[{"intvolume":"       137","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2010","title":"Plasma membrane-bound AGC3 kinases phosphorylate PIN auxin carriers at TPRXS(N/S) motifs to direct apical PIN recycling","date_created":"2018-12-11T12:01:12Z","date_published":"2010-10-01T00:00:00Z","oa_version":"None","_id":"3073","language":[{"iso":"eng"}],"abstract":[{"text":"Polar membrane cargo delivery is crucial for establishing cell polarity and for directional transport processes. In plants, polar trafficking mediates the dynamic asymmetric distribution of PIN FORMED (PIN) carriers, which drive polar cell-to-cell transport of the hormone auxin, thereby generating auxin maxima and minima that control development. The Arabidopsis PINOID (PID) protein kinase instructs apical PIN localization by phosphorylating PINs. Here, we identified the PID homologs WAG1 and WAG2 as new PIN polarity regulators. We show that the AGC3 kinases PID, WAG1 and WAG2, and not other plant AGC kinases, instruct recruitment of PINs into the apical recycling pathway by phosphorylating the middle serine in three conserved TPRXS(N/S) motifs within the PIN central hydrophilic loop. Our results put forward a model by which apolarly localized PID, WAG1 and WAG2 phosphorylate PINs at the plasma membrane after default non-polar PIN secretion, and trigger endocytosis-dependent apical PIN recycling. This phosphorylation-triggered apical PIN recycling competes with ARF-GEF GNOM-dependent basal recycling to promote apical PIN localization. In planta, expression domains of PID, WAG1 and WAG2 correlate with apical localization of PINs in those cell types, indicating the importance of these kinases for apical PIN localization. Our data show that by directing polar PIN localization and PIN-mediated polar auxin transport, the three AGC3 kinases redundantly regulate cotyledon development, root meristem size and gravitropic response, indicating their involvement in both programmed and adaptive plant development.","lang":"eng"}],"quality_controlled":"1","publication_status":"published","publist_id":"3627","type":"journal_article","day":"01","citation":{"chicago":"Dhonukshe, Pankaj, Fang Huang, Carlos Galván Ampudia, Ari Mähönen, Jürgen Kleine Vehn, Jian Xu, Ab Quint, et al. “Plasma Membrane-Bound AGC3 Kinases Phosphorylate PIN Auxin Carriers at TPRXS(N/S) Motifs to Direct Apical PIN Recycling.” <i>Development</i>. Company of Biologists, 2010. <a href=\"https://doi.org/10.1242/dev.052456\">https://doi.org/10.1242/dev.052456</a>.","ista":"Dhonukshe P, Huang F, Galván Ampudia C, Mähönen A, Kleine Vehn J, Xu J, Quint A, Prasad K, Friml J, Scheres B, Offringa R. 2010. Plasma membrane-bound AGC3 kinases phosphorylate PIN auxin carriers at TPRXS(N/S) motifs to direct apical PIN recycling. Development. 137(19), 3245–3255.","ama":"Dhonukshe P, Huang F, Galván Ampudia C, et al. Plasma membrane-bound AGC3 kinases phosphorylate PIN auxin carriers at TPRXS(N/S) motifs to direct apical PIN recycling. <i>Development</i>. 2010;137(19):3245-3255. doi:<a href=\"https://doi.org/10.1242/dev.052456\">10.1242/dev.052456</a>","apa":"Dhonukshe, P., Huang, F., Galván Ampudia, C., Mähönen, A., Kleine Vehn, J., Xu, J., … Offringa, R. (2010). Plasma membrane-bound AGC3 kinases phosphorylate PIN auxin carriers at TPRXS(N/S) motifs to direct apical PIN recycling. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.052456\">https://doi.org/10.1242/dev.052456</a>","ieee":"P. Dhonukshe <i>et al.</i>, “Plasma membrane-bound AGC3 kinases phosphorylate PIN auxin carriers at TPRXS(N/S) motifs to direct apical PIN recycling,” <i>Development</i>, vol. 137, no. 19. Company of Biologists, pp. 3245–3255, 2010.","short":"P. Dhonukshe, F. Huang, C. Galván Ampudia, A. Mähönen, J. Kleine Vehn, J. Xu, A. Quint, K. Prasad, J. Friml, B. Scheres, R. Offringa, Development 137 (2010) 3245–3255.","mla":"Dhonukshe, Pankaj, et al. “Plasma Membrane-Bound AGC3 Kinases Phosphorylate PIN Auxin Carriers at TPRXS(N/S) Motifs to Direct Apical PIN Recycling.” <i>Development</i>, vol. 137, no. 19, Company of Biologists, 2010, pp. 3245–55, doi:<a href=\"https://doi.org/10.1242/dev.052456\">10.1242/dev.052456</a>."},"article_processing_charge":"No","page":"3245 - 3255","status":"public","publisher":"Company of Biologists","extern":"1","issue":"19","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1242/dev.127415"}]},"doi":"10.1242/dev.052456","author":[{"last_name":"Dhonukshe","full_name":"Dhonukshe, Pankaj","first_name":"Pankaj"},{"last_name":"Huang","full_name":"Huang, Fang","first_name":"Fang"},{"last_name":"Galván Ampudia","full_name":"Galván Ampudia, Carlos","first_name":"Carlos"},{"full_name":"Mähönen, Ari","last_name":"Mähönen","first_name":"Ari"},{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine Vehn, Jürgen"},{"full_name":"Xu, Jian","last_name":"Xu","first_name":"Jian"},{"last_name":"Quint","full_name":"Quint, Ab","first_name":"Ab"},{"full_name":"Prasad, Kalika","last_name":"Prasad","first_name":"Kalika"},{"full_name":"Friml, Jiřĺ","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiřĺ","orcid":"0000-0002-8302-7596"},{"last_name":"Scheres","full_name":"Scheres, Ben","first_name":"Ben"},{"first_name":"Remko","last_name":"Offringa","full_name":"Offringa, Remko"}],"volume":137,"publication":"Development","date_updated":"2021-01-12T07:40:52Z","month":"10"},{"day":"01","citation":{"apa":"Ge, L., Peer, W., Robert, S., Swarup, R., Ye, S., Prigge, M., … Estelle, M. (2010). Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1 is required for polar auxin transport. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.110.074195\">https://doi.org/10.1105/tpc.110.074195</a>","ieee":"L. Ge <i>et al.</i>, “Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1 is required for polar auxin transport,” <i>Plant Cell</i>, vol. 22, no. 6. American Society of Plant Biologists, pp. 1749–1761, 2010.","short":"L. Ge, W. Peer, S. Robert, R. Swarup, S. Ye, M. Prigge, J. Cohen, J. Friml, A. Murphy, D. Tang, M. Estelle, Plant Cell 22 (2010) 1749–1761.","mla":"Ge, Lei, et al. “Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1 Is Required for Polar Auxin Transport.” <i>Plant Cell</i>, vol. 22, no. 6, American Society of Plant Biologists, 2010, pp. 1749–61, doi:<a href=\"https://doi.org/10.1105/tpc.110.074195\">10.1105/tpc.110.074195</a>.","chicago":"Ge, Lei, Wendy Peer, Stéphanie Robert, Ranjan Swarup, Songqing Ye, Michael Prigge, Jerry Cohen, et al. “Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1 Is Required for Polar Auxin Transport.” <i>Plant Cell</i>. American Society of Plant Biologists, 2010. <a href=\"https://doi.org/10.1105/tpc.110.074195\">https://doi.org/10.1105/tpc.110.074195</a>.","ista":"Ge L, Peer W, Robert S, Swarup R, Ye S, Prigge M, Cohen J, Friml J, Murphy A, Tang D, Estelle M. 2010. Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1 is required for polar auxin transport. Plant Cell. 22(6), 1749–1761.","ama":"Ge L, Peer W, Robert S, et al. Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1 is required for polar auxin transport. <i>Plant Cell</i>. 2010;22(6):1749-1761. doi:<a href=\"https://doi.org/10.1105/tpc.110.074195\">10.1105/tpc.110.074195</a>"},"abstract":[{"lang":"eng","text":"Auxin is an essential phytohormone that regulates many aspects of plant development. To identify new genes that function in auxin signaling, we performed a genetic screen for Arabidopsis thaliana mutants with an alteration in the expression of the auxin-responsive reporter DR5rev:GFP (for green fluorescent protein). One of the mutants recovered in this screen, called weak auxin response1 (wxr1), has a defect in auxin response and exhibits a variety of auxin-related growth defects in the root. Polar auxin transport is reduced in wxr1 seedlings, resulting in auxin accumulation in the hypocotyl and cotyledons and a reduction in auxin levels in the root apex. In addition, the levels of the PIN auxin transport proteins are reduced in the wxr1 root. We also show that WXR1 is ROOT UV-B SENSITIVE2 (RUS2), a member of the broadly conserved DUF647 domain protein family found in diverse eukaryotic organisms. Our data indicate that RUS2/WXR1 is required for auxin transport and to maintain the normal levels of PIN proteins in the root."}],"_id":"3074","quality_controlled":0,"publication_status":"published","type":"journal_article","publist_id":"3628","title":"Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1 is required for polar auxin transport","date_created":"2018-12-11T12:01:13Z","date_published":"2010-06-01T00:00:00Z","intvolume":"        22","year":"2010","volume":22,"author":[{"first_name":"Lei","full_name":"Ge, Lei","last_name":"Ge"},{"last_name":"Peer","full_name":"Peer, Wendy A","first_name":"Wendy"},{"last_name":"Robert","full_name":"Robert, Stéphanie","first_name":"Stéphanie"},{"full_name":"Swarup, Ranjan","last_name":"Swarup","first_name":"Ranjan"},{"first_name":"Songqing","full_name":"Ye, Songqing","last_name":"Ye"},{"first_name":"Michael","full_name":"Prigge, Michael J","last_name":"Prigge"},{"last_name":"Cohen","full_name":"Cohen, Jerry D","first_name":"Jerry"},{"last_name":"Friml","full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596"},{"first_name":"Angus","full_name":"Murphy, Angus S","last_name":"Murphy"},{"last_name":"Tang","full_name":"Tang, Ding","first_name":"Ding"},{"first_name":"Mark","full_name":"Estelle, Mark A","last_name":"Estelle"}],"date_updated":"2021-01-12T07:40:52Z","publication":"Plant Cell","month":"06","doi":"10.1105/tpc.110.074195","extern":1,"issue":"6","page":"1749 - 1761","status":"public","publisher":"American Society of Plant Biologists"},{"extern":1,"issue":"1","status":"public","page":"111 - 121","publisher":"Cell Press","month":"10","volume":143,"author":[{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"last_name":"Barbez","full_name":"Barbez, Elke","first_name":"Elke"},{"full_name":"Sauer, Michael","last_name":"Sauer","first_name":"Michael"},{"first_name":"Tomasz","last_name":"Paciorek","full_name":"Paciorek, Tomasz"},{"first_name":"Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","full_name":"Pawel Baster","last_name":"Baster"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"first_name":"Jing","last_name":"Zhang","full_name":"Zhang, Jing"},{"orcid":"0000-0002-1998-6741","first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","full_name":"Sibu Simon"},{"first_name":"Milada","last_name":"Čovanová","full_name":"Čovanová, Milada"},{"first_name":"Kenichiro","full_name":"Hayashi, Kenichiro","last_name":"Hayashi"},{"full_name":"Dhonukshe, Pankaj","last_name":"Dhonukshe","first_name":"Pankaj"},{"last_name":"Yang","full_name":"Yang, Zhenbiao","first_name":"Zhenbiao"},{"first_name":"Sebastian","full_name":"Bednarek, Sebastian Y","last_name":"Bednarek"},{"last_name":"Jones","full_name":"Jones, Alan M","first_name":"Alan"},{"last_name":"Luschnig","full_name":"Luschnig, Christian","first_name":"Christian"},{"first_name":"Fernando","full_name":"Aniento, Fernando","last_name":"Aniento"},{"last_name":"Zažímalová","full_name":"Zažímalová, Eva","first_name":"Eva"},{"last_name":"Friml","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"date_updated":"2021-01-12T07:40:52Z","publication":"Cell","doi":"10.1016/j.cell.2010.09.027","date_created":"2018-12-11T12:01:13Z","title":"ABP1 mediates auxin inhibition of clathrin-dependent endocytosis in Arabidopsis","date_published":"2010-10-01T00:00:00Z","year":"2010","intvolume":"       143","citation":{"apa":"Robert, S., Kleine Vehn, J., Barbez, E., Sauer, M., Paciorek, T., Baster, P., … Friml, J. (2010). ABP1 mediates auxin inhibition of clathrin-dependent endocytosis in Arabidopsis. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2010.09.027\">https://doi.org/10.1016/j.cell.2010.09.027</a>","mla":"Robert, Stéphanie, et al. “ABP1 Mediates Auxin Inhibition of Clathrin-Dependent Endocytosis in Arabidopsis.” <i>Cell</i>, vol. 143, no. 1, Cell Press, 2010, pp. 111–21, doi:<a href=\"https://doi.org/10.1016/j.cell.2010.09.027\">10.1016/j.cell.2010.09.027</a>.","short":"S. Robert, J. Kleine Vehn, E. Barbez, M. Sauer, T. Paciorek, P. Baster, S. Vanneste, J. Zhang, S. Simon, M. Čovanová, K. Hayashi, P. Dhonukshe, Z. Yang, S. Bednarek, A. Jones, C. Luschnig, F. Aniento, E. Zažímalová, J. Friml, Cell 143 (2010) 111–121.","ieee":"S. Robert <i>et al.</i>, “ABP1 mediates auxin inhibition of clathrin-dependent endocytosis in Arabidopsis,” <i>Cell</i>, vol. 143, no. 1. Cell Press, pp. 111–121, 2010.","chicago":"Robert, Stéphanie, Jürgen Kleine Vehn, Elke Barbez, Michael Sauer, Tomasz Paciorek, Pawel Baster, Steffen Vanneste, et al. “ABP1 Mediates Auxin Inhibition of Clathrin-Dependent Endocytosis in Arabidopsis.” <i>Cell</i>. Cell Press, 2010. <a href=\"https://doi.org/10.1016/j.cell.2010.09.027\">https://doi.org/10.1016/j.cell.2010.09.027</a>.","ama":"Robert S, Kleine Vehn J, Barbez E, et al. ABP1 mediates auxin inhibition of clathrin-dependent endocytosis in Arabidopsis. <i>Cell</i>. 2010;143(1):111-121. doi:<a href=\"https://doi.org/10.1016/j.cell.2010.09.027\">10.1016/j.cell.2010.09.027</a>","ista":"Robert S, Kleine Vehn J, Barbez E, Sauer M, Paciorek T, Baster P, Vanneste S, Zhang J, Simon S, Čovanová M, Hayashi K, Dhonukshe P, Yang Z, Bednarek S, Jones A, Luschnig C, Aniento F, Zažímalová E, Friml J. 2010. ABP1 mediates auxin inhibition of clathrin-dependent endocytosis in Arabidopsis. Cell. 143(1), 111–121."},"day":"01","quality_controlled":0,"publication_status":"published","type":"journal_article","publist_id":"3626","abstract":[{"text":"\nSpatial distribution of the plant hormone auxin regulates multiple aspects of plant development. These self-regulating auxin gradients are established by the action of PIN auxin transporters, whose activity is regulated by their constitutive cycling between the plasma membrane and endosomes. Here, we show that auxin signaling by the auxin receptor AUXIN-BINDING PROTEIN 1 (ABP1) inhibits the clathrin-mediated internalization of PIN proteins. ABP1 acts as a positive factor in clathrin recruitment to the plasma membrane, thereby promoting endocytosis. Auxin binding to ABP1 interferes with this action and leads to the inhibition of clathrin-mediated endocytosis. Our study demonstrates that ABP1 mediates a nontranscriptional auxin signaling that regulates the evolutionarily conserved process of clathrin-mediated endocytosis and suggests that this signaling may be essential for the developmentally important feedback of auxin on its own transport.","lang":"eng"}],"_id":"3075"},{"type":"journal_article","publist_id":"3625","quality_controlled":0,"publication_status":"published","abstract":[{"lang":"eng","text":"Auxin is a multifunctional hormone essential for plant development and pattern formation. A nuclear auxin-signaling system controlling auxin-induced gene expression is well established, but cytoplasmic auxin signaling, as in its coordination of cell polarization, is unexplored. We found a cytoplasmic auxin-signaling mechanism that modulates the interdigitated growth of Arabidopsis leaf epidermal pavement cells (PCs), which develop interdigitated lobes and indentations to form a puzzle-piece shape in a two-dimensional plane. PC interdigitation is compromised in leaves deficient in either auxin biosynthesis or its export mediated by PINFORMED 1 localized at the lobe tip. Auxin coordinately activates two Rho GTPases, ROP2 and ROP6, which promote the formation of complementary lobes and indentations, respectively. Activation of these ROPs by auxin occurs within 30 s and depends on AUXIN-BINDING PROTEIN 1. These findings reveal Rho GTPase-based auxin-signaling mechanisms, which modulate the spatial coordination of cell expansion across a field of cells."}],"_id":"3076","citation":{"ieee":"T. Xu <i>et al.</i>, “Cell surface- and Rho GTPase-based auxin signaling controls cellular interdigitation in Arabidopsis,” <i>Cell</i>, vol. 143, no. 1. Cell Press, pp. 99–110, 2010.","short":"T. Xu, M. Wen, S. Nagawa, Y. Fu, J. Chen, M. Wu, C. Perrot Rechenmann, J. Friml, A. Jones, Z. Yang, Cell 143 (2010) 99–110.","mla":"Xu, Tongda, et al. “Cell Surface- and Rho GTPase-Based Auxin Signaling Controls Cellular Interdigitation in Arabidopsis.” <i>Cell</i>, vol. 143, no. 1, Cell Press, 2010, pp. 99–110, doi:<a href=\"https://doi.org/10.1016/j.cell.2010.09.003\">10.1016/j.cell.2010.09.003</a>.","apa":"Xu, T., Wen, M., Nagawa, S., Fu, Y., Chen, J., Wu, M., … Yang, Z. (2010). Cell surface- and Rho GTPase-based auxin signaling controls cellular interdigitation in Arabidopsis. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2010.09.003\">https://doi.org/10.1016/j.cell.2010.09.003</a>","ista":"Xu T, Wen M, Nagawa S, Fu Y, Chen J, Wu M, Perrot Rechenmann C, Friml J, Jones A, Yang Z. 2010. Cell surface- and Rho GTPase-based auxin signaling controls cellular interdigitation in Arabidopsis. Cell. 143(1), 99–110.","ama":"Xu T, Wen M, Nagawa S, et al. Cell surface- and Rho GTPase-based auxin signaling controls cellular interdigitation in Arabidopsis. <i>Cell</i>. 2010;143(1):99-110. doi:<a href=\"https://doi.org/10.1016/j.cell.2010.09.003\">10.1016/j.cell.2010.09.003</a>","chicago":"Xu, Tongda, Mingzhang Wen, Shingo Nagawa, Ying Fu, Jin Chen, Ming Wu, Catherine Perrot Rechenmann, Jiří Friml, Alan Jones, and Zhenbiao Yang. “Cell Surface- and Rho GTPase-Based Auxin Signaling Controls Cellular Interdigitation in Arabidopsis.” <i>Cell</i>. Cell Press, 2010. <a href=\"https://doi.org/10.1016/j.cell.2010.09.003\">https://doi.org/10.1016/j.cell.2010.09.003</a>."},"day":"01","year":"2010","intvolume":"       143","date_published":"2010-10-01T00:00:00Z","date_created":"2018-12-11T12:01:14Z","title":"Cell surface- and Rho GTPase-based auxin signaling controls cellular interdigitation in Arabidopsis","doi":"10.1016/j.cell.2010.09.003","month":"10","publication":"Cell","date_updated":"2021-01-12T07:40:53Z","author":[{"first_name":"Tongda","full_name":"Xu, Tongda","last_name":"Xu"},{"first_name":"Mingzhang","last_name":"Wen","full_name":"Wen, Mingzhang"},{"first_name":"Shingo","full_name":"Nagawa, Shingo","last_name":"Nagawa"},{"first_name":"Ying","last_name":"Fu","full_name":"Fu, Ying"},{"first_name":"Jin","last_name":"Chen","full_name":"Chen, Jin-Gui"},{"full_name":"Wu, Ming-Jing","last_name":"Wu","first_name":"Ming"},{"first_name":"Catherine","last_name":"Perrot Rechenmann","full_name":"Perrot-Rechenmann, Catherine"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Jirí Friml","last_name":"Friml"},{"full_name":"Jones, Alan M","last_name":"Jones","first_name":"Alan"},{"first_name":"Zhenbiao","full_name":"Yang, Zhenbiao","last_name":"Yang"}],"volume":143,"publisher":"Cell Press","status":"public","page":"99 - 110","issue":"1","extern":1},{"issue":"2","extern":"1","pmid":1,"publisher":"American Society of Plant Biologists","status":"public","page":"458 - 462","date_updated":"2021-01-12T07:40:53Z","publication":"Plant Physiology","volume":154,"author":[{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Angharad","full_name":"Jones, Angharad","last_name":"Jones"}],"month":"10","oa":1,"doi":"10.1104/pp.110.161380","date_published":"2010-10-01T00:00:00Z","title":"Endoplasmic reticulum: The rising compartment in auxin biology","date_created":"2018-12-11T12:01:14Z","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/20921163"}],"intvolume":"       154","year":"2010","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","citation":{"mla":"Friml, Jiří, and Angharad Jones. “Endoplasmic Reticulum: The Rising Compartment in Auxin Biology.” <i>Plant Physiology</i>, vol. 154, no. 2, American Society of Plant Biologists, 2010, pp. 458–62, doi:<a href=\"https://doi.org/10.1104/pp.110.161380\">10.1104/pp.110.161380</a>.","ieee":"J. Friml and A. Jones, “Endoplasmic reticulum: The rising compartment in auxin biology,” <i>Plant Physiology</i>, vol. 154, no. 2. American Society of Plant Biologists, pp. 458–462, 2010.","short":"J. Friml, A. Jones, Plant Physiology 154 (2010) 458–462.","apa":"Friml, J., &#38; Jones, A. (2010). Endoplasmic reticulum: The rising compartment in auxin biology. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.110.161380\">https://doi.org/10.1104/pp.110.161380</a>","ama":"Friml J, Jones A. Endoplasmic reticulum: The rising compartment in auxin biology. <i>Plant Physiology</i>. 2010;154(2):458-462. doi:<a href=\"https://doi.org/10.1104/pp.110.161380\">10.1104/pp.110.161380</a>","ista":"Friml J, Jones A. 2010. Endoplasmic reticulum: The rising compartment in auxin biology. Plant Physiology. 154(2), 458–462.","chicago":"Friml, Jiří, and Angharad Jones. “Endoplasmic Reticulum: The Rising Compartment in Auxin Biology.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2010. <a href=\"https://doi.org/10.1104/pp.110.161380\">https://doi.org/10.1104/pp.110.161380</a>."},"_id":"3077","language":[{"iso":"eng"}],"external_id":{"pmid":["20921163"]},"publist_id":"3624","type":"journal_article","publication_status":"published"},{"day":"12","citation":{"chicago":"Sauer, Michael, and Jiří Friml. “Immunolocalization of Proteins in Plants .” In <i>Plant Developmental Biology</i>, edited by Lars Hennig and Claudia Köhler, 655:253–63. Humana Press, 2010. <a href=\"https://doi.org/10.1007/978-1-60761-765-5_17\">https://doi.org/10.1007/978-1-60761-765-5_17</a>.","ista":"Sauer M, Friml J. 2010.Immunolocalization of proteins in plants . In: Plant Developmental Biology. Methods in Molecular Biology, vol. 655, 253–263.","ama":"Sauer M, Friml J. Immunolocalization of proteins in plants . In: Hennig L, Köhler C, eds. <i>Plant Developmental Biology</i>. Vol 655. Humana Press; 2010:253-263. doi:<a href=\"https://doi.org/10.1007/978-1-60761-765-5_17\">10.1007/978-1-60761-765-5_17</a>","apa":"Sauer, M., &#38; Friml, J. (2010). Immunolocalization of proteins in plants . In L. Hennig &#38; C. Köhler (Eds.), <i>Plant Developmental Biology</i> (Vol. 655, pp. 253–263). Humana Press. <a href=\"https://doi.org/10.1007/978-1-60761-765-5_17\">https://doi.org/10.1007/978-1-60761-765-5_17</a>","short":"M. Sauer, J. Friml, in:, L. Hennig, C. Köhler (Eds.), Plant Developmental Biology, Humana Press, 2010, pp. 253–263.","ieee":"M. Sauer and J. Friml, “Immunolocalization of proteins in plants ,” in <i>Plant Developmental Biology</i>, vol. 655, L. Hennig and C. Köhler, Eds. Humana Press, 2010, pp. 253–263.","mla":"Sauer, Michael, and Jiří Friml. “Immunolocalization of Proteins in Plants .” <i>Plant Developmental Biology</i>, edited by Lars Hennig and Claudia Köhler, vol. 655, Humana Press, 2010, pp. 253–63, doi:<a href=\"https://doi.org/10.1007/978-1-60761-765-5_17\">10.1007/978-1-60761-765-5_17</a>."},"publication_status":"published","quality_controlled":0,"publist_id":"3623","type":"book_chapter","_id":"3078","abstract":[{"lang":"eng","text":"Rapid advances in the field of plant biology, especially in plant cell biology, have created the need for methods that allow the localization of proteins in situ at subcellular resolution. Although in many cases recombinant proteins with fluorescent proteins can fulfill this task, antibody-based immunological detection of proteins is a complementary technique, which avoids the risk of inducing side effects by a fusion protein, such as misexpression, mistargeting, altered stability, or toxicity. Moreover, recombinant protein techniques are applicable only to a rather limited set of model plants. The immunolocalization protocols presented here can be used to display protein localization patterns in different tissues of various plant species. This chapter describes a whole mount immunolocalization protocol, which has been extensively used in Arabidopsis roots and some above-ground tissues, and that also works in other species. Additionally, for bulky or hard tissue types, a variation of this protocol for paraffin-embedded sections is given."}],"date_created":"2018-12-11T12:01:14Z","title":"Immunolocalization of proteins in plants ","alternative_title":["Methods in Molecular Biology"],"date_published":"2010-08-12T00:00:00Z","year":"2010","intvolume":"       655","month":"08","volume":655,"author":[{"full_name":"Sauer, Michael","last_name":"Sauer","first_name":"Michael"},{"last_name":"Friml","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publication":"Plant Developmental Biology","date_updated":"2021-01-12T07:40:53Z","doi":"10.1007/978-1-60761-765-5_17","editor":[{"first_name":"Lars","full_name":"Hennig, Lars","last_name":"Hennig"},{"full_name":"Köhler, Claudia","last_name":"Köhler","first_name":"Claudia"}],"extern":1,"status":"public","page":"253 - 263","publisher":"Humana Press"},{"abstract":[{"lang":"eng","text":"Plant development is exceptionally flexible as manifested by its potential for organogenesis and regeneration, which are processes involving rearrangements of tissue polarities. Fundamental questions concern how individual cells can polarize in a coordinated manner to integrate into the multicellular context. In canalization models, the signaling molecule auxin acts as a polarizing cue, and feedback on the intercellular auxin flow is key for synchronized polarity rearrangements. We provide a novel mechanistic framework for canalization, based on up-to-date experimental data and minimal, biologically plausible assumptions. Our model combines the intracellular auxin signaling for expression of PINFORMED (PIN) auxin transporters and the theoretical postulation of extracellular auxin signaling for modulation of PIN subcellular dynamics. Computer simulations faithfully and robustly recapitulated the experimentally observed patterns of tissue polarity and asymmetric auxin distribution during formation and regeneration of vascular systems and during the competitive regulation of shoot branching by apical dominance. Additionally, our model generated new predictions that could be experimentally validated, highlighting a mechanistically conceivable explanation for the PIN polarization and canalization of the auxin flow in plants."}],"_id":"3079","publication_status":"published","quality_controlled":0,"publist_id":"3622","type":"journal_article","citation":{"apa":"Wabnik, K. T., Kleine Vehn, J., Balla, J., Sauer, M., Naramoto, S., Reinöhl, V., … Friml, J. (2010). Emergence of tissue polarization from synergy of intracellular and extracellular auxin signaling. <i>Molecular Systems Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/msb.2010.103\">https://doi.org/10.1038/msb.2010.103</a>","mla":"Wabnik, Krzysztof T., et al. “Emergence of Tissue Polarization from Synergy of Intracellular and Extracellular Auxin Signaling.” <i>Molecular Systems Biology</i>, vol. 6, Nature Publishing Group, 2010, doi:<a href=\"https://doi.org/10.1038/msb.2010.103\">10.1038/msb.2010.103</a>.","short":"K.T. Wabnik, J. Kleine Vehn, J. Balla, M. Sauer, S. Naramoto, V. Reinöhl, R. Merks, W. Govaerts, J. Friml, Molecular Systems Biology 6 (2010).","ieee":"K. T. Wabnik <i>et al.</i>, “Emergence of tissue polarization from synergy of intracellular and extracellular auxin signaling,” <i>Molecular Systems Biology</i>, vol. 6. Nature Publishing Group, 2010.","chicago":"Wabnik, Krzysztof T, Jürgen Kleine Vehn, Jozef Balla, Michael Sauer, Satoshi Naramoto, Vilém Reinöhl, Roeland Merks, Willy Govaerts, and Jiří Friml. “Emergence of Tissue Polarization from Synergy of Intracellular and Extracellular Auxin Signaling.” <i>Molecular Systems Biology</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/msb.2010.103\">https://doi.org/10.1038/msb.2010.103</a>.","ama":"Wabnik KT, Kleine Vehn J, Balla J, et al. Emergence of tissue polarization from synergy of intracellular and extracellular auxin signaling. <i>Molecular Systems Biology</i>. 2010;6. doi:<a href=\"https://doi.org/10.1038/msb.2010.103\">10.1038/msb.2010.103</a>","ista":"Wabnik KT, Kleine Vehn J, Balla J, Sauer M, Naramoto S, Reinöhl V, Merks R, Govaerts W, Friml J. 2010. Emergence of tissue polarization from synergy of intracellular and extracellular auxin signaling. Molecular Systems Biology. 6."},"day":"21","intvolume":"         6","year":"2010","title":"Emergence of tissue polarization from synergy of intracellular and extracellular auxin signaling","date_created":"2018-12-11T12:01:15Z","date_published":"2010-12-21T00:00:00Z","doi":"10.1038/msb.2010.103","volume":6,"author":[{"orcid":"0000-0001-7263-0560","first_name":"Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik","full_name":"Krzysztof Wabnik"},{"first_name":"Jürgen","full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn"},{"first_name":"Jozef","last_name":"Balla","full_name":"Balla, Jozef"},{"first_name":"Michael","last_name":"Sauer","full_name":"Sauer, Michael"},{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"full_name":"Reinöhl, Vilém","last_name":"Reinöhl","first_name":"Vilém"},{"full_name":"Merks, Roeland M","last_name":"Merks","first_name":"Roeland"},{"full_name":"Govaerts, Willy J","last_name":"Govaerts","first_name":"Willy"},{"full_name":"Jirí Friml","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"date_updated":"2021-01-12T07:40:54Z","publication":"Molecular Systems Biology","month":"12","status":"public","publisher":"Nature Publishing Group","extern":1},{"citation":{"ieee":"J. Kleine Vehn, Z. Ding, A. Jones, M. Tasaka, M. Morita, and J. Friml, “Gravity induced PIN transcytosis for polarization of auxin fluxes in gravity sensing root cells,” <i>PNAS</i>, vol. 107, no. 51. National Academy of Sciences, pp. 22344–22349, 2010.","short":"J. Kleine Vehn, Z. Ding, A. Jones, M. Tasaka, M. Morita, J. Friml, PNAS 107 (2010) 22344–22349.","mla":"Kleine Vehn, Jürgen, et al. “Gravity Induced PIN Transcytosis for Polarization of Auxin Fluxes in Gravity Sensing Root Cells.” <i>PNAS</i>, vol. 107, no. 51, National Academy of Sciences, 2010, pp. 22344–49, doi:<a href=\"https://doi.org/10.1073/pnas.1013145107\">10.1073/pnas.1013145107</a>.","apa":"Kleine Vehn, J., Ding, Z., Jones, A., Tasaka, M., Morita, M., &#38; Friml, J. (2010). Gravity induced PIN transcytosis for polarization of auxin fluxes in gravity sensing root cells. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1013145107\">https://doi.org/10.1073/pnas.1013145107</a>","ista":"Kleine Vehn J, Ding Z, Jones A, Tasaka M, Morita M, Friml J. 2010. Gravity induced PIN transcytosis for polarization of auxin fluxes in gravity sensing root cells. PNAS. 107(51), 22344–22349.","ama":"Kleine Vehn J, Ding Z, Jones A, Tasaka M, Morita M, Friml J. Gravity induced PIN transcytosis for polarization of auxin fluxes in gravity sensing root cells. <i>PNAS</i>. 2010;107(51):22344-22349. doi:<a href=\"https://doi.org/10.1073/pnas.1013145107\">10.1073/pnas.1013145107</a>","chicago":"Kleine Vehn, Jürgen, Zhaojun Ding, Angharad Jones, Masao Tasaka, Miyo Morita, and Jiří Friml. “Gravity Induced PIN Transcytosis for Polarization of Auxin Fluxes in Gravity Sensing Root Cells.” <i>PNAS</i>. National Academy of Sciences, 2010. <a href=\"https://doi.org/10.1073/pnas.1013145107\">https://doi.org/10.1073/pnas.1013145107</a>."},"day":"21","abstract":[{"text":"Auxin is an essential plant-specific regulator of patterning processes that also controls directional growth of roots and shoots. In response to gravity stimulation, the PIN3 auxin transporter polarizes to the bottomside of gravity-sensing root cells, presumably redirecting the auxin flux toward the lower side of the root and triggering gravitropic bending. By combining live-cell imaging techniques with pharmacological and genetic approaches, we demonstrate that PIN3 polarization does not require secretion of de novo synthesized proteins or protein degradation, but instead involves rapid, transient stimulation of PIN endocytosis, presumably via a clathrin-dependent pathway. Moreover, gravity-induced PIN3 polarization requires the activity of the guanine nucleotide exchange factors for ARF GTPases (ARF-GEF) GNOM-dependent polar-targeting path-ways and might involve endosome-based PIN3 translocation from one cell side to another. Our data suggest that gravity perception acts at several instances of PIN3 trafficking, ultimately leading to the polarization of PIN3, which presumably aligns auxin fluxes with gravity vector and mediates downstream root gravitropic response.","lang":"eng"}],"_id":"3080","quality_controlled":0,"publication_status":"published","type":"journal_article","publist_id":"3620","date_created":"2018-12-11T12:01:15Z","title":"Gravity induced PIN transcytosis for polarization of auxin fluxes in gravity sensing root cells","date_published":"2010-12-21T00:00:00Z","intvolume":"       107","year":"2010","volume":107,"author":[{"first_name":"Jürgen","full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn"},{"full_name":"Ding, Zhaojun","last_name":"Ding","first_name":"Zhaojun"},{"last_name":"Jones","full_name":"Jones, Angharad R","first_name":"Angharad"},{"first_name":"Masao","full_name":"Tasaka, Masao","last_name":"Tasaka"},{"last_name":"Morita","full_name":"Morita, Miyo T","first_name":"Miyo"},{"full_name":"Jirí Friml","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596"}],"publication":"PNAS","date_updated":"2021-01-12T07:40:55Z","month":"12","doi":"10.1073/pnas.1013145107","extern":1,"issue":"51","status":"public","page":"22344 - 22349","publisher":"National Academy of Sciences"},{"type":"journal_article","publist_id":"3621","quality_controlled":0,"publication_status":"published","abstract":[{"text":"Endocytosis is crucial for various cellular functions and development of multicellular organisms. In mammals and yeast, ADP-ribosylation factor (ARF) GTPases, key components of vesicle formation, and their regulators ARF-guanine nucleotide exchange factors (GEFs) and ARF-GTPase-activating protein (GAPs) mediate endocytosis. A similar role has not been established in plants,mainly because of the lack of the canonical ARF and ARF-GEF components that are involved in endocytosis in other eukaryotes. In this study, we revealed a regulatory mechanism of endocytosis in plants based on ARF GTPase activity.Weidentified that ARF-GEFGNOMand ARF-GAP VASCULAR NETWORK DEFECTIVE 3 (VAN3), both of which are involved in polar auxin transport-dependent morphogenesis, localize at the plasma membranes as well as in intracellular structures. Variable angle epifluorescence microscopy revealed that GNOM and VAN3 localize to partially overlapping discrete foci at the plasmamembranes that are regularly associated with the endocytic vesicle coat clathrin. Genetic studies revealed that GNOM and VAN3 activities are required for endocytosis and internalization of plasma membrane proteins, including PIN-FORMED auxin transporters. These findings identified ARF GTPase-based regulatory mechanisms for endocytosis in plants. GNOMand VAN3 previously were proposed to function solely at the recycling endosomes and trans-Golgi networks, respectively. Therefore our findings uncovered an additional cellular function of these prominent developmental regulators.","lang":"eng"}],"_id":"3081","day":"14","citation":{"chicago":"Naramoto, Satoshi, Jürgen Kleine Vehn, Stéphanie Robert, Masaru Fujimoto, Tomoko Dainobu, Tomasz Paciorek, Takashi Ueda, et al. “ADP Ribosylation Factor Machinery Mediates Endocytosis in Plant Cells.” <i>PNAS</i>. National Academy of Sciences, 2010. <a href=\"https://doi.org/10.1073/pnas.1016260107\">https://doi.org/10.1073/pnas.1016260107</a>.","ista":"Naramoto S, Kleine Vehn J, Robert S, Fujimoto M, Dainobu T, Paciorek T, Ueda T, Nakano A, Van Montagu M, Fukuda H, Friml J. 2010. ADP ribosylation factor machinery mediates endocytosis in plant cells. PNAS. 107(50), 21890–21895.","ama":"Naramoto S, Kleine Vehn J, Robert S, et al. ADP ribosylation factor machinery mediates endocytosis in plant cells. <i>PNAS</i>. 2010;107(50):21890-21895. doi:<a href=\"https://doi.org/10.1073/pnas.1016260107\">10.1073/pnas.1016260107</a>","apa":"Naramoto, S., Kleine Vehn, J., Robert, S., Fujimoto, M., Dainobu, T., Paciorek, T., … Friml, J. (2010). ADP ribosylation factor machinery mediates endocytosis in plant cells. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1016260107\">https://doi.org/10.1073/pnas.1016260107</a>","short":"S. Naramoto, J. Kleine Vehn, S. Robert, M. Fujimoto, T. Dainobu, T. Paciorek, T. Ueda, A. Nakano, M. Van Montagu, H. Fukuda, J. Friml, PNAS 107 (2010) 21890–21895.","ieee":"S. Naramoto <i>et al.</i>, “ADP ribosylation factor machinery mediates endocytosis in plant cells,” <i>PNAS</i>, vol. 107, no. 50. National Academy of Sciences, pp. 21890–21895, 2010.","mla":"Naramoto, Satoshi, et al. “ADP Ribosylation Factor Machinery Mediates Endocytosis in Plant Cells.” <i>PNAS</i>, vol. 107, no. 50, National Academy of Sciences, 2010, pp. 21890–95, doi:<a href=\"https://doi.org/10.1073/pnas.1016260107\">10.1073/pnas.1016260107</a>."},"year":"2010","intvolume":"       107","date_published":"2010-12-14T00:00:00Z","title":"ADP ribosylation factor machinery mediates endocytosis in plant cells","date_created":"2018-12-11T12:01:15Z","doi":"10.1073/pnas.1016260107","month":"12","date_updated":"2021-01-12T07:40:55Z","publication":"PNAS","volume":107,"author":[{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"last_name":"Fujimoto","full_name":"Fujimoto, Masaru","first_name":"Masaru"},{"last_name":"Dainobu","full_name":"Dainobu, Tomoko","first_name":"Tomoko"},{"first_name":"Tomasz","last_name":"Paciorek","full_name":"Paciorek, Tomasz"},{"last_name":"Ueda","full_name":"Ueda, Takashi","first_name":"Takashi"},{"first_name":"Akihiko","last_name":"Nakano","full_name":"Nakano, Akihiko"},{"last_name":"Van Montagu","full_name":"Van Montagu, Marc C","first_name":"Marc"},{"first_name":"Hiroo","last_name":"Fukuda","full_name":"Fukuda, Hiroo"},{"last_name":"Friml","full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596"}],"publisher":"National Academy of Sciences","status":"public","page":"21890 - 21895","issue":"50","extern":1},{"doi":"10.1016/j.neuron.2010.09.027","volume":68,"author":[{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Simon Hippenmeyer","last_name":"Hippenmeyer"},{"last_name":"Youn","full_name":"Youn, Yong H","first_name":"Yong"},{"full_name":"Moon, Hyang M","last_name":"Moon","first_name":"Hyang"},{"first_name":"Kazunari","last_name":"Miyamichi","full_name":"Miyamichi, Kazunari"},{"first_name":"Hui","last_name":"Zong","full_name":"Zong, Hui"},{"first_name":"Anthony","last_name":"Wynshaw Boris","full_name":"Wynshaw-Boris, Anthony"},{"last_name":"Luo","full_name":"Luo, Liqun","first_name":"Liqun"}],"date_updated":"2021-01-12T07:41:22Z","publication":"Neuron","month":"11","page":"695 - 709","status":"public","publisher":"Elsevier","extern":1,"issue":"4","abstract":[{"text":"Coordinated migration of newly born neurons to their prospective target laminae is a prerequisite for neural circuit assembly in the developing brain. The evolutionarily conserved LIS1/NDEL1 complex is essential for neuronal migration in the mammalian cerebral cortex. The cytoplasmic nature of LIS1 and NDEL1 proteins suggest that they regulate neuronal migration cell autonomously. Here, we extend mosaic analysis with double markers (MADM) to mouse chromosome 11 where Lis1, Ndel1, and 14-3-3e{open} (encoding a LIS1/NDEL1 signaling partner) are located. Analyses of sparse and uniquely labeled mutant cells in mosaic animals reveal distinct cell-autonomous functions for these three genes. Lis1 regulates neuronal migration efficiency in a dose-dependent manner, while Ndel1 is essential for a specific, previously uncharacterized, late step of neuronal migration: entry into the target lamina. Comparisons with previous genetic perturbations of Lis1 and Ndel1 also suggest a surprising degree of cell-nonautonomous function for these proteins in regulating neuronal migration.","lang":"eng"}],"_id":"3146","publication_status":"published","quality_controlled":0,"type":"journal_article","publist_id":"3550","citation":{"chicago":"Hippenmeyer, Simon, Yong Youn, Hyang Moon, Kazunari Miyamichi, Hui Zong, Anthony Wynshaw Boris, and Liqun Luo. “Genetic Mosaic Dissection of Lis1 and Ndel1 in Neuronal Migration.” <i>Neuron</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.neuron.2010.09.027\">https://doi.org/10.1016/j.neuron.2010.09.027</a>.","ista":"Hippenmeyer S, Youn Y, Moon H, Miyamichi K, Zong H, Wynshaw Boris A, Luo L. 2010. Genetic mosaic dissection of Lis1 and Ndel1 in neuronal migration. Neuron. 68(4), 695–709.","ama":"Hippenmeyer S, Youn Y, Moon H, et al. Genetic mosaic dissection of Lis1 and Ndel1 in neuronal migration. <i>Neuron</i>. 2010;68(4):695-709. doi:<a href=\"https://doi.org/10.1016/j.neuron.2010.09.027\">10.1016/j.neuron.2010.09.027</a>","apa":"Hippenmeyer, S., Youn, Y., Moon, H., Miyamichi, K., Zong, H., Wynshaw Boris, A., &#38; Luo, L. (2010). Genetic mosaic dissection of Lis1 and Ndel1 in neuronal migration. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2010.09.027\">https://doi.org/10.1016/j.neuron.2010.09.027</a>","ieee":"S. Hippenmeyer <i>et al.</i>, “Genetic mosaic dissection of Lis1 and Ndel1 in neuronal migration,” <i>Neuron</i>, vol. 68, no. 4. Elsevier, pp. 695–709, 2010.","short":"S. Hippenmeyer, Y. Youn, H. Moon, K. Miyamichi, H. Zong, A. Wynshaw Boris, L. Luo, Neuron 68 (2010) 695–709.","mla":"Hippenmeyer, Simon, et al. “Genetic Mosaic Dissection of Lis1 and Ndel1 in Neuronal Migration.” <i>Neuron</i>, vol. 68, no. 4, Elsevier, 2010, pp. 695–709, doi:<a href=\"https://doi.org/10.1016/j.neuron.2010.09.027\">10.1016/j.neuron.2010.09.027</a>."},"day":"18","intvolume":"        68","year":"2010","title":"Genetic mosaic dissection of Lis1 and Ndel1 in neuronal migration","date_created":"2018-12-11T12:01:39Z","date_published":"2010-11-18T00:00:00Z"},{"_id":"3153","abstract":[{"lang":"eng","text":"Human immune cells have to penetrate an endothelial barrier during their beneficial pursuit of infection and their destructive infiltration of tissues in autoimmune diseases. This transmigration requires Rap1 GTPase to activate integrin affinity. We define a new model system for this process by demonstrating, with live imaging and genetics, that during embryonic development Drosophila melanogaster immune cells penetrate an epithelial, Drosophila E-cadherin (DE-cadherin)-based tissue barrier. A mutant in RhoL, a GTPase homologue that is specifically expressed in haemocytes, blocks this invasive step but not other aspects of guided migration. RhoL mediates integrin adhesion caused by Drosophila Rap1 overexpression and moves Rap1 away from a concentration in the cytoplasm to the leading edge during invasive migration. These findings indicate that a programmed migratory step during Drosophila development bears striking molecular similarities to vertebrate immune cell transmigration during inflammation, and identify RhoL as a new regulator of invasion, adhesion and Rap1 localization. Our work establishes the utility of Drosophila for identifying novel components of immune cell transmigration and for understanding the in vivo interplay of immune cells with the barriers they penetrate."}],"publist_id":"3542","type":"journal_article","quality_controlled":0,"publication_status":"published","citation":{"apa":"Siekhaus, D. E., Haesemeyer, M., Moffitt, O., &#38; Lehmann, R. (2010). RhoL controls invasion and Rap1 localization during immune cell transmigration in Drosophila. <i>Nature Cell Biology</i>. Nature Publishing Group.","mla":"Siekhaus, Daria E., et al. “RhoL Controls Invasion and Rap1 Localization during Immune Cell Transmigration in Drosophila.” <i>Nature Cell Biology</i>, vol. 12, no. 6, Nature Publishing Group, 2010, pp. 605–10.","short":"D.E. Siekhaus, M. Haesemeyer, O. Moffitt, R. Lehmann, Nature Cell Biology 12 (2010) 605–610.","ieee":"D. E. Siekhaus, M. Haesemeyer, O. Moffitt, and R. Lehmann, “RhoL controls invasion and Rap1 localization during immune cell transmigration in Drosophila,” <i>Nature Cell Biology</i>, vol. 12, no. 6. Nature Publishing Group, pp. 605–610, 2010.","chicago":"Siekhaus, Daria E, Martin Haesemeyer, Olivia Moffitt, and Ruth Lehmann. “RhoL Controls Invasion and Rap1 Localization during Immune Cell Transmigration in Drosophila.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2010.","ama":"Siekhaus DE, Haesemeyer M, Moffitt O, Lehmann R. RhoL controls invasion and Rap1 localization during immune cell transmigration in Drosophila. <i>Nature Cell Biology</i>. 2010;12(6):605-610.","ista":"Siekhaus DE, Haesemeyer M, Moffitt O, Lehmann R. 2010. RhoL controls invasion and Rap1 localization during immune cell transmigration in Drosophila. Nature Cell Biology. 12(6), 605–610."},"day":"01","intvolume":"        12","year":"2010","date_published":"2010-06-01T00:00:00Z","date_created":"2018-12-11T12:01:42Z","title":"RhoL controls invasion and Rap1 localization during immune cell transmigration in Drosophila","main_file_link":[{"url":"10.1038/ncb2063 PubMed","open_access":"0"}],"publication":"Nature Cell Biology","date_updated":"2021-01-12T07:41:25Z","author":[{"last_name":"Siekhaus","full_name":"Daria Siekhaus","orcid":"0000-0001-8323-8353","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","full_name":"Haesemeyer, Martin","last_name":"Haesemeyer"},{"last_name":"Moffitt","full_name":"Moffitt, Olivia","first_name":"Olivia"},{"first_name":"Ruth","full_name":"Lehmann, Ruth","last_name":"Lehmann"}],"volume":12,"month":"06","publisher":"Nature Publishing Group","status":"public","page":"605 - 610","issue":"6","extern":1},{"status":"public","page":"465 - 479","publisher":"Springer","extern":1,"doi":"10.1007/978-3-642-15552-9_34","month":"08","author":[{"first_name":"Sara","full_name":"Vicente, Sara","last_name":"Vicente"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","full_name":"Vladimir Kolmogorov","last_name":"Kolmogorov"},{"full_name":"Rother, Carsten","last_name":"Rother","first_name":"Carsten"}],"volume":6312,"date_updated":"2021-01-12T07:41:46Z","year":"2010","intvolume":"      6312","main_file_link":[{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.330.6803df","open_access":"0"}],"title":"Cosegmentation revisited: Models and optimization","alternative_title":["LNCS"],"date_created":"2018-12-11T12:01:59Z","date_published":"2010-08-30T00:00:00Z","publication_status":"published","quality_controlled":0,"conference":{"name":"ECCV: European Conference on Computer Vision"},"type":"conference","publist_id":"3479","_id":"3201","abstract":[{"lang":"eng","text":"The problem of cosegmentation consists of segmenting the same object (or objects of the same class) in two or more distinct images. Recently a number of different models have been proposed for this problem. However, no comparison of such models and corresponding optimization techniques has been done so far. We analyze three existing models: the L1 norm model of Rother et al. [1], the L2 norm model of Mukherjee et al. [2] and the &quot;reward&quot; model of Hochbaum and Singh [3]. We also study a new model, which is a straightforward extension of the Boykov-Jolly model for single image segmentation [4]. In terms of optimization, we use a Dual Decomposition (DD) technique in addition to optimization methods in [1,2]. Experiments show a significant improvement of DD over published methods. Our main conclusion, however, is that the new model is the best overall because it: (i) has fewest parameters; (ii) is most robust in practice, and (iii) can be optimized well with an efficient EM-style procedure."}],"day":"30","citation":{"mla":"Vicente, Sara, et al. <i>Cosegmentation Revisited: Models and Optimization</i>. Vol. 6312, Springer, 2010, pp. 465–79, doi:<a href=\"https://doi.org/10.1007/978-3-642-15552-9_34\">10.1007/978-3-642-15552-9_34</a>.","ieee":"S. Vicente, V. Kolmogorov, and C. Rother, “Cosegmentation revisited: Models and optimization,” presented at the ECCV: European Conference on Computer Vision, 2010, vol. 6312, pp. 465–479.","short":"S. Vicente, V. Kolmogorov, C. Rother, in:, Springer, 2010, pp. 465–479.","apa":"Vicente, S., Kolmogorov, V., &#38; Rother, C. (2010). Cosegmentation revisited: Models and optimization (Vol. 6312, pp. 465–479). Presented at the ECCV: European Conference on Computer Vision, Springer. <a href=\"https://doi.org/10.1007/978-3-642-15552-9_34\">https://doi.org/10.1007/978-3-642-15552-9_34</a>","ama":"Vicente S, Kolmogorov V, Rother C. Cosegmentation revisited: Models and optimization. In: Vol 6312. Springer; 2010:465-479. doi:<a href=\"https://doi.org/10.1007/978-3-642-15552-9_34\">10.1007/978-3-642-15552-9_34</a>","ista":"Vicente S, Kolmogorov V, Rother C. 2010. Cosegmentation revisited: Models and optimization. ECCV: European Conference on Computer Vision, LNCS, vol. 6312, 465–479.","chicago":"Vicente, Sara, Vladimir Kolmogorov, and Carsten Rother. “Cosegmentation Revisited: Models and Optimization,” 6312:465–79. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-15552-9_34\">https://doi.org/10.1007/978-3-642-15552-9_34</a>."}},{"publist_id":"3480","type":"journal_article","publication_status":"published","quality_controlled":0,"_id":"3202","abstract":[{"text":"We consider the following problem: given an undirected weighted graph G = (V,E,c) with nonnegative weights, minimize function c(δ(Π))- λ|Π| for all values of parameter λ. Here Π is a partition of the set of nodes, the first term is the cost of edges whose endpoints belong to different components of the partition, and |Π| is the number of components. The current best known algorithm for this problem has complexity O(|V| 2) maximum flow computations. We improve it to |V| parametric maximum flow computations. We observe that the complexity can be improved further for families of graphs which admit a good separator, e.g. for planar graphs.","lang":"eng"}],"citation":{"ista":"Kolmogorov V. 2010. A faster algorithm for computing the principal sequence of partitions of a graph. Algorithmica. 56(4), 394–412.","ama":"Kolmogorov V. A faster algorithm for computing the principal sequence of partitions of a graph. <i>Algorithmica</i>. 2010;56(4):394-412. doi:<a href=\"https://doi.org/10.1007/s00453-008-9177-z\">10.1007/s00453-008-9177-z</a>","chicago":"Kolmogorov, Vladimir. “A Faster Algorithm for Computing the Principal Sequence of Partitions of a Graph.” <i>Algorithmica</i>. Springer, 2010. <a href=\"https://doi.org/10.1007/s00453-008-9177-z\">https://doi.org/10.1007/s00453-008-9177-z</a>.","short":"V. Kolmogorov, Algorithmica 56 (2010) 394–412.","ieee":"V. Kolmogorov, “A faster algorithm for computing the principal sequence of partitions of a graph,” <i>Algorithmica</i>, vol. 56, no. 4. Springer, pp. 394–412, 2010.","mla":"Kolmogorov, Vladimir. “A Faster Algorithm for Computing the Principal Sequence of Partitions of a Graph.” <i>Algorithmica</i>, vol. 56, no. 4, Springer, 2010, pp. 394–412, doi:<a href=\"https://doi.org/10.1007/s00453-008-9177-z\">10.1007/s00453-008-9177-z</a>.","apa":"Kolmogorov, V. (2010). A faster algorithm for computing the principal sequence of partitions of a graph. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-008-9177-z\">https://doi.org/10.1007/s00453-008-9177-z</a>"},"day":"01","year":"2010","intvolume":"        56","date_published":"2010-04-01T00:00:00Z","title":"A faster algorithm for computing the principal sequence of partitions of a graph","date_created":"2018-12-11T12:01:59Z","doi":"10.1007/s00453-008-9177-z","month":"04","publication":"Algorithmica","date_updated":"2021-01-12T07:41:46Z","author":[{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov"}],"volume":56,"publisher":"Springer","page":"394 - 412","status":"public","issue":"4","extern":1},{"month":"03","volume":5978,"author":[{"first_name":"Johan","last_name":"Håstad","full_name":"Håstad, Johan"},{"first_name":"Rafael","full_name":"Pass, Rafael","last_name":"Pass"},{"first_name":"Douglas","last_name":"Wikström","full_name":"Wikström, Douglas"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","full_name":"Krzysztof Pietrzak"}],"date_updated":"2021-01-12T07:41:59Z","doi":"10.1007/978-3-642-11799-2_1","extern":1,"page":"1 - 18","status":"public","publisher":"Springer","citation":{"ista":"Håstad J, Pass R, Wikström D, Pietrzak KZ. 2010. An efficient parallel repetition theorem. TCC: Theory of Cryptography Conference, LNCS, vol. 5978, 1–18.","ama":"Håstad J, Pass R, Wikström D, Pietrzak KZ. An efficient parallel repetition theorem. In: Vol 5978. Springer; 2010:1-18. doi:<a href=\"https://doi.org/10.1007/978-3-642-11799-2_1\">10.1007/978-3-642-11799-2_1</a>","chicago":"Håstad, Johan, Rafael Pass, Douglas Wikström, and Krzysztof Z Pietrzak. “An Efficient Parallel Repetition Theorem,” 5978:1–18. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-11799-2_1\">https://doi.org/10.1007/978-3-642-11799-2_1</a>.","short":"J. Håstad, R. Pass, D. Wikström, K.Z. Pietrzak, in:, Springer, 2010, pp. 1–18.","ieee":"J. Håstad, R. Pass, D. Wikström, and K. Z. Pietrzak, “An efficient parallel repetition theorem,” presented at the TCC: Theory of Cryptography Conference, 2010, vol. 5978, pp. 1–18.","mla":"Håstad, Johan, et al. <i>An Efficient Parallel Repetition Theorem</i>. Vol. 5978, Springer, 2010, pp. 1–18, doi:<a href=\"https://doi.org/10.1007/978-3-642-11799-2_1\">10.1007/978-3-642-11799-2_1</a>.","apa":"Håstad, J., Pass, R., Wikström, D., &#38; Pietrzak, K. Z. (2010). An efficient parallel repetition theorem (Vol. 5978, pp. 1–18). Presented at the TCC: Theory of Cryptography Conference, Springer. <a href=\"https://doi.org/10.1007/978-3-642-11799-2_1\">https://doi.org/10.1007/978-3-642-11799-2_1</a>"},"day":"26","publication_status":"published","quality_controlled":0,"conference":{"name":"TCC: Theory of Cryptography Conference"},"publist_id":"3446","type":"conference","abstract":[{"lang":"eng","text":"We present a general parallel-repetition theorem with an efficient reduction. As a corollary of this theorem we establish that parallel repetition reduces the soundness error at an exponential rate in any public-coin argument, and more generally, any argument where the verifier's messages, but not necessarily its decision to accept or reject, can be efficiently simulated with noticeable probability."}],"_id":"3233","date_created":"2018-12-11T12:02:10Z","title":"An efficient parallel repetition theorem","alternative_title":["LNCS"],"date_published":"2010-03-26T00:00:00Z","year":"2010","intvolume":"      5978"},{"date_published":"2010-03-26T00:00:00Z","title":"Leakage resilient signatures","alternative_title":["LNCS"],"date_created":"2018-12-11T12:02:10Z","intvolume":"      5978","year":"2010","citation":{"ista":"Faust S, Kiltz E, Pietrzak KZ, Rothblum G. 2010. Leakage resilient signatures. TCC: Theory of Cryptography Conference, LNCS, vol. 5978, 343–360.","ama":"Faust S, Kiltz E, Pietrzak KZ, Rothblum G. Leakage resilient signatures. In: Vol 5978. Springer; 2010:343-360. doi:<a href=\"https://doi.org/10.1007/978-3-642-11799-2_21\">10.1007/978-3-642-11799-2_21</a>","chicago":"Faust, Sebastian, Eike Kiltz, Krzysztof Z Pietrzak, and Guy Rothblum. “Leakage Resilient Signatures,” 5978:343–60. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-11799-2_21\">https://doi.org/10.1007/978-3-642-11799-2_21</a>.","ieee":"S. Faust, E. Kiltz, K. Z. Pietrzak, and G. Rothblum, “Leakage resilient signatures,” presented at the TCC: Theory of Cryptography Conference, 2010, vol. 5978, pp. 343–360.","short":"S. Faust, E. Kiltz, K.Z. Pietrzak, G. Rothblum, in:, Springer, 2010, pp. 343–360.","mla":"Faust, Sebastian, et al. <i>Leakage Resilient Signatures</i>. Vol. 5978, Springer, 2010, pp. 343–60, doi:<a href=\"https://doi.org/10.1007/978-3-642-11799-2_21\">10.1007/978-3-642-11799-2_21</a>.","apa":"Faust, S., Kiltz, E., Pietrzak, K. Z., &#38; Rothblum, G. (2010). Leakage resilient signatures (Vol. 5978, pp. 343–360). Presented at the TCC: Theory of Cryptography Conference, Springer. <a href=\"https://doi.org/10.1007/978-3-642-11799-2_21\">https://doi.org/10.1007/978-3-642-11799-2_21</a>"},"day":"26","abstract":[{"text":"The strongest standard security notion for digital signature schemes is unforgeability under chosen message attacks. In practice, however, this notion can be insufficient due to &quot;side-channel attacks&quot; which exploit leakage of information about the secret internal state. In this work we put forward the notion of &quot;leakage-resilient signatures,&quot; which strengthens the standard security notion by giving the adversary the additional power to learn a bounded amount of arbitrary information about the secret state that was accessed during every signature generation. This notion naturally implies security against all side-channel attacks as long as the amount of information leaked on each invocation is bounded and &quot;only computation leaks information.&quot; The main result of this paper is a construction which gives a (tree-based, stateful) leakage-resilient signature scheme based on any 3-time signature scheme. The amount of information that our scheme can safely leak per signature generation is 1/3 of the information the underlying 3-time signature scheme can leak in total. Signature schemes that remain secure even if a bounded total amount of information is leaked were recently constructed, hence instantiating our construction with these schemes gives the first constructions of provably secure leakage-resilient signature schemes. The above construction assumes that the signing algorithm can sample truly random bits, and thus an implementation would need some special hardware (randomness gates). Simply generating this randomness using a leakage-resilient stream-cipher will in general not work. Our second contribution is a sound general principle to replace uniform random bits in any leakage-resilient construction with pseudorandom ones: run two leakage-resilient stream-ciphers (with independent keys) in parallel and then apply a two-source extractor to their outputs. ","lang":"eng"}],"_id":"3234","publist_id":"3447","type":"conference","publication_status":"published","conference":{"name":"TCC: Theory of Cryptography Conference"},"quality_controlled":0,"extern":1,"publisher":"Springer","status":"public","page":"343 - 360","date_updated":"2021-01-12T07:41:59Z","author":[{"first_name":"Sebastian","full_name":"Faust, Sebastian","last_name":"Faust"},{"first_name":"Eike","last_name":"Kiltz","full_name":"Kiltz, Eike"},{"full_name":"Krzysztof Pietrzak","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654"},{"first_name":"Guy","last_name":"Rothblum","full_name":"Rothblum, Guy N"}],"volume":5978,"month":"03","doi":"10.1007/978-3-642-11799-2_21"},{"abstract":[{"lang":"eng","text":"A cryptographic primitive is leakage-resilient, if it remains secure even if an adversary can learn a bounded amount of arbitrary information about the computation with every invocation. As a consequence, the physical implementation of a leakage-resilient primitive is secure against every side-channel as long as the amount of information leaked per invocation is bounded. In this paper we prove positive and negative results about the feasibility of constructing leakage-resilient pseudorandom functions and permutations (i.e. block-ciphers). Our results are three fold: 1. We construct (from any standard PRF) a PRF which satisfies a relaxed notion of leakage-resilience where (1) the leakage function is fixed (and not adaptively chosen with each query.) and (2) the computation is split into several steps which leak individually (a &quot;step&quot; will be the invocation of the underlying PRF.) 2. We prove that a Feistel network with a super-logarithmic number of rounds, each instantiated with a leakage-resilient PRF, is a leakage resilient PRP. This reduction also holds for the non-adaptive notion just discussed, we thus get a block-cipher which is leakage-resilient (against non-adaptive leakage). 3. We propose generic side-channel attacks against Feistel networks. The attacks are generic in the sense that they work for any round functions (e.g. uniformly random functions) and only require some simple leakage from the inputs to the round functions. For example we show how to invert an r round Feistel network over 2n bits making 4•(n+1) r-2 forward queries, if with each query we are also given as leakage the Hamming weight of the inputs to the r round functions. This complements the result from the previous item showing that a super-constant number of rounds is necessary."}],"_id":"3235","type":"conference","publist_id":"3445","publication_status":"published","quality_controlled":0,"conference":{"name":"CRYPTO: International Cryptology Conference"},"citation":{"chicago":"Dodis, Yevgeniy, and Krzysztof Z Pietrzak. “Leakage Resilient Pseudorandom Functions and Side Channel Attacks on Feistel Networks,” 6223:21–40. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-14623-7_2\">https://doi.org/10.1007/978-3-642-14623-7_2</a>.","ista":"Dodis Y, Pietrzak KZ. 2010. Leakage resilient pseudorandom functions and side channel attacks on feistel networks. CRYPTO: International Cryptology Conference, LNCS, vol. 6223, 21–40.","ama":"Dodis Y, Pietrzak KZ. Leakage resilient pseudorandom functions and side channel attacks on feistel networks. In: Vol 6223. Springer; 2010:21-40. doi:<a href=\"https://doi.org/10.1007/978-3-642-14623-7_2\">10.1007/978-3-642-14623-7_2</a>","apa":"Dodis, Y., &#38; Pietrzak, K. Z. (2010). Leakage resilient pseudorandom functions and side channel attacks on feistel networks (Vol. 6223, pp. 21–40). Presented at the CRYPTO: International Cryptology Conference, Springer. <a href=\"https://doi.org/10.1007/978-3-642-14623-7_2\">https://doi.org/10.1007/978-3-642-14623-7_2</a>","short":"Y. Dodis, K.Z. Pietrzak, in:, Springer, 2010, pp. 21–40.","ieee":"Y. Dodis and K. Z. Pietrzak, “Leakage resilient pseudorandom functions and side channel attacks on feistel networks,” presented at the CRYPTO: International Cryptology Conference, 2010, vol. 6223, pp. 21–40.","mla":"Dodis, Yevgeniy, and Krzysztof Z. Pietrzak. <i>Leakage Resilient Pseudorandom Functions and Side Channel Attacks on Feistel Networks</i>. Vol. 6223, Springer, 2010, pp. 21–40, doi:<a href=\"https://doi.org/10.1007/978-3-642-14623-7_2\">10.1007/978-3-642-14623-7_2</a>."},"day":"30","intvolume":"      6223","year":"2010","date_published":"2010-09-30T00:00:00Z","title":"Leakage resilient pseudorandom functions and side channel attacks on feistel networks","alternative_title":["LNCS"],"date_created":"2018-12-11T12:02:10Z","doi":"10.1007/978-3-642-14623-7_2","date_updated":"2021-01-12T07:42:00Z","volume":6223,"author":[{"last_name":"Dodis","full_name":"Dodis, Yevgeniy","first_name":"Yevgeniy"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","full_name":"Krzysztof Pietrzak"}],"month":"09","publisher":"Springer","status":"public","page":"21 - 40","extern":1},{"extern":1,"publisher":"Springer","status":"public","page":"595 - 612","date_updated":"2021-01-12T07:42:01Z","volume":6477,"author":[{"last_name":"Kiltz","full_name":"Kiltz, Eike","first_name":"Eike"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","full_name":"Krzysztof Pietrzak"}],"month":"01","doi":"10.1007/978-3-642-17373-8_34","date_published":"2010-01-14T00:00:00Z","date_created":"2018-12-11T12:02:11Z","alternative_title":["LNCS"],"title":"Leakage resilient ElGamal encryption","intvolume":"      6477","year":"2010","citation":{"chicago":"Kiltz, Eike, and Krzysztof Z Pietrzak. “Leakage Resilient ElGamal Encryption,” 6477:595–612. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-17373-8_34\">https://doi.org/10.1007/978-3-642-17373-8_34</a>.","ista":"Kiltz E, Pietrzak KZ. 2010. Leakage resilient ElGamal encryption. ASIACRYPT: Theory and Application of Cryptology and Information Security, LNCS, vol. 6477, 595–612.","ama":"Kiltz E, Pietrzak KZ. Leakage resilient ElGamal encryption. In: Vol 6477. Springer; 2010:595-612. doi:<a href=\"https://doi.org/10.1007/978-3-642-17373-8_34\">10.1007/978-3-642-17373-8_34</a>","apa":"Kiltz, E., &#38; Pietrzak, K. Z. (2010). Leakage resilient ElGamal encryption (Vol. 6477, pp. 595–612). Presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Springer. <a href=\"https://doi.org/10.1007/978-3-642-17373-8_34\">https://doi.org/10.1007/978-3-642-17373-8_34</a>","short":"E. Kiltz, K.Z. Pietrzak, in:, Springer, 2010, pp. 595–612.","ieee":"E. Kiltz and K. Z. Pietrzak, “Leakage resilient ElGamal encryption,” presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, 2010, vol. 6477, pp. 595–612.","mla":"Kiltz, Eike, and Krzysztof Z. Pietrzak. <i>Leakage Resilient ElGamal Encryption</i>. Vol. 6477, Springer, 2010, pp. 595–612, doi:<a href=\"https://doi.org/10.1007/978-3-642-17373-8_34\">10.1007/978-3-642-17373-8_34</a>."},"day":"14","_id":"3237","abstract":[{"lang":"eng","text":"Blinding is a popular and well-known countermeasure to protect public-key cryptosystems against side-channel attacks. The high level idea is to randomize an exponentiation in order to prevent multiple measurements of the same operation on different data, as such measurements might allow the adversary to learn the secret exponent. Several variants of blinding have been proposed in the literature, using additive or multiplicative secret-sharing to blind either the base or the exponent. These countermeasures usually aim at preventing particular side-channel attacks (mostly power analysis) and come without any formal security guarantee. In this work we investigate to which extend blinding can provide provable security against a general class of side-channel attacks. Surprisingly, it turns out that in the context of public-key encryption some blinding techniques are more suited than others. In particular, we consider a multiplicatively blinded version of ElGamal public-key encryption where - we prove that the scheme, instantiated over bilinear groups of prime order p (where p - 1 is not smooth) is leakage resilient in the generic-group model. Here we consider the model of chosen-ciphertext security in the presence of continuous leakage, i.e., the scheme remains chosen-ciphertext secure even if with every decryption query the adversary can learn a bounded amount (roughly log(p)/2 bits) of arbitrary, adversarially chosen information about the computation. - we conjecture that the scheme, instantiated over arbitrary groups of prime order p (where p - 1 is not smooth) is leakage resilient. Previous to this work no encryption scheme secure against continuous leakage was known. Constructing a scheme that can be proven secure in the standard model remains an interesting open problem. "}],"type":"conference","publist_id":"3444","quality_controlled":0,"conference":{"name":"ASIACRYPT: Theory and Application of Cryptology and Information Security"},"publication_status":"published"},{"issue":"21","extern":1,"publisher":"National Academy of Sciences","status":"public","page":"9855 - 60","month":"01","date_updated":"2021-01-12T07:42:27Z","publication":"PNAS","author":[{"last_name":"Iyengar","full_name":"Iyengar, Atulya","first_name":"Atulya"},{"last_name":"Chakraborty Tuhin","full_name":"Chakraborty Tuhin, Subhra","first_name":"Subhra"},{"first_name":"Sarit","id":"3A578F32-F248-11E8-B48F-1D18A9856A87","full_name":"Sarit Goswami","last_name":"Goswami"},{"first_name":"Chun","last_name":"Wu","full_name":"Wu, Chun Fang"},{"first_name":"Obaid","last_name":"Siddiqi","full_name":"Siddiqi, Obaid"}],"volume":107,"doi":"10.1073/pnas.1003856107","date_published":"2010-01-01T00:00:00Z","title":"Post eclosion odor experience modifies olfactory receptor neuron coding in Drosophila","date_created":"2018-12-11T12:02:31Z","year":"2010","intvolume":"       107","day":"01","citation":{"chicago":"Iyengar, Atulya, Subhra Chakraborty Tuhin, Sarit Goswami, Chun Wu, and Obaid Siddiqi. “Post Eclosion Odor Experience Modifies Olfactory Receptor Neuron Coding in Drosophila.” <i>PNAS</i>. National Academy of Sciences, 2010. <a href=\"https://doi.org/10.1073/pnas.1003856107\">https://doi.org/10.1073/pnas.1003856107</a>.","ama":"Iyengar A, Chakraborty Tuhin S, Goswami S, Wu C, Siddiqi O. Post eclosion odor experience modifies olfactory receptor neuron coding in Drosophila. <i>PNAS</i>. 2010;107(21):9855-9860. doi:<a href=\"https://doi.org/10.1073/pnas.1003856107\">10.1073/pnas.1003856107</a>","ista":"Iyengar A, Chakraborty Tuhin S, Goswami S, Wu C, Siddiqi O. 2010. Post eclosion odor experience modifies olfactory receptor neuron coding in Drosophila. PNAS. 107(21), 9855–60.","apa":"Iyengar, A., Chakraborty Tuhin, S., Goswami, S., Wu, C., &#38; Siddiqi, O. (2010). Post eclosion odor experience modifies olfactory receptor neuron coding in Drosophila. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1003856107\">https://doi.org/10.1073/pnas.1003856107</a>","mla":"Iyengar, Atulya, et al. “Post Eclosion Odor Experience Modifies Olfactory Receptor Neuron Coding in Drosophila.” <i>PNAS</i>, vol. 107, no. 21, National Academy of Sciences, 2010, pp. 9855–60, doi:<a href=\"https://doi.org/10.1073/pnas.1003856107\">10.1073/pnas.1003856107</a>.","short":"A. Iyengar, S. Chakraborty Tuhin, S. Goswami, C. Wu, O. Siddiqi, PNAS 107 (2010) 9855–60.","ieee":"A. Iyengar, S. Chakraborty Tuhin, S. Goswami, C. Wu, and O. Siddiqi, “Post eclosion odor experience modifies olfactory receptor neuron coding in Drosophila,” <i>PNAS</i>, vol. 107, no. 21. National Academy of Sciences, pp. 9855–60, 2010."},"type":"journal_article","publist_id":"3347","quality_controlled":0,"publication_status":"published","abstract":[{"text":"Olfactory responses of Drosophila undergo pronounced changes after eclosion. The flies develop attraction to odors to which they are exposed and aversion to other odors. Behavioral adaptation is correlated with changes in the firing pattern of olfactory receptor neurons (ORNs). In this article, we present an information-theoretic analysis of the firing pattern of ORNs. Flies reared in a synthetic odorless medium were transferred after eclosion to three different media: (i) a synthetic medium relatively devoid of odor cues, (ii) synthetic medium infused with a single odorant, and (iii) complex cornmeal medium rich in odors. Recordings were made from an identified sensillum (type II), and the Jensen-Shannon divergence (D(JS)) was used to assess quantitatively the differences between ensemble spike responses to different odors. Analysis shows that prolonged exposure to ethyl acetate and several related esters increases sensitivity to these esters but does not improve the ability of the fly to distinguish between them. Flies exposed to cornmeal display varied sensitivity to these odorants and at the same time develop greater capacity to distinguish between odors. Deprivation of odor experience on an odorless synthetic medium leads to a loss of both sensitivity and acuity. Rich olfactory experience thus helps to shape the ORNs response and enhances its discriminative power. The experiments presented here demonstrate an experience-dependent adaptation at the level of the receptor neuron.","lang":"eng"}],"_id":"3294"},{"extern":"1","article_processing_charge":"No","publisher":"Georgia Institute of Technology","page":"1 - 175","status":"public","date_updated":"2023-02-23T11:21:00Z","author":[{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","orcid":"0000-0001-6646-5546"}],"month":"11","date_published":"2010-11-17T00:00:00Z","title":"Animating physical phenomena with embedded surface meshes","date_created":"2018-12-11T12:02:31Z","oa_version":"None","main_file_link":[{"url":"http://hdl.handle.net/1853/37256"}],"year":"2010","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"17","citation":{"chicago":"Wojtan, Chris. “Animating Physical Phenomena with Embedded Surface Meshes.” Georgia Institute of Technology, 2010.","ista":"Wojtan C. 2010. Animating physical phenomena with embedded surface meshes. Georgia Institute of Technology.","ama":"Wojtan C. Animating physical phenomena with embedded surface meshes. 2010:1-175.","apa":"Wojtan, C. (2010). <i>Animating physical phenomena with embedded surface meshes</i>. Georgia Institute of Technology.","short":"C. Wojtan, Animating Physical Phenomena with Embedded Surface Meshes, Georgia Institute of Technology, 2010.","ieee":"C. Wojtan, “Animating physical phenomena with embedded surface meshes,” Georgia Institute of Technology, 2010.","mla":"Wojtan, Chris. <i>Animating Physical Phenomena with Embedded Surface Meshes</i>. Georgia Institute of Technology, 2010, pp. 1–175."},"_id":"3296","supervisor":[{"first_name":"Irfan","full_name":"Essa, Irfan","last_name":"Essa"},{"full_name":"Liu, Karen","last_name":"Liu","first_name":"Karen"},{"full_name":"Mucha, Peter","last_name":"Mucha","first_name":"Peter"},{"last_name":"Rossignac","full_name":"Rossignac, Jarek","first_name":"Jarek"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Accurate computational representations of highly deformable surfaces are indispensable in the fields of computer animation, medical simulation, computer vision, digital modeling, and computational physics. The focus of this dissertation is on the animation of physics-based phenomena with highly detailed deformable surfaces represented by triangle meshes.\r\n \r\nWe first present results from an algorithm that generates continuum mechanics animations with intricate surface features. This method combines a finite element method with a tetrahedral mesh generator and a high resolution surface mesh, and it is orders of magnitude more efficient than previous approaches. Next, we present an efficient solution for the challenging problem of computing topological changes in detailed dynamic surface meshes. We then introduce a new physics-inspired surface tracking algorithm that is capable of preserving arbitrarily thin features and reproducing realistic fine-scale topological changes like Rayleigh-Plateau instabilities. This physics-inspired surface tracking technique also opens the door for a unique coupling between surficial finite element methods and volumetric finite difference methods, in order to simulate liquid surface tension phenomena more efficiently than any previous method. Due to its dramatic increase in computational resolution and efficiency, this method yielded the first computer simulations of a fully developed crown splash with droplet pinch off."}],"type":"dissertation","publist_id":"3345","publication_status":"published"},{"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998319/"}],"date_published":"2010-12-01T00:00:00Z","year":"2010","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"       186","citation":{"ama":"Weissman D, Feldman M, Fisher D. The rate of fitness-valley crossing in sexual populations. <i>Genetics</i>. 2010;186(4):1389-1410. doi:<a href=\"https://doi.org/10.1534/genetics.110.123240\">10.1534/genetics.110.123240</a>","ista":"Weissman D, Feldman M, Fisher D. 2010. The rate of fitness-valley crossing in sexual populations. Genetics. 186(4), 1389–1410.","chicago":"Weissman, Daniel, Marcus Feldman, and Daniel Fisher. “The Rate of Fitness-Valley Crossing in Sexual Populations.” <i>Genetics</i>. Genetics Society of America, 2010. <a href=\"https://doi.org/10.1534/genetics.110.123240\">https://doi.org/10.1534/genetics.110.123240</a>.","mla":"Weissman, Daniel, et al. “The Rate of Fitness-Valley Crossing in Sexual Populations.” <i>Genetics</i>, vol. 186, no. 4, Genetics Society of America, 2010, pp. 1389–410, doi:<a href=\"https://doi.org/10.1534/genetics.110.123240\">10.1534/genetics.110.123240</a>.","ieee":"D. Weissman, M. Feldman, and D. Fisher, “The rate of fitness-valley crossing in sexual populations,” <i>Genetics</i>, vol. 186, no. 4. Genetics Society of America, pp. 1389–1410, 2010.","short":"D. Weissman, M. Feldman, D. Fisher, Genetics 186 (2010) 1389–1410.","apa":"Weissman, D., Feldman, M., &#38; Fisher, D. (2010). The rate of fitness-valley crossing in sexual populations. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.110.123240\">https://doi.org/10.1534/genetics.110.123240</a>"},"day":"01","type":"journal_article","quality_controlled":"1","_id":"3303","abstract":[{"text":"Biological traits result in part from interactions between different genetic loci. This can lead to sign epistasis, in which a beneficial adaptation involves a combination of individually deleterious or neutral mutations; in this case, a population must cross a “fitness valley” to adapt. Recombination can assist this process by combining mutations from different individuals or retard it by breaking up the adaptive combination. Here, we analyze the simplest fitness valley, in which an adaptation requires one mutation at each of two loci to provide a fitness benefit. We present a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes. We find that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombination rates slow down valley crossing, with the transition between the two regimes occurring when the recombination rate between the loci is approximately equal to the selective advantage provided by the adaptation. In large populations, if the recombination rate is high and selection against single mutants is substantial, the time to cross the valley grows exponentially with population size, effectively meaning that the population cannot acquire the adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing time by up to several orders of magnitude relative to that in an asexual population. ","lang":"eng"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000285297000025"]},"scopus_import":"1","ec_funded":1,"issue":"4","page":"1389 - 1410","status":"public","isi":1,"date_updated":"2025-09-30T09:47:59Z","publication":"Genetics","oa_version":"Submitted Version","date_created":"2018-12-11T12:02:33Z","title":"The rate of fitness-valley crossing in sexual populations","publist_id":"3337","publication_status":"published","publisher":"Genetics Society of America","corr_author":"1","article_processing_charge":"No","project":[{"grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation"}],"department":[{"_id":"NiBa"}],"month":"12","author":[{"id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","full_name":"Weissman, Daniel","last_name":"Weissman"},{"full_name":"Feldman, Marcus","last_name":"Feldman","first_name":"Marcus"},{"last_name":"Fisher","full_name":"Fisher, Daniel","first_name":"Daniel"}],"volume":186,"acknowledgement":"This work was supported in part by a Robert N. Noyce Stanford Graduate Fellowship and European Research Council grant 250152 (to D.B.W.) and by National Institutes of Health grant GM 28016 (to M.W.F.).\r\nWe thank Michael Desai for many ideas and discussions and are grateful to Joanna Masel and an anonymous reviewer for their helpful suggestions. ","doi":"10.1534/genetics.110.123240","oa":1}]