[{"type":"journal_article","status":"public","_id":"2970","publist_id":"3739","author":[{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias"},{"full_name":"Wartlick, Ortrud","last_name":"Wartlick","first_name":"Ortrud"},{"last_name":"Julicher","full_name":"Julicher, Frank","first_name":"Frank"},{"first_name":"Marcos","full_name":"Gonzalez Gaitan, Marcos","last_name":"Gonzalez Gaitan"}],"title":"Investigating the principles of morphogen gradient formation: from tissues to cells","department":[{"_id":"ToBo"}],"date_updated":"2021-01-12T07:40:09Z","citation":{"apa":"Kicheva, A., Bollenbach, M. T., Wartlick, O., Julicher, F., & Gonzalez Gaitan, M. (2012). Investigating the principles of morphogen gradient formation: from tissues to cells. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2012.08.004","ama":"Kicheva A, Bollenbach MT, Wartlick O, Julicher F, Gonzalez Gaitan M. Investigating the principles of morphogen gradient formation: from tissues to cells. Current Opinion in Genetics & Development. 2012;22(6):527-532. doi:10.1016/j.gde.2012.08.004","short":"A. Kicheva, M.T. Bollenbach, O. Wartlick, F. Julicher, M. Gonzalez Gaitan, Current Opinion in Genetics & Development 22 (2012) 527–532.","ieee":"A. Kicheva, M. T. Bollenbach, O. Wartlick, F. Julicher, and M. Gonzalez Gaitan, “Investigating the principles of morphogen gradient formation: from tissues to cells,” Current Opinion in Genetics & Development, vol. 22, no. 6. Elsevier, pp. 527–532, 2012.","mla":"Kicheva, Anna, et al. “Investigating the Principles of Morphogen Gradient Formation: From Tissues to Cells.” Current Opinion in Genetics & Development, vol. 22, no. 6, Elsevier, 2012, pp. 527–32, doi:10.1016/j.gde.2012.08.004.","ista":"Kicheva A, Bollenbach MT, Wartlick O, Julicher F, Gonzalez Gaitan M. 2012. Investigating the principles of morphogen gradient formation: from tissues to cells. Current Opinion in Genetics & Development. 22(6), 527–532.","chicago":"Kicheva, Anna, Mark Tobias Bollenbach, Ortrud Wartlick, Frank Julicher, and Marcos Gonzalez Gaitan. “Investigating the Principles of Morphogen Gradient Formation: From Tissues to Cells.” Current Opinion in Genetics & Development. Elsevier, 2012. https://doi.org/10.1016/j.gde.2012.08.004."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","quality_controlled":"1","scopus_import":1,"month":"12","intvolume":" 22","abstract":[{"lang":"eng","text":"Morphogen gradients regulate the patterning and growth of many tissues, hence a key question is how they are established and maintained during development. Theoretical descriptions have helped to explain how gradient shape is controlled by the rates of morphogen production, spreading and degradation. These effective rates have been measured using fluorescence recovery after photobleaching (FRAP) and photoactivation. To unravel which molecular events determine the effective rates, such tissue-level assays have been combined with genetic analysis, high-resolution assays, and models that take into account interactions with receptors, extracellular components and trafficking. Nevertheless, because of the natural and experimental data variability, and the underlying assumptions of transport models, it remains challenging to conclusively distinguish between cellular mechanisms."}],"oa_version":"None","acknowledgement":"AK is currently supported by an MRC CDF. MGG and OW were supported by the Swiss National Science Foundation, grants from the Swiss SystemsX.ch initiative, LipidX-2008/011, an ERC advanced investigator grant and the Polish-Swiss research program.","page":"527 - 532","issue":"6","date_published":"2012-12-01T00:00:00Z","volume":22,"doi":"10.1016/j.gde.2012.08.004","date_created":"2018-12-11T12:00:37Z","year":"2012","publication_status":"published","day":"01","language":[{"iso":"eng"}],"publication":"Current Opinion in Genetics & Development"},{"status":"public","type":"conference","conference":{"location":"Graz, Austria","end_date":"2012-08-31","start_date":"2012-08-28","name":"Pattern Recognition"},"_id":"2971","department":[{"_id":"HeEd"}],"title":"Interactive labeling of image segmentation hierarchies","author":[{"last_name":"Zankl","full_name":"Zankl, Georg","first_name":"Georg"},{"first_name":"Yll","full_name":"Haxhimusa, Yll","last_name":"Haxhimusa"},{"last_name":"Ion","full_name":"Ion, Adrian","id":"29F89302-F248-11E8-B48F-1D18A9856A87","first_name":"Adrian"}],"publist_id":"3737","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Zankl G, Haxhimusa Y, Ion A. 2012. Interactive labeling of image segmentation hierarchies. Pattern Recognition vol. 7476, 11–20.","chicago":"Zankl, Georg, Yll Haxhimusa, and Adrian Ion. “Interactive Labeling of Image Segmentation Hierarchies,” 7476:11–20. Springer, 2012. https://doi.org/10.1007/978-3-642-32717-9_2.","ieee":"G. Zankl, Y. Haxhimusa, and A. Ion, “Interactive labeling of image segmentation hierarchies,” presented at the Pattern Recognition, Graz, Austria, 2012, vol. 7476, pp. 11–20.","short":"G. Zankl, Y. Haxhimusa, A. Ion, in:, Springer, 2012, pp. 11–20.","ama":"Zankl G, Haxhimusa Y, Ion A. Interactive labeling of image segmentation hierarchies. In: Vol 7476. Springer; 2012:11-20. doi:10.1007/978-3-642-32717-9_2","apa":"Zankl, G., Haxhimusa, Y., & Ion, A. (2012). Interactive labeling of image segmentation hierarchies (Vol. 7476, pp. 11–20). Presented at the Pattern Recognition, Graz, Austria: Springer. https://doi.org/10.1007/978-3-642-32717-9_2","mla":"Zankl, Georg, et al. Interactive Labeling of Image Segmentation Hierarchies. Vol. 7476, Springer, 2012, pp. 11–20, doi:10.1007/978-3-642-32717-9_2."},"date_updated":"2021-01-12T07:40:10Z","month":"01","intvolume":" 7476","quality_controlled":"1","scopus_import":1,"publisher":"Springer","oa_version":"None","abstract":[{"text":"We study the task of interactive semantic labeling of a segmentation hierarchy. To this end we propose a framework interleaving two components: an automatic labeling step, based on a Conditional Random Field whose dependencies are defined by the inclusion tree of the segmentation hierarchy, and an interaction step that integrates incremental input from a human user. Evaluated on two distinct datasets, the proposed interactive approach efficiently integrates human interventions and illustrates the advantages of structured prediction in an interactive framework. ","lang":"eng"}],"volume":7476,"date_published":"2012-01-01T00:00:00Z","doi":"10.1007/978-3-642-32717-9_2","date_created":"2018-12-11T12:00:37Z","page":"11 - 20","day":"01","language":[{"iso":"eng"}],"year":"2012","publication_status":"published"},{"type":"journal_article","status":"public","_id":"3105","author":[{"first_name":"Ryan","full_name":"Whitford, Ryan","last_name":"Whitford"},{"full_name":"Fernandez, Ana","last_name":"Fernandez","first_name":"Ana"},{"first_name":"Ricardo","full_name":"Tejos, Ricardo","last_name":"Tejos"},{"first_name":"Amparo","full_name":"Pérez, Amparo Cuéllar","last_name":"Pérez"},{"first_name":"Jürgen","full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"first_name":"Andrzej","last_name":"Drozdzecki","full_name":"Drozdzecki, Andrzej"},{"first_name":"Johannes","last_name":"Leitner","full_name":"Leitner, Johannes"},{"first_name":"Lindy","full_name":"Abas, Lindy","last_name":"Abas"},{"first_name":"Maarten","last_name":"Aerts","full_name":"Aerts, Maarten"},{"first_name":"Kurt","last_name":"Hoogewijs","full_name":"Hoogewijs, Kurt"},{"first_name":"Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","full_name":"Pawel Baster","last_name":"Baster"},{"full_name":"De Groodt, Ruth","last_name":"De Groodt","first_name":"Ruth"},{"first_name":"Yao","last_name":"Lin","full_name":"Lin, Yao-Cheng"},{"first_name":"Véronique","last_name":"Storme","full_name":"Storme, Véronique"},{"first_name":"Yves","full_name":"Van de Peer, Yves","last_name":"Van De Peer"},{"last_name":"Beeckman","full_name":"Beeckman, Tom","first_name":"Tom"},{"first_name":"Annemieke","last_name":"Madder","full_name":"Madder, Annemieke"},{"last_name":"Devreese","full_name":"Devreese, Bart","first_name":"Bart"},{"full_name":"Luschnig, Christian","last_name":"Luschnig","first_name":"Christian"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","last_name":"Friml"},{"first_name":"Pierre","last_name":"Hilson","full_name":"Hilson, Pierre"}],"publist_id":"3594","title":"GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses","date_updated":"2021-01-12T07:41:06Z","citation":{"apa":"Whitford, R., Fernandez, A., Tejos, R., Pérez, A., Kleine Vehn, J., Vanneste, S., … Hilson, P. (2012). GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2012.02.002","ama":"Whitford R, Fernandez A, Tejos R, et al. GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. Developmental Cell. 2012;22(3):678-685. doi:10.1016/j.devcel.2012.02.002","ieee":"R. Whitford et al., “GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses,” Developmental Cell, vol. 22, no. 3. Cell Press, pp. 678–685, 2012.","short":"R. Whitford, A. Fernandez, R. Tejos, A. Pérez, J. Kleine Vehn, S. Vanneste, A. Drozdzecki, J. Leitner, L. Abas, M. Aerts, K. Hoogewijs, P. Baster, R. De Groodt, Y. Lin, V. Storme, Y. Van De Peer, T. Beeckman, A. Madder, B. Devreese, C. Luschnig, J. Friml, P. Hilson, Developmental Cell 22 (2012) 678–685.","mla":"Whitford, Ryan, et al. “GOLVEN Secretory Peptides Regulate Auxin Carrier Turnover during Plant Gravitropic Responses.” Developmental Cell, vol. 22, no. 3, Cell Press, 2012, pp. 678–85, doi:10.1016/j.devcel.2012.02.002.","ista":"Whitford R, Fernandez A, Tejos R, Pérez A, Kleine Vehn J, Vanneste S, Drozdzecki A, Leitner J, Abas L, Aerts M, Hoogewijs K, Baster P, De Groodt R, Lin Y, Storme V, Van De Peer Y, Beeckman T, Madder A, Devreese B, Luschnig C, Friml J, Hilson P. 2012. GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. Developmental Cell. 22(3), 678–685.","chicago":"Whitford, Ryan, Ana Fernandez, Ricardo Tejos, Amparo Pérez, Jürgen Kleine Vehn, Steffen Vanneste, Andrzej Drozdzecki, et al. “GOLVEN Secretory Peptides Regulate Auxin Carrier Turnover during Plant Gravitropic Responses.” Developmental Cell. Cell Press, 2012. https://doi.org/10.1016/j.devcel.2012.02.002."},"extern":1,"quality_controlled":0,"publisher":"Cell Press","intvolume":" 22","month":"03","abstract":[{"text":"Growth and development are coordinated by an array of intercellular communications. Known plant signaling molecules include phytohormones and hormone peptides. Although both classes can be implicated in the same developmental processes, little is known about the interplay between phytohormone action and peptide signaling within the cellular microenvironment. We show that genes coding for small secretory peptides, designated GOLVEN (GLV), modulate the distribution of the phytohormone auxin. The deregulation of the GLV function impairs the formation of auxin gradients and alters the reorientation of shoots and roots after a gravity stimulus. Specifically, the GLV signal modulates the trafficking dynamics of the auxin efflux carrier PIN-FORMED2 involved in root tropic responses and meristem organization. Our work links the local action of secretory peptides with phytohormone transport. Root growth factor (RGF) or GOLVEN (GLV) secreted peptides have previously been implicated in meristem regulation. Whitford et al. now show that RGF/GLV peptides induce rapid relocalization of the auxin efflux regulator PIN2, regulate auxin gradients, and modulate auxin-dependent root responses to specific stimuli.","lang":"eng"}],"page":"678 - 685","date_created":"2018-12-11T12:01:25Z","volume":22,"doi":"10.1016/j.devcel.2012.02.002","issue":"3","date_published":"2012-03-13T00:00:00Z","publication_status":"published","year":"2012","publication":"Developmental Cell","day":"13"},{"_id":"3109","type":"journal_article","status":"public","date_updated":"2021-01-12T07:41:07Z","citation":{"ista":"Irani N, Di Rubbo S, Mylle E, Van Den Begin J, Schneider Pizoń J, Hniliková J, Šíša M, Buyst D, Vilarrasa Blasi J, Szatmári A, Van Damme D, Mishev K, Codreanu M, Kohout L, Strnad M, Caño Delgado A, Friml J, Madder A, Russinova E. 2012. Fluorescent castasterone reveals BRI1 signaling from the plasma membrane. Nature Chemical Biology. 8(6), 583–589.","chicago":"Irani, Niloufer, Simone Di Rubbo, Evelien Mylle, Jos Van Den Begin, Joanna Schneider Pizoń, Jaroslava Hniliková, Miroslav Šíša, et al. “Fluorescent Castasterone Reveals BRI1 Signaling from the Plasma Membrane.” Nature Chemical Biology. Nature Publishing Group, 2012. https://doi.org/10.1038/nchembio.958.","ieee":"N. Irani et al., “Fluorescent castasterone reveals BRI1 signaling from the plasma membrane,” Nature Chemical Biology, vol. 8, no. 6. Nature Publishing Group, pp. 583–589, 2012.","short":"N. Irani, S. Di Rubbo, E. Mylle, J. Van Den Begin, J. Schneider Pizoń, J. Hniliková, M. Šíša, D. Buyst, J. Vilarrasa Blasi, A. Szatmári, D. Van Damme, K. Mishev, M. Codreanu, L. Kohout, M. Strnad, A. Caño Delgado, J. Friml, A. Madder, E. Russinova, Nature Chemical Biology 8 (2012) 583–589.","ama":"Irani N, Di Rubbo S, Mylle E, et al. Fluorescent castasterone reveals BRI1 signaling from the plasma membrane. Nature Chemical Biology. 2012;8(6):583-589. doi:10.1038/nchembio.958","apa":"Irani, N., Di Rubbo, S., Mylle, E., Van Den Begin, J., Schneider Pizoń, J., Hniliková, J., … Russinova, E. (2012). Fluorescent castasterone reveals BRI1 signaling from the plasma membrane. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/nchembio.958","mla":"Irani, Niloufer, et al. “Fluorescent Castasterone Reveals BRI1 Signaling from the Plasma Membrane.” Nature Chemical Biology, vol. 8, no. 6, Nature Publishing Group, 2012, pp. 583–89, doi:10.1038/nchembio.958."},"extern":1,"publist_id":"3590","author":[{"last_name":"Irani","full_name":"Irani, Niloufer G","first_name":"Niloufer"},{"full_name":"Di Rubbo, Simone","last_name":"Di Rubbo","first_name":"Simone"},{"first_name":"Evelien","full_name":"Mylle, Evelien","last_name":"Mylle"},{"first_name":"Jos","full_name":"Van Den Begin, Jos","last_name":"Van Den Begin"},{"first_name":"Joanna","full_name":"Schneider-Pizoń, Joanna","last_name":"Schneider Pizoń"},{"first_name":"Jaroslava","full_name":"Hniliková, Jaroslava","last_name":"Hniliková"},{"last_name":"Šíša","full_name":"Šíša, Miroslav","first_name":"Miroslav"},{"last_name":"Buyst","full_name":"Buyst, Dieter","first_name":"Dieter"},{"first_name":"Josep","last_name":"Vilarrasa Blasi","full_name":"Vilarrasa-Blasi, Josep"},{"first_name":"Anna","last_name":"Szatmári","full_name":"Szatmári, Anna-Maria"},{"full_name":"Van Damme, Daniël","last_name":"Van Damme","first_name":"Daniël"},{"full_name":"Mishev, Kiril","last_name":"Mishev","first_name":"Kiril"},{"last_name":"Codreanu","full_name":"Codreanu, Mirela-Corina","first_name":"Mirela"},{"first_name":"Ladislav","last_name":"Kohout","full_name":"Kohout, Ladislav"},{"full_name":"Strnad, Miroslav","last_name":"Strnad","first_name":"Miroslav"},{"last_name":"Caño Delgado","full_name":"Caño-Delgado, Ana I","first_name":"Ana"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596"},{"last_name":"Madder","full_name":"Madder, Annemieke","first_name":"Annemieke"},{"full_name":"Russinova, Eugenia","last_name":"Russinova","first_name":"Eugenia"}],"title":"Fluorescent castasterone reveals BRI1 signaling from the plasma membrane","abstract":[{"text":"Receptor-mediated endocytosis is an integral part of signal transduction as it mediates signal attenuation and provides spatial and temporal dimensions to signaling events. One of the best-studied leucine-rich repeat receptor-like kinases in plants, BRASSINOSTEROID INSENSITIVE 1 (BRI1), perceives its ligand, the brassinosteroid (BR) hormone, at the cell surface and is constitutively endocytosed. However, the importance of endocytosis for BR signaling remains unclear. Here we developed a bioactive, fluorescent BR analog, Alexa Fluor 647-castasterone (AFCS), and visualized the endocytosis of BRI1-AFCS complexes in living Arabidopsis thaliana cells. Impairment of endocytosis dependent on clathrin and the guanine nucleotide exchange factor for ARF GTPases (ARF-GEF) GNOM enhanced BR signaling by retaining active BRI1-ligand complexes at the plasma membrane. Increasing the trans-Golgi network/early endosome pool of BRI1-BR complexes did not affect BR signaling. Our findings provide what is to our knowledge the first visualization of receptor-ligand complexes in plants and reveal clathrin-and ARF-GEF-dependent endocytic regulation of BR signaling from the plasma membrane.","lang":"eng"}],"publisher":"Nature Publishing Group","quality_controlled":0,"month":"06","intvolume":" 8","publication_status":"published","year":"2012","day":"01","publication":"Nature Chemical Biology","page":"583 - 589","date_published":"2012-06-01T00:00:00Z","issue":"6","volume":8,"doi":"10.1038/nchembio.958","date_created":"2018-12-11T12:01:26Z"},{"publication_status":"published","year":"2012","publication":"PNAS","day":"31","page":"1554 - 1559","date_created":"2018-12-11T12:01:24Z","doi":"10.1073/pnas.1121134109","volume":109,"issue":"5","date_published":"2012-01-31T00:00:00Z","abstract":[{"text":"\nGradients of the plant hormone auxin, which depend on its active intercellular transport, are crucial for the maintenance of root meristematic activity. This directional transport is largely orchestrated by a complex interaction of specific influx and efflux carriers that mediate the auxin flow into and out of cells, respectively. Besides these transport proteins, plant-specific polyphenolic compounds knownasflavonols have beenshownto act as endogenous regulators of auxin transport. However, only limited information is available on how flavonol synthesis is developmentally regulated. Using reduction-of-function and overexpression approaches in parallel, we demonstrate that the WRKY23 transcription factor is needed for proper root growth and development by stimulating the local biosynthesis of flavonols. The expression of WRKY23 itself is controlled by auxin through the AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 transcriptional response pathway. Our results suggest a model in which WRKY23 is part of a transcriptional feedback loop of auxin on its own transport through local regulation of flavonol biosynthesis.","lang":"eng"}],"publisher":"National Academy of Sciences","quality_controlled":0,"intvolume":" 109","month":"01","citation":{"ista":"Grunewald W, De Smet I, Lewis D, Löfke C, Jansen L, Goeminne G, Vanden Bossche R, Karimi M, De Rybel B, Vanholme B, Teichmann T, Boerjan W, Van Montagu M, Gheysen G, Muday G, Friml J, Beeckman T. 2012. Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis. PNAS. 109(5), 1554–1559.","chicago":"Grunewald, Wim, Ive De Smet, Daniel Lewis, Christian Löfke, Leentje Jansen, Geert Goeminne, Robin Vanden Bossche, et al. “Transcription Factor WRKY23 Assists Auxin Distribution Patterns during Arabidopsis Root Development through Local Control on Flavonol Biosynthesis.” PNAS. National Academy of Sciences, 2012. https://doi.org/10.1073/pnas.1121134109.","apa":"Grunewald, W., De Smet, I., Lewis, D., Löfke, C., Jansen, L., Goeminne, G., … Beeckman, T. (2012). Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1121134109","ama":"Grunewald W, De Smet I, Lewis D, et al. Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis. PNAS. 2012;109(5):1554-1559. doi:10.1073/pnas.1121134109","ieee":"W. Grunewald et al., “Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis,” PNAS, vol. 109, no. 5. National Academy of Sciences, pp. 1554–1559, 2012.","short":"W. Grunewald, I. De Smet, D. Lewis, C. Löfke, L. Jansen, G. Goeminne, R. Vanden Bossche, M. Karimi, B. De Rybel, B. Vanholme, T. Teichmann, W. Boerjan, M. Van Montagu, G. Gheysen, G. Muday, J. Friml, T. Beeckman, PNAS 109 (2012) 1554–1559.","mla":"Grunewald, Wim, et al. “Transcription Factor WRKY23 Assists Auxin Distribution Patterns during Arabidopsis Root Development through Local Control on Flavonol Biosynthesis.” PNAS, vol. 109, no. 5, National Academy of Sciences, 2012, pp. 1554–59, doi:10.1073/pnas.1121134109."},"date_updated":"2021-01-12T07:41:05Z","extern":1,"author":[{"first_name":"Wim","full_name":"Grunewald, Wim","last_name":"Grunewald"},{"full_name":"De Smet, Ive","last_name":"De Smet","first_name":"Ive"},{"full_name":"Lewis, Daniel R","last_name":"Lewis","first_name":"Daniel"},{"full_name":"Löfke, Christian","last_name":"Löfke","first_name":"Christian"},{"first_name":"Leentje","full_name":"Jansen, Leentje","last_name":"Jansen"},{"first_name":"Geert","full_name":"Goeminne, Geert","last_name":"Goeminne"},{"first_name":"Robin","last_name":"Vanden Bossche","full_name":"Vanden Bossche, Robin"},{"full_name":"Karimi, Mansour","last_name":"Karimi","first_name":"Mansour"},{"first_name":"Bert","last_name":"De Rybel","full_name":"De Rybel, Bert"},{"first_name":"Bartel","last_name":"Vanholme","full_name":"Vanholme, Bartel"},{"first_name":"Thomas","last_name":"Teichmann","full_name":"Teichmann, Thomas"},{"first_name":"Wout","last_name":"Boerjan","full_name":"Boerjan, Wout"},{"first_name":"Marc","last_name":"Van Montagu","full_name":"Van Montagu, Marc C"},{"full_name":"Gheysen, Godelieve","last_name":"Gheysen","first_name":"Godelieve"},{"first_name":"Gloria","full_name":"Muday, Gloria K","last_name":"Muday"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"last_name":"Beeckman","full_name":"Beeckman, Tom","first_name":"Tom"}],"publist_id":"3595","title":"Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis","_id":"3104","type":"journal_article","status":"public"},{"page":"119 - 122","date_created":"2018-12-11T12:01:26Z","doi":"10.1038/nature11001","date_published":"2012-05-03T00:00:00Z","volume":485,"issue":"7396","publication_status":"published","year":"2012","publication":"Nature","day":"03","quality_controlled":0,"publisher":"Nature Publishing Group","intvolume":" 485","month":"05","abstract":[{"lang":"eng","text":"The phytohormone auxin acts as a prominent signal, providing, by its local accumulation or depletion in selected cells, a spatial and temporal reference for changes in the developmental program. The distribution of auxin depends on both auxin metabolism (biosynthesis, conjugation and degradation) and cellular auxin transport. We identified in silico a novel putative auxin transport facilitator family, called PIN-LIKES (PILS). Here we illustrate that PILS proteins are required for auxin-dependent regulation of plant growth by determining the cellular sensitivity to auxin. PILS proteins regulate intracellular auxin accumulation at the endoplasmic reticulum and thus auxin availability for nuclear auxin signalling. PILS activity affects the level of endogenous auxin indole-3-acetic acid (IAA), presumably via intracellular accumulation and metabolism. Our findings reveal that the transport machinery to compartmentalize auxin within the cell is of an unexpected molecular complexity and demonstrate this compartmentalization to be functionally important for a number of developmental processes."}],"publist_id":"3591","author":[{"first_name":"Elke","last_name":"Barbez","full_name":"Barbez, Elke"},{"last_name":"Kubeš","full_name":"Kubeš, Martin","first_name":"Martin"},{"first_name":"Jakub","full_name":"Rolčík, Jakub","last_name":"Rolčík"},{"last_name":"Béziat","full_name":"Béziat, Chloe","first_name":"Chloe"},{"full_name":"Pěnčík, Aleš","last_name":"Pěnčík","first_name":"Aleš"},{"last_name":"Wang","full_name":"Wang, Bangjun","first_name":"Bangjun"},{"first_name":"Michel","full_name":"Rosquete, Michel Ruiz","last_name":"Rosquete"},{"first_name":"Jinsheng","last_name":"Zhu","full_name":"Zhu, Jinsheng"},{"last_name":"Dobrev","full_name":"Dobrev, Petre I","first_name":"Petre"},{"first_name":"Yuree","full_name":"Lee, Yuree","last_name":"Lee"},{"last_name":"Zašímalová","full_name":"Zašímalová, Eva","first_name":"Eva"},{"last_name":"Petrášek","full_name":"Petrášek, Jan","first_name":"Jan"},{"last_name":"Geisler","full_name":"Geisler, Markus","first_name":"Markus"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml"},{"last_name":"Kleine Vehn","full_name":"Kleine-Vehn, Jürgen","first_name":"Jürgen"}],"title":"A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants","citation":{"ista":"Barbez E, Kubeš M, Rolčík J, Béziat C, Pěnčík A, Wang B, Rosquete M, Zhu J, Dobrev P, Lee Y, Zašímalová E, Petrášek J, Geisler M, Friml J, Kleine Vehn J. 2012. A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature. 485(7396), 119–122.","chicago":"Barbez, Elke, Martin Kubeš, Jakub Rolčík, Chloe Béziat, Aleš Pěnčík, Bangjun Wang, Michel Rosquete, et al. “A Novel Putative Auxin Carrier Family Regulates Intracellular Auxin Homeostasis in Plants.” Nature. Nature Publishing Group, 2012. https://doi.org/10.1038/nature11001.","ama":"Barbez E, Kubeš M, Rolčík J, et al. A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature. 2012;485(7396):119-122. doi:10.1038/nature11001","apa":"Barbez, E., Kubeš, M., Rolčík, J., Béziat, C., Pěnčík, A., Wang, B., … Kleine Vehn, J. (2012). A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11001","ieee":"E. Barbez et al., “A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants,” Nature, vol. 485, no. 7396. Nature Publishing Group, pp. 119–122, 2012.","short":"E. Barbez, M. Kubeš, J. Rolčík, C. Béziat, A. Pěnčík, B. Wang, M. Rosquete, J. Zhu, P. Dobrev, Y. Lee, E. Zašímalová, J. Petrášek, M. Geisler, J. Friml, J. Kleine Vehn, Nature 485 (2012) 119–122.","mla":"Barbez, Elke, et al. “A Novel Putative Auxin Carrier Family Regulates Intracellular Auxin Homeostasis in Plants.” Nature, vol. 485, no. 7396, Nature Publishing Group, 2012, pp. 119–22, doi:10.1038/nature11001."},"date_updated":"2021-01-12T07:41:07Z","extern":1,"type":"journal_article","status":"public","_id":"3108"},{"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"3106","publist_id":"3593","author":[{"first_name":"Shingo","full_name":"Nagawa, Shingo","last_name":"Nagawa"},{"full_name":"Xu, Tongda","last_name":"Xu","first_name":"Tongda"},{"last_name":"Lin","full_name":"Lin, Deshu","first_name":"Deshu"},{"first_name":"Pankaj","last_name":"Dhonukshe","full_name":"Dhonukshe, Pankaj"},{"last_name":"Zhang","full_name":"Zhang, Xingxing","first_name":"Xingxing"},{"orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"first_name":"Ben","last_name":"Scheres","full_name":"Scheres, Ben"},{"first_name":"Ying","full_name":"Fu, Ying","last_name":"Fu"},{"first_name":"Zhenbiao","full_name":"Yang, Zhenbiao","last_name":"Yang"}],"title":"ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis","date_updated":"2021-01-12T07:41:06Z","citation":{"chicago":"Nagawa, Shingo, Tongda Xu, Deshu Lin, Pankaj Dhonukshe, Xingxing Zhang, Jiří Friml, Ben Scheres, Ying Fu, and Zhenbiao Yang. “ROP GTPase-Dependent Actin Microfilaments Promote PIN1 Polarization by Localized Inhibition of Clathrin-Dependent Endocytosis.” PLoS Biology. Public Library of Science, 2012. https://doi.org/10.1371/journal.pbio.1001299.","ista":"Nagawa S, Xu T, Lin D, Dhonukshe P, Zhang X, Friml J, Scheres B, Fu Y, Yang Z. 2012. ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS Biology. 10(4).","mla":"Nagawa, Shingo, et al. “ROP GTPase-Dependent Actin Microfilaments Promote PIN1 Polarization by Localized Inhibition of Clathrin-Dependent Endocytosis.” PLoS Biology, vol. 10, no. 4, Public Library of Science, 2012, doi:10.1371/journal.pbio.1001299.","apa":"Nagawa, S., Xu, T., Lin, D., Dhonukshe, P., Zhang, X., Friml, J., … Yang, Z. (2012). ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1001299","ama":"Nagawa S, Xu T, Lin D, et al. ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS Biology. 2012;10(4). doi:10.1371/journal.pbio.1001299","short":"S. Nagawa, T. Xu, D. Lin, P. Dhonukshe, X. Zhang, J. Friml, B. Scheres, Y. Fu, Z. Yang, PLoS Biology 10 (2012).","ieee":"S. Nagawa et al., “ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis,” PLoS Biology, vol. 10, no. 4. Public Library of Science, 2012."},"extern":1,"publisher":"Public Library of Science","quality_controlled":0,"month":"04","intvolume":" 10","abstract":[{"text":"Cell polarization via asymmetrical distribution of structures or molecules is essential for diverse cellular functions and development of organisms, but how polarity is developmentally controlled has been poorly understood. In plants, the asymmetrical distribution of the PIN-FORMED (PIN) proteins involved in the cellular efflux of the quintessential phytohormone auxin plays a central role in developmental patterning, morphogenesis, and differential growth. Recently we showed that auxin promotes cell interdigitation by activating the Rho family ROP GTPases in leaf epidermal pavement cells. Here we found that auxin activation of the ROP2 signaling pathway regulates the asymmetric distribution of PIN1 by inhibiting its endocytosis. ROP2 inhibits PIN1 endocytosis via the accumulation of cortical actin microfilaments induced by the ROP2 effector protein RIC4. Our findings suggest a link between the developmental auxin signal and polar PIN1 distribution via Rho-dependent cytoskeletal reorganization and reveal the conservation of a design principle for cell polarization that is based on Rho GTPase-mediated inhibition of endocytosis.","lang":"eng"}],"issue":"4","doi":"10.1371/journal.pbio.1001299","volume":10,"date_published":"2012-04-01T00:00:00Z","license":"https://creativecommons.org/licenses/by/4.0/","date_created":"2018-12-11T12:01:25Z","publication_status":"published","year":"2012","day":"01","publication":"PLoS Biology"},{"page":"415 - 416","date_created":"2018-12-11T12:01:26Z","volume":8,"issue":"5","date_published":"2012-05-01T00:00:00Z","doi":"10.1038/nchembio.943","year":"2012","publication_status":"published","language":[{"iso":"eng"}],"publication":"Nature Chemical Biology","day":"01","quality_controlled":"1","publisher":"Nature Publishing Group","intvolume":" 8","month":"05","oa_version":"None","author":[{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"publist_id":"3592","title":"Plant signaling: Deconstructing auxin sensing","date_updated":"2021-01-12T07:41:06Z","citation":{"ista":"Vanneste S, Friml J. 2012. Plant signaling: Deconstructing auxin sensing, Nature Publishing Group,p.","chicago":"Vanneste, Steffen, and Jiří Friml. Plant Signaling: Deconstructing Auxin Sensing. Nature Chemical Biology. Vol. 8. Nature Publishing Group, 2012. https://doi.org/10.1038/nchembio.943.","ama":"Vanneste S, Friml J. Plant Signaling: Deconstructing Auxin Sensing. Vol 8. Nature Publishing Group; 2012:415-416. doi:10.1038/nchembio.943","apa":"Vanneste, S., & Friml, J. (2012). Plant signaling: Deconstructing auxin sensing. Nature Chemical Biology (Vol. 8, pp. 415–416). Nature Publishing Group. https://doi.org/10.1038/nchembio.943","ieee":"S. Vanneste and J. Friml, Plant signaling: Deconstructing auxin sensing, vol. 8, no. 5. Nature Publishing Group, 2012, pp. 415–416.","short":"S. Vanneste, J. Friml, Plant Signaling: Deconstructing Auxin Sensing, Nature Publishing Group, 2012.","mla":"Vanneste, Steffen, and Jiří Friml. “Plant Signaling: Deconstructing Auxin Sensing.” Nature Chemical Biology, vol. 8, no. 5, Nature Publishing Group, 2012, pp. 415–16, doi:10.1038/nchembio.943."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","type":"other_academic_publication","status":"public","_id":"3107"},{"citation":{"ista":"Raveendran K, Thuerey N, Wojtan C, Turk G. 2012. Controlling liquids using meshes. Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 255–264.","chicago":"Raveendran, Karthik, Nils Thuerey, Chris Wojtan, and Greg Turk. “Controlling Liquids Using Meshes.” In Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, 255–64. ACM, 2012.","short":"K. Raveendran, N. Thuerey, C. Wojtan, G. Turk, in:, Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, ACM, 2012, pp. 255–264.","ieee":"K. Raveendran, N. Thuerey, C. Wojtan, and G. Turk, “Controlling liquids using meshes,” in Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, Aire-la-Ville, Switzerland, 2012, pp. 255–264.","apa":"Raveendran, K., Thuerey, N., Wojtan, C., & Turk, G. (2012). Controlling liquids using meshes. In Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation (pp. 255–264). Aire-la-Ville, Switzerland: ACM.","ama":"Raveendran K, Thuerey N, Wojtan C, Turk G. Controlling liquids using meshes. In: Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. ACM; 2012:255-264.","mla":"Raveendran, Karthik, et al. “Controlling Liquids Using Meshes.” Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, ACM, 2012, pp. 255–64."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"3580","author":[{"first_name":"Karthik","last_name":"Raveendran","full_name":"Raveendran, Karthik"},{"full_name":"Thuerey, Nils","last_name":"Thuerey","first_name":"Nils"},{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Greg","last_name":"Turk","full_name":"Turk, Greg"}],"title":"Controlling liquids using meshes","acknowledgement":"This work was partially funded by NSF grants CCF-0811485 and IIS-1130934. We would like to thank Scanline VFX for additional funding. We would like to thank Jie Tan as well as our anonymous reviewers for their useful suggestions and feedback.","publisher":"ACM","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2012","day":"29","publication":"Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation","page":"255 - 264","date_published":"2012-07-29T00:00:00Z","date_created":"2018-12-11T12:01:30Z","_id":"3119","type":"conference","conference":{"name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation","start_date":"2012-07-29","location":"Aire-la-Ville, Switzerland","end_date":"2012-07-31"},"status":"public","pubrep_id":"600","date_updated":"2023-02-23T11:13:07Z","ddc":["000"],"file_date_updated":"2020-07-14T12:46:00Z","department":[{"_id":"ChWo"}],"abstract":[{"lang":"eng","text":"We present an approach for artist-directed animation of liquids using multiple levels of control over the simulation, ranging from the overall tracking of desired shapes to highly detailed secondary effects such as dripping streams, separating sheets of fluid, surface waves and ripples. The first portion of our technique is a volume preserving morph that allows the animator to produce a plausible fluid-like motion from a sparse set of control meshes. By rasterizing the resulting control meshes onto the simulation grid, the mesh velocities act as boundary conditions during the projection step of the fluid simulation. We can then blend this motion together with uncontrolled fluid velocities to achieve a more relaxed control over the fluid that captures natural inertial effects. Our method can produce highly detailed liquid surfaces with control over sub-grid details by using a mesh-based surface tracker on top of a coarse grid-based fluid simulation. We can create ripples and waves on the fluid surface attracting the surface mesh to the control mesh with spring-like forces and also by running a wave simulation over the surface mesh. Our video results demonstrate how our control scheme can be used to create animated characters and shapes that are made of water.\r\n"}],"oa_version":"Submitted Version","scopus_import":1,"month":"07","publication_status":"published","file":[{"file_name":"IST-2016-600-v1+1_ControllingLiquids_Preprint.pdf","date_created":"2018-12-12T10:11:23Z","creator":"system","file_size":4939370,"date_updated":"2020-07-14T12:46:00Z","file_id":"4877","checksum":"babda64c24cf90a4d05ae86d712bed08","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"table_of_contents","url":"http://dl.acm.org/citation.cfm?id=2422393"}]}},{"acknowledgement":"This work is supported by the SNF fellowship PBEZP2-134464.\r\nWe would like to thank Xiaochen Hu for implementing mesh con- version tools, Duygu Ceylan for helping with the rendering, and Art Tevs for the human performance data comparison. We also thank Nils Thuerey and Christopher Batty for helpful discussions. ","oa":1,"quality_controlled":"1","publisher":"ACM","publication":"ACM Transactions on Graphics","day":"01","year":"2012","has_accepted_license":"1","date_created":"2018-12-11T12:01:29Z","doi":"10.1145/2185520.2185549","date_published":"2012-07-01T00:00:00Z","article_number":"53","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bojsen-Hansen M, Li H, Wojtan C. 2012. Tracking surfaces with evolving topology. ACM Transactions on Graphics. 31(4), 53.","chicago":"Bojsen-Hansen, Morten, Hao Li, and Chris Wojtan. “Tracking Surfaces with Evolving Topology.” ACM Transactions on Graphics. ACM, 2012. https://doi.org/10.1145/2185520.2185549.","apa":"Bojsen-Hansen, M., Li, H., & Wojtan, C. (2012). Tracking surfaces with evolving topology. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2185520.2185549","ama":"Bojsen-Hansen M, Li H, Wojtan C. Tracking surfaces with evolving topology. ACM Transactions on Graphics. 2012;31(4). doi:10.1145/2185520.2185549","ieee":"M. Bojsen-Hansen, H. Li, and C. Wojtan, “Tracking surfaces with evolving topology,” ACM Transactions on Graphics, vol. 31, no. 4. ACM, 2012.","short":"M. Bojsen-Hansen, H. Li, C. Wojtan, ACM Transactions on Graphics 31 (2012).","mla":"Bojsen-Hansen, Morten, et al. “Tracking Surfaces with Evolving Topology.” ACM Transactions on Graphics, vol. 31, no. 4, 53, ACM, 2012, doi:10.1145/2185520.2185549."},"title":"Tracking surfaces with evolving topology","article_processing_charge":"No","publist_id":"3581","author":[{"last_name":"Bojsen-Hansen","full_name":"Bojsen-Hansen, Morten","orcid":"0000-0002-4417-3224","first_name":"Morten","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hao","full_name":"Li, Hao","last_name":"Li"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Submitted Version","abstract":[{"text":"We present a method for recovering a temporally coherent, deforming triangle mesh with arbitrarily changing topology from an incoherent sequence of static closed surfaces. We solve this problem using the surface geometry alone, without any prior information like surface templates or velocity fields. Our system combines a proven strategy for triangle mesh improvement, a robust multi-resolution non-rigid registration routine, and a reliable technique for changing surface mesh topology. We also introduce a novel topological constraint enforcement algorithm to ensure that the output and input always have similar topology. We apply our technique to a series of diverse input data from video reconstructions, physics simulations, and artistic morphs. The structured output of our algorithm allows us to efficiently track information like colors and displacement maps, recover velocity information, and solve PDEs on the mesh as a post process.","lang":"eng"}],"intvolume":" 31","month":"07","alternative_title":["SIGGRAPH"],"scopus_import":"1","language":[{"iso":"eng"}],"file":[{"checksum":"1e219c5bf4e5552c1290c62eefa5cd60","file_id":"5359","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2016-602-v1+1_topoReg.pdf","date_created":"2018-12-12T10:18:37Z","file_size":44538518,"date_updated":"2020-07-14T12:46:00Z","creator":"system"}],"publication_status":"published","issue":"4","volume":31,"_id":"3118","pubrep_id":"602","status":"public","article_type":"original","type":"journal_article","ddc":["000"],"date_updated":"2022-05-24T08:21:11Z","file_date_updated":"2020-07-14T12:46:00Z","department":[{"_id":"ChWo"}]}]