[{"abstract":[{"lang":"eng","text":"We describe a new implementation of the Edmonds’s algorithm for computing a perfect matching of minimum cost, to which we refer as Blossom V. A key feature of our implementation is a combination of two ideas that were shown to be effective for this problem: the “variable dual updates” approach of Cook and Rohe (INFORMS J Comput 11(2):138–148, 1999) and the use of priority queues. We achieve this by maintaining an auxiliary graph whose nodes correspond to alternating trees in the Edmonds’s algorithm. While our use of priority queues does not improve the worst-case complexity, it appears to lead to an efficient technique. In the majority of our tests Blossom V outperformed previous implementations of Cook and Rohe (INFORMS J Comput 11(2):138–148, 1999) and Mehlhorn and Schäfer (J Algorithmics Exp (JEA) 7:4, 2002), sometimes by an order of magnitude. We also show that for large VLSI instances it is beneficial to update duals by solving a linear program, contrary to a conjecture by Cook and Rohe.\n\n"}],"publication_status":"published","month":"07","_id":"2932","date_published":"2009-07-01T00:00:00Z","date_created":"2018-12-11T12:00:25Z","quality_controlled":0,"volume":1,"intvolume":"         1","issue":"1","page":"43 - 67","extern":1,"date_updated":"2021-01-12T07:00:47Z","author":[{"first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","day":"01","publist_id":"3804","publisher":"Springer","citation":{"short":"V. Kolmogorov, Mathematical Programming Computation 1 (2009) 43–67.","ista":"Kolmogorov V. 2009. Blossom V: A new implementation of a minimum cost perfect matching algorithm. Mathematical Programming Computation. 1(1), 43–67.","ama":"Kolmogorov V. Blossom V: A new implementation of a minimum cost perfect matching algorithm. <i>Mathematical Programming Computation</i>. 2009;1(1):43-67. doi:<a href=\"https://doi.org/10.1007/s12532-009-0002-8\">10.1007/s12532-009-0002-8</a>","apa":"Kolmogorov, V. (2009). Blossom V: A new implementation of a minimum cost perfect matching algorithm. <i>Mathematical Programming Computation</i>. Springer. <a href=\"https://doi.org/10.1007/s12532-009-0002-8\">https://doi.org/10.1007/s12532-009-0002-8</a>","ieee":"V. Kolmogorov, “Blossom V: A new implementation of a minimum cost perfect matching algorithm,” <i>Mathematical Programming Computation</i>, vol. 1, no. 1. Springer, pp. 43–67, 2009.","mla":"Kolmogorov, Vladimir. “Blossom V: A New Implementation of a Minimum Cost Perfect Matching Algorithm.” <i>Mathematical Programming Computation</i>, vol. 1, no. 1, Springer, 2009, pp. 43–67, doi:<a href=\"https://doi.org/10.1007/s12532-009-0002-8\">10.1007/s12532-009-0002-8</a>.","chicago":"Kolmogorov, Vladimir. “Blossom V: A New Implementation of a Minimum Cost Perfect Matching Algorithm.” <i>Mathematical Programming Computation</i>. Springer, 2009. <a href=\"https://doi.org/10.1007/s12532-009-0002-8\">https://doi.org/10.1007/s12532-009-0002-8</a>."},"doi":"10.1007/s12532-009-0002-8","year":"2009","publication":"Mathematical Programming Computation","status":"public","title":"Blossom V: A new implementation of a minimum cost perfect matching algorithm"},{"title":"Parasitic nematodes modulate PIN mediated auxin transport to facilitate infection","publication":"PLoS Pathogens","status":"public","year":"2009","publisher":"Public Library of Science","citation":{"mla":"Grunewald, Wim, et al. “Parasitic Nematodes Modulate PIN Mediated Auxin Transport to Facilitate Infection.” <i>PLoS Pathogens</i>, vol. 5, no. 1, Public Library of Science, 2009, doi:<a href=\"https://doi.org/ 10.1371/journal.ppat.1000266\"> 10.1371/journal.ppat.1000266</a>.","chicago":"Grunewald, Wim, Bernard Cannoot, Jiří Friml, and Godelieve Gheysen. “Parasitic Nematodes Modulate PIN Mediated Auxin Transport to Facilitate Infection.” <i>PLoS Pathogens</i>. Public Library of Science, 2009. <a href=\"https://doi.org/ 10.1371/journal.ppat.1000266\">https://doi.org/ 10.1371/journal.ppat.1000266</a>.","apa":"Grunewald, W., Cannoot, B., Friml, J., &#38; Gheysen, G. (2009). Parasitic nematodes modulate PIN mediated auxin transport to facilitate infection. <i>PLoS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/ 10.1371/journal.ppat.1000266\">https://doi.org/ 10.1371/journal.ppat.1000266</a>","ieee":"W. Grunewald, B. Cannoot, J. Friml, and G. Gheysen, “Parasitic nematodes modulate PIN mediated auxin transport to facilitate infection,” <i>PLoS Pathogens</i>, vol. 5, no. 1. Public Library of Science, 2009.","short":"W. Grunewald, B. Cannoot, J. Friml, G. Gheysen, PLoS Pathogens 5 (2009).","ista":"Grunewald W, Cannoot B, Friml J, Gheysen G. 2009. Parasitic nematodes modulate PIN mediated auxin transport to facilitate infection. PLoS Pathogens. 5(1).","ama":"Grunewald W, Cannoot B, Friml J, Gheysen G. Parasitic nematodes modulate PIN mediated auxin transport to facilitate infection. <i>PLoS Pathogens</i>. 2009;5(1). doi:<a href=\"https://doi.org/ 10.1371/journal.ppat.1000266\"> 10.1371/journal.ppat.1000266</a>"},"doi":" 10.1371/journal.ppat.1000266","publist_id":"3656","day":"01","type":"journal_article","author":[{"full_name":"Grunewald, Wim","last_name":"Grunewald","first_name":"Wim"},{"first_name":"Bernard","last_name":"Cannoot","full_name":"Cannoot, Bernard"},{"first_name":"Jirí","last_name":"Friml","full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"last_name":"Gheysen","first_name":"Godelieve","full_name":"Gheysen, Godelieve"}],"date_updated":"2021-01-12T07:40:40Z","extern":1,"issue":"1","intvolume":"         5","volume":5,"quality_controlled":0,"date_created":"2018-12-11T12:01:03Z","date_published":"2009-01-01T00:00:00Z","_id":"3046","month":"01","publication_status":"published","abstract":[{"text":"Plant-parasitic nematodes are destructive plant pathogens that cause significant yield losses. They induce highly specialized feeding sites (NFS) in infected plant roots from which they withdraw nutrients. In order to establish these NFS, it is thought that the nematodes manipulate the molecular and physiological pathways of their hosts. Evidence is accumulating that the plant signalling molecule auxin is involved in the initiation and development of the feeding sites of sedentary plant-parasitic nematodes. Intercellular transport of auxin is essential for various aspects of plant growth and development. Here, we analysed the spatial and temporal expression of PIN auxin transporters during the early events of NFS establishment using promoter-GUS/GFP fusion lines. Additionally, single and double pin mutants were used in infection studies to analyse the role of the different PIN proteins during cyst nematode infection. Based on our results, we postulate a model in which PIN1-mediated auxin transport is needed to deliver auxin to the initial syncytial cell, whereas PIN3 and PIN4 distribute the accumulated auxin laterally and are involved in the radial expansion of the NFS. Our data demonstrate that cyst nematodes are able to hijack the auxin distribution network in order to facilitate the infection process. © 2009 Grunewald et al","lang":"eng"}]},{"author":[{"full_name":"Titapiwatanakun, Boosaree","first_name":"Boosaree","last_name":"Titapiwatanakun"},{"full_name":"Blakeslee, Joshua","first_name":"Joshua","last_name":"Blakeslee"},{"last_name":"Bandyopadhyay","first_name":"Anindita","full_name":"Bandyopadhyay, Anindita"},{"full_name":"Yang, Haibing","last_name":"Yang","first_name":"Haibing"},{"last_name":"Mravec","first_name":"Jozef","full_name":"Mravec, Jozef"},{"full_name":"Sauer, Michael","last_name":"Sauer","first_name":"Michael"},{"last_name":"Cheng","first_name":"Yan","full_name":"Cheng, Yan"},{"first_name":"Jiří","last_name":"Adamec","full_name":"Adamec, Jiří"},{"full_name":"Nagashima, Akitomo","first_name":"Akitomo","last_name":"Nagashima"},{"first_name":"Markus","last_name":"Geisler","full_name":"Geisler, Markus"},{"full_name":"Sakai, Tatsuya","last_name":"Sakai","first_name":"Tatsuya"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596"},{"full_name":"Peer, Wendy A","first_name":"Wendy","last_name":"Peer"},{"full_name":"Murphy, Angus S","first_name":"Angus","last_name":"Murphy"}],"day":"01","type":"journal_article","publist_id":"3655","status":"public","publication":"Plant Journal","year":"2009","title":"ABCB19 PGP19 stabilises PIN1 in membrane microdomains in Arabidopsis","publisher":"Wiley-Blackwell","citation":{"ieee":"B. Titapiwatanakun <i>et al.</i>, “ABCB19 PGP19 stabilises PIN1 in membrane microdomains in Arabidopsis,” <i>Plant Journal</i>, vol. 57, no. 1. Wiley-Blackwell, pp. 27–44, 2009.","apa":"Titapiwatanakun, B., Blakeslee, J., Bandyopadhyay, A., Yang, H., Mravec, J., Sauer, M., … Murphy, A. (2009). ABCB19 PGP19 stabilises PIN1 in membrane microdomains in Arabidopsis. <i>Plant Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1365-313X.2008.03668.x\">https://doi.org/10.1111/j.1365-313X.2008.03668.x</a>","mla":"Titapiwatanakun, Boosaree, et al. “ABCB19 PGP19 Stabilises PIN1 in Membrane Microdomains in Arabidopsis.” <i>Plant Journal</i>, vol. 57, no. 1, Wiley-Blackwell, 2009, pp. 27–44, doi:<a href=\"https://doi.org/10.1111/j.1365-313X.2008.03668.x\">10.1111/j.1365-313X.2008.03668.x</a>.","chicago":"Titapiwatanakun, Boosaree, Joshua Blakeslee, Anindita Bandyopadhyay, Haibing Yang, Jozef Mravec, Michael Sauer, Yan Cheng, et al. “ABCB19 PGP19 Stabilises PIN1 in Membrane Microdomains in Arabidopsis.” <i>Plant Journal</i>. Wiley-Blackwell, 2009. <a href=\"https://doi.org/10.1111/j.1365-313X.2008.03668.x\">https://doi.org/10.1111/j.1365-313X.2008.03668.x</a>.","short":"B. Titapiwatanakun, J. Blakeslee, A. Bandyopadhyay, H. Yang, J. Mravec, M. Sauer, Y. Cheng, J. Adamec, A. Nagashima, M. Geisler, T. Sakai, J. Friml, W. Peer, A. Murphy, Plant Journal 57 (2009) 27–44.","ista":"Titapiwatanakun B, Blakeslee J, Bandyopadhyay A, Yang H, Mravec J, Sauer M, Cheng Y, Adamec J, Nagashima A, Geisler M, Sakai T, Friml J, Peer W, Murphy A. 2009. ABCB19 PGP19 stabilises PIN1 in membrane microdomains in Arabidopsis. Plant Journal. 57(1), 27–44.","ama":"Titapiwatanakun B, Blakeslee J, Bandyopadhyay A, et al. ABCB19 PGP19 stabilises PIN1 in membrane microdomains in Arabidopsis. <i>Plant Journal</i>. 2009;57(1):27-44. doi:<a href=\"https://doi.org/10.1111/j.1365-313X.2008.03668.x\">10.1111/j.1365-313X.2008.03668.x</a>"},"doi":"10.1111/j.1365-313X.2008.03668.x","_id":"3047","publication_status":"published","month":"01","abstract":[{"lang":"eng","text":"\n\nAuxin transport is mediated at the cellular level by three independent mechanisms that are characterised by the PIN-formed (PIN), P-glycoprotein (ABCB/PGP) and AUX/LAX transport proteins. The PIN and ABCB transport proteins, best represented by PIN1 and ABCB19 (PGP19), have been shown to coordinately regulate auxin efflux. When PIN1 and ABCB19 coincide on the plasma membrane, their interaction enhances the rate and specificity of auxin efflux and the dynamic cycling of PIN1 is reduced. However, ABCB19 function is not regulated by the dynamic cellular trafficking mechanisms that regulate PIN1 in apical tissues, as localisation of ABCB19 on the plasma membrane was not inhibited by short-term treatments with latrunculin B, oryzalin, brefeldin A (BFA) or wortmannin - all of which have been shown to alter PIN1 and/or PIN2 plasma membrane localisation. When taken up by endocytosis, the styryl dye FM4-64 labels diffuse rather than punctuate intracellular bodies in abcb19 (pgp19), and some aggregations of PIN1 induced by short-term BFA treatment did not disperse after BFA washout in abcb19. Although the subcellular localisations of ABCB19 and PIN1 in the reciprocal mutant backgrounds were like those in wild type, PIN1 plasma membrane localisation in abcb19 roots was more easily perturbed by the detergent Triton X-100, but not other non-ionic detergents. ABCB19 is stably associated with sterol/sphingolipid-enriched membrane fractions containing BIG/TIR3 and partitions into Triton X-100 detergent-resistant membrane (DRM) fractions. In the wild type, PIN1 was also present in DRMs, but was less abundant in abcb19 DRMs. These observations suggested a rationale for the observed lack of auxin transport activity when PIN1 is expressed in a non-plant heterologous system. PIN1 was therefore expressed in Schizosaccharomyces pombe, which has plant-like sterol-enriched microdomains, and catalysed auxin transport in these cells. These data suggest that ABCB19 stabilises PIN1 localisation at the plasma membrane in discrete cellular subdomains where PIN1 and ABCB19 expression overlaps. "}],"volume":57,"intvolume":"        57","quality_controlled":0,"date_created":"2018-12-11T12:01:03Z","date_published":"2009-01-01T00:00:00Z","date_updated":"2021-01-12T07:40:40Z","page":"27 - 44","issue":"1","extern":1},{"date_published":"2009-03-10T00:00:00Z","quality_controlled":0,"date_created":"2018-12-11T12:01:03Z","intvolume":"        19","volume":19,"page":"391 - 397","extern":1,"issue":"5","date_updated":"2021-01-12T07:40:41Z","publication_status":"published","month":"03","abstract":[{"lang":"eng","text":"Endocytic vesicle trafficking is crucial for regulating activity and localization of plasma membrane components, but the process is still poorly genetically defined in plants. Membrane proteins of the PIN-FORMED (PIN) family exhibit polar localization in plant cells and facilitate cellular efflux of the plant hormone auxin, thereby regulating multiple developmental processes [1, 2]. PIN proteins undergo constitutive endocytosis and GNOM ARF GEF-dependent recycling [3-5], and their localization is under extensive regulation by developmental and environmental cues [6-9]. We designed a fluorescence imaging-based screen to identify Arabidopsis thaliana mutants defective in internalization of proteins including PINs from the plasma membrane. We identified three mutant loci, BFA-visualized endocytic trafficking defective1 (ben1) through ben3 that do not efficiently accumulate PIN1-GFP in intracellular compartments after inhibition of recycling and secretion by fungal toxin brefeldin A (BFA). Fine mapping revealed that BEN1 encodes an ARF GEF vesicle trafficking regulator from the functionally uncharacterized BIG class. ben1 mutant has been previously implicated in pathogen response [10] and shows cell polarity, BFA sensitivity, and growth defects. BEN1 is involved in endocytosis of plasma membrane proteins and localizes to early endocytic compartments distinct from GNOM-positive endosomes. Our results identify BEN1 as the ARF GEF mediating early endosomal traffic."}],"_id":"3048","publist_id":"3653","publisher":"Cell Press","doi":"10.1016/j.cub.2009.01.057","citation":{"apa":"Tanaka, H., Kitakura, S., De Rycke, R., De Groodt, R., &#38; Friml, J. (2009). Fluorescence imaging based screen identifies ARF GEF component of early endosomal trafficking. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2009.01.057\">https://doi.org/10.1016/j.cub.2009.01.057</a>","ieee":"H. Tanaka, S. Kitakura, R. De Rycke, R. De Groodt, and J. Friml, “Fluorescence imaging based screen identifies ARF GEF component of early endosomal trafficking,” <i>Current Biology</i>, vol. 19, no. 5. Cell Press, pp. 391–397, 2009.","mla":"Tanaka, Hirokazu, et al. “Fluorescence Imaging Based Screen Identifies ARF GEF Component of Early Endosomal Trafficking.” <i>Current Biology</i>, vol. 19, no. 5, Cell Press, 2009, pp. 391–97, doi:<a href=\"https://doi.org/10.1016/j.cub.2009.01.057\">10.1016/j.cub.2009.01.057</a>.","chicago":"Tanaka, Hirokazu, Saeko Kitakura, Riet De Rycke, Ruth De Groodt, and Jiří Friml. “Fluorescence Imaging Based Screen Identifies ARF GEF Component of Early Endosomal Trafficking.” <i>Current Biology</i>. Cell Press, 2009. <a href=\"https://doi.org/10.1016/j.cub.2009.01.057\">https://doi.org/10.1016/j.cub.2009.01.057</a>.","short":"H. Tanaka, S. Kitakura, R. De Rycke, R. De Groodt, J. Friml, Current Biology 19 (2009) 391–397.","ama":"Tanaka H, Kitakura S, De Rycke R, De Groodt R, Friml J. Fluorescence imaging based screen identifies ARF GEF component of early endosomal trafficking. <i>Current Biology</i>. 2009;19(5):391-397. doi:<a href=\"https://doi.org/10.1016/j.cub.2009.01.057\">10.1016/j.cub.2009.01.057</a>","ista":"Tanaka H, Kitakura S, De Rycke R, De Groodt R, Friml J. 2009. Fluorescence imaging based screen identifies ARF GEF component of early endosomal trafficking. Current Biology. 19(5), 391–397."},"year":"2009","status":"public","publication":"Current Biology","title":"Fluorescence imaging based screen identifies ARF GEF component of early endosomal trafficking","author":[{"full_name":"Tanaka, Hirokazu","last_name":"Tanaka","first_name":"Hirokazu"},{"first_name":"Saeko","last_name":"Kitakura","full_name":"Kitakura, Saeko"},{"last_name":"De Rycke","first_name":"Riet","full_name":"De Rycke, Riet M"},{"last_name":"De Groodt","first_name":"Ruth","full_name":"De Groodt, Ruth"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml","last_name":"Friml","first_name":"Jirí"}],"type":"journal_article","day":"10"},{"month":"03","abstract":[{"lang":"eng","text":"Postembryonic de novo organogenesis represents an important competence evolved in plants that allows their physiological and developmental adaptation to changing environmental conditions. The phytohormones auxin and cytokinin (CK) are important regulators of the developmental fate of pluripotent plant cells. However, the molecular nature of their interaction(s) in control of plant organogenesis is largely unknown. Here, we show that CK modulates auxin-induced organogenesis (AIO) via regulation of the efflux-dependent intercellular auxin distribution. We used the hypocotyl explants-based in vitro system to study the mechanism underlying de novo organogenesis. We show that auxin, but not CK, is capable of triggering organogenesis in hypocotyl explants. The AIO is accompanied by endogenous CK production and tissue-specific activation of CK signaling. CK affects differential auxin distribution, and the CK-mediated modulation of organogenesis is simulated by inhibition of polar auxin transport. CK reduces auxin efflux from cultured tobacco cells and regulates expression of auxin efflux carriers from the PIN family in hypocotyl explants. Moreover, endogenous CK levels influence PIN transcription and are necessary to maintain intercellular auxin distribution in planta. Based on these findings, we propose a model in which auxin acts as a trigger of the organogenic processes, whose output is modulated by the endogenously produced CKs. We propose that an important mechanism of this CK action is its effect on auxin distribution via regulation of expression of auxin efflux carriers."}],"publication_status":"published","_id":"3049","extern":1,"issue":"9","page":"3609 - 3614","date_updated":"2021-01-12T07:40:41Z","date_published":"2009-03-03T00:00:00Z","date_created":"2018-12-11T12:01:04Z","quality_controlled":0,"intvolume":"       106","volume":106,"type":"journal_article","day":"03","author":[{"full_name":"Pernisová, Markéta","last_name":"Pernisová","first_name":"Markéta"},{"last_name":"Klíma","first_name":"Petr","full_name":"Klíma, Petr"},{"full_name":"Horák, Jakub","last_name":"Horák","first_name":"Jakub"},{"full_name":"Válková, Martina","last_name":"Válková","first_name":"Martina"},{"last_name":"Malbeck","first_name":"Jiří","full_name":"Malbeck, Jiří"},{"full_name":"Souček, Přemysl","first_name":"Přemysl","last_name":"Souček"},{"full_name":"Reichman, Pavel","first_name":"Pavel","last_name":"Reichman"},{"first_name":"Klára","last_name":"Hoyerová","full_name":"Hoyerová, Klára"},{"first_name":"Jaroslava","last_name":"Dubová","full_name":"Dubová, Jaroslava"},{"full_name":"Jirí Friml","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"last_name":"Zažímalová","first_name":"Eva","full_name":"Zažímalová, Eva"},{"first_name":"Jan","last_name":"Hejátko","full_name":"Hejátko, Jan"}],"publisher":"National Academy of Sciences","doi":"10.1073/pnas.0811539106","citation":{"short":"M. Pernisová, P. Klíma, J. Horák, M. Válková, J. Malbeck, P. Souček, P. Reichman, K. Hoyerová, J. Dubová, J. Friml, E. Zažímalová, J. Hejátko, PNAS 106 (2009) 3609–3614.","ama":"Pernisová M, Klíma P, Horák J, et al. Cytokinins modulate auxin induced organogenesis in plants via regulation of the auxin efflux. <i>PNAS</i>. 2009;106(9):3609-3614. doi:<a href=\"https://doi.org/10.1073/pnas.0811539106\">10.1073/pnas.0811539106</a>","ista":"Pernisová M, Klíma P, Horák J, Válková M, Malbeck J, Souček P, Reichman P, Hoyerová K, Dubová J, Friml J, Zažímalová E, Hejátko J. 2009. Cytokinins modulate auxin induced organogenesis in plants via regulation of the auxin efflux. PNAS. 106(9), 3609–3614.","apa":"Pernisová, M., Klíma, P., Horák, J., Válková, M., Malbeck, J., Souček, P., … Hejátko, J. (2009). Cytokinins modulate auxin induced organogenesis in plants via regulation of the auxin efflux. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0811539106\">https://doi.org/10.1073/pnas.0811539106</a>","ieee":"M. Pernisová <i>et al.</i>, “Cytokinins modulate auxin induced organogenesis in plants via regulation of the auxin efflux,” <i>PNAS</i>, vol. 106, no. 9. National Academy of Sciences, pp. 3609–3614, 2009.","mla":"Pernisová, Markéta, et al. “Cytokinins Modulate Auxin Induced Organogenesis in Plants via Regulation of the Auxin Efflux.” <i>PNAS</i>, vol. 106, no. 9, National Academy of Sciences, 2009, pp. 3609–14, doi:<a href=\"https://doi.org/10.1073/pnas.0811539106\">10.1073/pnas.0811539106</a>.","chicago":"Pernisová, Markéta, Petr Klíma, Jakub Horák, Martina Válková, Jiří Malbeck, Přemysl Souček, Pavel Reichman, et al. “Cytokinins Modulate Auxin Induced Organogenesis in Plants via Regulation of the Auxin Efflux.” <i>PNAS</i>. National Academy of Sciences, 2009. <a href=\"https://doi.org/10.1073/pnas.0811539106\">https://doi.org/10.1073/pnas.0811539106</a>."},"title":"Cytokinins modulate auxin induced organogenesis in plants via regulation of the auxin efflux","year":"2009","status":"public","publication":"PNAS","publist_id":"3654"},{"publist_id":"3652","publisher":"National Academy of Sciences","citation":{"mla":"Růžička, Kamil, et al. “Cytokinin Regulates Root Meristem Activity via Modulation of the Polar Auxin Transport.” <i>PNAS</i>, vol. 106, no. 11, National Academy of Sciences, 2009, pp. 4284–89, doi:<a href=\"https://doi.org/10.1073/pnas.0900060106\">10.1073/pnas.0900060106</a>.","chicago":"Růžička, Kamil, Mária Šimášková, Jérôme Duclercq, Jan Petrášek, Eva Zažímalová, Sibu Simon, Jiří Friml, Marc Van Montagu, and Eva Benková. “Cytokinin Regulates Root Meristem Activity via Modulation of the Polar Auxin Transport.” <i>PNAS</i>. National Academy of Sciences, 2009. <a href=\"https://doi.org/10.1073/pnas.0900060106\">https://doi.org/10.1073/pnas.0900060106</a>.","apa":"Růžička, K., Šimášková, M., Duclercq, J., Petrášek, J., Zažímalová, E., Simon, S., … Benková, E. (2009). Cytokinin regulates root meristem activity via modulation of the polar auxin transport. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0900060106\">https://doi.org/10.1073/pnas.0900060106</a>","ieee":"K. Růžička <i>et al.</i>, “Cytokinin regulates root meristem activity via modulation of the polar auxin transport,” <i>PNAS</i>, vol. 106, no. 11. National Academy of Sciences, pp. 4284–4289, 2009.","short":"K. Růžička, M. Šimášková, J. Duclercq, J. Petrášek, E. Zažímalová, S. Simon, J. Friml, M. Van Montagu, E. Benková, PNAS 106 (2009) 4284–4289.","ista":"Růžička K, Šimášková M, Duclercq J, Petrášek J, Zažímalová E, Simon S, Friml J, Van Montagu M, Benková E. 2009. Cytokinin regulates root meristem activity via modulation of the polar auxin transport. PNAS. 106(11), 4284–4289.","ama":"Růžička K, Šimášková M, Duclercq J, et al. Cytokinin regulates root meristem activity via modulation of the polar auxin transport. <i>PNAS</i>. 2009;106(11):4284-4289. doi:<a href=\"https://doi.org/10.1073/pnas.0900060106\">10.1073/pnas.0900060106</a>"},"doi":"10.1073/pnas.0900060106","status":"public","publication":"PNAS","title":"Cytokinin regulates root meristem activity via modulation of the polar auxin transport","year":"2009","author":[{"full_name":"Růžička, Kamil","first_name":"Kamil","last_name":"Růžička"},{"full_name":"Šimášková, Mária","last_name":"Šimášková","first_name":"Mária"},{"full_name":"Duclercq, Jérôme","first_name":"Jérôme","last_name":"Duclercq"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"full_name":"Zažímalová, Eva","first_name":"Eva","last_name":"Zažímalová"},{"orcid":"0000-0002-1998-6741","first_name":"Sibu","last_name":"Simon","full_name":"Sibu Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"full_name":"Van Montagu, Marc C","last_name":"Van Montagu","first_name":"Marc"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Eva Benková","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739"}],"type":"journal_article","day":"17","date_published":"2009-03-17T00:00:00Z","quality_controlled":0,"date_created":"2018-12-11T12:01:04Z","intvolume":"       106","volume":106,"page":"4284 - 4289","extern":1,"issue":"11","date_updated":"2021-01-12T07:40:42Z","month":"03","publication_status":"published","abstract":[{"lang":"eng","text":"Plant development is governed by signaling molecules called phytohormones. Typically, in certain developmental processes more than 1 hormone is implicated and, thus, coordination of their overlapping activities is crucial for correct plant development. However, molecular mechanisms underlying the hormonal crosstalk are only poorly understood. Multiple hormones including cytokinin and auxin have been implicated in the regulation of root development. Here we dissect the roles of cytokinin in modulating growth of the primary root. We show that cytokinin effect on root elongation occurs through ethylene signaling whereas cytokinin effect on the root meristem size involves ethylene-independent modulation of transport-dependent asymmetric auxin distribution. Exogenous or endogenous modification of cytokinin levels and cytokinin signaling lead to specific changes in transcription of several auxin efflux carrier genes from the PIN family having a direct impact on auxin efflux from cultured cells and on auxin distribution in the root apex. We propose a novel model for cytokinin action in regulating root growth: Cytokinin influences cell-to-cell auxin transport by modification of expression of several auxin transport components and thus modulates auxin distribution important for regulation of activity and size of the root meristem."}],"_id":"3050"},{"type":"journal_article","author":[{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/19303857","open_access":"1"}],"publisher":"Cell Press","doi":"10.1016/j.cell.2009.03.009","title":"SnapShot: Auxin signaling and transport","status":"public","year":"2009","oa_version":"Published Version","publist_id":"3650","month":"03","_id":"3051","issue":"6","page":"1172 - 1172","external_id":{"pmid":["    19303857"]},"date_updated":"2021-01-12T07:40:42Z","article_type":"original","date_published":"2009-03-20T00:00:00Z","quality_controlled":"1","language":[{"iso":"eng"}],"day":"20","citation":{"apa":"Weijers, D., &#38; Friml, J. (2009). SnapShot: Auxin signaling and transport. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2009.03.009\">https://doi.org/10.1016/j.cell.2009.03.009</a>","ieee":"D. Weijers and J. Friml, “SnapShot: Auxin signaling and transport,” <i>Cell</i>, vol. 136, no. 6. Cell Press, pp. 1172–1172, 2009.","mla":"Weijers, Dolf, and Jiří Friml. “SnapShot: Auxin Signaling and Transport.” <i>Cell</i>, vol. 136, no. 6, Cell Press, 2009, pp. 1172–1172, doi:<a href=\"https://doi.org/10.1016/j.cell.2009.03.009\">10.1016/j.cell.2009.03.009</a>.","chicago":"Weijers, Dolf, and Jiří Friml. “SnapShot: Auxin Signaling and Transport.” <i>Cell</i>. Cell Press, 2009. <a href=\"https://doi.org/10.1016/j.cell.2009.03.009\">https://doi.org/10.1016/j.cell.2009.03.009</a>.","short":"D. Weijers, J. Friml, Cell 136 (2009) 1172–1172.","ama":"Weijers D, Friml J. SnapShot: Auxin signaling and transport. <i>Cell</i>. 2009;136(6):1172-1172. doi:<a href=\"https://doi.org/10.1016/j.cell.2009.03.009\">10.1016/j.cell.2009.03.009</a>","ista":"Weijers D, Friml J. 2009. SnapShot: Auxin signaling and transport. Cell. 136(6), 1172–1172."},"publication":"Cell","oa":1,"publication_status":"published","extern":"1","pmid":1,"date_created":"2018-12-11T12:01:05Z","volume":136,"intvolume":"       136","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication_status":"published","abstract":[{"text":"The dynamic, differential distribution of the hormone auxin within plant tissues controls an impressive variety of developmental processes, which tailor plant growth and morphology to environmental conditions. Various environmental and endogenous signals can be integrated into changes in auxin distribution through their effects on local auxin biosynthesis and intercellular auxin transport. Individual cells interpret auxin largely by a nuclear signaling pathway that involves the F box protein TIR1 acting as an auxin receptor. Auxin-dependent TIR1 activity leads to ubiquitination-based degradation of transcriptional repressors and complex transcriptional reprogramming. Thus, auxin appears to be a versatile trigger of preprogrammed developmental changes in plant cells.","lang":"eng"}],"date_created":"2018-12-11T12:01:05Z","volume":136,"intvolume":"       136","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","pmid":1,"day":"20","oa":1,"citation":{"apa":"Vanneste, S., &#38; Friml, J. (2009). Auxin: A trigger for change in plant development. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2009.03.001\">https://doi.org/10.1016/j.cell.2009.03.001</a>","ieee":"S. Vanneste and J. Friml, “Auxin: A trigger for change in plant development,” <i>Cell</i>, vol. 136, no. 6. Cell Press, pp. 1005–1016, 2009.","mla":"Vanneste, Steffen, and Jiří Friml. “Auxin: A Trigger for Change in Plant Development.” <i>Cell</i>, vol. 136, no. 6, Cell Press, 2009, pp. 1005–16, doi:<a href=\"https://doi.org/10.1016/j.cell.2009.03.001\">10.1016/j.cell.2009.03.001</a>.","chicago":"Vanneste, Steffen, and Jiří Friml. “Auxin: A Trigger for Change in Plant Development.” <i>Cell</i>. Cell Press, 2009. <a href=\"https://doi.org/10.1016/j.cell.2009.03.001\">https://doi.org/10.1016/j.cell.2009.03.001</a>.","short":"S. Vanneste, J. Friml, Cell 136 (2009) 1005–1016.","ama":"Vanneste S, Friml J. Auxin: A trigger for change in plant development. <i>Cell</i>. 2009;136(6):1005-1016. doi:<a href=\"https://doi.org/10.1016/j.cell.2009.03.001\">10.1016/j.cell.2009.03.001</a>","ista":"Vanneste S, Friml J. 2009. Auxin: A trigger for change in plant development. Cell. 136(6), 1005–1016."},"publication":"Cell","month":"03","_id":"3052","quality_controlled":"1","date_published":"2009-03-20T00:00:00Z","language":[{"iso":"eng"}],"page":"1005 - 1016","issue":"6","external_id":{"pmid":["    19303845"]},"date_updated":"2021-01-12T07:40:43Z","author":[{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/19303845","open_access":"1"}],"type":"journal_article","publist_id":"3651","oa_version":"Published Version","publisher":"Cell Press","doi":"10.1016/j.cell.2009.03.001","year":"2009","title":"Auxin: A trigger for change in plant development","status":"public"},{"date_updated":"2021-01-12T07:40:43Z","extern":"1","issue":"4","page":"189 - 193","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":14,"language":[{"iso":"eng"}],"intvolume":"        14","date_published":"2009-04-01T00:00:00Z","date_created":"2018-12-11T12:01:05Z","_id":"3053","publication_status":"published","month":"04","year":"2009","title":"A morphogenetic trigger: Is there an emerging concept in plant developmental biology?","publication":"Trends in Plant Science","status":"public","citation":{"ieee":"E. Benková, M. Ivanchenko, J. Friml, S. Shishkova, and J. Dubrovsky, “A morphogenetic trigger: Is there an emerging concept in plant developmental biology?,” <i>Trends in Plant Science</i>, vol. 14, no. 4. Cell Press, pp. 189–193, 2009.","apa":"Benková, E., Ivanchenko, M., Friml, J., Shishkova, S., &#38; Dubrovsky, J. (2009). A morphogenetic trigger: Is there an emerging concept in plant developmental biology? <i>Trends in Plant Science</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tplants.2009.01.006\">https://doi.org/10.1016/j.tplants.2009.01.006</a>","chicago":"Benková, Eva, Maria Ivanchenko, Jiří Friml, Svetlana Shishkova, and Joseph Dubrovsky. “A Morphogenetic Trigger: Is There an Emerging Concept in Plant Developmental Biology?” <i>Trends in Plant Science</i>. Cell Press, 2009. <a href=\"https://doi.org/10.1016/j.tplants.2009.01.006\">https://doi.org/10.1016/j.tplants.2009.01.006</a>.","mla":"Benková, Eva, et al. “A Morphogenetic Trigger: Is There an Emerging Concept in Plant Developmental Biology?” <i>Trends in Plant Science</i>, vol. 14, no. 4, Cell Press, 2009, pp. 189–93, doi:<a href=\"https://doi.org/10.1016/j.tplants.2009.01.006\">10.1016/j.tplants.2009.01.006</a>.","ista":"Benková E, Ivanchenko M, Friml J, Shishkova S, Dubrovsky J. 2009. A morphogenetic trigger: Is there an emerging concept in plant developmental biology? Trends in Plant Science. 14(4), 189–193.","ama":"Benková E, Ivanchenko M, Friml J, Shishkova S, Dubrovsky J. A morphogenetic trigger: Is there an emerging concept in plant developmental biology? <i>Trends in Plant Science</i>. 2009;14(4):189-193. doi:<a href=\"https://doi.org/10.1016/j.tplants.2009.01.006\">10.1016/j.tplants.2009.01.006</a>","short":"E. Benková, M. Ivanchenko, J. Friml, S. Shishkova, J. Dubrovsky, Trends in Plant Science 14 (2009) 189–193."},"doi":"10.1016/j.tplants.2009.01.006","publisher":"Cell Press","oa_version":"None","publist_id":"3649","day":"01","type":"journal_article","author":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739"},{"last_name":"Ivanchenko","first_name":"Maria","full_name":"Ivanchenko, Maria"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"full_name":"Shishkova, Svetlana","first_name":"Svetlana","last_name":"Shishkova"},{"full_name":"Dubrovsky, Joseph","last_name":"Dubrovsky","first_name":"Joseph"}]},{"_id":"3054","month":"05","abstract":[{"text":"As multicellular organisms, plants, like animals, use endogenous signaling molecules to coordinate their own physiology and development. To compensate for the absence of a cardiovascular system, plants have evolved specialized transport pathways to distribute signals and nutrients. The main transport streams include the xylem flow of the nutrients from the root to the shoot and the phloem flow of materials from the photosynthetic active tissues. These long-distance transport processes are complemented by several intercellular transport mechanisms (apoplastic, symplastic and transcellular transport). A prominent example of transcellular flow is transport of the phytohormone auxin within tissues. The process is mediated by influx and efflux carriers, whose polar localization in the plasma membrane determines the directionality of the flow. This polar auxin transport generates auxin maxima and gradients within tissues that are instrumental in the diverse regulation of various plant developmental processes, including embryogenesis, organogenesis, vascular tissue formation and tropisms.","lang":"eng"}],"publication_status":"published","date_updated":"2021-01-12T07:40:43Z","external_id":{"pmid":["    19377459"]},"issue":"5","page":"325 - 332","extern":"1","pmid":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":5,"language":[{"iso":"eng"}],"intvolume":"         5","date_published":"2009-05-01T00:00:00Z","quality_controlled":"1","date_created":"2018-12-11T12:01:06Z","day":"01","type":"journal_article","author":[{"last_name":"Robert","first_name":"Hélène","full_name":"Robert, Hélène"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí"}],"title":"Auxin and other signals on the move in plants","year":"2009","publication":"Nature Chemical Biology","status":"public","doi":"10.1038/nchembio.170","citation":{"ama":"Robert H, Friml J. Auxin and other signals on the move in plants. <i>Nature Chemical Biology</i>. 2009;5(5):325-332. doi:<a href=\"https://doi.org/10.1038/nchembio.170\">10.1038/nchembio.170</a>","ista":"Robert H, Friml J. 2009. Auxin and other signals on the move in plants. Nature Chemical Biology. 5(5), 325–332.","short":"H. Robert, J. Friml, Nature Chemical Biology 5 (2009) 325–332.","chicago":"Robert, Hélène, and Jiří Friml. “Auxin and Other Signals on the Move in Plants.” <i>Nature Chemical Biology</i>. Nature Publishing Group, 2009. <a href=\"https://doi.org/10.1038/nchembio.170\">https://doi.org/10.1038/nchembio.170</a>.","mla":"Robert, Hélène, and Jiří Friml. “Auxin and Other Signals on the Move in Plants.” <i>Nature Chemical Biology</i>, vol. 5, no. 5, Nature Publishing Group, 2009, pp. 325–32, doi:<a href=\"https://doi.org/10.1038/nchembio.170\">10.1038/nchembio.170</a>.","ieee":"H. Robert and J. Friml, “Auxin and other signals on the move in plants,” <i>Nature Chemical Biology</i>, vol. 5, no. 5. Nature Publishing Group, pp. 325–332, 2009.","apa":"Robert, H., &#38; Friml, J. (2009). Auxin and other signals on the move in plants. <i>Nature Chemical Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nchembio.170\">https://doi.org/10.1038/nchembio.170</a>"},"publisher":"Nature Publishing Group","oa_version":"None","publist_id":"3648"},{"abstract":[{"lang":"eng","text":"ACAP-type ARF GTPase activating proteins (ARF-GAPs) regulate multiple cellular processes, including endocytosis, secretion, phagocytosis, cell adhesion and cell migration. However, the regulation of ACAP functions by other cellular proteins is poorly understood. We have reported previously that a plant ACAP, VAN3, plays a pivotal role in plant venation continuity. Here, we report on newly identified VAN3 regulators: the CVP2 (cotyledon vascular pattern 2) 5 PTase, which is considered to degrade IP3 and also to produce PtdIns(4)P from PtdIns(4,5)P2; and a PH domain-containing protein, VAB (VAN3 binding protein). Combinational mutations of both CVP2 and its closest homologue CVL1 (CVP2 like 1) phenocopied the strong allele of van3 mutants, showing severe vascular continuity. The phenotype of double mutants between van3, cvp2 and vab suggested that VAN3, CVP2 and VAB function in vascular pattern formation in the same pathway. Localization analysis revealed that both CVP2 and VAB colocalize with VAN3 in the trans- Golgi network (TGN), supporting their functions in the same pathway. The subcellular localization of VAN3 was dependent on its PH domain, and mislocalization of VAN3 was induced in cvp2 or vab mutants. These results suggest that CVP2 and VAB cooperatively regulate the subcellular localization of VAN3 through the interaction between its PH domain and phosphoinositides and/or inositol phosphates. In addition, PtdIns(4)P, to which VAN3 binds preferentially, enhanced the ARF-GAP activity of VAN3, whereas IP3 inhibited it. These results suggest the existence of PtdIns(4)P and/or IP3-dependent subcellular targeting and regulation of VAN3 ACAP activity that governs plant vascular tissue continuity."}],"month":"05","publication_status":"published","_id":"3055","date_created":"2018-12-11T12:01:06Z","date_published":"2009-05-01T00:00:00Z","quality_controlled":0,"intvolume":"       136","volume":136,"page":"1529 - 1538","extern":1,"issue":"9","date_updated":"2021-01-12T07:40:44Z","author":[{"last_name":"Naramoto","first_name":"Satoshi","full_name":"Naramoto, Satoshi"},{"full_name":"Sawa, Shinichiro","first_name":"Shinichiro","last_name":"Sawa"},{"full_name":"Koizumi, Koji","first_name":"Koji","last_name":"Koizumi"},{"full_name":"Uemura, Tomohiro","last_name":"Uemura","first_name":"Tomohiro"},{"first_name":"Takashi","last_name":"Ueda","full_name":"Ueda, Takashi"},{"full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"Akihiko","last_name":"Nakano","full_name":"Nakano, Akihiko"},{"first_name":"Hiroo","last_name":"Fukuda","full_name":"Fukuda, Hiroo"}],"type":"journal_article","day":"01","publist_id":"3647","citation":{"apa":"Naramoto, S., Sawa, S., Koizumi, K., Uemura, T., Ueda, T., Friml, J., … Fukuda, H. (2009). Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity in plants. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.030098\">https://doi.org/10.1242/dev.030098</a>","ieee":"S. Naramoto <i>et al.</i>, “Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity in plants,” <i>Development</i>, vol. 136, no. 9. Company of Biologists, pp. 1529–1538, 2009.","mla":"Naramoto, Satoshi, et al. “Phosphoinositide-Dependent Regulation of VAN3 ARF-GAP Localization and Activity Essential for Vascular Tissue Continuity in Plants.” <i>Development</i>, vol. 136, no. 9, Company of Biologists, 2009, pp. 1529–38, doi:<a href=\"https://doi.org/10.1242/dev.030098\">10.1242/dev.030098</a>.","chicago":"Naramoto, Satoshi, Shinichiro Sawa, Koji Koizumi, Tomohiro Uemura, Takashi Ueda, Jiří Friml, Akihiko Nakano, and Hiroo Fukuda. “Phosphoinositide-Dependent Regulation of VAN3 ARF-GAP Localization and Activity Essential for Vascular Tissue Continuity in Plants.” <i>Development</i>. Company of Biologists, 2009. <a href=\"https://doi.org/10.1242/dev.030098\">https://doi.org/10.1242/dev.030098</a>.","short":"S. Naramoto, S. Sawa, K. Koizumi, T. Uemura, T. Ueda, J. Friml, A. Nakano, H. Fukuda, Development 136 (2009) 1529–1538.","ista":"Naramoto S, Sawa S, Koizumi K, Uemura T, Ueda T, Friml J, Nakano A, Fukuda H. 2009. Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity in plants. Development. 136(9), 1529–1538.","ama":"Naramoto S, Sawa S, Koizumi K, et al. Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity in plants. <i>Development</i>. 2009;136(9):1529-1538. doi:<a href=\"https://doi.org/10.1242/dev.030098\">10.1242/dev.030098</a>"},"doi":"10.1242/dev.030098","publisher":"Company of Biologists","publication":"Development","status":"public","year":"2009","title":"Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity in plants"},{"author":[{"first_name":"Karim","last_name":"Sorefan","full_name":"Sorefan, Karim"},{"full_name":"Girin, Thomas","first_name":"Thomas","last_name":"Girin"},{"last_name":"Liljegren","first_name":"Sarah","full_name":"Liljegren, Sarah J"},{"last_name":"Ljung","first_name":"Karin","full_name":"Ljung, Karin"},{"first_name":"Pedro","last_name":"Robles","full_name":"Robles, Pedro"},{"last_name":"Galván Ampudia","first_name":"Carlos","full_name":"Galván-Ampudia, Carlos S"},{"full_name":"Offringa, Remko","first_name":"Remko","last_name":"Offringa"},{"full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"Yanofsky, Martin F","first_name":"Martin","last_name":"Yanofsky"},{"last_name":"Østergaard","first_name":"Lars","full_name":"Østergaard, Lars"}],"day":"28","type":"journal_article","publist_id":"3646","status":"public","publication":"Nature","year":"2009","title":"A regulated auxin minimum is required for seed dispersal in Arabidopsis","citation":{"apa":"Sorefan, K., Girin, T., Liljegren, S., Ljung, K., Robles, P., Galván Ampudia, C., … Østergaard, L. (2009). A regulated auxin minimum is required for seed dispersal in Arabidopsis. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature07875\">https://doi.org/10.1038/nature07875</a>","ieee":"K. Sorefan <i>et al.</i>, “A regulated auxin minimum is required for seed dispersal in Arabidopsis,” <i>Nature</i>, vol. 459, no. 7246. Nature Publishing Group, pp. 583–586, 2009.","mla":"Sorefan, Karim, et al. “A Regulated Auxin Minimum Is Required for Seed Dispersal in Arabidopsis.” <i>Nature</i>, vol. 459, no. 7246, Nature Publishing Group, 2009, pp. 583–86, doi:<a href=\"https://doi.org/10.1038/nature07875\">10.1038/nature07875</a>.","chicago":"Sorefan, Karim, Thomas Girin, Sarah Liljegren, Karin Ljung, Pedro Robles, Carlos Galván Ampudia, Remko Offringa, Jiří Friml, Martin Yanofsky, and Lars Østergaard. “A Regulated Auxin Minimum Is Required for Seed Dispersal in Arabidopsis.” <i>Nature</i>. Nature Publishing Group, 2009. <a href=\"https://doi.org/10.1038/nature07875\">https://doi.org/10.1038/nature07875</a>.","short":"K. Sorefan, T. Girin, S. Liljegren, K. Ljung, P. Robles, C. Galván Ampudia, R. Offringa, J. Friml, M. Yanofsky, L. Østergaard, Nature 459 (2009) 583–586.","ama":"Sorefan K, Girin T, Liljegren S, et al. A regulated auxin minimum is required for seed dispersal in Arabidopsis. <i>Nature</i>. 2009;459(7246):583-586. doi:<a href=\"https://doi.org/10.1038/nature07875\">10.1038/nature07875</a>","ista":"Sorefan K, Girin T, Liljegren S, Ljung K, Robles P, Galván Ampudia C, Offringa R, Friml J, Yanofsky M, Østergaard L. 2009. A regulated auxin minimum is required for seed dispersal in Arabidopsis. Nature. 459(7246), 583–586."},"doi":"10.1038/nature07875","publisher":"Nature Publishing Group","_id":"3056","publication_status":"published","abstract":[{"lang":"eng","text":"Local hormone maxima are essential for the development of multicellular structures and organs. For example, steroid hormones accumulate in specific cell types of the animal fetus to induce sexual differentiation and concentration peaks of the plant hormone auxin direct organ initiation and mediate tissue patterning. Here we provide an example of a regulated local hormone minimum required during organogenesis. Our results demonstrate that formation of a local auxin minimum is necessary for specification of the valve margin separation layer where Arabidopsis fruit opening takes place. Consequently, ectopic production of auxin, specifically in valve margin cells, leads to a complete loss of proper cell fate determination. The valve margin identity factor INDEHISCENT (IND) is responsible for forming the auxin minimum by coordinating auxin efflux in separation-layer cells. We propose that the simplicity of formation and maintenance make local hormone minima particularly well suited to specify a small number of cells such as the stripes at the valve margins."}],"month":"05","intvolume":"       459","volume":459,"date_published":"2009-05-28T00:00:00Z","date_created":"2018-12-11T12:01:06Z","quality_controlled":0,"date_updated":"2021-01-12T07:40:44Z","page":"583 - 586","issue":"7246","extern":1},{"date_created":"2018-12-11T12:01:07Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":136,"intvolume":"       136","pmid":1,"extern":"1","publication_status":"published","abstract":[{"text":"The differential distribution of the plant signaling molecule auxin is required for many aspects of plant development. Local auxin maxima and gradients arise as a result of local auxin metabolism and, predominantly, from directional cell-to-cell transport. In this primer, we discuss how the coordinated activity of several auxin influx and efflux systems, which transport auxin across the plasma membrane, mediates directional auxin flow. This activity crucially contributes to the correct setting of developmental cues in embryogenesis, organogenesis, vascular tissue formation and directional growth in response to environmental stimuli.","lang":"eng"}],"oa":1,"citation":{"ieee":"J. Petrášek and J. Friml, “Auxin transport routes in plant development,” <i>Development</i>, vol. 136, no. 16. Company of Biologists, pp. 2675–2688, 2009.","apa":"Petrášek, J., &#38; Friml, J. (2009). Auxin transport routes in plant development. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.030353\">https://doi.org/10.1242/dev.030353</a>","mla":"Petrášek, Jan, and Jiří Friml. “Auxin Transport Routes in Plant Development.” <i>Development</i>, vol. 136, no. 16, Company of Biologists, 2009, pp. 2675–88, doi:<a href=\"https://doi.org/10.1242/dev.030353\">10.1242/dev.030353</a>.","chicago":"Petrášek, Jan, and Jiří Friml. “Auxin Transport Routes in Plant Development.” <i>Development</i>. Company of Biologists, 2009. <a href=\"https://doi.org/10.1242/dev.030353\">https://doi.org/10.1242/dev.030353</a>.","short":"J. Petrášek, J. Friml, Development 136 (2009) 2675–2688.","ista":"Petrášek J, Friml J. 2009. Auxin transport routes in plant development. Development. 136(16), 2675–2688.","ama":"Petrášek J, Friml J. Auxin transport routes in plant development. <i>Development</i>. 2009;136(16):2675-2688. doi:<a href=\"https://doi.org/10.1242/dev.030353\">10.1242/dev.030353</a>"},"publication":"Development","day":"15","quality_controlled":"1","date_published":"2009-08-15T00:00:00Z","language":[{"iso":"eng"}],"page":"2675 - 2688","issue":"16","external_id":{"pmid":["    19633168"]},"date_updated":"2021-01-12T07:40:45Z","month":"08","_id":"3057","oa_version":"Published Version","publist_id":"3644","doi":"10.1242/dev.030353","publisher":"Company of Biologists","year":"2009","status":"public","title":"Auxin transport routes in plant development","author":[{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/19633168"}],"type":"journal_article"},{"author":[{"full_name":"Mravec, Jozef","first_name":"Jozef","last_name":"Mravec"},{"last_name":"Skůpa","first_name":"Petr","full_name":"Skůpa, Petr"},{"last_name":"Bailly","first_name":"Aurélien","full_name":"Bailly, Aurélien"},{"first_name":"Klára","last_name":"Hoyerová","full_name":"Hoyerová, Klára"},{"first_name":"Pavel","last_name":"Křeček","full_name":"Křeček, Pavel"},{"full_name":"Bielach, Agnieszka","last_name":"Bielach","first_name":"Agnieszka"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"first_name":"Jing","last_name":"Zhang","full_name":"Zhang, Jing"},{"full_name":"Gaykova, Vassilena","first_name":"Vassilena","last_name":"Gaykova"},{"last_name":"Stierhof","first_name":"York","full_name":"Stierhof, York-Dieter"},{"last_name":"Dobrev","first_name":"Petre","full_name":"Dobrev, Petre I"},{"last_name":"Schwarzerová","first_name":"Kateřina","full_name":"Schwarzerová, Kateřina"},{"full_name":"Rolčík, Jakub","first_name":"Jakub","last_name":"Rolčík"},{"full_name":"Seifertová, Daniela","last_name":"Seifertová","first_name":"Daniela"},{"last_name":"Luschnig","first_name":"Christian","full_name":"Luschnig, Christian"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Eva Benková","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739"},{"last_name":"Zažímalová","first_name":"Eva","full_name":"Zažímalová, Eva"},{"first_name":"Markus","last_name":"Geisler","full_name":"Geisler, Markus"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml"}],"day":"25","type":"journal_article","publist_id":"3645","title":"Subcellular homeostasis of phytohormone auxin is mediated by the ER localized PIN5 transporter","year":"2009","publication":"Nature","status":"public","doi":"10.1038/nature08066","citation":{"short":"J. Mravec, P. Skůpa, A. Bailly, K. Hoyerová, P. Křeček, A. Bielach, J. Petrášek, J. Zhang, V. Gaykova, Y. Stierhof, P. Dobrev, K. Schwarzerová, J. Rolčík, D. Seifertová, C. Luschnig, E. Benková, E. Zažímalová, M. Geisler, J. Friml, Nature 459 (2009) 1136–1140.","ama":"Mravec J, Skůpa P, Bailly A, et al. Subcellular homeostasis of phytohormone auxin is mediated by the ER localized PIN5 transporter. <i>Nature</i>. 2009;459(7250):1136-1140. doi:<a href=\"https://doi.org/10.1038/nature08066\">10.1038/nature08066</a>","ista":"Mravec J, Skůpa P, Bailly A, Hoyerová K, Křeček P, Bielach A, Petrášek J, Zhang J, Gaykova V, Stierhof Y, Dobrev P, Schwarzerová K, Rolčík J, Seifertová D, Luschnig C, Benková E, Zažímalová E, Geisler M, Friml J. 2009. Subcellular homeostasis of phytohormone auxin is mediated by the ER localized PIN5 transporter. Nature. 459(7250), 1136–1140.","apa":"Mravec, J., Skůpa, P., Bailly, A., Hoyerová, K., Křeček, P., Bielach, A., … Friml, J. (2009). Subcellular homeostasis of phytohormone auxin is mediated by the ER localized PIN5 transporter. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature08066\">https://doi.org/10.1038/nature08066</a>","ieee":"J. Mravec <i>et al.</i>, “Subcellular homeostasis of phytohormone auxin is mediated by the ER localized PIN5 transporter,” <i>Nature</i>, vol. 459, no. 7250. Nature Publishing Group, pp. 1136–1140, 2009.","mla":"Mravec, Jozef, et al. “Subcellular Homeostasis of Phytohormone Auxin Is Mediated by the ER Localized PIN5 Transporter.” <i>Nature</i>, vol. 459, no. 7250, Nature Publishing Group, 2009, pp. 1136–40, doi:<a href=\"https://doi.org/10.1038/nature08066\">10.1038/nature08066</a>.","chicago":"Mravec, Jozef, Petr Skůpa, Aurélien Bailly, Klára Hoyerová, Pavel Křeček, Agnieszka Bielach, Jan Petrášek, et al. “Subcellular Homeostasis of Phytohormone Auxin Is Mediated by the ER Localized PIN5 Transporter.” <i>Nature</i>. Nature Publishing Group, 2009. <a href=\"https://doi.org/10.1038/nature08066\">https://doi.org/10.1038/nature08066</a>."},"publisher":"Nature Publishing Group","_id":"3058","abstract":[{"lang":"eng","text":"The plant signalling molecule auxin provides positional informa-tion in a variety of developmental processes by means of its differential distribution (gradients) within plant tissues. Thus, cellular auxin levels often determine the developmental output of auxin signalling. Conceptually, transmembrane transport and metabolic processes regulate the steady-state levels of auxin in any given cell2,3. In particular, PIN auxin-efflux-carrier-mediated, directional transport between cells is crucial for generating auxin gradients2,4,5. Here we show that Arabidopsis thaliana PIN5, an atypical member of the PIN gene family, encodes a functional auxin transporter that is required for auxin-mediated develop-ment. PIN5 does not have a direct role in cell-to-cell transport but regulates intracellular auxin homeostasis and metabolism. PIN5 localizes, unlike other characterized plasma membrane PIN proteins, to endoplasmic reticulum (ER), presumably medi-ating auxin flow from the cytosol to the lumen of the ER. The ER localization of other PIN5-like transporters (including the moss PIN) indicates that the diversification of PIN protein functions in mediating auxin homeostasis at the ER, and cell-to-cell auxin transport at the plasma membrane, represent an ancient event during the evolution of land plants."}],"publication_status":"published","month":"06","intvolume":"       459","volume":459,"date_created":"2018-12-11T12:01:07Z","date_published":"2009-06-25T00:00:00Z","quality_controlled":0,"date_updated":"2021-01-12T07:40:45Z","extern":1,"issue":"7250","page":"1136 - 1140"},{"date_updated":"2021-01-12T07:40:45Z","extern":1,"page":"3839 - 3849","issue":"12","intvolume":"        21","volume":21,"quality_controlled":0,"date_published":"2009-12-01T00:00:00Z","date_created":"2018-12-11T12:01:07Z","_id":"3059","month":"12","abstract":[{"lang":"eng","text":"The phytohormone auxin plays a major role in embryonic and postembryonic plant development. The temporal and spatial distribution of auxin largely depends on the subcellular polar localization of members of the PIN-FORMED (PIN) auxin efflux carrier family. The Ser/Thr protein kinase PINOID (PID) catalyzes PIN phosphorylation and crucially contributes to the regulation of apical-basal PIN polarity. The GTP exchange factor on ADP-ribosylation factors (ARF-GEF), GNOM preferentially mediates PIN recycling at the basal side of the cell. Interference with GNOM activity leads to dynamic PIN transcytosis between different sides of the cell. Our genetic, pharmacological, and cell biological approaches illustrate that PID and GNOM influence PIN polarity and plant development in an antagonistic manner and that the PID-dependent PIN phosphorylation results in GNOM-independent polar PIN targeting. The data suggest that PID and the protein phosphatase 2A not only regulate the static PIN polarity, but also act antagonistically on the rate of GNOM-dependent polar PIN transcytosis. We propose a model that includes PID-dependent PIN phosphorylation at the plasma membrane and the subsequent sorting of PIN proteins to a GNOM-independent pathway for polarity alterations during developmental processes, such as lateral root formation and leaf vasculature development."}],"publication_status":"published","title":"PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis","year":"2009","status":"public","publication":"Plant Cell","citation":{"ista":"Kleine Vehn J, Huang F, Naramoto S, Zhang J, Michniewicz M, Offringa R, Friml J. 2009. PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis. Plant Cell. 21(12), 3839–3849.","ama":"Kleine Vehn J, Huang F, Naramoto S, et al. PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis. <i>Plant Cell</i>. 2009;21(12):3839-3849. doi:<a href=\"https://doi.org/10.1105/tpc.109.071639\">10.1105/tpc.109.071639</a>","short":"J. Kleine Vehn, F. Huang, S. Naramoto, J. Zhang, M. Michniewicz, R. Offringa, J. Friml, Plant Cell 21 (2009) 3839–3849.","chicago":"Kleine Vehn, Jürgen, Fang Huang, Satoshi Naramoto, Jing Zhang, Marta Michniewicz, Remko Offringa, and Jiří Friml. “PIN Auxin Efflux Carrier Polarity Is Regulated by PINOID Kinase Mediated Recruitment into GNOM Independent Trafficking in Arabidopsis.” <i>Plant Cell</i>. American Society of Plant Biologists, 2009. <a href=\"https://doi.org/10.1105/tpc.109.071639\">https://doi.org/10.1105/tpc.109.071639</a>.","mla":"Kleine Vehn, Jürgen, et al. “PIN Auxin Efflux Carrier Polarity Is Regulated by PINOID Kinase Mediated Recruitment into GNOM Independent Trafficking in Arabidopsis.” <i>Plant Cell</i>, vol. 21, no. 12, American Society of Plant Biologists, 2009, pp. 3839–49, doi:<a href=\"https://doi.org/10.1105/tpc.109.071639\">10.1105/tpc.109.071639</a>.","apa":"Kleine Vehn, J., Huang, F., Naramoto, S., Zhang, J., Michniewicz, M., Offringa, R., &#38; Friml, J. (2009). PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.109.071639\">https://doi.org/10.1105/tpc.109.071639</a>","ieee":"J. Kleine Vehn <i>et al.</i>, “PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis,” <i>Plant Cell</i>, vol. 21, no. 12. American Society of Plant Biologists, pp. 3839–3849, 2009."},"doi":"10.1105/tpc.109.071639","publisher":"American Society of Plant Biologists","publist_id":"3643","day":"01","type":"journal_article","author":[{"last_name":"Kleine Vehn","first_name":"Jürgen","full_name":"Kleine-Vehn, Jürgen"},{"last_name":"Huang","first_name":"Fang","full_name":"Huang, Fang"},{"full_name":"Naramoto, Satoshi","last_name":"Naramoto","first_name":"Satoshi"},{"full_name":"Zhang, Jing","first_name":"Jing","last_name":"Zhang"},{"full_name":"Michniewicz, Marta","last_name":"Michniewicz","first_name":"Marta"},{"full_name":"Offringa, Remko","first_name":"Remko","last_name":"Offringa"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"}]},{"doi":"10.1016/j.pbi.2009.10.009","citation":{"short":"K. Schumacher, J. Friml, Current Opinion in Plant Biology 12 (2009) 651–652.","ista":"Schumacher K, Friml J. 2009. Cell biology. Current Opinion in Plant Biology. 12(6), 651–652.","ama":"Schumacher K, Friml J. Cell biology. <i>Current Opinion in Plant Biology</i>. 2009;12(6):651-652. doi:<a href=\"https://doi.org/10.1016/j.pbi.2009.10.009\">10.1016/j.pbi.2009.10.009</a>","mla":"Schumacher, Karin, and Jiří Friml. “Cell Biology.” <i>Current Opinion in Plant Biology</i>, vol. 12, no. 6, Elsevier, 2009, pp. 651–52, doi:<a href=\"https://doi.org/10.1016/j.pbi.2009.10.009\">10.1016/j.pbi.2009.10.009</a>.","chicago":"Schumacher, Karin, and Jiří Friml. “Cell Biology.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.pbi.2009.10.009\">https://doi.org/10.1016/j.pbi.2009.10.009</a>.","apa":"Schumacher, K., &#38; Friml, J. (2009). Cell biology. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2009.10.009\">https://doi.org/10.1016/j.pbi.2009.10.009</a>","ieee":"K. Schumacher and J. Friml, “Cell biology,” <i>Current Opinion in Plant Biology</i>, vol. 12, no. 6. Elsevier, pp. 651–652, 2009."},"publisher":"Elsevier","title":"Cell biology","publication":"Current Opinion in Plant Biology","status":"public","year":"2009","oa_version":"None","publist_id":"3641","type":"journal_article","day":"01","author":[{"first_name":"Karin","last_name":"Schumacher","full_name":"Schumacher, Karin"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"}],"extern":"1","page":"651 - 652","issue":"6","article_type":"letter_note","date_updated":"2021-01-12T07:40:46Z","quality_controlled":"1","date_published":"2009-12-01T00:00:00Z","date_created":"2018-12-11T12:01:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":12,"language":[{"iso":"eng"}],"intvolume":"        12","month":"12","publication_status":"published","_id":"3060"},{"author":[{"full_name":"Křeček, Pavel","last_name":"Křeček","first_name":"Pavel"},{"full_name":"Skůpa, Petr","first_name":"Petr","last_name":"Skůpa"},{"first_name":"Jiří","last_name":"Libus","full_name":"Libus, Jiří"},{"full_name":"Naramoto, Satoshi","first_name":"Satoshi","last_name":"Naramoto"},{"first_name":"Ricardo","last_name":"Tejos","full_name":"Tejos, Ricardo"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"},{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812941/"}],"type":"journal_article","day":"29","oa_version":"Published Version","oa":1,"publist_id":"3640","publisher":"BioMed Central","doi":"10.1186/gb-2009-10-12-249","citation":{"ama":"Křeček P, Skůpa P, Libus J, et al. The PIN-FORMED (PIN) protein family of auxin transporters. <i>Genome Biology</i>. 2009;10(12). doi:<a href=\"https://doi.org/10.1186/gb-2009-10-12-249\">10.1186/gb-2009-10-12-249</a>","ista":"Křeček P, Skůpa P, Libus J, Naramoto S, Tejos R, Friml J, Zažímalová E. 2009. The PIN-FORMED (PIN) protein family of auxin transporters. Genome Biology. 10(12).","short":"P. Křeček, P. Skůpa, J. Libus, S. Naramoto, R. Tejos, J. Friml, E. Zažímalová, Genome Biology 10 (2009).","chicago":"Křeček, Pavel, Petr Skůpa, Jiří Libus, Satoshi Naramoto, Ricardo Tejos, Jiří Friml, and Eva Zažímalová. “The PIN-FORMED (PIN) Protein Family of Auxin Transporters.” <i>Genome Biology</i>. BioMed Central, 2009. <a href=\"https://doi.org/10.1186/gb-2009-10-12-249\">https://doi.org/10.1186/gb-2009-10-12-249</a>.","mla":"Křeček, Pavel, et al. “The PIN-FORMED (PIN) Protein Family of Auxin Transporters.” <i>Genome Biology</i>, vol. 10, no. 12, BioMed Central, 2009, doi:<a href=\"https://doi.org/10.1186/gb-2009-10-12-249\">10.1186/gb-2009-10-12-249</a>.","ieee":"P. Křeček <i>et al.</i>, “The PIN-FORMED (PIN) protein family of auxin transporters,” <i>Genome Biology</i>, vol. 10, no. 12. BioMed Central, 2009.","apa":"Křeček, P., Skůpa, P., Libus, J., Naramoto, S., Tejos, R., Friml, J., &#38; Zažímalová, E. (2009). The PIN-FORMED (PIN) protein family of auxin transporters. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/gb-2009-10-12-249\">https://doi.org/10.1186/gb-2009-10-12-249</a>"},"status":"public","publication":"Genome Biology","title":"The PIN-FORMED (PIN) protein family of auxin transporters","year":"2009","abstract":[{"text":"The PIN-FORMED (PIN) proteins are secondary transporters acting in the efflux of the plant signal molecule auxin from cells. They are asymmetrically localized within cells and their polarity determines the directionality of intercellular auxin flow. PIN genes are found exclusively in the genomes of multicellular plants and play an important role in regulating asymmetric auxin distribution in multiple developmental processes, including embryogenesis, organogenesis, tissue differentiation and tropic responses. All PIN proteins have a similar structure with amino- and carboxy-terminal hydrophobic, membrane-spanning domains separated by a central hydrophilic domain. The structure of the hydrophobic domains is well conserved. The hydrophilic domain is more divergent and it determines eight groups within the protein family. The activity of PIN proteins is regulated at multiple levels, including transcription, protein stability, subcellular localization and transport activity. Different endogenous and environmental signals can modulate PIN activity and thus modulate auxin-distribution-dependent development. A large group of PIN proteins, including the most ancient members known from mosses, localize to the endoplasmic reticulum and they regulate the subcellular compartmentalization of auxin and thus auxin metabolism. Further work is needed to establish the physiological importance of this unexpected mode of auxin homeostasis regulation. Furthermore, the evolution of PIN-based transport, PIN protein structure and more detailed biochemical characterization of the transport function are important topics for further studies.","lang":"eng"}],"publication_status":"published","month":"12","_id":"3061","date_created":"2018-12-11T12:01:08Z","date_published":"2009-12-29T00:00:00Z","quality_controlled":"1","intvolume":"        10","volume":10,"language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","pmid":1,"issue":"12","extern":"1","date_updated":"2021-01-12T07:40:46Z","external_id":{"pmid":["20053306"]}},{"oa":1,"publist_id":"3484","title":"An analysis of convex relaxations for MAP estimation of discrete MRFs","status":"public","year":"2009","publication":"Journal of Machine Learning Research","citation":{"apa":"Kumar, M. P., Kolmogorov, V., &#38; Torr, P. (2009). An analysis of convex relaxations for MAP estimation of discrete MRFs. <i>Journal of Machine Learning Research</i>. Microtome Publishing.","ieee":"M. P. Kumar, V. Kolmogorov, and P. Torr, “An analysis of convex relaxations for MAP estimation of discrete MRFs,” <i>Journal of Machine Learning Research</i>, vol. 10. Microtome Publishing, pp. 71–106, 2009.","chicago":"Kumar, M Pawan, Vladimir Kolmogorov, and Philip Torr. “An Analysis of Convex Relaxations for MAP Estimation of Discrete MRFs.” <i>Journal of Machine Learning Research</i>. Microtome Publishing, 2009.","mla":"Kumar, M. Pawan, et al. “An Analysis of Convex Relaxations for MAP Estimation of Discrete MRFs.” <i>Journal of Machine Learning Research</i>, vol. 10, Microtome Publishing, 2009, pp. 71–106.","ista":"Kumar MP, Kolmogorov V, Torr P. 2009. An analysis of convex relaxations for MAP estimation of discrete MRFs. Journal of Machine Learning Research. 10, 71–106.","ama":"Kumar MP, Kolmogorov V, Torr P. An analysis of convex relaxations for MAP estimation of discrete MRFs. <i>Journal of Machine Learning Research</i>. 2009;10:71-106.","short":"M.P. Kumar, V. Kolmogorov, P. Torr, Journal of Machine Learning Research 10 (2009) 71–106."},"publisher":"Microtome Publishing","main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-00773608"}],"author":[{"last_name":"Kumar","first_name":"M Pawan","full_name":"Kumar, M Pawan"},{"full_name":"Vladimir Kolmogorov","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Torr","first_name":"Philip","full_name":"Torr, Philip H"}],"day":"01","type":"journal_article","volume":10,"intvolume":"        10","date_published":"2009-01-01T00:00:00Z","date_created":"2018-12-11T12:01:57Z","quality_controlled":0,"date_updated":"2021-01-12T07:41:44Z","page":"71 - 106","extern":1,"_id":"3197","month":"01","abstract":[{"lang":"eng","text":"The problem of obtaining the maximum a posteriori estimate of a general discrete Markov random field (i.e., a Markov random field defined using a discrete set of labels) is known to be NP-hard. However, due to its central importance in many applications, several approximation algorithms have been proposed in the literature. In this paper, we present an analysis of three such algorithms based on convex relaxations: (i) LP-S: the linear programming (LP) relaxation proposed by Schlesinger (1976) for a special case and independently in Chekuri et al. (2001), Koster et al. (1998), and Wainwright et al. (2005) for the general case; (ii) QP-RL: the quadratic programming (QP) relaxation of Ravikumar and Lafferty (2006); and (iii) SOCP-MS: the second order cone programming (SOCP) relaxation first proposed by Muramatsu and Suzuki (2003) for two label problems and later extended by Kumar et al. (2006) for a general label set.\n\nWe show that the SOCP-MS and the QP-RL relaxations are equivalent. Furthermore, we prove that despite the flexibility in the form of the constraints/objective function offered by QP and SOCP, the LP-S relaxation strictly dominates (i.e., provides a better approximation than) QP-RL and SOCP-MS. We generalize these results by defining a large class of SOCP (and equivalent QP) relaxations which is dominated by the LP-S relaxation. Based on these results we propose some novel SOCP relaxations which define constraints using random variables that form cycles or cliques in the graphical model representation of the random field. Using some examples we show that the new SOCP relaxations strictly dominate the previous approaches."}],"publication_status":"published"},{"publist_id":"3482","title":"Joint optimization of segmentation and appearance models","year":"2009","status":"public","citation":{"ieee":"S. Vicente, V. Kolmogorov, and C. Rother, “Joint optimization of segmentation and appearance models,” presented at the ICCV: International Conference on Computer Vision, 2009, pp. 755–762.","apa":"Vicente, S., Kolmogorov, V., &#38; Rother, C. (2009). Joint optimization of segmentation and appearance models (pp. 755–762). Presented at the ICCV: International Conference on Computer Vision, IEEE. <a href=\"https://doi.org/10.1109/ICCV.2009.5459287\">https://doi.org/10.1109/ICCV.2009.5459287</a>","chicago":"Vicente, Sara, Vladimir Kolmogorov, and Carsten Rother. “Joint Optimization of Segmentation and Appearance Models,” 755–62. IEEE, 2009. <a href=\"https://doi.org/10.1109/ICCV.2009.5459287\">https://doi.org/10.1109/ICCV.2009.5459287</a>.","mla":"Vicente, Sara, et al. <i>Joint Optimization of Segmentation and Appearance Models</i>. IEEE, 2009, pp. 755–62, doi:<a href=\"https://doi.org/10.1109/ICCV.2009.5459287\">10.1109/ICCV.2009.5459287</a>.","ama":"Vicente S, Kolmogorov V, Rother C. Joint optimization of segmentation and appearance models. In: IEEE; 2009:755-762. doi:<a href=\"https://doi.org/10.1109/ICCV.2009.5459287\">10.1109/ICCV.2009.5459287</a>","ista":"Vicente S, Kolmogorov V, Rother C. 2009. Joint optimization of segmentation and appearance models. ICCV: International Conference on Computer Vision, 755–762.","short":"S. Vicente, V. Kolmogorov, C. Rother, in:, IEEE, 2009, pp. 755–762."},"doi":"10.1109/ICCV.2009.5459287","publisher":"IEEE","main_file_link":[{"open_access":"0","url":"http://www.robots.ox.ac.uk/~vgg/rg/papers/segmentationappearance.pdf"}],"author":[{"full_name":"Vicente, Sara","last_name":"Vicente","first_name":"Sara"},{"full_name":"Vladimir Kolmogorov","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carsten","last_name":"Rother","full_name":"Rother, Carsten"}],"day":"01","conference":{"name":"ICCV: International Conference on Computer Vision"},"type":"conference","date_published":"2009-05-01T00:00:00Z","date_created":"2018-12-11T12:01:58Z","quality_controlled":0,"date_updated":"2021-01-12T07:41:44Z","extern":1,"page":"755 - 762","_id":"3199","abstract":[{"lang":"eng","text":"Many interactive image segmentation approaches use an objective function which includes appearance models as an unknown variable. Since the resulting optimization problem is NP-hard the segmentation and appearance are typically optimized separately, in an EM-style fashion. One contribution of this paper is to express the objective function purely in terms of the unknown segmentation, using higher-order cliques. This formulation reveals an interesting bias of the model towards balanced segmentations. Furthermore, it enables us to develop a new dual decomposition optimization procedure, which provides additionally a lower bound. Hence, we are able to improve on existing optimizers, and verify that for a considerable number of real world examples we even achieve global optimality. This is important since we are able, for the first time, to analyze the deficiencies of the model. Another contribution is to establish a property of a particular dual decomposition approach which involves convex functions depending on foreground area. As a consequence, we show that the optimal decomposition for our problem can be computed efficiently via a parametric maxflow algorithm."}],"month":"05","publication_status":"published"},{"date_updated":"2021-01-12T07:41:45Z","page":"378 - 393","issue":"4","extern":1,"volume":6,"intvolume":"         6","quality_controlled":0,"date_created":"2018-12-11T12:01:58Z","date_published":"2009-11-01T00:00:00Z","_id":"3200","publication_status":"published","abstract":[{"text":"Motivated by various applications to computer vision, we consider the convex cost tension problem, which is the dual of the convex cost flow problem. In this paper, we first propose a primal algorithm for computing an optimal solution of the problem. Our primal algorithm iteratively updates primal variables by solving associated minimum cut problems. We show that the time complexity of the primal algorithm is O (K {dot operator} T (n, m)), where K is the range of primal variables and T (n, m) is the time needed to compute a minimum cut in a graph with n nodes and m edges. We then develop an improved version of the primal algorithm, called the primal-dual algorithm, by making good use of dual variables in addition to primal variables. Although its time complexity is the same as that of the primal algorithm, we can expect a better performance in practice. We finally consider an application to a computer vision problem called the panoramic image stitching.","lang":"eng"}],"month":"11","year":"2009","publication":"Discrete Optimization","title":"New algorithms for convex cost tension problem with application to computer vision","status":"public","citation":{"ista":"Kolmogorov V, Shioura A. 2009. New algorithms for convex cost tension problem with application to computer vision. Discrete Optimization. 6(4), 378–393.","ama":"Kolmogorov V, Shioura A. New algorithms for convex cost tension problem with application to computer vision. <i>Discrete Optimization</i>. 2009;6(4):378-393. doi:<a href=\"https://doi.org/10.1016/j.disopt.2009.04.006\">10.1016/j.disopt.2009.04.006</a>","short":"V. Kolmogorov, A. Shioura, Discrete Optimization 6 (2009) 378–393.","chicago":"Kolmogorov, Vladimir, and Akiyoshi Shioura. “New Algorithms for Convex Cost Tension Problem with Application to Computer Vision.” <i>Discrete Optimization</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.disopt.2009.04.006\">https://doi.org/10.1016/j.disopt.2009.04.006</a>.","mla":"Kolmogorov, Vladimir, and Akiyoshi Shioura. “New Algorithms for Convex Cost Tension Problem with Application to Computer Vision.” <i>Discrete Optimization</i>, vol. 6, no. 4, Elsevier, 2009, pp. 378–93, doi:<a href=\"https://doi.org/10.1016/j.disopt.2009.04.006\">10.1016/j.disopt.2009.04.006</a>.","ieee":"V. Kolmogorov and A. Shioura, “New algorithms for convex cost tension problem with application to computer vision,” <i>Discrete Optimization</i>, vol. 6, no. 4. Elsevier, pp. 378–393, 2009.","apa":"Kolmogorov, V., &#38; Shioura, A. (2009). New algorithms for convex cost tension problem with application to computer vision. <i>Discrete Optimization</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.disopt.2009.04.006\">https://doi.org/10.1016/j.disopt.2009.04.006</a>"},"doi":"10.1016/j.disopt.2009.04.006","publisher":"Elsevier","publist_id":"3483","day":"01","type":"journal_article","author":[{"last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Vladimir Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Shioura","first_name":"Akiyoshi","full_name":"Shioura, Akiyoshi"}]}]