[{"intvolume":"        78","date_created":"2018-12-11T11:59:37Z","page":"109 - 114","year":"2006","publication":"Fluid Mechanics and its Applications","volume":78,"publisher":"Springer","date_published":"2006-01-18T00:00:00Z","title":"Observation of nonlinear travelling waves in turbulent pipe flow","quality_controlled":0,"type":"journal_article","month":"01","date_updated":"2021-01-12T06:59:45Z","publication_status":"published","day":"18","citation":{"mla":"Hof, Björn, et al. “Observation of Nonlinear Travelling Waves in Turbulent Pipe Flow.” <i>Fluid Mechanics and Its Applications</i>, vol. 78, Springer, 2006, pp. 109–14, doi:<a href=\"https://doi.org/10.1007/1-4020-4159-4_11\">10.1007/1-4020-4159-4_11</a>.","apa":"Hof, B., Van Doorne, C., Westerweel, J., &#38; Nieuwstadt, F. (2006). Observation of nonlinear travelling waves in turbulent pipe flow. <i>Fluid Mechanics and Its Applications</i>. Springer. <a href=\"https://doi.org/10.1007/1-4020-4159-4_11\">https://doi.org/10.1007/1-4020-4159-4_11</a>","ista":"Hof B, Van Doorne C, Westerweel J, Nieuwstadt F. 2006. Observation of nonlinear travelling waves in turbulent pipe flow. Fluid Mechanics and its Applications. 78, 109–114.","ieee":"B. Hof, C. Van Doorne, J. Westerweel, and F. Nieuwstadt, “Observation of nonlinear travelling waves in turbulent pipe flow,” <i>Fluid Mechanics and its Applications</i>, vol. 78. Springer, pp. 109–114, 2006.","chicago":"Hof, Björn, Casimir Van Doorne, Jerry Westerweel, and Frans Nieuwstadt. “Observation of Nonlinear Travelling Waves in Turbulent Pipe Flow.” <i>Fluid Mechanics and Its Applications</i>. Springer, 2006. <a href=\"https://doi.org/10.1007/1-4020-4159-4_11\">https://doi.org/10.1007/1-4020-4159-4_11</a>.","short":"B. Hof, C. Van Doorne, J. Westerweel, F. Nieuwstadt, Fluid Mechanics and Its Applications 78 (2006) 109–114.","ama":"Hof B, Van Doorne C, Westerweel J, Nieuwstadt F. Observation of nonlinear travelling waves in turbulent pipe flow. <i>Fluid Mechanics and its Applications</i>. 2006;78:109-114. doi:<a href=\"https://doi.org/10.1007/1-4020-4159-4_11\">10.1007/1-4020-4159-4_11</a>"},"extern":1,"author":[{"full_name":"Björn Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","last_name":"Hof"},{"last_name":"Van Doorne","first_name":"Casimir","full_name":"van Doorne, Casimir W"},{"full_name":"Westerweel, Jerry","first_name":"Jerry","last_name":"Westerweel"},{"full_name":"Nieuwstadt, Frans T","first_name":"Frans","last_name":"Nieuwstadt"}],"status":"public","_id":"2792","abstract":[{"text":"Transition to turbulence in pipe flow has posed a riddle in fluid dynamics since the pioneering experiments of Reynolds[1]. Although the laminar flow is linearly stable for all flow rates, practical pipe flows become turbulent at large enough flow speeds. Turbulence arises suddenly and fully without distinct steps and without a clear critical point. The complexity of this problem has puzzled mathematicians, physicists and engineers for more than a century and no satisfactory explanation of this problem has been given. In a very recent theoretical approach it has been suggested that unstable solutions of the Navier Stokes equations may hold the key to understanding this problem. In numerical studies such unstable states have been identified as exact solutions for the idealized case of a pipe with periodic boundary conditions[2, 3]. These solutions have the form of waves extending through the entire pipe and travelling in the streamwise direction at a phase speed close to the bulk velocity of the fluid. With the aid of a recently developed high-speed stereoscopic Particle Image Velocimetry (PIV) system, we were able to observe transients of such unstable solutions in turbulent pipe flow[4].","lang":"eng"}],"doi":"10.1007/1-4020-4159-4_11","publist_id":"4097"},{"publisher":"American Association of Immunologists","quality_controlled":0,"title":"Stochastic Monoallelic Expression of IL 10 in T Cells","date_published":"2006-01-01T00:00:00Z","page":"5358 - 5364","date_created":"2018-12-11T12:00:11Z","intvolume":"       177","volume":177,"publication":"Journal of Immunology","year":"2006","_id":"2894","status":"public","abstract":[{"lang":"eng","text":"IL-10 is a potent anti-inflammatory and immunomodulatory cytokine, exerting major effects in the degree and quality of the immune response. Using a newly generated IL-10 reporter mouse model, which easily allows the study of IL-10 expression from each allele in a single cell, we report here for the first time that IL-10 is predominantly monoallelic expressed in CD4+ T cells. Furthermore, we have compelling evidence that this expression pattern is not due to parental imprinting, allelic exclusion, or strong allelic bias. Instead, our results support a stochastic regulation mechanism, in which the probability to initiate allelic transcription depends on the strength of TCR signaling and subsequent capacity to overcome restrictions imposed by chromatin hypoacetylation. In vivo Ag-experienced T cells show a higher basal probability to transcribe IL-10 when compared with naive cells, yet still show mostly monoallelic IL-10 expression. Finally, statistical analysis on allelic expression data shows transcriptional independence between both alleles. We conclude that CD4+ T cells have a low probability for IL-10 allelic activation resulting in a predominantly monoallelic expression pattern, and that IL-10 expression appears to be stochastically regulated by controlling the frequency of expressing cells, rather than absolute protein levels per cell."}],"publist_id":"3864","doi":"10.4049/jimmunol.177.8.5358 ","issue":"8","month":"01","type":"journal_article","author":[{"last_name":"Calado","first_name":"Dinis","full_name":"Calado, Dinis P"},{"last_name":"Paixao","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Tiago Paixao","orcid":"0000-0003-2361-3953"},{"full_name":"Holmberg, Dan","first_name":"Dan","last_name":"Holmberg"},{"last_name":"Haury","full_name":"Haury, Matthias","first_name":"Matthias"}],"extern":1,"day":"01","citation":{"ieee":"D. Calado, T. Paixao, D. Holmberg, and M. Haury, “Stochastic Monoallelic Expression of IL 10 in T Cells,” <i>Journal of Immunology</i>, vol. 177, no. 8. American Association of Immunologists, pp. 5358–5364, 2006.","chicago":"Calado, Dinis, Tiago Paixao, Dan Holmberg, and Matthias Haury. “Stochastic Monoallelic Expression of IL 10 in T Cells.” <i>Journal of Immunology</i>. American Association of Immunologists, 2006. <a href=\"https://doi.org/10.4049/jimmunol.177.8.5358 \">https://doi.org/10.4049/jimmunol.177.8.5358 </a>.","short":"D. Calado, T. Paixao, D. Holmberg, M. Haury, Journal of Immunology 177 (2006) 5358–5364.","ama":"Calado D, Paixao T, Holmberg D, Haury M. Stochastic Monoallelic Expression of IL 10 in T Cells. <i>Journal of Immunology</i>. 2006;177(8):5358-5364. doi:<a href=\"https://doi.org/10.4049/jimmunol.177.8.5358 \">10.4049/jimmunol.177.8.5358 </a>","apa":"Calado, D., Paixao, T., Holmberg, D., &#38; Haury, M. (2006). Stochastic Monoallelic Expression of IL 10 in T Cells. <i>Journal of Immunology</i>. American Association of Immunologists. <a href=\"https://doi.org/10.4049/jimmunol.177.8.5358 \">https://doi.org/10.4049/jimmunol.177.8.5358 </a>","mla":"Calado, Dinis, et al. “Stochastic Monoallelic Expression of IL 10 in T Cells.” <i>Journal of Immunology</i>, vol. 177, no. 8, American Association of Immunologists, 2006, pp. 5358–64, doi:<a href=\"https://doi.org/10.4049/jimmunol.177.8.5358 \">10.4049/jimmunol.177.8.5358 </a>.","ista":"Calado D, Paixao T, Holmberg D, Haury M. 2006. Stochastic Monoallelic Expression of IL 10 in T Cells. Journal of Immunology. 177(8), 5358–5364."},"date_updated":"2021-01-12T07:00:32Z","publication_status":"published"},{"doi":"10.1007/0-387-28831-7_26","publist_id":"3816","abstract":[{"lang":"eng","text":"Most binocular stereo algorithms assume that all scene elements are visible from both cameras. Scene elements that are visible from only one camera, known as occlusions, pose an important challenge for stereo. Occlusions are important for segmentation, because they appear near discontinuities. However, stereo algorithms tend to ignore occlusions because of their difficulty. One reason is that occlusions require the input images to be treated symmetrically, which complicates the problem formulation. Worse, certain depth maps imply physically impossible scene configurations, and must be excluded from the output. In this chapter we approach the problem of binocular stereo with occlusions from an energy minimization viewpoint. We begin by reviewing traditional stereo methods that do not handle occlusions. If occlusions are ignored, it is easy to formulate the stereo problem as a pixel labeling problem, which leads to an energy function that is common in early vision. This kind of energy function can he minimized using graph cuts, which is a combinatorial optimization technique that has proven to be very effective for low-level vision problems. Motivated by this, we have designed two graph cut stereo algorithms that are designed to handle occlusions. These algorithms produce promising experimental results on real data with ground truth."}],"_id":"2921","status":"public","publication_status":"published","date_updated":"2021-01-12T07:00:42Z","extern":1,"author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov","first_name":"Vladimir","last_name":"Kolmogorov"},{"last_name":"Zabih","full_name":"Zabih, Ramin","first_name":"Ramin"}],"citation":{"short":"V. Kolmogorov, R. Zabih, in:, Handbook of Mathematical Models in Computer Vision, Springer, 2006, pp. 423–427.","ama":"Kolmogorov V, Zabih R. Graph cut algorithms for binocular stereo with occlusions. In: <i>Handbook of Mathematical Models in Computer Vision</i>. Springer; 2006:423-427. doi:<a href=\"https://doi.org/10.1007/0-387-28831-7_26\">10.1007/0-387-28831-7_26</a>","chicago":"Kolmogorov, Vladimir, and Ramin Zabih. “Graph Cut Algorithms for Binocular Stereo with Occlusions.” In <i>Handbook of Mathematical Models in Computer Vision</i>, 423–27. Springer, 2006. <a href=\"https://doi.org/10.1007/0-387-28831-7_26\">https://doi.org/10.1007/0-387-28831-7_26</a>.","ieee":"V. Kolmogorov and R. Zabih, “Graph cut algorithms for binocular stereo with occlusions,” in <i>Handbook of Mathematical Models in Computer Vision</i>, Springer, 2006, pp. 423–427.","ista":"Kolmogorov V, Zabih R. 2006.Graph cut algorithms for binocular stereo with occlusions. In: Handbook of Mathematical Models in Computer Vision. , 423–427.","mla":"Kolmogorov, Vladimir, and Ramin Zabih. “Graph Cut Algorithms for Binocular Stereo with Occlusions.” <i>Handbook of Mathematical Models in Computer Vision</i>, Springer, 2006, pp. 423–27, doi:<a href=\"https://doi.org/10.1007/0-387-28831-7_26\">10.1007/0-387-28831-7_26</a>.","apa":"Kolmogorov, V., &#38; Zabih, R. (2006). Graph cut algorithms for binocular stereo with occlusions. In <i>Handbook of Mathematical Models in Computer Vision</i> (pp. 423–427). Springer. <a href=\"https://doi.org/10.1007/0-387-28831-7_26\">https://doi.org/10.1007/0-387-28831-7_26</a>"},"day":"01","month":"01","type":"book_chapter","date_published":"2006-01-01T00:00:00Z","title":"Graph cut algorithms for binocular stereo with occlusions","quality_controlled":0,"publisher":"Springer","year":"2006","publication":"Handbook of Mathematical Models in Computer Vision","date_created":"2018-12-11T12:00:21Z","page":"423 - 427"},{"status":"public","_id":"3002","editor":[{"full_name":"Mujib, Abdul","first_name":"Abdul","last_name":"Mujib"},{"full_name":"Šamaj, Jozef","first_name":"Jozef","last_name":"Šamaj"}],"publist_id":"3699","doi":"10.1007/7089_020","abstract":[{"text":"Arabidopsis thaliana is currently the most important model organism for basic molecular plant research. It is also a favourable model for developmental biology, as its embryogenesis follows a nearly invariant pattern of cell divisions and cell type specifications. Study of embryogenesis can involve genetic, physiological or biochemical approaches, but is always limited by the inaccessibility of the embryos which develop deep inside maternal tissue. Thus, for developmental studies, there is an increasing demand for methods which allow embryogenesis under artificial conditions, providing better accessibility to experimental manipulation. In this chapter, we address theoretical aspects of embryo culture, give some thoughts on which embryo culture system is suited best for which application and finally discuss three current methods which have been successfully used in Arabidopsis embryo culture. © 2006 Springer-Verlag Berlin Heidelberg.","lang":"eng"}],"alternative_title":["Plant Cell Monographs"],"type":"book_chapter","month":"01","publication_status":"published","date_updated":"2021-01-12T07:40:23Z","citation":{"chicago":"Sauer, Michael, and Jiří Friml. “In Vitro Culture of Arabidopsis Embryos.” In <i>Somatic Embryogenesis</i>, edited by Abdul Mujib and Jozef Šamaj, 2:343–54. Springer, 2006. <a href=\"https://doi.org/10.1007/7089_020\">https://doi.org/10.1007/7089_020</a>.","ama":"Sauer M, Friml J. In vitro culture of Arabidopsis embryos. In: Mujib A, Šamaj J, eds. <i>Somatic Embryogenesis</i>. Vol 2. Springer; 2006:343-354. doi:<a href=\"https://doi.org/10.1007/7089_020\">10.1007/7089_020</a>","short":"M. Sauer, J. Friml, in:, A. Mujib, J. Šamaj (Eds.), Somatic Embryogenesis, Springer, 2006, pp. 343–354.","ieee":"M. Sauer and J. Friml, “In vitro culture of Arabidopsis embryos,” in <i>Somatic Embryogenesis</i>, vol. 2, A. Mujib and J. Šamaj, Eds. Springer, 2006, pp. 343–354.","mla":"Sauer, Michael, and Jiří Friml. “In Vitro Culture of Arabidopsis Embryos.” <i>Somatic Embryogenesis</i>, edited by Abdul Mujib and Jozef Šamaj, vol. 2, Springer, 2006, pp. 343–54, doi:<a href=\"https://doi.org/10.1007/7089_020\">10.1007/7089_020</a>.","apa":"Sauer, M., &#38; Friml, J. (2006). In vitro culture of Arabidopsis embryos. In A. Mujib &#38; J. Šamaj (Eds.), <i>Somatic Embryogenesis</i> (Vol. 2, pp. 343–354). Springer. <a href=\"https://doi.org/10.1007/7089_020\">https://doi.org/10.1007/7089_020</a>","ista":"Sauer M, Friml J. 2006.In vitro culture of Arabidopsis embryos. In: Somatic Embryogenesis. Plant Cell Monographs, vol. 2, 343–354."},"day":"01","extern":1,"author":[{"last_name":"Sauer","first_name":"Michael","full_name":"Sauer, Michael"},{"orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml"}],"publisher":"Springer","date_published":"2006-01-01T00:00:00Z","title":"In vitro culture of Arabidopsis embryos","quality_controlled":0,"intvolume":"         2","date_created":"2018-12-11T12:00:48Z","page":"343 - 354","year":"2006","publication":"Somatic Embryogenesis","volume":2},{"volume":11,"language":[{"iso":"eng"}],"publication":"Trends in Plant Science","year":"2006","page":"12 - 14","date_created":"2018-12-11T12:00:49Z","intvolume":"        11","date_published":"2006-01-01T00:00:00Z","title":"Apical-basal polarity: Why plant cells don't stand on their heads","publisher":"Cell Press","author":[{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","first_name":"Jirí"},{"first_name":"Philip","full_name":"Benfey, Philip","last_name":"Benfey"},{"last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"},{"last_name":"Bennett","first_name":"Malcolm","full_name":"Bennett, Malcolm"},{"full_name":"Berleth, Thomas","first_name":"Thomas","last_name":"Berleth"},{"last_name":"Geldner","first_name":"Niko","full_name":"Geldner, Niko"},{"last_name":"Grebe","full_name":"Grebe, Markus","first_name":"Markus"},{"first_name":"Marcus","full_name":"Heisler, Marcus","last_name":"Heisler"},{"last_name":"Hejátko","full_name":"Hejátko, Jan","first_name":"Jan"},{"first_name":"Gerd","full_name":"Jürgens, Gerd","last_name":"Jürgens"},{"last_name":"Laux","full_name":"Laux, Thomas","first_name":"Thomas"},{"last_name":"Lindsey","full_name":"Lindsey, Keith","first_name":"Keith"},{"first_name":"Wolfgang","full_name":"Lukowitz, Wolfgang","last_name":"Lukowitz"},{"last_name":"Luschnig","first_name":"Christian","full_name":"Luschnig, Christian"},{"full_name":"Offringa, Remko","first_name":"Remko","last_name":"Offringa"},{"last_name":"Scheres","full_name":"Scheres, Ben","first_name":"Ben"},{"last_name":"Swarup","first_name":"Ranjan","full_name":"Swarup, Ranjan"},{"last_name":"Torres Ruiz","first_name":"Ramón","full_name":"Torres Ruiz, Ramón"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"last_name":"Zažímalová","first_name":"Eva","full_name":"Zažímalová, Eva"}],"extern":"1","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Friml J, Benfey P, Benková E, Bennett M, Berleth T, Geldner N, Grebe M, Heisler M, Hejátko J, Jürgens G, Laux T, Lindsey K, Lukowitz W, Luschnig C, Offringa R, Scheres B, Swarup R, Torres Ruiz R, Weijers D, Zažímalová E. 2006. Apical-basal polarity: Why plant cells don’t stand on their heads. Trends in Plant Science. 11(1), 12–14.","mla":"Friml, Jiří, et al. “Apical-Basal Polarity: Why Plant Cells Don’t Stand on Their Heads.” <i>Trends in Plant Science</i>, vol. 11, no. 1, Cell Press, 2006, pp. 12–14, doi:<a href=\"https://doi.org/10.1016/j.tplants.2005.11.010\">10.1016/j.tplants.2005.11.010</a>.","apa":"Friml, J., Benfey, P., Benková, E., Bennett, M., Berleth, T., Geldner, N., … Zažímalová, E. (2006). Apical-basal polarity: Why plant cells don’t stand on their heads. <i>Trends in Plant Science</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tplants.2005.11.010\">https://doi.org/10.1016/j.tplants.2005.11.010</a>","short":"J. Friml, P. Benfey, E. Benková, M. Bennett, T. Berleth, N. Geldner, M. Grebe, M. Heisler, J. Hejátko, G. Jürgens, T. Laux, K. Lindsey, W. Lukowitz, C. Luschnig, R. Offringa, B. Scheres, R. Swarup, R. Torres Ruiz, D. Weijers, E. Zažímalová, Trends in Plant Science 11 (2006) 12–14.","ama":"Friml J, Benfey P, Benková E, et al. Apical-basal polarity: Why plant cells don’t stand on their heads. <i>Trends in Plant Science</i>. 2006;11(1):12-14. doi:<a href=\"https://doi.org/10.1016/j.tplants.2005.11.010\">10.1016/j.tplants.2005.11.010</a>","chicago":"Friml, Jiří, Philip Benfey, Eva Benková, Malcolm Bennett, Thomas Berleth, Niko Geldner, Markus Grebe, et al. “Apical-Basal Polarity: Why Plant Cells Don’t Stand on Their Heads.” <i>Trends in Plant Science</i>. Cell Press, 2006. <a href=\"https://doi.org/10.1016/j.tplants.2005.11.010\">https://doi.org/10.1016/j.tplants.2005.11.010</a>.","ieee":"J. Friml <i>et al.</i>, “Apical-basal polarity: Why plant cells don’t stand on their heads,” <i>Trends in Plant Science</i>, vol. 11, no. 1. Cell Press, pp. 12–14, 2006."},"date_updated":"2021-01-12T07:40:24Z","oa_version":"None","publication_status":"published","month":"01","type":"journal_article","publist_id":"3697","doi":"10.1016/j.tplants.2005.11.010","issue":"1","_id":"3005","status":"public"},{"publication_status":"published","date_updated":"2021-01-12T07:40:24Z","extern":1,"author":[{"last_name":"Dhonukshe","full_name":"Dhonukshe, Pankaj","first_name":"Pankaj"},{"first_name":"František","full_name":"Baluška, František","last_name":"Baluška"},{"last_name":"Schlicht","full_name":"Schlicht, Markus","first_name":"Markus"},{"full_name":"Hlavacka, Andrej","first_name":"Andrej","last_name":"Hlavacka"},{"last_name":"Šamaj","first_name":"Jozef","full_name":"Šamaj, Jozef"},{"full_name":"Jirí Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"first_name":"Theodorus","full_name":"Gadella, Theodorus W","last_name":"Gadella"}],"day":"01","citation":{"chicago":"Dhonukshe, Pankaj, František Baluška, Markus Schlicht, Andrej Hlavacka, Jozef Šamaj, Jiří Friml, and Theodorus Gadella. “Endocytosis of Cell Surface Material Mediates Cell Plate Formation during Plant Cytokinesis.” <i>Developmental Cell</i>. Cell Press, 2006. <a href=\"https://doi.org/10.1016/j.devcel.2005.11.015\">https://doi.org/10.1016/j.devcel.2005.11.015</a>.","short":"P. Dhonukshe, F. Baluška, M. Schlicht, A. Hlavacka, J. Šamaj, J. Friml, T. Gadella, Developmental Cell 10 (2006) 137–150.","ama":"Dhonukshe P, Baluška F, Schlicht M, et al. Endocytosis of cell surface material mediates cell plate formation during plant cytokinesis. <i>Developmental Cell</i>. 2006;10(1):137-150. doi:<a href=\"https://doi.org/10.1016/j.devcel.2005.11.015\">10.1016/j.devcel.2005.11.015</a>","ieee":"P. Dhonukshe <i>et al.</i>, “Endocytosis of cell surface material mediates cell plate formation during plant cytokinesis,” <i>Developmental Cell</i>, vol. 10, no. 1. Cell Press, pp. 137–150, 2006.","mla":"Dhonukshe, Pankaj, et al. “Endocytosis of Cell Surface Material Mediates Cell Plate Formation during Plant Cytokinesis.” <i>Developmental Cell</i>, vol. 10, no. 1, Cell Press, 2006, pp. 137–50, doi:<a href=\"https://doi.org/10.1016/j.devcel.2005.11.015\">10.1016/j.devcel.2005.11.015</a>.","apa":"Dhonukshe, P., Baluška, F., Schlicht, M., Hlavacka, A., Šamaj, J., Friml, J., &#38; Gadella, T. (2006). Endocytosis of cell surface material mediates cell plate formation during plant cytokinesis. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2005.11.015\">https://doi.org/10.1016/j.devcel.2005.11.015</a>","ista":"Dhonukshe P, Baluška F, Schlicht M, Hlavacka A, Šamaj J, Friml J, Gadella T. 2006. Endocytosis of cell surface material mediates cell plate formation during plant cytokinesis. Developmental Cell. 10(1), 137–150."},"month":"01","type":"journal_article","issue":"1","publist_id":"3696","abstract":[{"lang":"eng","text":"Dividing plant cells perform a remarkable task of building a new cell wall within the cytoplasm in a few minutes. A long-standing paradigm claims that this primordial cell wall, known as the cell plate, is generated by delivery of newly synthesized material from Golgi apparatus-originated secretory vesicles. Here, we show that, in diverse plant species, cell surface material, including plasma membrane proteins, cell wall components, and exogenously applied endocytic tracers, is rapidly delivered to the forming cell plate. Importantly, this occurs even when de novo protein synthesis is blocked. In addition, cytokinesis-specific syntaxin KNOLLE as well as plasma membrane (PM) resident proteins localize to endosomes that fuse to initiate the cell plate. The rate of endocytosis is strongly enhanced during cell plate formation, and its genetic or pharmacological inhibition leads to cytokinesis defects. Our results reveal that endocytic delivery of cell surface material significantly contributes to cell plate formation during plant cytokinesis. "}],"doi":"10.1016/j.devcel.2005.11.015","_id":"3006","status":"public","year":"2006","volume":10,"publication":"Developmental Cell","intvolume":"        10","date_created":"2018-12-11T12:00:49Z","page":"137 - 150","date_published":"2006-01-01T00:00:00Z","title":"Endocytosis of cell surface material mediates cell plate formation during plant cytokinesis","quality_controlled":0,"publisher":"Cell Press"},{"status":"public","_id":"3007","issue":"3","publist_id":"3694","doi":"10.1038/ncb1369","abstract":[{"text":"Root gravitropism describes the orientation of root growth along the gravity vector and is mediated by differential cell elongation in the root meristem. This response requires the coordinated, asymmetric distribution of the phytohormone auxin within the root meristem, and depends on the concerted activities of PIN proteins and AUX1 - members of the auxin transport pathway. Here, we show that intracellular trafficking and proteasome activity combine to control PIN2 degradation during root gravitropism. Following gravi-stimulation, proteasome-dependent variations in PIN2 localization and degradation at the upper and lower sides of the root result in asymmetric distribution of PIN2. Ubiquitination of PIN2 occurs in a proteasome-dependent manner, indicating that the proteasome is involved in the control of PIN2 turnover. Stabilization of PIN2 affects its abundance and distribution, and leads to defects in auxin distribution and gravitropic responses. We describe the effects of auxin on PIN2 localization and protein levels, indicating that redistribution of auxin during the gravitropic response may be involved in the regulation of PIN2 protein.","lang":"eng"}],"type":"journal_article","month":"03","date_updated":"2021-01-12T07:40:25Z","publication_status":"published","citation":{"ieee":"L. Abas <i>et al.</i>, “Intracellular trafficking and proteolysis of the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism,” <i>Nature Cell Biology</i>, vol. 8, no. 3. Nature Publishing Group, pp. 249–256, 2006.","ama":"Abas L, Benjamins R, Malenica N, et al. Intracellular trafficking and proteolysis of the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism. <i>Nature Cell Biology</i>. 2006;8(3):249-256. doi:<a href=\"https://doi.org/10.1038/ncb1369\">10.1038/ncb1369</a>","short":"L. Abas, R. Benjamins, N. Malenica, T. Paciorek, J. Wiśniewska, J. Moulinier Anzola, T. Sieberer, J. Friml, C. Luschnig, Nature Cell Biology 8 (2006) 249–256.","chicago":"Abas, Lindy, René Benjamins, Nenad Malenica, Tomasz Paciorek, Justyna Wiśniewska, Jeanette Moulinier Anzola, Tobias Sieberer, Jiří Friml, and Christian Luschnig. “Intracellular Trafficking and Proteolysis of the Arabidopsis Auxin-Efflux Facilitator PIN2 Are Involved in Root Gravitropism.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2006. <a href=\"https://doi.org/10.1038/ncb1369\">https://doi.org/10.1038/ncb1369</a>.","ista":"Abas L, Benjamins R, Malenica N, Paciorek T, Wiśniewska J, Moulinier Anzola J, Sieberer T, Friml J, Luschnig C. 2006. Intracellular trafficking and proteolysis of the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism. Nature Cell Biology. 8(3), 249–256.","apa":"Abas, L., Benjamins, R., Malenica, N., Paciorek, T., Wiśniewska, J., Moulinier Anzola, J., … Luschnig, C. (2006). Intracellular trafficking and proteolysis of the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb1369\">https://doi.org/10.1038/ncb1369</a>","mla":"Abas, Lindy, et al. “Intracellular Trafficking and Proteolysis of the Arabidopsis Auxin-Efflux Facilitator PIN2 Are Involved in Root Gravitropism.” <i>Nature Cell Biology</i>, vol. 8, no. 3, Nature Publishing Group, 2006, pp. 249–56, doi:<a href=\"https://doi.org/10.1038/ncb1369\">10.1038/ncb1369</a>."},"day":"01","author":[{"last_name":"Abas","first_name":"Lindy","full_name":"Abas, Lindy"},{"last_name":"Benjamins","first_name":"René","full_name":"Benjamins, René"},{"last_name":"Malenica","first_name":"Nenad","full_name":"Malenica, Nenad"},{"first_name":"Tomasz","full_name":"Paciorek, Tomasz","last_name":"Paciorek"},{"first_name":"Justyna","full_name":"Wiśniewska, Justyna","last_name":"Wiśniewska"},{"full_name":"Moulinier-Anzola, Jeanette C","first_name":"Jeanette","last_name":"Moulinier Anzola"},{"full_name":"Sieberer, Tobias","first_name":"Tobias","last_name":"Sieberer"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Jirí Friml"},{"last_name":"Luschnig","full_name":"Luschnig, Christian","first_name":"Christian"}],"extern":1,"publisher":"Nature Publishing Group","title":"Intracellular trafficking and proteolysis of the Arabidopsis auxin-efflux facilitator PIN2 are involved in root gravitropism","date_published":"2006-03-01T00:00:00Z","quality_controlled":0,"date_created":"2018-12-11T12:00:50Z","intvolume":"         8","page":"249 - 256","year":"2006","publication":"Nature Cell Biology","volume":8},{"publisher":"American Association for the Advancement of Science","title":"A molecular framework for plant regeneration","date_published":"2006-01-20T00:00:00Z","quality_controlled":0,"date_created":"2018-12-11T12:00:50Z","intvolume":"       311","page":"385 - 388","year":"2006","publication":"Science","volume":311,"status":"public","_id":"3008","issue":"5759","abstract":[{"lang":"eng","text":"Plants and some animals have a profound capacity to regenerate organs from adult tissues. Molecular mechanisms for regeneration have, however, been largely unexplored. Here we investigate a local regeneration response in Arabidopsis roots. Laser-induced wounding disrupts the flow of auxin-a cell-fate-instructive plant hormone-in root tips, and we demonstrate that resulting cell-fate changes require the PLETHORA, SHORTROOT, and SCARECROW transcription factors. These transcription factors regulate the expression and polar position of PIN auxin efflux-facilitating membrane proteins to reconstitute auxin transport in renewed root tips. Thus, a regeneration mechanism using embryonic root stem-cell patterning factors first responds to and subsequently stabilizes a new hormone distribution."}],"publist_id":"3695","doi":"10.1126/science.1121790","type":"journal_article","month":"01","publication_status":"published","date_updated":"2021-01-12T07:40:25Z","day":"20","citation":{"mla":"Xu, Jian, et al. “A Molecular Framework for Plant Regeneration.” <i>Science</i>, vol. 311, no. 5759, American Association for the Advancement of Science, 2006, pp. 385–88, doi:<a href=\"https://doi.org/10.1126/science.1121790\">10.1126/science.1121790</a>.","apa":"Xu, J., Hofhuis, H., Heidstra, R., Sauer, M., Friml, J., &#38; Scheres, B. (2006). A molecular framework for plant regeneration. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1121790\">https://doi.org/10.1126/science.1121790</a>","ista":"Xu J, Hofhuis H, Heidstra R, Sauer M, Friml J, Scheres B. 2006. A molecular framework for plant regeneration. Science. 311(5759), 385–388.","ieee":"J. Xu, H. Hofhuis, R. Heidstra, M. Sauer, J. Friml, and B. Scheres, “A molecular framework for plant regeneration,” <i>Science</i>, vol. 311, no. 5759. American Association for the Advancement of Science, pp. 385–388, 2006.","chicago":"Xu, Jian, Hugo Hofhuis, Renze Heidstra, Michael Sauer, Jiří Friml, and Ben Scheres. “A Molecular Framework for Plant Regeneration.” <i>Science</i>. American Association for the Advancement of Science, 2006. <a href=\"https://doi.org/10.1126/science.1121790\">https://doi.org/10.1126/science.1121790</a>.","short":"J. Xu, H. Hofhuis, R. Heidstra, M. Sauer, J. Friml, B. Scheres, Science 311 (2006) 385–388.","ama":"Xu J, Hofhuis H, Heidstra R, Sauer M, Friml J, Scheres B. A molecular framework for plant regeneration. <i>Science</i>. 2006;311(5759):385-388. doi:<a href=\"https://doi.org/10.1126/science.1121790\">10.1126/science.1121790</a>"},"extern":1,"author":[{"last_name":"Xu","full_name":"Xu, Jian","first_name":"Jian"},{"last_name":"Hofhuis","full_name":"Hofhuis, Hugo","first_name":"Hugo"},{"full_name":"Heidstra, Renze","first_name":"Renze","last_name":"Heidstra"},{"first_name":"Michael","full_name":"Sauer, Michael","last_name":"Sauer"},{"orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml"},{"full_name":"Scheres, Ben","first_name":"Ben","last_name":"Scheres"}]},{"author":[{"last_name":"Paciorek","full_name":"Paciorek, Tomasz","first_name":"Tomasz"},{"last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"oa":1,"extern":"1","citation":{"ieee":"T. Paciorek and J. Friml, “Auxin signaling,” <i>Journal of Cell Science</i>, vol. 119, no. 7. Company of Biologists, pp. 1199–1202, 2006.","short":"T. Paciorek, J. Friml, Journal of Cell Science 119 (2006) 1199–1202.","ama":"Paciorek T, Friml J. Auxin signaling. <i>Journal of Cell Science</i>. 2006;119(7):1199-1202. doi:<a href=\"https://doi.org/10.1242/jcs.02910\">10.1242/jcs.02910</a>","chicago":"Paciorek, Tomasz, and Jiří Friml. “Auxin Signaling.” <i>Journal of Cell Science</i>. Company of Biologists, 2006. <a href=\"https://doi.org/10.1242/jcs.02910\">https://doi.org/10.1242/jcs.02910</a>.","ista":"Paciorek T, Friml J. 2006. Auxin signaling. Journal of Cell Science. 119(7), 1199–1202.","mla":"Paciorek, Tomasz, and Jiří Friml. “Auxin Signaling.” <i>Journal of Cell Science</i>, vol. 119, no. 7, Company of Biologists, 2006, pp. 1199–202, doi:<a href=\"https://doi.org/10.1242/jcs.02910\">10.1242/jcs.02910</a>.","apa":"Paciorek, T., &#38; Friml, J. (2006). Auxin signaling. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.02910\">https://doi.org/10.1242/jcs.02910</a>"},"day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:40:25Z","oa_version":"Published Version","publication_status":"published","month":"01","type":"journal_article","publist_id":"3693","doi":"10.1242/jcs.02910","external_id":{"pmid":["    16554435"]},"issue":"7","_id":"3009","status":"public","pmid":1,"language":[{"iso":"eng"}],"volume":119,"publication":"Journal of Cell Science","year":"2006","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/16554435","open_access":"1"}],"page":"1199 - 1202","intvolume":"       119","date_created":"2018-12-11T12:00:50Z","quality_controlled":"1","date_published":"2006-01-01T00:00:00Z","title":"Auxin signaling","publisher":"Company of Biologists"},{"type":"journal_article","month":"04","publication_status":"published","date_updated":"2021-01-12T07:40:26Z","citation":{"chicago":"Scarpella, Enrico, Danielle Marcos, Jiří Friml, and Thomas Berleth. “Control of Leaf Vascular Patterning by Polar Auxin Transport.” <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press, 2006. <a href=\"https://doi.org/10.1101/gad.1402406\">https://doi.org/10.1101/gad.1402406</a>.","short":"E. Scarpella, D. Marcos, J. Friml, T. Berleth, Genes and Development 20 (2006) 1015–1027.","ama":"Scarpella E, Marcos D, Friml J, Berleth T. Control of leaf vascular patterning by polar auxin transport. <i>Genes and Development</i>. 2006;20(8):1015-1027. doi:<a href=\"https://doi.org/10.1101/gad.1402406\">10.1101/gad.1402406</a>","ieee":"E. Scarpella, D. Marcos, J. Friml, and T. Berleth, “Control of leaf vascular patterning by polar auxin transport,” <i>Genes and Development</i>, vol. 20, no. 8. Cold Spring Harbor Laboratory Press, pp. 1015–1027, 2006.","apa":"Scarpella, E., Marcos, D., Friml, J., &#38; Berleth, T. (2006). Control of leaf vascular patterning by polar auxin transport. <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.1402406\">https://doi.org/10.1101/gad.1402406</a>","mla":"Scarpella, Enrico, et al. “Control of Leaf Vascular Patterning by Polar Auxin Transport.” <i>Genes and Development</i>, vol. 20, no. 8, Cold Spring Harbor Laboratory Press, 2006, pp. 1015–27, doi:<a href=\"https://doi.org/10.1101/gad.1402406\">10.1101/gad.1402406</a>.","ista":"Scarpella E, Marcos D, Friml J, Berleth T. 2006. Control of leaf vascular patterning by polar auxin transport. Genes and Development. 20(8), 1015–1027."},"day":"15","author":[{"first_name":"Enrico","full_name":"Scarpella, Enrico","last_name":"Scarpella"},{"first_name":"Danielle","full_name":"Marcos, Danielle","last_name":"Marcos"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Jirí Friml","last_name":"Friml"},{"full_name":"Berleth, Thomas","first_name":"Thomas","last_name":"Berleth"}],"extern":1,"status":"public","_id":"3010","issue":"8","doi":"10.1101/gad.1402406","publist_id":"3692","abstract":[{"text":"The formation of the leaf vascular pattern has fascinated biologists for centuries. In the early leaf primordium, complex networks of procambial cells emerge from homogeneous subepidermal tissue. The molecular nature of the underlying positional information is unknown, but various lines of evidence implicate gradually restricted transport routes of the plant hormone auxin in defining sites of procambium formation. Here we show that a crucial member of the AtPIN family of auxin-efflux-associated proteins, AtPIN1, is expressed prior to pre-procambial and procambial cell fate markers in domains that become restricted toward sites of procambium formation. Subcellular AtPIN1 polarity indicates that auxin is directed to distinct &quot;convergence points&quot; in the epidermis, from where it defines the positions of major veins. Integrated polarities in all emerging veins indicate auxin drainage toward pre-existing veins, but veins display divergent polarities as they become connected at both ends. Auxin application and transport inhibition reveal that convergence point positioning and AtPIN1 expression domain dynamics are self-organizing, auxin-transport-dependent processes. We derive a model for self-regulated, reiterative patterning of all vein orders and postulate at its onset a common epidermal auxin-focusing mechanism for major-vein positioning and phyllotactic patterning.","lang":"eng"}],"intvolume":"        20","date_created":"2018-12-11T12:00:51Z","page":"1015 - 1027","year":"2006","publication":"Genes and Development","volume":20,"publisher":"Cold Spring Harbor Laboratory Press","date_published":"2006-04-15T00:00:00Z","title":"Control of leaf vascular patterning by polar auxin transport","quality_controlled":0},{"month":"05","type":"journal_article","publication_status":"published","date_updated":"2021-01-12T07:40:27Z","author":[{"last_name":"Wiśniewska","first_name":"Justyna","full_name":"Wiśniewska, Justyna"},{"full_name":"Xu, Jian","first_name":"Jian","last_name":"Xu"},{"first_name":"Daniela","full_name":"Seifertová, Daniela","last_name":"Seifertová"},{"first_name":"Philip","full_name":"Brewer, Philip B","last_name":"Brewer"},{"full_name":"Růžička, Kamil","first_name":"Kamil","last_name":"Růžička"},{"full_name":"Blilou, Ikram","first_name":"Ikram","last_name":"Blilou"},{"first_name":"David","full_name":"Rouquié, David","last_name":"Rouquié"},{"orcid":"0000-0002-8510-9739","full_name":"Eva Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"},{"full_name":"Scheres, Ben","first_name":"Ben","last_name":"Scheres"},{"orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"extern":1,"day":"12","citation":{"mla":"Wiśniewska, Justyna, et al. “Polar PIN Localization Directs Auxin Flow in Plants.” <i>Science</i>, vol. 312, no. 5775, American Association for the Advancement of Science, 2006, doi:<a href=\"https://doi.org/10.1126/science.1121356\">10.1126/science.1121356</a>.","apa":"Wiśniewska, J., Xu, J., Seifertová, D., Brewer, P., Růžička, K., Blilou, I., … Friml, J. (2006). Polar PIN localization directs auxin flow in plants. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1121356\">https://doi.org/10.1126/science.1121356</a>","ista":"Wiśniewska J, Xu J, Seifertová D, Brewer P, Růžička K, Blilou I, Rouquié D, Benková E, Scheres B, Friml J. 2006. Polar PIN localization directs auxin flow in plants. Science. 312(5775).","chicago":"Wiśniewska, Justyna, Jian Xu, Daniela Seifertová, Philip Brewer, Kamil Růžička, Ikram Blilou, David Rouquié, Eva Benková, Ben Scheres, and Jiří Friml. “Polar PIN Localization Directs Auxin Flow in Plants.” <i>Science</i>. American Association for the Advancement of Science, 2006. <a href=\"https://doi.org/10.1126/science.1121356\">https://doi.org/10.1126/science.1121356</a>.","short":"J. Wiśniewska, J. Xu, D. Seifertová, P. Brewer, K. Růžička, I. Blilou, D. Rouquié, E. Benková, B. Scheres, J. Friml, Science 312 (2006).","ama":"Wiśniewska J, Xu J, Seifertová D, et al. Polar PIN localization directs auxin flow in plants. <i>Science</i>. 2006;312(5775). doi:<a href=\"https://doi.org/10.1126/science.1121356\">10.1126/science.1121356</a>","ieee":"J. Wiśniewska <i>et al.</i>, “Polar PIN localization directs auxin flow in plants,” <i>Science</i>, vol. 312, no. 5775. American Association for the Advancement of Science, 2006."},"_id":"3011","status":"public","issue":"5775","publist_id":"3691","doi":"10.1126/science.1121356","abstract":[{"text":"Polar flow of the phytohormone auxin requires plasma membrane‐associated PIN proteins and underlies multiple developmental processes in plants. Here we address the importance of the polarity of subcellular PIN localization for the directionality of auxin transport in Arabidopsis thaliana. Expression of different PINs in the root epidermis revealed the importance of PIN polar positions for directional auxin flow and root gravitropic growth. Interfering with sequence-embedded polarity signals directly demonstrates that PIN polarity is a primary factor in determining the direction of auxin flow in meristematic tissues. This finding provides a crucial piece in the puzzle of how auxin flow can be redirected via rapid changes in PIN polarity.","lang":"eng"}],"date_created":"2018-12-11T12:00:51Z","intvolume":"       312","year":"2006","volume":312,"publication":"Science","publisher":"American Association for the Advancement of Science","date_published":"2006-05-12T00:00:00Z","title":"Polar PIN localization directs auxin flow in plants","quality_controlled":0},{"publisher":"American Association for the Advancement of Science","quality_controlled":0,"title":"PIN proteins perform a rate-limiting function in cellular auxin efflux","date_published":"2006-05-12T00:00:00Z","page":"914 - 918","date_created":"2018-12-11T12:00:51Z","intvolume":"       312","volume":312,"publication":"Science","year":"2006","_id":"3012","status":"public","abstract":[{"text":"Intercellular flow of the phytohormone auxin underpins multiple developmental processes in plants. Plant-specific pin-formed (PIN) proteins and several phosphoglycoprotein (PGP) transporters are crucial factors in auxin transport-related development, yet the molecular function of PINs remains unknown. Here, we show that PINs mediate auxin efflux from mammalian and yeast cells without needing additional plant-specific factors. Conditional gain-of-function alleles and quantitative measurements of auxin accumulation in Arabidopsis and tobacco cultured cells revealed that the action of PINs in auxin efflux is distinct from PGP, rate-limiting, specific to auxins, and sensitive to auxin transport inhibitors. This suggests a direct involvement of PINs in catalyzing cellular auxin efflux.","lang":"eng"}],"doi":"10.1126/science.1123542","publist_id":"3690","issue":"5775","month":"05","type":"journal_article","extern":1,"author":[{"first_name":"Jan","full_name":"Petrášek, Jan","last_name":"Petrášek"},{"full_name":"Mravec, Jozef","first_name":"Jozef","last_name":"Mravec"},{"last_name":"Bouchard","full_name":"Bouchard, Rodolphe","first_name":"Rodolphe"},{"first_name":"Joshua","full_name":"Blakeslee, Joshua","last_name":"Blakeslee"},{"id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda F","full_name":"Melinda Abas","last_name":"Abas"},{"last_name":"Seifertová","first_name":"Daniela","full_name":"Seifertová, Daniela"},{"first_name":"Justyna","full_name":"Wiśniewska, Justyna","last_name":"Wiśniewska"},{"last_name":"Tadele","first_name":"Zerihun","full_name":"Tadele, Zerihun"},{"last_name":"Kubeš","full_name":"Kubeš, Martin","first_name":"Martin"},{"last_name":"Čovanová","first_name":"Milada","full_name":"Čovanová, Milada"},{"last_name":"Dhonukshe","first_name":"Pankaj","full_name":"Dhonukshe, Pankaj"},{"first_name":"Petr","full_name":"Skůpa, Petr","last_name":"Skůpa"},{"orcid":"0000-0002-8510-9739","full_name":"Eva Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"},{"last_name":"Perry","first_name":"Lucie","full_name":"Perry, Lucie"},{"last_name":"Křeček","first_name":"Pavel","full_name":"Křeček, Pavel"},{"last_name":"Lee","first_name":"Ok","full_name":"Lee, Ok Ran"},{"last_name":"Fink","first_name":"Gerald","full_name":"Fink, Gerald R"},{"first_name":"Markus","full_name":"Geisler, Markus","last_name":"Geisler"},{"last_name":"Murphy","full_name":"Murphy, Angus S","first_name":"Angus"},{"last_name":"Luschnig","first_name":"Christian","full_name":"Luschnig, Christian"},{"last_name":"Zažímalová","first_name":"Eva","full_name":"Zažímalová, Eva"},{"last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596"}],"citation":{"apa":"Petrášek, J., Mravec, J., Bouchard, R., Blakeslee, J., Abas, M. F., Seifertová, D., … Friml, J. (2006). PIN proteins perform a rate-limiting function in cellular auxin efflux. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1123542\">https://doi.org/10.1126/science.1123542</a>","mla":"Petrášek, Jan, et al. “PIN Proteins Perform a Rate-Limiting Function in Cellular Auxin Efflux.” <i>Science</i>, vol. 312, no. 5775, American Association for the Advancement of Science, 2006, pp. 914–18, doi:<a href=\"https://doi.org/10.1126/science.1123542\">10.1126/science.1123542</a>.","ista":"Petrášek J, Mravec J, Bouchard R, Blakeslee J, Abas MF, Seifertová D, Wiśniewska J, Tadele Z, Kubeš M, Čovanová M, Dhonukshe P, Skůpa P, Benková E, Perry L, Křeček P, Lee O, Fink G, Geisler M, Murphy A, Luschnig C, Zažímalová E, Friml J. 2006. PIN proteins perform a rate-limiting function in cellular auxin efflux. Science. 312(5775), 914–918.","ieee":"J. Petrášek <i>et al.</i>, “PIN proteins perform a rate-limiting function in cellular auxin efflux,” <i>Science</i>, vol. 312, no. 5775. American Association for the Advancement of Science, pp. 914–918, 2006.","chicago":"Petrášek, Jan, Jozef Mravec, Rodolphe Bouchard, Joshua Blakeslee, Melinda F Abas, Daniela Seifertová, Justyna Wiśniewska, et al. “PIN Proteins Perform a Rate-Limiting Function in Cellular Auxin Efflux.” <i>Science</i>. American Association for the Advancement of Science, 2006. <a href=\"https://doi.org/10.1126/science.1123542\">https://doi.org/10.1126/science.1123542</a>.","ama":"Petrášek J, Mravec J, Bouchard R, et al. PIN proteins perform a rate-limiting function in cellular auxin efflux. <i>Science</i>. 2006;312(5775):914-918. doi:<a href=\"https://doi.org/10.1126/science.1123542\">10.1126/science.1123542</a>","short":"J. Petrášek, J. Mravec, R. Bouchard, J. Blakeslee, M.F. Abas, D. Seifertová, J. Wiśniewska, Z. Tadele, M. Kubeš, M. Čovanová, P. Dhonukshe, P. Skůpa, E. Benková, L. Perry, P. Křeček, O. Lee, G. Fink, M. Geisler, A. Murphy, C. Luschnig, E. Zažímalová, J. Friml, Science 312 (2006) 914–918."},"day":"12","date_updated":"2021-01-12T07:40:27Z","publication_status":"published"},{"page":"104 - 107","date_created":"2018-12-11T12:00:52Z","intvolume":"         1","volume":1,"publication":"Nature Protocols","year":"2006","publisher":"Nature Publishing Group","quality_controlled":0,"title":"Immunocytochemical technique for protein localization in sections of plant tissues","date_published":"2006-06-01T00:00:00Z","month":"06","type":"journal_article","author":[{"last_name":"Paciorek","full_name":"Paciorek, Tomasz","first_name":"Tomasz"},{"first_name":"Michael","full_name":"Sauer, Michael","last_name":"Sauer"},{"full_name":"Balla, Jozef","first_name":"Jozef","last_name":"Balla"},{"last_name":"Wiśniewska","full_name":"Wiśniewska, Justyna","first_name":"Justyna"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"extern":1,"day":"01","citation":{"ieee":"T. Paciorek, M. Sauer, J. Balla, J. Wiśniewska, and J. Friml, “Immunocytochemical technique for protein localization in sections of plant tissues,” <i>Nature Protocols</i>, vol. 1, no. 1. Nature Publishing Group, pp. 104–107, 2006.","ama":"Paciorek T, Sauer M, Balla J, Wiśniewska J, Friml J. Immunocytochemical technique for protein localization in sections of plant tissues. <i>Nature Protocols</i>. 2006;1(1):104-107. doi:<a href=\"https://doi.org/10.1038/nprot.2006.16\">10.1038/nprot.2006.16</a>","short":"T. Paciorek, M. Sauer, J. Balla, J. Wiśniewska, J. Friml, Nature Protocols 1 (2006) 104–107.","chicago":"Paciorek, Tomasz, Michael Sauer, Jozef Balla, Justyna Wiśniewska, and Jiří Friml. “Immunocytochemical Technique for Protein Localization in Sections of Plant Tissues.” <i>Nature Protocols</i>. Nature Publishing Group, 2006. <a href=\"https://doi.org/10.1038/nprot.2006.16\">https://doi.org/10.1038/nprot.2006.16</a>.","ista":"Paciorek T, Sauer M, Balla J, Wiśniewska J, Friml J. 2006. Immunocytochemical technique for protein localization in sections of plant tissues. Nature Protocols. 1(1), 104–107.","apa":"Paciorek, T., Sauer, M., Balla, J., Wiśniewska, J., &#38; Friml, J. (2006). Immunocytochemical technique for protein localization in sections of plant tissues. <i>Nature Protocols</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nprot.2006.16\">https://doi.org/10.1038/nprot.2006.16</a>","mla":"Paciorek, Tomasz, et al. “Immunocytochemical Technique for Protein Localization in Sections of Plant Tissues.” <i>Nature Protocols</i>, vol. 1, no. 1, Nature Publishing Group, 2006, pp. 104–07, doi:<a href=\"https://doi.org/10.1038/nprot.2006.16\">10.1038/nprot.2006.16</a>."},"publication_status":"published","date_updated":"2021-01-12T07:40:27Z","_id":"3013","status":"public","publist_id":"3689","doi":"10.1038/nprot.2006.16","abstract":[{"text":"There is a growing demand for methods that allow rapid and reliable in situ localization of proteins in plant cells. The immunocytochemistry protocol presented here can be used routinely to observe protein localization patterns in tissue sections of various plant species. This protocol is especially suitable for plant species with more-complex tissue architecture (such as maize, Zea mays), which makes it difficult to use an easier whole-mount procedure for protein localization. To facilitate the antibody-antigen reaction, it is necessary to include a wax-embedding and tissue-sectioning step. The protocol consists of the following procedures: chemical fixation of tissue, dehydration, wax embedding, sectioning, dewaxing, rehydration, blocking and antibody incubation. The detailed protocol, recommended controls and troubleshooting are presented here, along with examples of applications.","lang":"eng"}],"issue":"1"},{"publist_id":"3687","doi":"10.1038/nprot.2006.226","abstract":[{"text":"Plant biology is currently confronted with an overflow of expression profile data provided by high-throughput microarray transcription analyses. However, the tissue and cellular resolution of these techniques is limited. Thus, it is still necessary to examine the expression pattern of selected candidate genes at a cellular level. Here we present an in situ mRNA hybridization method that is routinely used in the analysis of gene expression patterns. The protocol is optimized for mRNA localizations in sectioned tissue of Arabidopsis seedlings including embryos, roots, hypocotyls, young primary leaves and flowers. The detailed protocol, recommended controls and troubleshooting are presented along with examples of application. The total time for the process is 10 days.","lang":"eng"}],"issue":"3","status":"public","_id":"3014","citation":{"apa":"Brewer, P., Heisler, M., Hejátko, J., Friml, J., &#38; Benková, E. (2006). In situ hybridization for mRNA detection in Arabidopsis tissue sections. <i>Nature Protocols</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nprot.2006.226\">https://doi.org/10.1038/nprot.2006.226</a>","mla":"Brewer, Philip, et al. “In Situ Hybridization for MRNA Detection in Arabidopsis Tissue Sections.” <i>Nature Protocols</i>, vol. 1, no. 3, Nature Publishing Group, 2006, pp. 1462–67, doi:<a href=\"https://doi.org/10.1038/nprot.2006.226\">10.1038/nprot.2006.226</a>.","ista":"Brewer P, Heisler M, Hejátko J, Friml J, Benková E. 2006. In situ hybridization for mRNA detection in Arabidopsis tissue sections. Nature Protocols. 1(3), 1462–1467.","chicago":"Brewer, Philip, Marcus Heisler, Jan Hejátko, Jiří Friml, and Eva Benková. “In Situ Hybridization for MRNA Detection in Arabidopsis Tissue Sections.” <i>Nature Protocols</i>. Nature Publishing Group, 2006. <a href=\"https://doi.org/10.1038/nprot.2006.226\">https://doi.org/10.1038/nprot.2006.226</a>.","ama":"Brewer P, Heisler M, Hejátko J, Friml J, Benková E. In situ hybridization for mRNA detection in Arabidopsis tissue sections. <i>Nature Protocols</i>. 2006;1(3):1462-1467. doi:<a href=\"https://doi.org/10.1038/nprot.2006.226\">10.1038/nprot.2006.226</a>","short":"P. Brewer, M. Heisler, J. Hejátko, J. Friml, E. Benková, Nature Protocols 1 (2006) 1462–1467.","ieee":"P. Brewer, M. Heisler, J. Hejátko, J. Friml, and E. Benková, “In situ hybridization for mRNA detection in Arabidopsis tissue sections,” <i>Nature Protocols</i>, vol. 1, no. 3. Nature Publishing Group, pp. 1462–1467, 2006."},"day":"01","author":[{"first_name":"Philip","full_name":"Brewer, Philip B","last_name":"Brewer"},{"first_name":"Marcus","full_name":"Heisler, Marcus G","last_name":"Heisler"},{"first_name":"Jan","full_name":"Hejátko, Jan","last_name":"Hejátko"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Jirí Friml","last_name":"Friml"},{"first_name":"Eva","full_name":"Eva Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková"}],"extern":1,"date_updated":"2021-01-12T07:40:28Z","publication_status":"published","type":"journal_article","month":"08","quality_controlled":0,"title":"In situ hybridization for mRNA detection in Arabidopsis tissue sections","date_published":"2006-08-01T00:00:00Z","publisher":"Nature Publishing Group","publication":"Nature Protocols","volume":1,"year":"2006","page":"1462 - 1467","date_created":"2018-12-11T12:00:52Z","intvolume":"         1"},{"page":"98 - 103","date_created":"2018-12-11T12:00:52Z","intvolume":"         1","volume":1,"publication":"Nature Protocols","year":"2006","publisher":"Nature Publishing Group","quality_controlled":0,"date_published":"2006-06-01T00:00:00Z","title":"Immunocytochemical techniques for whole mount in situ protein localization in plants","month":"06","type":"journal_article","author":[{"last_name":"Sauer","full_name":"Sauer, Michael","first_name":"Michael"},{"last_name":"Paciorek","full_name":"Paciorek, Tomasz","first_name":"Tomasz"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Eva Benková"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596"}],"extern":1,"day":"01","citation":{"ieee":"M. Sauer, T. Paciorek, E. Benková, and J. Friml, “Immunocytochemical techniques for whole mount in situ protein localization in plants,” <i>Nature Protocols</i>, vol. 1, no. 1. Nature Publishing Group, pp. 98–103, 2006.","ama":"Sauer M, Paciorek T, Benková E, Friml J. Immunocytochemical techniques for whole mount in situ protein localization in plants. <i>Nature Protocols</i>. 2006;1(1):98-103. doi:<a href=\"https://doi.org/10.1038/nprot.2006.15\">10.1038/nprot.2006.15</a>","short":"M. Sauer, T. Paciorek, E. Benková, J. Friml, Nature Protocols 1 (2006) 98–103.","chicago":"Sauer, Michael, Tomasz Paciorek, Eva Benková, and Jiří Friml. “Immunocytochemical Techniques for Whole Mount in Situ Protein Localization in Plants.” <i>Nature Protocols</i>. Nature Publishing Group, 2006. <a href=\"https://doi.org/10.1038/nprot.2006.15\">https://doi.org/10.1038/nprot.2006.15</a>.","ista":"Sauer M, Paciorek T, Benková E, Friml J. 2006. Immunocytochemical techniques for whole mount in situ protein localization in plants. Nature Protocols. 1(1), 98–103.","mla":"Sauer, Michael, et al. “Immunocytochemical Techniques for Whole Mount in Situ Protein Localization in Plants.” <i>Nature Protocols</i>, vol. 1, no. 1, Nature Publishing Group, 2006, pp. 98–103, doi:<a href=\"https://doi.org/10.1038/nprot.2006.15\">10.1038/nprot.2006.15</a>.","apa":"Sauer, M., Paciorek, T., Benková, E., &#38; Friml, J. (2006). Immunocytochemical techniques for whole mount in situ protein localization in plants. <i>Nature Protocols</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nprot.2006.15\">https://doi.org/10.1038/nprot.2006.15</a>"},"publication_status":"published","date_updated":"2021-01-12T07:40:28Z","_id":"3015","status":"public","doi":"10.1038/nprot.2006.15","publist_id":"3688","abstract":[{"text":"As the field of plant molecular biology is swiftly advancing, a need has been created for methods that allow rapid and reliable in situ localization of proteins in plant cells. Here we describe a whole-mount 'immunolocalization' technique for various plant tissues, including roots, hypocotyls, cotyledons, young primary leaves and embryos of Arabidopsis thaliana and other species. The detailed protocol, recommended controls and troubleshooting are presented, along with examples of applications. The protocol consists of five main procedures: tissue fixation, tissue permeation, blocking, primary and secondary antibody incubation. Notably, the first procedure (tissue fixation) includes several steps (4-12) that are absolutely necessary for protein localization in hypocotyls, cotyledons and young primary leaves but should be omitted for other tissues. The protocol is usually done in 3 days, but could also be completed in 2 days.","lang":"eng"}],"issue":"1"},{"publication_status":"published","date_updated":"2021-11-16T07:53:09Z","oa_version":"None","citation":{"ama":"Sauer M, Balla J, Luschnig C, et al. Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity. <i>Genes and Development</i>. 2006;20(20):2902-2911. doi:<a href=\"https://doi.org/10.1101/gad.390806\">10.1101/gad.390806</a>","short":"M. Sauer, J. Balla, C. Luschnig, J. Wiśniewska, V. Reinöhl, J. Friml, E. Benková, Genes and Development 20 (2006) 2902–2911.","chicago":"Sauer, Michael, Jozef Balla, Christian Luschnig, Justyna Wiśniewska, Vilém Reinöhl, Jiří Friml, and Eva Benková. “Canalization of Auxin Flow by Aux/IAA-ARF-Dependent Feedback Regulation of PIN Polarity.” <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press, 2006. <a href=\"https://doi.org/10.1101/gad.390806\">https://doi.org/10.1101/gad.390806</a>.","ieee":"M. Sauer <i>et al.</i>, “Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity,” <i>Genes and Development</i>, vol. 20, no. 20. Cold Spring Harbor Laboratory Press, pp. 2902–2911, 2006.","ista":"Sauer M, Balla J, Luschnig C, Wiśniewska J, Reinöhl V, Friml J, Benková E. 2006. Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity. Genes and Development. 20(20), 2902–2911.","apa":"Sauer, M., Balla, J., Luschnig, C., Wiśniewska, J., Reinöhl, V., Friml, J., &#38; Benková, E. (2006). Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity. <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.390806\">https://doi.org/10.1101/gad.390806</a>","mla":"Sauer, Michael, et al. “Canalization of Auxin Flow by Aux/IAA-ARF-Dependent Feedback Regulation of PIN Polarity.” <i>Genes and Development</i>, vol. 20, no. 20, Cold Spring Harbor Laboratory Press, 2006, pp. 2902–11, doi:<a href=\"https://doi.org/10.1101/gad.390806\">10.1101/gad.390806</a>."},"day":"15","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","author":[{"first_name":"Michael","full_name":"Sauer, Michael","last_name":"Sauer"},{"full_name":"Balla, Jozef","first_name":"Jozef","last_name":"Balla"},{"last_name":"Luschnig","full_name":"Luschnig, Christian","first_name":"Christian"},{"full_name":"Wiśniewska, Justyna","first_name":"Justyna","last_name":"Wiśniewska"},{"first_name":"Vilém","full_name":"Reinöhl, Vilém","last_name":"Reinöhl"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva"}],"type":"journal_article","month":"10","related_material":{"link":[{"relation":"erratum","url":"http://genesdev.cshlp.org/content/21/11/1431.short"}]},"issue":"20","abstract":[{"lang":"eng","text":"Plant development is characterized by a profound ability to regenerate and form tissues with new axes of polarity. An unsolved question concerns how the position within a tissue and cues from neighboring cells are integrated to specify the polarity of individual cells. The canalization hypothesis proposes a feedback effect of the phytohormone auxin on the directionality of intercellular auxin flow as a means to polarize tissues. Here we identify a cellular and molecular mechanism for canalization. Local auxin application, wounding, or auxin accumulation during de novo organ formation lead to rearrangements in the subcellular polar localization of PIN auxin transport components. This auxin effect on PIN polarity is cell-specific, does not depend on PIN transcription, and involves the Aux/IAA-ARF (indole-3-acetic acid-auxin response factor) signaling pathway. Our data suggest that auxin acts as polarizing cue, which links individual cell polarity with tissue and organ polarity through control of PIN polar targeting. This feedback regulation provides a conceptual framework for polarization during multiple regenerative and patterning processes in plants."}],"publist_id":"3686","doi":"10.1101/gad.390806","status":"public","_id":"3016","year":"2006","publication":"Genes and Development","volume":20,"language":[{"iso":"eng"}],"article_processing_charge":"No","date_created":"2018-12-11T12:00:53Z","intvolume":"        20","page":"2902 - 2911","date_published":"2006-10-15T00:00:00Z","title":"Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity","publisher":"Cold Spring Harbor Laboratory Press"},{"publication_status":"published","date_updated":"2021-01-12T07:40:29Z","oa_version":"None","author":[{"full_name":"Tanaka, Hirokazu","first_name":"Hirokazu","last_name":"Tanaka"},{"last_name":"Dhonukshe","full_name":"Dhonukshe, Pankaj","first_name":"Pankaj"},{"last_name":"Brewer","first_name":"Philip","full_name":"Brewer, Philip"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","first_name":"Jirí"}],"extern":"1","citation":{"apa":"Tanaka, H., Dhonukshe, P., Brewer, P., &#38; Friml, J. (2006). Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development. <i>Cellular and Molecular Life Sciences</i>. Birkhäuser. <a href=\"https://doi.org/10.1007/s00018-006-6116-5\">https://doi.org/10.1007/s00018-006-6116-5</a>","mla":"Tanaka, Hirokazu, et al. “Spatiotemporal Asymmetric Auxin Distribution: A Means to Coordinate Plant Development.” <i>Cellular and Molecular Life Sciences</i>, vol. 63, no. 23, Birkhäuser, 2006, pp. 2738–54, doi:<a href=\"https://doi.org/10.1007/s00018-006-6116-5\">10.1007/s00018-006-6116-5</a>.","ista":"Tanaka H, Dhonukshe P, Brewer P, Friml J. 2006. Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development. Cellular and Molecular Life Sciences. 63(23), 2738–2754.","ieee":"H. Tanaka, P. Dhonukshe, P. Brewer, and J. Friml, “Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development,” <i>Cellular and Molecular Life Sciences</i>, vol. 63, no. 23. Birkhäuser, pp. 2738–2754, 2006.","chicago":"Tanaka, Hirokazu, Pankaj Dhonukshe, Philip Brewer, and Jiří Friml. “Spatiotemporal Asymmetric Auxin Distribution: A Means to Coordinate Plant Development.” <i>Cellular and Molecular Life Sciences</i>. Birkhäuser, 2006. <a href=\"https://doi.org/10.1007/s00018-006-6116-5\">https://doi.org/10.1007/s00018-006-6116-5</a>.","short":"H. Tanaka, P. Dhonukshe, P. Brewer, J. Friml, Cellular and Molecular Life Sciences 63 (2006) 2738–2754.","ama":"Tanaka H, Dhonukshe P, Brewer P, Friml J. Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development. <i>Cellular and Molecular Life Sciences</i>. 2006;63(23):2738-2754. doi:<a href=\"https://doi.org/10.1007/s00018-006-6116-5\">10.1007/s00018-006-6116-5</a>"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","month":"12","type":"journal_article","issue":"23","doi":"10.1007/s00018-006-6116-5","abstract":[{"text":"The plant hormone auxin plays crucial roles in regulating plant growth development, including embryo and root patterning, organ formation, vascular tissue differentiation and growth responses to environmental stimuli. Asymmetric auxin distribution patterns have been observed within tissues, and these so-called auxin gradients change dynamically during different developmental processes. Most auxin is synthesized in the shoot and distributed directionally throughout the plant. This polar auxin transport is mediated by auxin influx and efflux facilitators, whose subcellular polar localizations guide the direction of auxin flow. The polar localization of PIN auxin efflux carriers changes in response to developmental and external cues in order to channel auxin flow in a regulated manner for organized growth. Auxin itself modulates the expression and subcellular localization of PIN proteins, contributing to a complex pattern of feedback regulation. Here we review the available information mainly from studies of a model plant, Arabidopsis thaliana, on the generation of auxin gradients, the regulation of polar auxin transport and further downstream cellular events.","lang":"eng"}],"publist_id":"3685","_id":"3017","status":"public","year":"2006","language":[{"iso":"eng"}],"volume":63,"publication":"Cellular and Molecular Life Sciences","date_created":"2018-12-11T12:00:53Z","intvolume":"        63","page":"2738 - 2754","title":"Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development","date_published":"2006-12-01T00:00:00Z","quality_controlled":"1","publisher":"Birkhäuser"},{"year":"2006","publication":"Plant Cell","volume":18,"intvolume":"        18","date_created":"2018-12-11T12:00:53Z","page":"3171 - 3181","title":"Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1","date_published":"2006-11-01T00:00:00Z","quality_controlled":0,"publisher":"American Society of Plant Biologists","date_updated":"2021-01-12T07:40:29Z","publication_status":"published","day":"01","citation":{"ieee":"J. Kleine Vehn, P. Dhonukshe, R. Swarup, M. Bennett, and J. Friml, “Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1,” <i>Plant Cell</i>, vol. 18, no. 11. American Society of Plant Biologists, pp. 3171–3181, 2006.","short":"J. Kleine Vehn, P. Dhonukshe, R. Swarup, M. Bennett, J. Friml, Plant Cell 18 (2006) 3171–3181.","ama":"Kleine Vehn J, Dhonukshe P, Swarup R, Bennett M, Friml J. Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1. <i>Plant Cell</i>. 2006;18(11):3171-3181. doi:<a href=\"https://doi.org/10.1105/tpc.106.042770\">10.1105/tpc.106.042770</a>","chicago":"Kleine Vehn, Jürgen, Pankaj Dhonukshe, Ranjan Swarup, Malcolm Bennett, and Jiří Friml. “Subcellular Trafficking of the Arabidopsis Auxin Influx Carrier AUX1 Uses a Novel Pathway Distinct from PIN1.” <i>Plant Cell</i>. American Society of Plant Biologists, 2006. <a href=\"https://doi.org/10.1105/tpc.106.042770\">https://doi.org/10.1105/tpc.106.042770</a>.","ista":"Kleine Vehn J, Dhonukshe P, Swarup R, Bennett M, Friml J. 2006. Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1. Plant Cell. 18(11), 3171–3181.","mla":"Kleine Vehn, Jürgen, et al. “Subcellular Trafficking of the Arabidopsis Auxin Influx Carrier AUX1 Uses a Novel Pathway Distinct from PIN1.” <i>Plant Cell</i>, vol. 18, no. 11, American Society of Plant Biologists, 2006, pp. 3171–81, doi:<a href=\"https://doi.org/10.1105/tpc.106.042770\">10.1105/tpc.106.042770</a>.","apa":"Kleine Vehn, J., Dhonukshe, P., Swarup, R., Bennett, M., &#38; Friml, J. (2006). Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.106.042770\">https://doi.org/10.1105/tpc.106.042770</a>"},"author":[{"first_name":"Jürgen","full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn"},{"full_name":"Dhonukshe, Pankaj","first_name":"Pankaj","last_name":"Dhonukshe"},{"first_name":"Ranjan","full_name":"Swarup, Ranjan","last_name":"Swarup"},{"first_name":"Malcolm","full_name":"Bennett, Malcolm","last_name":"Bennett"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Jirí Friml"}],"extern":1,"type":"journal_article","month":"11","issue":"11","abstract":[{"text":"The directional flow of the plant hormone auxin mediates multiple developmental processes, including patterning and tropisms. Apical and basal plasma membrane localization of AUXIN-RESISTANT1 (AUX1) and PIN-FORMED1 (PIN1) auxin transport components underpins the directionality of intercellular auxin flow in Arabidopsis thaliana roots. Here, we examined the mechanism of polar trafficking of AUX1. Real-time live cell analysis along with subcellular markers revealed that AUX1 resides at the apical plasma membrane of protophloem cells and at highly dynamic subpopulations of Golgi apparatus and endosomes in all cell types. Plasma membrane and intracellular pools of AUX1 are interconnected by actin-dependent constitutive trafficking, which is not sensitive to the vesicle trafficking inhibitor brefeldin A. AUX1 subcellular dynamics are not influenced by the auxin influx inhibitor NOA but are blocked by the auxin efflux inhibitors TIBA and PBA. Furthermore, auxin transport inhibitors and interference with the sterol composition of membranes disrupt polar AUX1 distribution at the plasma membrane. Compared with PIN1 trafficking, AUX1 dynamics display different sensitivities to trafficking inhibitors and are independent of the endosomal trafficking regulator ARF GEF GNOM. Hence, AUX1 uses a novel trafficking pathway in plants that is distinct from PIN trafficking, providing an additional mechanism for the fine regulation of auxin transport.","lang":"eng"}],"doi":"10.1105/tpc.106.042770","publist_id":"3684","status":"public","_id":"3018"},{"status":"public","_id":"3020","doi":"10.1038/nprot.2006.333","abstract":[{"text":"High throughput microarray transcription analyses provide us with the expression profiles for large amounts of plant genes. However, their tissue and cellular resolution is limited. Thus, for detailed functional analysis, it is still necessary to examine the expression pattern of selected candidate genes at a cellular level. Here, we present an in situ mRNA hybridization method that is routinely used for the analysis of plant gene expression patterns. The protocol is optimized for whole mount mRNA localizations in Arabidopsis seedling tissues including embryos, roots, hypocotyls and young primary leaves. It can also be used for comparable tissues in other species. Part of the protocol can also be automated and performed by a liquid handling robot. Here we present a detailed protocol, recommended controls and troubleshooting, along with examples of several applications. The total time to carry out the entire procedure is ∼7 d, depending on the tissue used.","lang":"eng"}],"publist_id":"3683","issue":"4","type":"journal_article","month":"11","citation":{"mla":"Hejátko, Jan, et al. “In Situ Hybridization Technique for MRNA Detection in Whole Mount Arabidopsis Samples.” <i>Nature Protocols</i>, vol. 1, no. 4, Nature Publishing Group, 2006, pp. 1939–46, doi:<a href=\"https://doi.org/10.1038/nprot.2006.333\">10.1038/nprot.2006.333</a>.","apa":"Hejátko, J., Blilou, I., Brewer, P., Friml, J., Scheres, B., &#38; Benková, E. (2006). In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples. <i>Nature Protocols</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nprot.2006.333\">https://doi.org/10.1038/nprot.2006.333</a>","ista":"Hejátko J, Blilou I, Brewer P, Friml J, Scheres B, Benková E. 2006. In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples. Nature Protocols. 1(4), 1939–1946.","ieee":"J. Hejátko, I. Blilou, P. Brewer, J. Friml, B. Scheres, and E. Benková, “In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples,” <i>Nature Protocols</i>, vol. 1, no. 4. Nature Publishing Group, pp. 1939–1946, 2006.","chicago":"Hejátko, Jan, Ikram Blilou, Philip Brewer, Jiří Friml, Ben Scheres, and Eva Benková. “In Situ Hybridization Technique for MRNA Detection in Whole Mount Arabidopsis Samples.” <i>Nature Protocols</i>. Nature Publishing Group, 2006. <a href=\"https://doi.org/10.1038/nprot.2006.333\">https://doi.org/10.1038/nprot.2006.333</a>.","ama":"Hejátko J, Blilou I, Brewer P, Friml J, Scheres B, Benková E. In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples. <i>Nature Protocols</i>. 2006;1(4):1939-1946. doi:<a href=\"https://doi.org/10.1038/nprot.2006.333\">10.1038/nprot.2006.333</a>","short":"J. Hejátko, I. Blilou, P. Brewer, J. Friml, B. Scheres, E. Benková, Nature Protocols 1 (2006) 1939–1946."},"day":"01","extern":1,"author":[{"last_name":"Hejátko","first_name":"Jan","full_name":"Hejátko, Jan"},{"last_name":"Blilou","first_name":"Ikram","full_name":"Blilou, Ikram"},{"last_name":"Brewer","full_name":"Brewer, Philip B","first_name":"Philip"},{"full_name":"Jirí Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"last_name":"Scheres","full_name":"Scheres, Ben","first_name":"Ben"},{"last_name":"Benková","full_name":"Eva Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"date_updated":"2021-01-12T07:40:30Z","publication_status":"published","publisher":"Nature Publishing Group","quality_controlled":0,"title":"In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples","date_published":"2006-11-01T00:00:00Z","page":"1939 - 1946","date_created":"2018-12-11T12:00:54Z","intvolume":"         1","publication":"Nature Protocols","volume":1,"year":"2006"},{"date_published":"2006-06-14T00:00:00Z","title":"In vivo migration A germ cell perspective","quality_controlled":0,"publisher":"Annual Reviews","year":"2006","volume":22,"publication":"Annual Review of Cell and Developmental Biology","date_created":"2018-12-11T12:01:42Z","intvolume":"        22","page":"237 - 265","doi":"10.1146/annurev.cellbio.22.010305.103337","abstract":[{"text":"The basic concepts of the molecular machinery that mediates cell migration have been gleaned from cell culture systems. However, the three-dimensional environment within an organism presents migrating cells with a much greater challenge. They must move between and among other cells while interpreting multiple attractive and repulsive cues to choose their proper path. They must coordinate their cell adhesion with their surroundings and know when to start and stop moving. New insights into the control of these remaining mysteries have emerged from genetic dissection and live imaging of germ cell migration in Drosophila, zebrafish, and mouse embryos. In this review, we first describe germ cell migration in cellular and mechanistic detail in these different model systems. We then compare these systems to highlight the emerging principles. Finally, we contrast the migration of germ cells with that of immune and cancer cells to outline the conserved and different mechanisms.","lang":"eng"}],"publist_id":"3543","_id":"3152","status":"public","publication_status":"published","date_updated":"2021-01-12T07:41:25Z","author":[{"full_name":"Kunwar, Prabhat S","first_name":"Prabhat","last_name":"Kunwar"},{"last_name":"Siekhaus","full_name":"Daria Siekhaus","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353"},{"last_name":"Lehmann","full_name":"Lehmann, Ruth","first_name":"Ruth"}],"extern":1,"citation":{"ista":"Kunwar P, Siekhaus DE, Lehmann R. 2006. In vivo migration A germ cell perspective. Annual Review of Cell and Developmental Biology. 22, 237–265.","mla":"Kunwar, Prabhat, et al. “In Vivo Migration A Germ Cell Perspective.” <i>Annual Review of Cell and Developmental Biology</i>, vol. 22, Annual Reviews, 2006, pp. 237–65, doi:<a href=\"https://doi.org/10.1146/annurev.cellbio.22.010305.103337\">10.1146/annurev.cellbio.22.010305.103337</a>.","apa":"Kunwar, P., Siekhaus, D. E., &#38; Lehmann, R. (2006). In vivo migration A germ cell perspective. <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev.cellbio.22.010305.103337\">https://doi.org/10.1146/annurev.cellbio.22.010305.103337</a>","ieee":"P. Kunwar, D. E. Siekhaus, and R. Lehmann, “In vivo migration A germ cell perspective,” <i>Annual Review of Cell and Developmental Biology</i>, vol. 22. Annual Reviews, pp. 237–265, 2006.","ama":"Kunwar P, Siekhaus DE, Lehmann R. In vivo migration A germ cell perspective. <i>Annual Review of Cell and Developmental Biology</i>. 2006;22:237-265. doi:<a href=\"https://doi.org/10.1146/annurev.cellbio.22.010305.103337\">10.1146/annurev.cellbio.22.010305.103337</a>","short":"P. Kunwar, D.E. Siekhaus, R. Lehmann, Annual Review of Cell and Developmental Biology 22 (2006) 237–265.","chicago":"Kunwar, Prabhat, Daria E Siekhaus, and Ruth Lehmann. “In Vivo Migration A Germ Cell Perspective.” <i>Annual Review of Cell and Developmental Biology</i>. Annual Reviews, 2006. <a href=\"https://doi.org/10.1146/annurev.cellbio.22.010305.103337\">https://doi.org/10.1146/annurev.cellbio.22.010305.103337</a>."},"day":"14","month":"06","type":"journal_article"}]