michael, and Jiří Friml. “In Vitro Culture of Arabidopsis Embryos .” <i>Plant Embryogenesis</i>, edited by María Suárez and Peter Bozhkov, vol. 427, Humana Press, 2008, pp. 71–76, doi:<a href=\"https://doi.org/10.1007/978-1-59745-273-1_5\">10.1007/978-1-59745-273-1_5</a>.","ista":"Sauer M, Friml J. 2008.In vitro culture of Arabidopsis embryos . In: Plant Embryogenesis. Methods In Molecular Biology, vol. 427, 71–76.","ieee":"M. Sauer and J. Friml, “In vitro culture of Arabidopsis embryos ,” in <i>Plant Embryogenesis</i>, vol. 427, M. Suárez and P. Bozhkov, Eds. Humana Press, 2008, pp. 71–76."},"extern":1,"title":"In vitro culture of Arabidopsis embryos ","status":"public","type":"book_chapter","doi":"10.1007/978-1-59745-273-1_5","date_created":"2018-12-11T12:00:59Z","page":"71 - 76","_id":"3035","intvolume":"       427","quality_controlled":0,"editor":[{"full_name":"Suárez, María F","last_name":"Suárez","first_name":"María"},{"last_name":"Bozhkov","first_name":"Peter","full_name":"Bozhkov,  Peter V"}]},{"month":"06","publication":"PNAS","publist_id":"3666","day":"24","year":"2008","publication_status":"published","date_updated":"2021-01-12T07:40:36Z","issue":"25","author":[{"full_name":"Dubrovsky, Joseph G","first_name":"Joseph","last_name":"Dubrovsky"},{"first_name":"Michael","last_name":"Sauer","full_name":"Sauer, Michael"},{"last_name":"Napsucialy Mendivil","first_name":"Selene","full_name":"Napsucialy-Mendivil, Selene"},{"last_name":"Ivanchenko","first_name":"Maria","full_name":"Ivanchenko, Maria G"},{"full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"full_name":"Shishkova, Svetlana","first_name":"Svetlana","last_name":"Shishkova"},{"full_name":"Celenza, John","first_name":"John","last_name":"Celenza"},{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Eva Benková"}],"abstract":[{"lang":"eng","text":"Plants exhibit an exceptional adaptability to different environmental conditions. To a large extent, this adaptability depends on their ability to initiate and form new organs throughout their entire postembryonic life. Plant shoot and root systems unceasingly branch and form axillary shoots or lateral roots, respectively. The first event in the formation of a new organ is specification of founder cells. Several plant hormones, prominent among them auxin, have been implicated in the acquisition of founder cell identity by differentiated cells, but the mechanisms underlying this process are largely elusive. Here, we show that auxin and its local accumulation in root pericycle cells is a necessary and sufficient signal to respecify these cells into lateral root founder cells. Analysis of the alf4-1 mutant suggests that specification of founder cells and the subsequent activation of cell division leading to primordium formation represent two genetically separable events. Time-lapse experiments show that the activation of an auxin response is the earliest detectable event in founder cell specification. Accordingly, local activation of auxin response correlates absolutely with the acquisition of founder cell identity and precedes the actual formation of a lateral root primordium through patterned cell division. Local production and subsequent accumulation of auxin in single pericycle cells induced by Cre-Lox-based activation of auxin synthesis converts them into founder cells. Thus, auxin is the local instructive signal that is sufficient for acquisition of founder cell identity and can be considered a morphogenetic trigger in postembryonic plant organogenesis."}],"volume":105,"date_published":"2008-06-24T00:00:00Z","doi":"10.1073/pnas.0712307105","date_created":"2018-12-11T12:00:59Z","page":"8790 - 8794","_id":"3036","intvolume":"       105","quality_controlled":0,"publisher":"National Academy of Sciences","extern":1,"citation":{"ieee":"J. Dubrovsky <i>et al.</i>, “Auxin acts as a local morphogenetic trigger to specify lateral root founder cells,” <i>PNAS</i>, vol. 105, no. 25. National Academy of Sciences, pp. 8790–8794, 2008.","ista":"Dubrovsky J, Sauer M, Napsucialy Mendivil S, Ivanchenko M, Friml J, Shishkova S, Celenza J, Benková E. 2008. Auxin acts as a local morphogenetic trigger to specify lateral root founder cells. PNAS. 105(25), 8790–8794.","short":"J. Dubrovsky, M. Sauer, S. Napsucialy Mendivil, M. Ivanchenko, J. Friml, S. Shishkova, J. Celenza, E. Benková, PNAS 105 (2008) 8790–8794.","chicago":"Dubrovsky, Joseph, Michael Sauer, Selene Napsucialy Mendivil, Maria Ivanchenko, Jiří Friml, Svetlana Shishkova, John Celenza, and Eva Benková. “Auxin Acts as a Local Morphogenetic Trigger to Specify Lateral Root Founder Cells.” <i>PNAS</i>. National Academy of Sciences, 2008. <a href=\"https://doi.org/10.1073/pnas.0712307105\">https://doi.org/10.1073/pnas.0712307105</a>.","ama":"Dubrovsky J, Sauer M, Napsucialy Mendivil S, et al. Auxin acts as a local morphogenetic trigger to specify lateral root founder cells. <i>PNAS</i>. 2008;105(25):8790-8794. doi:<a href=\"https://doi.org/10.1073/pnas.0712307105\">10.1073/pnas.0712307105</a>","mla":"Dubrovsky, Joseph, et al. “Auxin Acts as a Local Morphogenetic Trigger to Specify Lateral Root Founder Cells.” <i>PNAS</i>, vol. 105, no. 25, National Academy of Sciences, 2008, pp. 8790–94, doi:<a href=\"https://doi.org/10.1073/pnas.0712307105\">10.1073/pnas.0712307105</a>.","apa":"Dubrovsky, J., Sauer, M., Napsucialy Mendivil, S., Ivanchenko, M., Friml, J., Shishkova, S., … Benková, E. (2008). Auxin acts as a local morphogenetic trigger to specify lateral root founder cells. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0712307105\">https://doi.org/10.1073/pnas.0712307105</a>"},"title":"Auxin acts as a local morphogenetic trigger to specify lateral root founder cells","type":"journal_article","status":"public"},{"external_id":{"pmid":["18678746"]},"date_created":"2018-12-11T12:01:00Z","doi":"10.1104/pp.108.121756","intvolume":"       147","page":"1553 - 1559","_id":"3037","quality_controlled":"1","citation":{"apa":"Feraru, E., &#38; Friml, J. (2008). PIN polar targeting. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.108.121756\">https://doi.org/10.1104/pp.108.121756</a>","mla":"Feraru, Elena, and Jiří Friml. “PIN Polar Targeting.” <i>Plant Physiology</i>, vol. 147, no. 4, American Society of Plant Biologists, 2008, pp. 1553–59, doi:<a href=\"https://doi.org/10.1104/pp.108.121756\">10.1104/pp.108.121756</a>.","short":"E. Feraru, J. Friml, Plant Physiology 147 (2008) 1553–1559.","ama":"Feraru E, Friml J. PIN polar targeting. <i>Plant Physiology</i>. 2008;147(4):1553-1559. doi:<a href=\"https://doi.org/10.1104/pp.108.121756\">10.1104/pp.108.121756</a>","chicago":"Feraru, Elena, and Jiří Friml. “PIN Polar Targeting.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2008. <a href=\"https://doi.org/10.1104/pp.108.121756\">https://doi.org/10.1104/pp.108.121756</a>.","ista":"Feraru E, Friml J. 2008. PIN polar targeting. Plant Physiology. 147(4), 1553–1559.","ieee":"E. Feraru and J. Friml, “PIN polar targeting,” <i>Plant Physiology</i>, vol. 147, no. 4. American Society of Plant Biologists, pp. 1553–1559, 2008."},"extern":"1","pmid":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2492634/","open_access":"1"}],"publisher":"American Society of Plant Biologists","title":"PIN polar targeting","status":"public","type":"journal_article","oa_version":"Published Version","publication":"Plant Physiology","month":"08","year":"2008","language":[{"iso":"eng"}],"publist_id":"3664","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"04","publication_status":"published","oa":1,"date_updated":"2021-01-12T07:40:36Z","issue":"4","author":[{"last_name":"Feraru","first_name":"Elena","full_name":"Feraru, Elena"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"}],"date_published":"2008-08-04T00:00:00Z","volume":147},{"publication_status":"published","date_updated":"2021-01-12T07:40:37Z","month":"07","publication":"Nature Cell Biology","year":"2008","day":"11","publist_id":"3665","author":[{"last_name":"Swarup","first_name":"Kamal","full_name":"Swarup, Kamal"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Eva Benková","first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739"},{"full_name":"Swarup, Ranjan","first_name":"Ranjan","last_name":"Swarup"},{"full_name":"Casimiro, Ilda","first_name":"Ilda","last_name":"Casimiro"},{"last_name":"Péret","first_name":"Benjamin","full_name":"Péret, Benjamin"},{"full_name":"Yang, Yaodong","first_name":"Yaodong","last_name":"Yang"},{"first_name":"Geraint","last_name":"Parry","full_name":"Parry, Geraint"},{"last_name":"Nielsen","first_name":"Erik","full_name":"Nielsen, Erik"},{"first_name":"Ive","last_name":"De Smet","full_name":"De Smet, Ive"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"full_name":"Levesque, Mitchell P","first_name":"Mitchell","last_name":"Levesque"},{"first_name":"David","last_name":"Carrier","full_name":"Carrier, David"},{"first_name":"Nicholas","last_name":"James","full_name":"James, Nicholas"},{"first_name":"Vanessa","last_name":"Calvo","full_name":"Calvo, Vanessa"},{"full_name":"Ljung, Karin","last_name":"Ljung","first_name":"Karin"},{"full_name":"Kramer, Eric","first_name":"Eric","last_name":"Kramer"},{"first_name":"Rebecca","last_name":"Roberts","full_name":"Roberts, Rebecca"},{"full_name":"Graham, Neil","first_name":"Neil","last_name":"Graham"},{"full_name":"Marillonnet, Sylvestre","first_name":"Sylvestre","last_name":"Marillonnet"},{"first_name":"Kanu","last_name":"Patel","full_name":"Patel, Kanu"},{"last_name":"Jones","first_name":"Jonathan","full_name":"Jones, Jonathan D"},{"full_name":"Taylor, Christopher G","first_name":"Christopher","last_name":"Taylor"},{"full_name":"Schachtman, Daniel P","last_name":"Schachtman","first_name":"Daniel"},{"first_name":"Sean","last_name":"May","full_name":"May, Sean"},{"full_name":"Sandberg, Göran","first_name":"Göran","last_name":"Sandberg"},{"full_name":"Benfey, Philip N","last_name":"Benfey","first_name":"Philip"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ian","last_name":"Kerr","full_name":"Kerr, Ian"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, Tom"},{"first_name":"Laurent","last_name":"Laplaze","full_name":"Laplaze, Laurent"},{"first_name":"Malcolm","last_name":"Bennett","full_name":"Bennett, Malcolm J"}],"date_published":"2008-07-11T00:00:00Z","abstract":[{"text":"Lateral roots originate deep within the parental root from a small number of founder cells at the periphery of vascular tissues and must emerge through intervening layers of tissues. We describe how the hormone auxin, which originates from the developing lateral root, acts as a local inductive signal which re-programmes adjacent cells. Auxin induces the expression of a previously uncharacterized auxin influx carrier LAX3 in cortical and epidermal cells directly overlaying new primordia. Increased LAX3 activity reinforces the auxin-dependent induction of a selection of cell-wall-remodelling enzymes, which are likely to promote cell separation in advance of developing lateral root primordia.","lang":"eng"}],"volume":10,"issue":"8","quality_controlled":0,"date_created":"2018-12-11T12:01:00Z","doi":"10.1038/ncb1754","intvolume":"        10","page":"946 - 954","_id":"3038","title":"The auxin influx carrier LAX3 promotes lateral root emergence","type":"journal_article","status":"public","citation":{"ieee":"K. Swarup <i>et al.</i>, “The auxin influx carrier LAX3 promotes lateral root emergence,” <i>Nature Cell Biology</i>, vol. 10, no. 8. Nature Publishing Group, pp. 946–954, 2008.","ista":"Swarup K, Benková E, Swarup R, Casimiro I, Péret B, Yang Y, Parry G, Nielsen E, De Smet I, Vanneste S, Levesque M, Carrier D, James N, Calvo V, Ljung K, Kramer E, Roberts R, Graham N, Marillonnet S, Patel K, Jones J, Taylor C, Schachtman D, May S, Sandberg G, Benfey P, Friml J, Kerr I, Beeckman T, Laplaze L, Bennett M. 2008. The auxin influx carrier LAX3 promotes lateral root emergence. Nature Cell Biology. 10(8), 946–954.","short":"K. Swarup, E. Benková, R. Swarup, I. Casimiro, B. Péret, Y. Yang, G. Parry, E. Nielsen, I. De Smet, S. Vanneste, M. Levesque, D. Carrier, N. James, V. Calvo, K. Ljung, E. Kramer, R. Roberts, N. Graham, S. Marillonnet, K. Patel, J. Jones, C. Taylor, D. Schachtman, S. May, G. Sandberg, P. Benfey, J. Friml, I. Kerr, T. Beeckman, L. Laplaze, M. Bennett, Nature Cell Biology 10 (2008) 946–954.","ama":"Swarup K, Benková E, Swarup R, et al. The auxin influx carrier LAX3 promotes lateral root emergence. <i>Nature Cell Biology</i>. 2008;10(8):946-954. doi:<a href=\"https://doi.org/10.1038/ncb1754\">10.1038/ncb1754</a>","chicago":"Swarup, Kamal, Eva Benková, Ranjan Swarup, Ilda Casimiro, Benjamin Péret, Yaodong Yang, Geraint Parry, et al. “The Auxin Influx Carrier LAX3 Promotes Lateral Root Emergence.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2008. <a href=\"https://doi.org/10.1038/ncb1754\">https://doi.org/10.1038/ncb1754</a>.","mla":"Swarup, Kamal, et al. “The Auxin Influx Carrier LAX3 Promotes Lateral Root Emergence.” <i>Nature Cell Biology</i>, vol. 10, no. 8, Nature Publishing Group, 2008, pp. 946–54, doi:<a href=\"https://doi.org/10.1038/ncb1754\">10.1038/ncb1754</a>.","apa":"Swarup, K., Benková, E., Swarup, R., Casimiro, I., Péret, B., Yang, Y., … Bennett, M. (2008). The auxin influx carrier LAX3 promotes lateral root emergence. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb1754\">https://doi.org/10.1038/ncb1754</a>"},"extern":1,"publisher":"Nature Publishing Group"},{"quality_controlled":0,"doi":"10.1126/science.1160158","date_created":"2018-12-11T12:01:00Z","page":"594 - 597","_id":"3039","intvolume":"       322","title":"Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root","status":"public","type":"journal_article","publisher":"American Association for the Advancement of Science","extern":1,"citation":{"ieee":"I. De Smet <i>et al.</i>, “Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root,” <i>Science</i>, vol. 322, no. 5901. American Association for the Advancement of Science, pp. 594–597, 2008.","ista":"De Smet I, Vassileva V, De Rybel B, Levesque M, Grunewald W, Van Damme D, Van Noorden G, Naudts M, Van Isterdael G, De Clercq R, Wang J, Meuli N, Vanneste S, Friml J, Hilson P, Jürgens G, Ingram G, Inzé D, Benfey P, Beeckman T. 2008. Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root. Science. 322(5901), 594–597.","mla":"De Smet, Ive, et al. “Receptor-like Kinase ACR4 Restricts Formative Cell Divisions in the Arabidopsis Root.” <i>Science</i>, vol. 322, no. 5901, American Association for the Advancement of Science, 2008, pp. 594–97, doi:<a href=\"https://doi.org/10.1126/science.1160158\">10.1126/science.1160158</a>.","apa":"De Smet, I., Vassileva, V., De Rybel, B., Levesque, M., Grunewald, W., Van Damme, D., … Beeckman, T. (2008). Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1160158\">https://doi.org/10.1126/science.1160158</a>","ama":"De Smet I, Vassileva V, De Rybel B, et al. Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root. <i>Science</i>. 2008;322(5901):594-597. doi:<a href=\"https://doi.org/10.1126/science.1160158\">10.1126/science.1160158</a>","short":"I. De Smet, V. Vassileva, B. De Rybel, M. Levesque, W. Grunewald, D. Van Damme, G. Van Noorden, M. Naudts, G. Van Isterdael, R. De Clercq, J. Wang, N. Meuli, S. Vanneste, J. Friml, P. Hilson, G. Jürgens, G. Ingram, D. Inzé, P. Benfey, T. Beeckman, Science 322 (2008) 594–597.","chicago":"De Smet, Ive, Valya Vassileva, Bert De Rybel, Mitchell Levesque, Wim Grunewald, Daniël Van Damme, Giel Van Noorden, et al. “Receptor-like Kinase ACR4 Restricts Formative Cell Divisions in the Arabidopsis Root.” <i>Science</i>. American Association for the Advancement of Science, 2008. <a href=\"https://doi.org/10.1126/science.1160158\">https://doi.org/10.1126/science.1160158</a>."},"publication_status":"published","date_updated":"2021-01-12T07:40:37Z","month":"10","publication":"Science","publist_id":"3663","day":"24","year":"2008","author":[{"first_name":"Ive","last_name":"De Smet","full_name":"De Smet, Ive"},{"first_name":"Valya","last_name":"Vassileva","full_name":"Vassileva, Valya"},{"full_name":"De Rybel, Bert","last_name":"De Rybel","first_name":"Bert"},{"last_name":"Levesque","first_name":"Mitchell","full_name":"Levesque, Mitchell P"},{"last_name":"Grunewald","first_name":"Wim","full_name":"Grunewald, Wim"},{"last_name":"Van Damme","first_name":"Daniël","full_name":"Van Damme, Daniël"},{"last_name":"Van Noorden","first_name":"Giel","full_name":"Van Noorden, Giel"},{"last_name":"Naudts","first_name":"Mirande","full_name":"Naudts, Mirande"},{"first_name":"Gert","last_name":"Van Isterdael","full_name":"Van Isterdael, Gert"},{"last_name":"De Clercq","first_name":"Rebecca","full_name":"De Clercq, Rebecca"},{"full_name":"Wang, Jean Y","first_name":"Jean","last_name":"Wang"},{"full_name":"Meuli, Nicholas","last_name":"Meuli","first_name":"Nicholas"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml"},{"last_name":"Hilson","first_name":"Pierre","full_name":"Hilson, Pierre"},{"full_name":"Jürgens, Gerd","last_name":"Jürgens","first_name":"Gerd"},{"first_name":"Gwyneth","last_name":"Ingram","full_name":"Ingram, Gwyneth C"},{"full_name":"Inzé, Dirk","first_name":"Dirk","last_name":"Inzé"},{"first_name":"Philip","last_name":"Benfey","full_name":"Benfey, Philip N"},{"last_name":"Beeckman","first_name":"Tom","full_name":"Beeckman, Tom"}],"abstract":[{"text":"During the development of multicellular organisms, organogenesis and pattern formation depend on formative divisions to specify and maintain pools of stem cells. In higher plants, these activities are essential to shape the final root architecture because the functioning of root apical meristems and the de novo formation of lateral roots entirely rely on it. We used transcript profiling on sorted pericycle cells undergoing lateral root initiation to identify the receptor-like kinase ACR4 of Arabidopsis as a key factor both in promoting formative cell divisions in the pericycle and in constraining the number of these divisions once organogenesis has been started. In the root tip meristem, ACR4 shows a similar action by controlling cell proliferation activity in the columella cell lineage. Thus, ACR4 function reveals a common mechanism of formative cell division control in the main root tip meristem and during lateral root initiation.","lang":"eng"}],"volume":322,"date_published":"2008-10-24T00:00:00Z","issue":"5901"},{"issue":"6","author":[{"full_name":"Kleine-Vehn, Jürgen","first_name":"Jürgen","last_name":"Kleine Vehn"},{"first_name":"Łukasz","last_name":"Łangowski","full_name":"Łangowski, Łukasz"},{"first_name":"Justyna","last_name":"Wiśniewska","full_name":"Wiśniewska, Justyna"},{"full_name":"Dhonukshe, Pankaj","last_name":"Dhonukshe","first_name":"Pankaj"},{"first_name":"Philip","last_name":"Brewer","full_name":"Brewer, Philip B"},{"full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596"}],"volume":1,"abstract":[{"text":"The polar, sub-cellular localization of PIN auxin efflux carriers determines the direction of intercellular auxin flow, thus defining the spatial aspect of auxin signalling. Dynamic, transcytosis-like relocalizations of PIN proteins occur in response to external and internal signals, integrating these signals into changes in auxin distribution. Here, we examine the cellular and molecular mechanisms of polar PIN delivery and transcytosis. The mechanisms of the ARF-GEF-dependent polar targeting and transcytosis are well conserved and show little variations among diverse Arabidopsis ecotypes consistent with their fundamental importance in regulating plant development. At the cellular level, we refine previous findings on the role of the actin cytoskeleton in apical and basal PIN targeting, and identify a previously unknown role for microtubules, specifically in basal targeting. PIN protein delivery to different sides of the cell is mediated by ARF-dependent trafficking with a previously unknown complex level of distinct ARF-GEF vesicle trafficking regulators. Our data suggest that alternative recruitment of PIN proteins by these distinct pathways can account for cell type- and cargo-specific aspects of polar targeting, as well as for polarity changes in response to different signals. The resulting dynamic PIN positioning to different sides of cells defines a three-dimensional pattern of auxin fluxes within plant tissues.","lang":"eng"}],"date_published":"2008-01-01T00:00:00Z","month":"01","publication":"Molecular Plant","day":"01","publist_id":"3662","year":"2008","publication_status":"published","date_updated":"2021-01-12T07:40:38Z","publisher":"Oxford University Press","extern":1,"citation":{"short":"J. Kleine Vehn, Ł. Łangowski, J. Wiśniewska, P. Dhonukshe, P. Brewer, J. Friml, Molecular Plant 1 (2008) 1056–1066.","chicago":"Kleine Vehn, Jürgen, Łukasz Łangowski, Justyna Wiśniewska, Pankaj Dhonukshe, Philip Brewer, and Jiří Friml. “Cellular and Molecular Requirements for Polar PIN Targeting and Transcytosis in Plants.” <i>Molecular Plant</i>. Oxford University Press, 2008. <a href=\"https://doi.org/10.1093/mp/ssn062\">https://doi.org/10.1093/mp/ssn062</a>.","ama":"Kleine Vehn J, Łangowski Ł, Wiśniewska J, Dhonukshe P, Brewer P, Friml J. Cellular and molecular requirements for polar PIN targeting and transcytosis in plants. <i>Molecular Plant</i>. 2008;1(6):1056-1066. doi:<a href=\"https://doi.org/10.1093/mp/ssn062\">10.1093/mp/ssn062</a>","mla":"Kleine Vehn, Jürgen, et al. “Cellular and Molecular Requirements for Polar PIN Targeting and Transcytosis in Plants.” <i>Molecular Plant</i>, vol. 1, no. 6, Oxford University Press, 2008, pp. 1056–66, doi:<a href=\"https://doi.org/10.1093/mp/ssn062\">10.1093/mp/ssn062</a>.","apa":"Kleine Vehn, J., Łangowski, Ł., Wiśniewska, J., Dhonukshe, P., Brewer, P., &#38; Friml, J. (2008). Cellular and molecular requirements for polar PIN targeting and transcytosis in plants. <i>Molecular Plant</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mp/ssn062\">https://doi.org/10.1093/mp/ssn062</a>","ieee":"J. Kleine Vehn, Ł. Łangowski, J. Wiśniewska, P. Dhonukshe, P. Brewer, and J. Friml, “Cellular and molecular requirements for polar PIN targeting and transcytosis in plants,” <i>Molecular Plant</i>, vol. 1, no. 6. Oxford University Press, pp. 1056–1066, 2008.","ista":"Kleine Vehn J, Łangowski Ł, Wiśniewska J, Dhonukshe P, Brewer P, Friml J. 2008. Cellular and molecular requirements for polar PIN targeting and transcytosis in plants. Molecular Plant. 1(6), 1056–1066."},"title":"Cellular and molecular requirements for polar PIN targeting and transcytosis in plants","type":"journal_article","status":"public","doi":"10.1093/mp/ssn062","date_created":"2018-12-11T12:01:01Z","page":"1056 - 1066","_id":"3040","intvolume":"         1","quality_controlled":0},{"issue":"45","author":[{"first_name":"Diana","last_name":"Santelia","full_name":"Santelia, Diana"},{"full_name":"Henrichs, Sina","last_name":"Henrichs","first_name":"Sina"},{"last_name":"Vincenzetti","first_name":"Vincent","full_name":"Vincenzetti, Vincent"},{"last_name":"Sauer","first_name":"Michael","full_name":"Sauer, Michael"},{"last_name":"Bigler","first_name":"Laurent","full_name":"Bigler, Laurent"},{"full_name":"Klein, Markus B","last_name":"Klein","first_name":"Markus"},{"full_name":"Bailly, Aurélien","last_name":"Bailly","first_name":"Aurélien"},{"last_name":"Lee","first_name":"Yuree","full_name":"Lee, Yuree"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"full_name":"Geisler, Markus","last_name":"Geisler","first_name":"Markus"},{"full_name":"Martinoia, Enrico","last_name":"Martinoia","first_name":"Enrico"}],"volume":283,"abstract":[{"lang":"eng","text":"The rate, polarity, and symmetry of the flow of the plant hormone auxin are determined by the polar cellular localization of PIN-FORMED (PIN) auxin efflux carriers. Flavonoids, a class of secondary plant metabolites, have been suspected to modulate auxin transport and tropic responses. Nevertheless, the identity of specific flavonoid compounds involved and their molecular function and targets in vivo are essentially unknown. Here we show that the root elongation zone of agravitropic pin2/eir1/wav6/agr1 has an altered pattern and amount of flavonol glycosides. Application of nanomolar concentrations of flavonols to pin2 roots is sufficient to partially restore root gravitropism. By employing a quantitative cell biological approach, we demonstrate that flavonoids partially restore the formation of lateral auxin gradients in the absence of PIN2. Chemical complementation by flavonoids correlates with an asymmetric distribution of the PIN1 protein. pin2 complementation probably does not result from inhibition of auxin efflux, as supply of the auxin transport inhibitor N-1-naphthylphthalamic acid failed to restore pin2 gravitropism. We propose that flavonoids promote asymmetric PIN shifts during gravity stimulation, thus redirecting basipetal auxin streams necessary for root bending. © 2008 by The American Society for Biochemistry and Molecular Biology, Inc."}],"date_published":"2008-11-07T00:00:00Z","publication":"Journal of Biological Chemistry","month":"11","day":"07","publist_id":"3661","year":"2008","publication_status":"published","date_updated":"2021-01-12T07:40:38Z","publisher":"American Society for Biochemistry and Molecular Biology","extern":1,"citation":{"ieee":"D. Santelia <i>et al.</i>, “Flavonoids redirect PIN mediated polar auxin fluxes during root gravitropic responses,” <i>Journal of Biological Chemistry</i>, vol. 283, no. 45. American Society for Biochemistry and Molecular Biology, pp. 31218–31226, 2008.","ista":"Santelia D, Henrichs S, Vincenzetti V, Sauer M, Bigler L, Klein M, Bailly A, Lee Y, Friml J, Geisler M, Martinoia E. 2008. Flavonoids redirect PIN mediated polar auxin fluxes during root gravitropic responses. Journal of Biological Chemistry. 283(45), 31218–31226.","mla":"Santelia, Diana, et al. “Flavonoids Redirect PIN Mediated Polar Auxin Fluxes during Root Gravitropic Responses.” <i>Journal of Biological Chemistry</i>, vol. 283, no. 45, American Society for Biochemistry and Molecular Biology, 2008, pp. 31218–26, doi:<a href=\"https://doi.org/ 10.1074/jbc.M710122200\"> 10.1074/jbc.M710122200</a>.","apa":"Santelia, D., Henrichs, S., Vincenzetti, V., Sauer, M., Bigler, L., Klein, M., … Martinoia, E. (2008). Flavonoids redirect PIN mediated polar auxin fluxes during root gravitropic responses. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology. <a href=\"https://doi.org/ 10.1074/jbc.M710122200\">https://doi.org/ 10.1074/jbc.M710122200</a>","short":"D. Santelia, S. Henrichs, V. Vincenzetti, M. Sauer, L. Bigler, M. Klein, A. Bailly, Y. Lee, J. Friml, M. Geisler, E. Martinoia, Journal of Biological Chemistry 283 (2008) 31218–31226.","chicago":"Santelia, Diana, Sina Henrichs, Vincent Vincenzetti, Michael Sauer, Laurent Bigler, Markus Klein, Aurélien Bailly, et al. “Flavonoids Redirect PIN Mediated Polar Auxin Fluxes during Root Gravitropic Responses.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry and Molecular Biology, 2008. <a href=\"https://doi.org/ 10.1074/jbc.M710122200\">https://doi.org/ 10.1074/jbc.M710122200</a>.","ama":"Santelia D, Henrichs S, Vincenzetti V, et al. Flavonoids redirect PIN mediated polar auxin fluxes during root gravitropic responses. <i>Journal of Biological Chemistry</i>. 2008;283(45):31218-31226. doi:<a href=\"https://doi.org/ 10.1074/jbc.M710122200\"> 10.1074/jbc.M710122200</a>"},"title":"Flavonoids redirect PIN mediated polar auxin fluxes during root gravitropic responses","type":"journal_article","status":"public","date_created":"2018-12-11T12:01:01Z","doi":" 10.1074/jbc.M710122200","page":"31218 - 31226","_id":"3041","intvolume":"       283","quality_controlled":0},{"page":"17812 - 17817","_id":"3042","intvolume":"       105","doi":"10.1073/pnas.0808073105","date_created":"2018-12-11T12:01:01Z","quality_controlled":0,"publisher":"National Academy of Sciences","citation":{"short":"J. Kleine Vehn, J. Leitner, M. Zwiewka, M. Sauer, L. Abas, C. Luschnig, J. Friml, PNAS 105 (2008) 17812–17817.","ama":"Kleine Vehn J, Leitner J, Zwiewka M, et al. Differential degradation of PIN2 auxin efflux carrier by retromer dependent vacuolar targeting. <i>PNAS</i>. 2008;105(46):17812-17817. doi:<a href=\"https://doi.org/10.1073/pnas.0808073105\">10.1073/pnas.0808073105</a>","chicago":"Kleine Vehn, Jürgen, Johannes Leitner, Marta Zwiewka, Michael Sauer, Lindy Abas, Christian Luschnig, and Jiří Friml. “Differential Degradation of PIN2 Auxin Efflux Carrier by Retromer Dependent Vacuolar Targeting.” <i>PNAS</i>. National Academy of Sciences, 2008. <a href=\"https://doi.org/10.1073/pnas.0808073105\">https://doi.org/10.1073/pnas.0808073105</a>.","mla":"Kleine Vehn, Jürgen, et al. “Differential Degradation of PIN2 Auxin Efflux Carrier by Retromer Dependent Vacuolar Targeting.” <i>PNAS</i>, vol. 105, no. 46, National Academy of Sciences, 2008, pp. 17812–17, doi:<a href=\"https://doi.org/10.1073/pnas.0808073105\">10.1073/pnas.0808073105</a>.","apa":"Kleine Vehn, J., Leitner, J., Zwiewka, M., Sauer, M., Abas, L., Luschnig, C., &#38; Friml, J. (2008). Differential degradation of PIN2 auxin efflux carrier by retromer dependent vacuolar targeting. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0808073105\">https://doi.org/10.1073/pnas.0808073105</a>","ieee":"J. Kleine Vehn <i>et al.</i>, “Differential degradation of PIN2 auxin efflux carrier by retromer dependent vacuolar targeting,” <i>PNAS</i>, vol. 105, no. 46. National Academy of Sciences, pp. 17812–17817, 2008.","ista":"Kleine Vehn J, Leitner J, Zwiewka M, Sauer M, Abas L, Luschnig C, Friml J. 2008. Differential degradation of PIN2 auxin efflux carrier by retromer dependent vacuolar targeting. PNAS. 105(46), 17812–17817."},"extern":1,"status":"public","type":"journal_article","title":"Differential degradation of PIN2 auxin efflux carrier by retromer dependent vacuolar targeting","publist_id":"3659","day":"18","year":"2008","month":"11","publication":"PNAS","date_updated":"2021-01-12T07:40:39Z","publication_status":"published","issue":"46","volume":105,"abstract":[{"lang":"eng","text":"All eukaryotic cells present at the cell surface a specific set of plasma membrane proteins that modulate responses to internal and external cues and whose activity is also regulated by protein degradation. We characterized the lytic vacuole-dependent degradation of membrane proteins in Arabidopsis thaliana by means of in vivo visualization of vacuolar targeting combined with quantitative protein analysis. We show that the vacuolar targeting pathway is used by multiple cargos including PIN-FORMED (PIN) efflux carriers for the phytohormone auxin. In vivo visualization of PIN2 vacuolar targeting revealed its differential degradation in response to environmental signals, such as gravity. In contrast to polar PIN delivery to the basal plasma membrane, which depends on the vesicle trafficking regulator ARF-GEF GNOM, PIN sorting to the lytic vacuolar pathway requires additional brefeldin A-sensitive ARF-GEF activity. Furthermore, we identified putative retromer components SORTING NEXIN1 (SNX1) and VACUOLAR PROTEIN SORTING29 (VPS29) as important factors in this pathway and propose that the retromer complex acts to retrieve PIN proteins from a late/pre-vacuolar compartment back to the recycling pathways. Our data suggest that ARF GEF- and retromer-dependent processes regulate PIN sorting to the vacuole in an antagonistic manner and illustrate instrumentalization of this mechanism for fine-tuning the auxin fluxes during gravitropic response."}],"date_published":"2008-11-18T00:00:00Z","author":[{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"last_name":"Leitner","first_name":"Johannes","full_name":"Leitner, Johannes"},{"last_name":"Zwiewka","first_name":"Marta","full_name":"Zwiewka, Marta"},{"last_name":"Sauer","first_name":"Michael","full_name":"Sauer, Michael"},{"first_name":"Lindy","last_name":"Abas","full_name":"Abas, Lindy"},{"first_name":"Christian","last_name":"Luschnig","full_name":"Luschnig, Christian"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"}]},{"date_published":"2008-11-10T00:00:00Z","volume":24,"abstract":[{"lang":"eng","text":"Plant development is characterized by a profound phenotypic plasticity that often involves redefining of the developmental fate and polarity of cells within differentiated tissues. The plant hormone auxin and its directional intercellular transport play a major role in these processes because they provide positional information and link cell polarity with tissue patterning. This plant-specific mechanism of transport-dependent auxin gradients depends on subcellular dynamics of auxin transport components, in particular on endocytic recycling and polar targeting. Recent insights into these cellular processes in plants have revealed important parallels to yeast and animal systems, including clathrin-dependent endocytosis, retromer function, and transcytosis, but have also emphasized unique features of plant cells such as diversity of polar targeting pathways; integration of environmental signals into subcellular trafficking; and the link between endocytosis, cell polarity, and cell fate specification. We review these advances and focus on the translation of the subcellular dynamics to the regulation of whole-plant development."}],"author":[{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine Vehn, Jürgen"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"date_updated":"2021-01-12T07:40:39Z","publication_status":"published","language":[{"iso":"eng"}],"year":"2008","day":"10","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"3660","month":"11","publication":"Annual Review of Cell and Developmental Biology","oa_version":"None","type":"journal_article","status":"public","title":"Polar targeting and endocytic recycling in auxin-dependent plant development","extern":"1","pmid":1,"citation":{"ista":"Kleine Vehn J, Friml J. 2008. Polar targeting and endocytic recycling in auxin-dependent plant development. Annual Review of Cell and Developmental Biology. 24, 447–473.","ieee":"J. Kleine Vehn and J. Friml, “Polar targeting and endocytic recycling in auxin-dependent plant development,” <i>Annual Review of Cell and Developmental Biology</i>, vol. 24. Annual Reviews, pp. 447–473, 2008.","mla":"Kleine Vehn, Jürgen, and Jiří Friml. “Polar Targeting and Endocytic Recycling in Auxin-Dependent Plant Development.” <i>Annual Review of Cell and Developmental Biology</i>, vol. 24, Annual Reviews, 2008, pp. 447–73, doi:<a href=\"https://doi.org/10.1146/annurev.cellbio.24.110707.175254\">10.1146/annurev.cellbio.24.110707.175254</a>.","apa":"Kleine Vehn, J., &#38; Friml, J. (2008). Polar targeting and endocytic recycling in auxin-dependent plant development. <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev.cellbio.24.110707.175254\">https://doi.org/10.1146/annurev.cellbio.24.110707.175254</a>","chicago":"Kleine Vehn, Jürgen, and Jiří Friml. “Polar Targeting and Endocytic Recycling in Auxin-Dependent Plant Development.” <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews, 2008. <a href=\"https://doi.org/10.1146/annurev.cellbio.24.110707.175254\">https://doi.org/10.1146/annurev.cellbio.24.110707.175254</a>.","short":"J. Kleine Vehn, J. Friml, Annual Review of Cell and Developmental Biology 24 (2008) 447–473.","ama":"Kleine Vehn J, Friml J. Polar targeting and endocytic recycling in auxin-dependent plant development. <i>Annual Review of Cell and Developmental Biology</i>. 2008;24:447-473. doi:<a href=\"https://doi.org/10.1146/annurev.cellbio.24.110707.175254\">10.1146/annurev.cellbio.24.110707.175254</a>"},"publisher":"Annual Reviews","quality_controlled":"1","intvolume":"        24","page":"447 - 473","_id":"3043","external_id":{"pmid":["    18837671"]},"doi":"10.1146/annurev.cellbio.24.110707.175254","date_created":"2018-12-11T12:01:02Z"},{"author":[{"full_name":"Mravec, Jozef","first_name":"Jozef","last_name":"Mravec"},{"last_name":"Kubeš","first_name":"Martin","full_name":"Kubeš, Martin"},{"last_name":"Bielach","first_name":"Agnieszka","full_name":"Bielach, Agnieszka"},{"full_name":"Gaykova, Vassilena","first_name":"Vassilena","last_name":"Gaykova"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"full_name":"Skůpa, Petr","first_name":"Petr","last_name":"Skůpa"},{"full_name":"Chand, Suresh","first_name":"Suresh","last_name":"Chand"},{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Eva Benková"},{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml"}],"abstract":[{"lang":"eng","text":"The signalling molecule auxin controls plant morphogenesis via its activity gradients, which are produced by intercellular auxin transport. Cellular auxin efflux is the rate-limiting step in this process and depends on PIN and phosphoglycoprotein (PGP) auxin transporters. Mutual roles for these proteins in auxin transport are unclear, as is the significance of their interactions for plant development. Here, we have analysed the importance of the functional interaction between PIN- and PGP-dependent auxin transport in development. We show by analysis of inducible overexpression lines that PINs and PGPs define distinct auxin transport mechanisms: both mediate auxin efflux but they play diverse developmental roles. Components of both systems are expressed during embryogenesis, organogenesis and tropisms, and they interact genetically in both synergistic and antagonistic fashions. A concerted action of PIN- and PGP-dependent efflux systems is required for asymmetric auxin distribution during these processes. We propose a model in which PGP-mediated efflux controls auxin levels in auxin channel-forming cells and, thus, auxin availability for PIN-dependent vectorial auxin movement."}],"volume":135,"date_published":"2008-10-15T00:00:00Z","issue":"20","publication_status":"published","date_updated":"2021-01-12T07:40:39Z","month":"10","publication":"Development","publist_id":"3658","day":"15","year":"2008","title":"Interaction of PIN and PGP transport mechanisms in auxin distribution-dependent development","status":"public","type":"journal_article","publisher":"Company of Biologists","citation":{"ama":"Mravec J, Kubeš M, Bielach A, et al. Interaction of PIN and PGP transport mechanisms in auxin distribution-dependent development. <i>Development</i>. 2008;135(20):3345-3354. doi:<a href=\"https://doi.org/10.1242/dev.021071\">10.1242/dev.021071</a>","chicago":"Mravec, Jozef, Martin Kubeš, Agnieszka Bielach, Vassilena Gaykova, Jan Petrášek, Petr Skůpa, Suresh Chand, Eva Benková, Eva Zažímalová, and Jiří Friml. “Interaction of PIN and PGP Transport Mechanisms in Auxin Distribution-Dependent Development.” <i>Development</i>. Company of Biologists, 2008. <a href=\"https://doi.org/10.1242/dev.021071\">https://doi.org/10.1242/dev.021071</a>.","short":"J. Mravec, M. Kubeš, A. Bielach, V. Gaykova, J. Petrášek, P. Skůpa, S. Chand, E. Benková, E. Zažímalová, J. Friml, Development 135 (2008) 3345–3354.","apa":"Mravec, J., Kubeš, M., Bielach, A., Gaykova, V., Petrášek, J., Skůpa, P., … Friml, J. (2008). Interaction of PIN and PGP transport mechanisms in auxin distribution-dependent development. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.021071\">https://doi.org/10.1242/dev.021071</a>","mla":"Mravec, Jozef, et al. “Interaction of PIN and PGP Transport Mechanisms in Auxin Distribution-Dependent Development.” <i>Development</i>, vol. 135, no. 20, Company of Biologists, 2008, pp. 3345–54, doi:<a href=\"https://doi.org/10.1242/dev.021071\">10.1242/dev.021071</a>.","ista":"Mravec J, Kubeš M, Bielach A, Gaykova V, Petrášek J, Skůpa P, Chand S, Benková E, Zažímalová E, Friml J. 2008. Interaction of PIN and PGP transport mechanisms in auxin distribution-dependent development. Development. 135(20), 3345–3354.","ieee":"J. Mravec <i>et al.</i>, “Interaction of PIN and PGP transport mechanisms in auxin distribution-dependent development,” <i>Development</i>, vol. 135, no. 20. Company of Biologists, pp. 3345–3354, 2008."},"extern":1,"quality_controlled":0,"doi":"10.1242/dev.021071","date_created":"2018-12-11T12:01:02Z","_id":"3044","page":"3345 - 3354","intvolume":"       135"},{"author":[{"full_name":"Dhonukshe, Pankaj","first_name":"Pankaj","last_name":"Dhonukshe"},{"full_name":"Tanaka, Hirokazu","first_name":"Hirokazu","last_name":"Tanaka"},{"last_name":"Goh","first_name":"Tatsuaki","full_name":"Goh, Tatsuaki"},{"first_name":"Kazuo","last_name":"Ebine","full_name":"Ebine, Kazuo"},{"full_name":"Mähönen, Ari Pekka","first_name":"Ari","last_name":"Mähönen"},{"first_name":"Kalika","last_name":"Prasad","full_name":"Prasad, Kalika"},{"full_name":"Blilou, Ikram","first_name":"Ikram","last_name":"Blilou"},{"first_name":"Niko","last_name":"Geldner","full_name":"Geldner, Niko"},{"full_name":"Xu, Jian","first_name":"Jian","last_name":"Xu"},{"first_name":"Tomohiro","last_name":"Uemura","full_name":"Uemura, Tomohiro"},{"full_name":"Chory, Joanne","first_name":"Joanne","last_name":"Chory"},{"full_name":"Ueda, Takashi","first_name":"Takashi","last_name":"Ueda"},{"full_name":"Nakano, Akihiko","last_name":"Nakano","first_name":"Akihiko"},{"last_name":"Scheres","first_name":"Ben","full_name":"Scheres, Ben"},{"first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2008-12-18T00:00:00Z","volume":456,"abstract":[{"lang":"eng","text":"Dynamically polarized membrane proteins define different cell boundaries and have an important role in intercellular communication - a vital feature of multicellular development. Efflux carriers for the signalling molecule auxin from the PIN family are landmarks of cell polarity in plants and have a crucial involvement in auxin distribution-dependent development including embryo patterning, organogenesis and tropisms. Polar PIN localization determines the direction of intercellular auxin flow, yet the mechanisms generating PIN polarity remain unclear. Here we identify an endocytosis-dependent mechanism of PIN polarity generation and analyse its developmental implications. Real-time PIN tracking showed that after synthesis, PINs are initially delivered to the plasma membrane in a non-polar manner and their polarity is established by subsequent endocytic recycling. Interference with PIN endocytosis either by auxin or by manipulation of the Arabidopsis Rab5 GTPase pathway prevents PIN polarization. Failure of PIN polarization transiently alters asymmetric auxin distribution during embryogenesis and increases the local auxin response in apical embryo regions. This results in ectopic expression of auxin pathway-associated root-forming master regulators in embryonic leaves and promotes homeotic transformation of leaves to roots. Our results indicate a two-step mechanism for the generation of PIN polar localization and the essential role of endocytosis in this process. It also highlights the link between endocytosis-dependent polarity of individual cells and auxin distribution-dependent cell fate establishment for multicellular patterning."}],"issue":"7224","publication_status":"published","date_updated":"2021-01-12T07:40:40Z","month":"12","publication":"Nature","year":"2008","publist_id":"3657","day":"18","title":"Generation of cell polarity in plants links endocytosis auxin distribution and cell fate decisions","status":"public","type":"journal_article","citation":{"chicago":"Dhonukshe, Pankaj, Hirokazu Tanaka, Tatsuaki Goh, Kazuo Ebine, Ari Mähönen, Kalika Prasad, Ikram Blilou, et al. “Generation of Cell Polarity in Plants Links Endocytosis Auxin Distribution and Cell Fate Decisions.” <i>Nature</i>. Nature Publishing Group, 2008. <a href=\"https://doi.org/10.1038/nature07409\">https://doi.org/10.1038/nature07409</a>.","short":"P. Dhonukshe, H. Tanaka, T. Goh, K. Ebine, A. Mähönen, K. Prasad, I. Blilou, N. Geldner, J. Xu, T. Uemura, J. Chory, T. Ueda, A. Nakano, B. Scheres, J. Friml, Nature 456 (2008) 962–966.","ama":"Dhonukshe P, Tanaka H, Goh T, et al. Generation of cell polarity in plants links endocytosis auxin distribution and cell fate decisions. <i>Nature</i>. 2008;456(7224):962-966. doi:<a href=\"https://doi.org/10.1038/nature07409\">10.1038/nature07409</a>","mla":"Dhonukshe, Pankaj, et al. “Generation of Cell Polarity in Plants Links Endocytosis Auxin Distribution and Cell Fate Decisions.” <i>Nature</i>, vol. 456, no. 7224, Nature Publishing Group, 2008, pp. 962–66, doi:<a href=\"https://doi.org/10.1038/nature07409\">10.1038/nature07409</a>.","apa":"Dhonukshe, P., Tanaka, H., Goh, T., Ebine, K., Mähönen, A., Prasad, K., … Friml, J. (2008). Generation of cell polarity in plants links endocytosis auxin distribution and cell fate decisions. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature07409\">https://doi.org/10.1038/nature07409</a>","ista":"Dhonukshe P, Tanaka H, Goh T, Ebine K, Mähönen A, Prasad K, Blilou I, Geldner N, Xu J, Uemura T, Chory J, Ueda T, Nakano A, Scheres B, Friml J. 2008. Generation of cell polarity in plants links endocytosis auxin distribution and cell fate decisions. Nature. 456(7224), 962–966.","ieee":"P. Dhonukshe <i>et al.</i>, “Generation of cell polarity in plants links endocytosis auxin distribution and cell fate decisions,” <i>Nature</i>, vol. 456, no. 7224. Nature Publishing Group, pp. 962–966, 2008."},"extern":1,"publisher":"Nature Publishing Group","quality_controlled":0,"date_created":"2018-12-11T12:01:02Z","doi":"10.1038/nature07409","intvolume":"       456","page":"962 - 966","_id":"3045"},{"page":"480 - 487","_id":"3194","doi":"10.1145/1390156.1390217","date_created":"2018-12-11T12:01:56Z","quality_controlled":0,"main_file_link":[{"open_access":"0","url":"http://research.microsoft.com/pubs/77356/icml08-partoptmrf.pdf"}],"citation":{"ieee":"P. Kohli, A. Shekhovtsov, C. Rother, V. Kolmogorov, and P. Torr, “On partial optimality in multi label MRFs,” presented at the ICML: International Conference on Machine Learning, 2008, pp. 480–487.","ista":"Kohli P, Shekhovtsov A, Rother C, Kolmogorov V, Torr P. 2008. On partial optimality in multi label MRFs. ICML: International Conference on Machine Learning, 480–487.","short":"P. Kohli, A. Shekhovtsov, C. Rother, V. Kolmogorov, P. Torr, in:, Omnipress, 2008, pp. 480–487.","chicago":"Kohli, Pushmeet, Alexander Shekhovtsov, Carsten Rother, Vladimir Kolmogorov, and Philip Torr. “On Partial Optimality in Multi Label MRFs,” 480–87. Omnipress, 2008. <a href=\"https://doi.org/10.1145/1390156.1390217\">https://doi.org/10.1145/1390156.1390217</a>.","ama":"Kohli P, Shekhovtsov A, Rother C, Kolmogorov V, Torr P. On partial optimality in multi label MRFs. In: Omnipress; 2008:480-487. doi:<a href=\"https://doi.org/10.1145/1390156.1390217\">10.1145/1390156.1390217</a>","mla":"Kohli, Pushmeet, et al. <i>On Partial Optimality in Multi Label MRFs</i>. Omnipress, 2008, pp. 480–87, doi:<a href=\"https://doi.org/10.1145/1390156.1390217\">10.1145/1390156.1390217</a>.","apa":"Kohli, P., Shekhovtsov, A., Rother, C., Kolmogorov, V., &#38; Torr, P. (2008). On partial optimality in multi label MRFs (pp. 480–487). Presented at the ICML: International Conference on Machine Learning, Omnipress. <a href=\"https://doi.org/10.1145/1390156.1390217\">https://doi.org/10.1145/1390156.1390217</a>"},"extern":1,"publisher":"Omnipress","status":"public","type":"conference","title":"On partial optimality in multi label MRFs","year":"2008","day":"01","publist_id":"3486","month":"01","date_updated":"2021-01-12T07:41:42Z","conference":{"name":"ICML: International Conference on Machine Learning"},"publication_status":"published","date_published":"2008-01-01T00:00:00Z","abstract":[{"text":"We consider the problem of optimizing multilabel MRFs, which is in general NP-hard and ubiquitous in low-level computer vision. One approach for its solution is to formulate it as an integer linear programming and relax the integrality constraints. The approach we consider in this paper is to first convert the multi-label MRF into an equivalent binary-label MRF and then to relax it. The resulting relaxation can be efficiently solved using a maximum flow algorithm. Its solution provides us with a partially optimal labelling of the binary variables. This partial labelling is then easily transferred to the multi-label problem. We study the theoretical properties of the new relaxation and compare it with the standard one. Specifically, we compare tightness, and characterize a subclass of problems where the two relaxations coincide. We propose several combined algorithms based on the technique and demonstrate their performance on challenging computer vision problems.","lang":"eng"}],"author":[{"full_name":"Kohli, Pushmeet","first_name":"Pushmeet","last_name":"Kohli"},{"last_name":"Shekhovtsov","first_name":"Alexander","full_name":"Shekhovtsov, Alexander"},{"last_name":"Rother","first_name":"Carsten","full_name":"Rother, Carsten"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov","last_name":"Kolmogorov","first_name":"Vladimir"},{"first_name":"Philip","last_name":"Torr","full_name":"Torr, Philip H"}]},{"quality_controlled":0,"doi":"10.1109/CVPR.2008.4587440","date_created":"2018-12-11T12:01:57Z","_id":"3195","title":"Graph cut based image segmentation with connectivity priors","type":"conference","status":"public","publisher":"IEEE","extern":1,"citation":{"ista":"Vicente S, Kolmogorov V, Rother C. 2008. Graph cut based image segmentation with connectivity priors. CVPR: Computer Vision and Pattern Recognition.","ieee":"S. Vicente, V. Kolmogorov, and C. Rother, “Graph cut based image segmentation with connectivity priors,” presented at the CVPR: Computer Vision and Pattern Recognition, 2008.","short":"S. Vicente, V. Kolmogorov, C. Rother, in:, IEEE, 2008.","ama":"Vicente S, Kolmogorov V, Rother C. Graph cut based image segmentation with connectivity priors. In: IEEE; 2008. doi:<a href=\"https://doi.org/10.1109/CVPR.2008.4587440\">10.1109/CVPR.2008.4587440</a>","chicago":"Vicente, Sara, Vladimir Kolmogorov, and Carsten Rother. “Graph Cut Based Image Segmentation with Connectivity Priors.” IEEE, 2008. <a href=\"https://doi.org/10.1109/CVPR.2008.4587440\">https://doi.org/10.1109/CVPR.2008.4587440</a>.","mla":"Vicente, Sara, et al. <i>Graph Cut Based Image Segmentation with Connectivity Priors</i>. IEEE, 2008, doi:<a href=\"https://doi.org/10.1109/CVPR.2008.4587440\">10.1109/CVPR.2008.4587440</a>.","apa":"Vicente, S., Kolmogorov, V., &#38; Rother, C. (2008). Graph cut based image segmentation with connectivity priors. Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. <a href=\"https://doi.org/10.1109/CVPR.2008.4587440\">https://doi.org/10.1109/CVPR.2008.4587440</a>"},"main_file_link":[{"url":"http://research.microsoft.com/pubs/80485/CVPR08-ConnectedGC.pdf","open_access":"0"}],"publication_status":"published","conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"date_updated":"2021-01-12T07:41:43Z","month":"08","publist_id":"3487","day":"05","year":"2008","author":[{"last_name":"Vicente","first_name":"Sara","full_name":"Vicente, Sara"},{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov"},{"last_name":"Rother","first_name":"Carsten","full_name":"Rother, Carsten"}],"abstract":[{"lang":"eng","text":"Graph cut is a popular technique for interactive image segmentation. However, it has certain shortcomings. In particular, graph cut has problems with segmenting thin elongated objects due to the ldquoshrinking biasrdquo. To overcome this problem, we propose to impose an additional connectivity prior, which is a very natural assumption about objects. We formulate several versions of the connectivity constraint and show that the corresponding optimization problems are all NP-hard. For some of these versions we propose two optimization algorithms: (i) a practical heuristic technique which we call DijkstraGC, and (ii) a slow method based on problem decomposition which provides a lower bound on the problem. We use the second technique to verify that for some practical examples DijkstraGC is able to find the global minimum."}],"date_published":"2008-08-05T00:00:00Z"},{"extern":1,"citation":{"ista":"Szeliski R, Zabih R, Scharstein D, Veksler O, Kolmogorov V, Agarwala A, Tappen M, Rother C. 2008. A comparative study of energy minimization methods for Markov random fields with smoothness-based priors. IEEE Transactions on Pattern Analysis and Machine Intelligence. 30(6), 1068–1080.","ieee":"R. Szeliski <i>et al.</i>, “A comparative study of energy minimization methods for Markov random fields with smoothness-based priors,” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 30, no. 6. IEEE, pp. 1068–1080, 2008.","mla":"Szeliski, Richard, et al. “A Comparative Study of Energy Minimization Methods for Markov Random Fields with Smoothness-Based Priors.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 30, no. 6, IEEE, 2008, pp. 1068–80, doi:<a href=\"https://doi.org/10.1109/TPAMI.2007.70844\">10.1109/TPAMI.2007.70844</a>.","apa":"Szeliski, R., Zabih, R., Scharstein, D., Veksler, O., Kolmogorov, V., Agarwala, A., … Rother, C. (2008). A comparative study of energy minimization methods for Markov random fields with smoothness-based priors. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE. <a href=\"https://doi.org/10.1109/TPAMI.2007.70844\">https://doi.org/10.1109/TPAMI.2007.70844</a>","short":"R. Szeliski, R. Zabih, D. Scharstein, O. Veksler, V. Kolmogorov, A. Agarwala, M. Tappen, C. Rother, IEEE Transactions on Pattern Analysis and Machine Intelligence 30 (2008) 1068–1080.","ama":"Szeliski R, Zabih R, Scharstein D, et al. A comparative study of energy minimization methods for Markov random fields with smoothness-based priors. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. 2008;30(6):1068-1080. doi:<a href=\"https://doi.org/10.1109/TPAMI.2007.70844\">10.1109/TPAMI.2007.70844</a>","chicago":"Szeliski, Richard, Ramin Zabih, Daniel Scharstein, Olga Veksler, Vladimir Kolmogorov, Aseem Agarwala, Marshall Tappen, and Carsten Rother. “A Comparative Study of Energy Minimization Methods for Markov Random Fields with Smoothness-Based Priors.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE, 2008. <a href=\"https://doi.org/10.1109/TPAMI.2007.70844\">https://doi.org/10.1109/TPAMI.2007.70844</a>."},"publisher":"IEEE","title":"A comparative study of energy minimization methods for Markov random fields with smoothness-based priors","type":"journal_article","status":"public","doi":"10.1109/TPAMI.2007.70844","date_created":"2018-12-11T12:01:57Z","intvolume":"        30","_id":"3196","page":"1068 - 1080","quality_controlled":0,"issue":"6","author":[{"last_name":"Szeliski","first_name":"Richard","full_name":"Szeliski, Richard S"},{"last_name":"Zabih","first_name":"Ramin","full_name":"Zabih, Ramin"},{"full_name":"Scharstein, Daniel","last_name":"Scharstein","first_name":"Daniel"},{"full_name":"Veksler, Olga","last_name":"Veksler","first_name":"Olga"},{"full_name":"Vladimir Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"},{"first_name":"Aseem","last_name":"Agarwala","full_name":"Agarwala, Aseem"},{"full_name":"Tappen, Marshall F","last_name":"Tappen","first_name":"Marshall"},{"last_name":"Rother","first_name":"Carsten","full_name":"Rother, Carsten"}],"date_published":"2008-06-01T00:00:00Z","volume":30,"abstract":[{"text":"Among the most exciting advances in early vision has been the development of efficient energy minimization algorithms for pixel-labeling tasks such as depth or texture computation. It has been known for decades that such problems can be elegantly expressed as Markov random fields, yet the resulting energy minimization problems have been widely viewed as intractable. Algorithms such as graph cuts and loopy belief propagation (LBP) have proven to be very powerful: For example, such methods form the basis for almost all the top-performing stereo methods. However, the trade-offs among different energy minimization algorithms are still not well understood. In this paper, we describe a set of energy minimization benchmarks and use them to compare the solution quality and runtime of several common energy minimization algorithms. We investigate three promising methods-graph cuts, LBP, and tree-reweighted message passing-in addition to the well-known older iterated conditional mode (ICM) algorithm. Our benchmark problems are drawn from published energy functions used for stereo, image stitching, interactive segmentation, and denoising. We also provide a general-purpose software interface that allows vision researchers to easily switch between optimization methods. The benchmarks, code, images, and results are available at http://vision.middlebury.edu/MRF/.","lang":"eng"}],"month":"06","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","year":"2008","publist_id":"3488","day":"01","publication_status":"published","date_updated":"2021-01-12T07:41:43Z"},{"quality_controlled":0,"date_created":"2018-12-11T12:01:58Z","doi":"10.1007/978-3-540-88688-4_44","intvolume":"      5303","_id":"3198","page":"596 - 609","title":"Feature correspondence via graph matching: Models and global optimization","status":"public","type":"conference","main_file_link":[{"url":"http://research-srv.microsoft.com/pubs/70610/eccv08-MatchingMRF.pdf","open_access":"0"}],"extern":1,"citation":{"ieee":"L. Torresani, V. Kolmogorov, and C. Rother, “Feature correspondence via graph matching: Models and global optimization,” presented at the ECCV: European Conference on Computer Vision, 2008, vol. 5303, pp. 596–609.","ista":"Torresani L, Kolmogorov V, Rother C. 2008. Feature correspondence via graph matching: Models and global optimization. ECCV: European Conference on Computer Vision, LNCS, vol. 5303, 596–609.","ama":"Torresani L, Kolmogorov V, Rother C. Feature correspondence via graph matching: Models and global optimization. In: Vol 5303. Springer; 2008:596-609. doi:<a href=\"https://doi.org/10.1007/978-3-540-88688-4_44\">10.1007/978-3-540-88688-4_44</a>","chicago":"Torresani, Lorenzo, Vladimir Kolmogorov, and Carsten Rother. “Feature Correspondence via Graph Matching: Models and Global Optimization,” 5303:596–609. Springer, 2008. <a href=\"https://doi.org/10.1007/978-3-540-88688-4_44\">https://doi.org/10.1007/978-3-540-88688-4_44</a>.","short":"L. Torresani, V. Kolmogorov, C. Rother, in:, Springer, 2008, pp. 596–609.","apa":"Torresani, L., Kolmogorov, V., &#38; Rother, C. (2008). Feature correspondence via graph matching: Models and global optimization (Vol. 5303, pp. 596–609). Presented at the ECCV: European Conference on Computer Vision, Springer. <a href=\"https://doi.org/10.1007/978-3-540-88688-4_44\">https://doi.org/10.1007/978-3-540-88688-4_44</a>","mla":"Torresani, Lorenzo, et al. <i>Feature Correspondence via Graph Matching: Models and Global Optimization</i>. Vol. 5303, Springer, 2008, pp. 596–609, doi:<a href=\"https://doi.org/10.1007/978-3-540-88688-4_44\">10.1007/978-3-540-88688-4_44</a>."},"publisher":"Springer","conference":{"name":"ECCV: European Conference on Computer Vision"},"publication_status":"published","date_updated":"2021-01-12T07:41:44Z","month":"01","year":"2008","publist_id":"3485","day":"01","author":[{"full_name":"Torresani, Lorenzo","last_name":"Torresani","first_name":"Lorenzo"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov","last_name":"Kolmogorov","first_name":"Vladimir"},{"last_name":"Rother","first_name":"Carsten","full_name":"Rother, Carsten"}],"date_published":"2008-01-01T00:00:00Z","abstract":[{"lang":"eng","text":"In this paper we present a new approach for establishing correspondences between sparse image features related by an unknown non-rigid mapping and corrupted by clutter and occlusion, such as points extracted from a pair of images containing a human figure in distinct poses. We formulate this matching task as an energy minimization problem by defining a complex objective function of the appearance and the spatial arrangement of the features. Optimization of this energy is an instance of graph matching, which is in general a NP-hard problem. We describe a novel graph matching optimization technique, which we refer to as dual decomposition (DD), and demonstrate on a variety of examples that this method outperforms existing graph matching algorithms. In the majority of our examples DD is able to find the global minimum within a minute. The ability to globally optimize the objective allows us to accurately learn the parameters of our matching model from training examples. We show on several matching tasks that our learned model yields results superior to those of state-of-the-art methods. "}],"volume":5303,"alternative_title":["LNCS"]},{"publication_status":"published","conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"date_updated":"2021-01-12T07:41:55Z","month":"04","publist_id":"3456","day":"28","year":"2008","author":[{"first_name":"Yevgeniy","last_name":"Dodis","full_name":"Dodis, Yevgeniy"},{"orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Krzysztof Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Puniya, Prashant","first_name":"Prashant","last_name":"Puniya"}],"abstract":[{"lang":"eng","text":"We propose a new mode of operation, enciphered CBC, for domain extension of length-preserving functions (like block ciphers), which is a variation on the popular CBC mode of operation. Our new mode is twice slower than CBC, but has many (property-preserving) properties not enjoyed by CBC and other known modes. Most notably, it yields the first constant-rate Variable Input Length (VIL) MAC from any length preserving Fixed Input Length (FIL) MAC. This answers the question of Dodis and Puniya from Eurocrypt 2007. Further, our mode is a secure domain extender for PRFs (with basically the same security as encrypted CBC). This provides a hedge against the security of the block cipher: if the block cipher is pseudorandom, one gets a VIL-PRF, while if it is &quot;only&quot; unpredictable, one &quot;at least&quot; gets a VIL-MAC. Additionally, our mode yields a VIL random oracle (and, hence, a collision-resistant hash function) when instantiated with length-preserving random functions, or even random permutations (which can be queried from both sides). This means that one does not have to re-key the block cipher during the computation, which was critically used in most previous constructions (analyzed in the ideal cipher model). "}],"volume":4965,"date_published":"2008-04-28T00:00:00Z","alternative_title":["LNCS"],"quality_controlled":0,"date_created":"2018-12-11T12:02:07Z","doi":"10.1007/978-3-540-78967-3_12","page":"198 - 219","_id":"3224","intvolume":"      4965","title":"A new mode of operation for block ciphers and length preserving MACs","type":"conference","status":"public","publisher":"Springer","extern":1,"citation":{"apa":"Dodis, Y., Pietrzak, K. Z., &#38; Puniya, P. (2008). A new mode of operation for block ciphers and length preserving MACs (Vol. 4965, pp. 198–219). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. <a href=\"https://doi.org/10.1007/978-3-540-78967-3_12\">https://doi.org/10.1007/978-3-540-78967-3_12</a>","mla":"Dodis, Yevgeniy, et al. <i>A New Mode of Operation for Block Ciphers and Length Preserving MACs</i>. Vol. 4965, Springer, 2008, pp. 198–219, doi:<a href=\"https://doi.org/10.1007/978-3-540-78967-3_12\">10.1007/978-3-540-78967-3_12</a>.","chicago":"Dodis, Yevgeniy, Krzysztof Z Pietrzak, and Prashant Puniya. “A New Mode of Operation for Block Ciphers and Length Preserving MACs,” 4965:198–219. Springer, 2008. <a href=\"https://doi.org/10.1007/978-3-540-78967-3_12\">https://doi.org/10.1007/978-3-540-78967-3_12</a>.","ama":"Dodis Y, Pietrzak KZ, Puniya P. A new mode of operation for block ciphers and length preserving MACs. In: Vol 4965. Springer; 2008:198-219. doi:<a href=\"https://doi.org/10.1007/978-3-540-78967-3_12\">10.1007/978-3-540-78967-3_12</a>","short":"Y. Dodis, K.Z. Pietrzak, P. Puniya, in:, Springer, 2008, pp. 198–219.","ieee":"Y. Dodis, K. Z. Pietrzak, and P. Puniya, “A new mode of operation for block ciphers and length preserving MACs,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2008, vol. 4965, pp. 198–219.","ista":"Dodis Y, Pietrzak KZ, Puniya P. 2008. A new mode of operation for block ciphers and length preserving MACs. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 4965, 198–219."}}]