[{"issue":"8","status":"public","page":"2352 - 2359","date_updated":"2021-01-12T07:41:00Z","publication":"Molecular BioSystems","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/21660355","open_access":"1"}],"date_published":"2011-06-10T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2011","intvolume":"         7","citation":{"ista":"Wabnik KT, Govaerts W, Friml J, Kleine Vehn J. 2011. Feedback models for polarized auxin transport: An emerging trend. Molecular BioSystems. 7(8), 2352–2359.","ama":"Wabnik KT, Govaerts W, Friml J, Kleine Vehn J. Feedback models for polarized auxin transport: An emerging trend. <i>Molecular BioSystems</i>. 2011;7(8):2352-2359. doi:<a href=\"https://doi.org/10.1039/c1mb05109a\">10.1039/c1mb05109a</a>","chicago":"Wabnik, Krzysztof T, Willy Govaerts, Jiří Friml, and Jürgen Kleine Vehn. “Feedback Models for Polarized Auxin Transport: An Emerging Trend.” <i>Molecular BioSystems</i>. Royal Society of Chemistry, 2011. <a href=\"https://doi.org/10.1039/c1mb05109a\">https://doi.org/10.1039/c1mb05109a</a>.","short":"K.T. Wabnik, W. Govaerts, J. Friml, J. Kleine Vehn, Molecular BioSystems 7 (2011) 2352–2359.","ieee":"K. T. Wabnik, W. Govaerts, J. Friml, and J. Kleine Vehn, “Feedback models for polarized auxin transport: An emerging trend,” <i>Molecular BioSystems</i>, vol. 7, no. 8. Royal Society of Chemistry, pp. 2352–2359, 2011.","mla":"Wabnik, Krzysztof T., et al. “Feedback Models for Polarized Auxin Transport: An Emerging Trend.” <i>Molecular BioSystems</i>, vol. 7, no. 8, Royal Society of Chemistry, 2011, pp. 2352–59, doi:<a href=\"https://doi.org/10.1039/c1mb05109a\">10.1039/c1mb05109a</a>.","apa":"Wabnik, K. T., Govaerts, W., Friml, J., &#38; Kleine Vehn, J. (2011). Feedback models for polarized auxin transport: An emerging trend. <i>Molecular BioSystems</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c1mb05109a\">https://doi.org/10.1039/c1mb05109a</a>"},"day":"10","quality_controlled":"1","type":"journal_article","external_id":{"pmid":["21660355"]},"_id":"3092","abstract":[{"text":"The phytohormone auxin is vital to plant growth and development. A unique property of auxin among all other plant hormones is its cell-to-cell polar transport that requires activity of polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the substantial molecular insight into the cellular PIN polarization, the mechanistic understanding for developmentally and environmentally regulated PIN polarization is scarce. The long-standing belief that auxin modulates its own transport by means of a positive feedback mechanism has inspired both experimentalists and theoreticians for more than two decades. Recently, theoretical models for auxin-dependent patterning in plants include the feedback between auxin transport and the PIN protein localization. These computer models aid to assess the complexity of plant development by testing and predicting plausible scenarios for various developmental processes that occur in planta. Although the majority of these models rely on purely heuristic principles, the most recent mechanistic models tentatively integrate biologically testable components into known cellular processes that underlie the PIN polarity regulation. The existing and emerging computational approaches to describe PIN polarization are presented and discussed in the light of recent experimental data on the PIN polar targeting.","lang":"eng"}],"language":[{"iso":"eng"}],"pmid":1,"extern":"1","publisher":"Royal Society of Chemistry","month":"06","volume":7,"author":[{"full_name":"Wabnik, Krzysztof T","last_name":"Wabnik","orcid":"0000-0001-7263-0560","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T"},{"last_name":"Govaerts","full_name":"Govaerts, Willy","first_name":"Willy"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml"},{"first_name":"Jürgen","full_name":"Kleine Vehn, Jürgen","last_name":"Kleine Vehn"}],"doi":"10.1039/c1mb05109a","oa":1,"oa_version":"Published Version","title":"Feedback models for polarized auxin transport: An emerging trend","date_created":"2018-12-11T12:01:20Z","publication_status":"published","publist_id":"3608"},{"issue":"32","extern":1,"publisher":"National Academy of Sciences","page":"E450 - E458","status":"public","month":"08","publication":"PNAS","date_updated":"2021-01-12T07:41:00Z","author":[{"first_name":"Marie","full_name":"Barberon, Marie","last_name":"Barberon"},{"first_name":"Enric","last_name":"Zelazny","full_name":"Zelazny, Enric"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"first_name":"Geneviève","full_name":"Conéjéro, Geneviève","last_name":"Conéjéro"},{"first_name":"Cathy","last_name":"Curie","full_name":"Curie, Cathy"},{"last_name":"Friml","full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vert, Grégory","last_name":"Vert","first_name":"Grégory"}],"volume":108,"doi":"10.1073/pnas.1100659108","date_published":"2011-08-09T00:00:00Z","title":"Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1 transporter controls iron uptake in plants","date_created":"2018-12-11T12:01:20Z","year":"2011","intvolume":"       108","day":"09","citation":{"chicago":"Barberon, Marie, Enric Zelazny, Stéphanie Robert, Geneviève Conéjéro, Cathy Curie, Jiří Friml, and Grégory Vert. “Monoubiquitin Dependent Endocytosis of the Iron Regulated Transporter 1 IRT1 Transporter Controls Iron Uptake in Plants.” <i>PNAS</i>. National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1100659108\">https://doi.org/10.1073/pnas.1100659108</a>.","ama":"Barberon M, Zelazny E, Robert S, et al. Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1 transporter controls iron uptake in plants. <i>PNAS</i>. 2011;108(32):E450-E458. doi:<a href=\"https://doi.org/10.1073/pnas.1100659108\">10.1073/pnas.1100659108</a>","ista":"Barberon M, Zelazny E, Robert S, Conéjéro G, Curie C, Friml J, Vert G. 2011. Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1 transporter controls iron uptake in plants. PNAS. 108(32), E450–E458.","apa":"Barberon, M., Zelazny, E., Robert, S., Conéjéro, G., Curie, C., Friml, J., &#38; Vert, G. (2011). Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1 transporter controls iron uptake in plants. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1100659108\">https://doi.org/10.1073/pnas.1100659108</a>","mla":"Barberon, Marie, et al. “Monoubiquitin Dependent Endocytosis of the Iron Regulated Transporter 1 IRT1 Transporter Controls Iron Uptake in Plants.” <i>PNAS</i>, vol. 108, no. 32, National Academy of Sciences, 2011, pp. E450–58, doi:<a href=\"https://doi.org/10.1073/pnas.1100659108\">10.1073/pnas.1100659108</a>.","short":"M. Barberon, E. Zelazny, S. Robert, G. Conéjéro, C. Curie, J. Friml, G. Vert, PNAS 108 (2011) E450–E458.","ieee":"M. Barberon <i>et al.</i>, “Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1 transporter controls iron uptake in plants,” <i>PNAS</i>, vol. 108, no. 32. National Academy of Sciences, pp. E450–E458, 2011."},"type":"journal_article","publist_id":"3607","quality_controlled":0,"publication_status":"published","_id":"3093","abstract":[{"text":"\nPlants take up iron from the soil using the IRON-REGULATED TRANSPORTER 1 (IRT1) high-affinity iron transporter at the root surface. Sophisticated regulatory mechanisms allow plants to tightly control the levels of IRT1, ensuring optimal absorption of essential but toxic iron. Here, we demonstrate that overexpression of Arabidopsis thaliana IRT1 leads to constitutive IRT1 protein accumulation, metal overload, and oxidative stress. IRT1 is unexpectedly found in trans-Golgi network/early endosomes of root hair cells, and its levels and localization are unaffected by iron nutrition. Using pharmacological approaches, we show that IRT1 cycles to the plasma membrane to perform iron and metal uptake at the cell surface and is sent to the vacuole for proper turnover. We also prove that IRT1 is monoubiquitinated on several cytosol-exposed residues in vivo and that mutation of two putative monoubiquitination target residues in IRT1 triggers stabilization at the plasma membrane and leads to extreme lethality. Together, these data suggest a model in which monoubiquitin-dependent internalization/sorting and turnover keep the plasma membrane pool of IRT1 low to ensure proper iron uptake and to prevent metal toxicity. More generally, our work demonstrates the existence of monoubiquitin-dependent trafficking to lytic vacuoles in plants and points to proteasome-independent turnover of plasma membrane proteins.","lang":"eng"}]},{"day":"01","citation":{"ama":"Rakusová H, Gallego Bartolomé J, Vanstraelen M, et al. Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana. <i>Plant Journal</i>. 2011;67(5):817-826. doi:<a href=\"https://doi.org/10.1111/j.1365-313X.2011.04636.x\">10.1111/j.1365-313X.2011.04636.x</a>","ista":"Rakusová H, Gallego Bartolomé J, Vanstraelen M, Robert H, Alabadí D, Blázquez M, Benková E, Friml J. 2011. Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana. Plant Journal. 67(5), 817–826.","chicago":"Rakusová, Hana, Javier Gallego Bartolomé, Marleen Vanstraelen, Hélène Robert, David Alabadí, Miguel Blázquez, Eva Benková, and Jiří Friml. “Polarization of PIN3 Dependent Auxin Transport for Hypocotyl Gravitropic Response in Arabidopsis Thaliana.” <i>Plant Journal</i>. Wiley-Blackwell, 2011. <a href=\"https://doi.org/10.1111/j.1365-313X.2011.04636.x\">https://doi.org/10.1111/j.1365-313X.2011.04636.x</a>.","mla":"Rakusová, Hana, et al. “Polarization of PIN3 Dependent Auxin Transport for Hypocotyl Gravitropic Response in Arabidopsis Thaliana.” <i>Plant Journal</i>, vol. 67, no. 5, Wiley-Blackwell, 2011, pp. 817–26, doi:<a href=\"https://doi.org/10.1111/j.1365-313X.2011.04636.x\">10.1111/j.1365-313X.2011.04636.x</a>.","short":"H. Rakusová, J. Gallego Bartolomé, M. Vanstraelen, H. Robert, D. Alabadí, M. Blázquez, E. Benková, J. Friml, Plant Journal 67 (2011) 817–826.","ieee":"H. Rakusová <i>et al.</i>, “Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana,” <i>Plant Journal</i>, vol. 67, no. 5. Wiley-Blackwell, pp. 817–826, 2011.","apa":"Rakusová, H., Gallego Bartolomé, J., Vanstraelen, M., Robert, H., Alabadí, D., Blázquez, M., … Friml, J. (2011). Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana. <i>Plant Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1365-313X.2011.04636.x\">https://doi.org/10.1111/j.1365-313X.2011.04636.x</a>"},"publist_id":"3606","type":"journal_article","publication_status":"published","quality_controlled":0,"_id":"3094","abstract":[{"text":"Summary Gravitropism aligns plant growth with gravity. It involves gravity perception and the asymmetric distribution of the phytohormone auxin. Here we provide insights into the mechanism for hypocotyl gravitropic growth. We show that the Arabidopsis thaliana PIN3 auxin transporter is required for the asymmetric auxin distribution for the gravitropic response. Gravistimulation polarizes PIN3 to the bottom side of hypocotyl endodermal cells, which correlates with an increased auxin response at the lower hypocotyl side. Both PIN3 polarization and hypocotyl bending require the activity of the trafficking regulator GNOM and the protein kinase PINOID. Our data suggest that gravity-induced PIN3 polarization diverts the auxin flow to mediate the asymmetric distribution of auxin for gravitropic shoot bending.","lang":"eng"}],"date_published":"2011-09-01T00:00:00Z","date_created":"2018-12-11T12:01:21Z","title":"Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana","year":"2011","intvolume":"        67","month":"09","publication":"Plant Journal","date_updated":"2021-01-12T07:41:01Z","volume":67,"author":[{"first_name":"Hana","last_name":"Rakusová","full_name":"Rakusová, Hana"},{"last_name":"Gallego Bartolomé","full_name":"Gallego-Bartolomé, Javier","first_name":"Javier"},{"first_name":"Marleen","last_name":"Vanstraelen","full_name":"Vanstraelen, Marleen"},{"first_name":"Hélène","last_name":"Robert","full_name":"Robert, Hélène S"},{"full_name":"Alabadí, David","last_name":"Alabadí","first_name":"David"},{"last_name":"Blázquez","full_name":"Blázquez, Miguel A","first_name":"Miguel"},{"full_name":"Eva Benková","last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Jirí Friml","last_name":"Friml"}],"doi":"10.1111/j.1365-313X.2011.04636.x","issue":"5","extern":1,"publisher":"Wiley-Blackwell","status":"public","page":"817 - 826"},{"publisher":"Wiley-Blackwell","status":"public","page":"970 - 983","issue":"4","extern":1,"doi":" 10.1111/j.1469-8137.2011.03757.x","publication":"New Phytologist","date_updated":"2021-01-12T07:41:01Z","author":[{"first_name":"Joseph","last_name":"Dubrovsky","full_name":"Dubrovsky, Joseph G"},{"first_name":"Selene","last_name":"Napsucialy Mendivil","full_name":"Napsucialy-Mendivil, Selene"},{"last_name":"Duclercq","full_name":"Duclercq, Jérôme","first_name":"Jérôme"},{"last_name":"Cheng","full_name":"Cheng, Yan","first_name":"Yan"},{"first_name":"Svetlana","full_name":"Shishkova, Svetlana O","last_name":"Shishkova"},{"full_name":"Ivanchenko, Maria G","last_name":"Ivanchenko","first_name":"Maria"},{"full_name":"Jirí Friml","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"last_name":"Murphy","full_name":"Murphy, Angus S","first_name":"Angus"},{"full_name":"Eva Benková","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739"}],"volume":191,"month":"01","intvolume":"       191","year":"2011","date_published":"2011-01-01T00:00:00Z","date_created":"2018-12-11T12:01:21Z","title":"Auxin minimum defines a developmental window for lateral root initiation","abstract":[{"text":"Root system architecture depends on lateral root (LR) initiation that takes place in a relatively narrow developmental window (DW). Here, we analyzed the role of auxin gradients established along the parent root in defining this DW for LR initiation. Correlations between auxin distribution and response, and spatiotemporal control of LR initiation were analyzed in Arabidopsis thaliana and tomato (Solanum lycopersicum). In both Arabidopsis and tomato roots, a well defined zone, where auxin content and response are minimal, demarcates the position of a DW for founder cell specification and LR initiation. We show that in the zone of auxin minimum pericycle cells have highest probability to become founder cells and that auxin perception via the TIR1/AFB pathway, and polar auxin transport, are essential for the establishment of this zone. Altogether, this study reveals that the same morphogen-like molecule, auxin, can act simultaneously as a morphogenetic trigger of LR founder cell identity and as a gradient-dependent signal defining positioning of the founder cell specification. This auxin minimum zone might represent an important control mechanism ensuring the LR initiation steadiness and the acropetal LR initiation pattern. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.","lang":"eng"}],"_id":"3095","publist_id":"3605","type":"journal_article","quality_controlled":0,"publication_status":"published","citation":{"ama":"Dubrovsky J, Napsucialy Mendivil S, Duclercq J, et al. Auxin minimum defines a developmental window for lateral root initiation. <i>New Phytologist</i>. 2011;191(4):970-983. doi:<a href=\"https://doi.org/ 10.1111/j.1469-8137.2011.03757.x\"> 10.1111/j.1469-8137.2011.03757.x</a>","ista":"Dubrovsky J, Napsucialy Mendivil S, Duclercq J, Cheng Y, Shishkova S, Ivanchenko M, Friml J, Murphy A, Benková E. 2011. Auxin minimum defines a developmental window for lateral root initiation. New Phytologist. 191(4), 970–983.","chicago":"Dubrovsky, Joseph, Selene Napsucialy Mendivil, Jérôme Duclercq, Yan Cheng, Svetlana Shishkova, Maria Ivanchenko, Jiří Friml, Angus Murphy, and Eva Benková. “Auxin Minimum Defines a Developmental Window for Lateral Root Initiation.” <i>New Phytologist</i>. Wiley-Blackwell, 2011. <a href=\"https://doi.org/ 10.1111/j.1469-8137.2011.03757.x\">https://doi.org/ 10.1111/j.1469-8137.2011.03757.x</a>.","mla":"Dubrovsky, Joseph, et al. “Auxin Minimum Defines a Developmental Window for Lateral Root Initiation.” <i>New Phytologist</i>, vol. 191, no. 4, Wiley-Blackwell, 2011, pp. 970–83, doi:<a href=\"https://doi.org/ 10.1111/j.1469-8137.2011.03757.x\"> 10.1111/j.1469-8137.2011.03757.x</a>.","short":"J. Dubrovsky, S. Napsucialy Mendivil, J. Duclercq, Y. Cheng, S. Shishkova, M. Ivanchenko, J. Friml, A. Murphy, E. Benková, New Phytologist 191 (2011) 970–983.","ieee":"J. Dubrovsky <i>et al.</i>, “Auxin minimum defines a developmental window for lateral root initiation,” <i>New Phytologist</i>, vol. 191, no. 4. Wiley-Blackwell, pp. 970–983, 2011.","apa":"Dubrovsky, J., Napsucialy Mendivil, S., Duclercq, J., Cheng, Y., Shishkova, S., Ivanchenko, M., … Benková, E. (2011). Auxin minimum defines a developmental window for lateral root initiation. <i>New Phytologist</i>. Wiley-Blackwell. <a href=\"https://doi.org/ 10.1111/j.1469-8137.2011.03757.x\">https://doi.org/ 10.1111/j.1469-8137.2011.03757.x</a>"},"day":"01"},{"doi":"10.1016/j.tplants.2011.05.002","author":[{"last_name":"Wabnik","full_name":"Wabnik, Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T","orcid":"0000-0001-7263-0560"},{"first_name":"Jürgen","full_name":"Kleine Vehn, Jürgen","last_name":"Kleine Vehn"},{"last_name":"Govaerts","full_name":"Govaerts, Willy","first_name":"Willy"},{"last_name":"Friml","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596"}],"volume":16,"publication":"Trends in Plant Science","date_updated":"2021-01-12T07:41:01Z","month":"09","status":"public","page":"468 - 475","publisher":"Cell Press","extern":"1","issue":"9","_id":"3096","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Carrier-dependent, intercellular auxin transport is central to the developmental patterning of higher plants (tracheophytes). The evolution of this polar auxin transport might be linked to the translocation of some PIN auxin efflux carriers from their presumably ancestral localization at the endoplasmic reticulum (ER) to the polar domains at the plasma membrane. Here we propose an eventually ancient mechanism of intercellular auxin distribution by ER-localized auxin transporters involving intracellular auxin retention and switch-like release from the ER. The proposed model integrates feedback circuits utilizing the conserved nuclear auxin signaling for the regulation of PIN transcription and a hypothetical ER-based signaling for the regulation of PIN-dependent transport activity at the ER. Computer simulations of the model revealed its plausibility for generating auxin channels and localized auxin maxima highlighting the possibility of this alternative mechanism for polar auxin transport."}],"publication_status":"published","quality_controlled":"1","publist_id":"3604","type":"journal_article","citation":{"ieee":"K. T. Wabnik, J. Kleine Vehn, W. Govaerts, and J. Friml, “Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization,” <i>Trends in Plant Science</i>, vol. 16, no. 9. Cell Press, pp. 468–475, 2011.","short":"K.T. Wabnik, J. Kleine Vehn, W. Govaerts, J. Friml, Trends in Plant Science 16 (2011) 468–475.","mla":"Wabnik, Krzysztof T., et al. “Prototype Cell-to-Cell Auxin Transport Mechanism by Intracellular Auxin Compartmentalization.” <i>Trends in Plant Science</i>, vol. 16, no. 9, Cell Press, 2011, pp. 468–75, doi:<a href=\"https://doi.org/10.1016/j.tplants.2011.05.002\">10.1016/j.tplants.2011.05.002</a>.","apa":"Wabnik, K. T., Kleine Vehn, J., Govaerts, W., &#38; Friml, J. (2011). Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization. <i>Trends in Plant Science</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tplants.2011.05.002\">https://doi.org/10.1016/j.tplants.2011.05.002</a>","ista":"Wabnik KT, Kleine Vehn J, Govaerts W, Friml J. 2011. Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization. Trends in Plant Science. 16(9), 468–475.","ama":"Wabnik KT, Kleine Vehn J, Govaerts W, Friml J. Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization. <i>Trends in Plant Science</i>. 2011;16(9):468-475. doi:<a href=\"https://doi.org/10.1016/j.tplants.2011.05.002\">10.1016/j.tplants.2011.05.002</a>","chicago":"Wabnik, Krzysztof T, Jürgen Kleine Vehn, Willy Govaerts, and Jiří Friml. “Prototype Cell-to-Cell Auxin Transport Mechanism by Intracellular Auxin Compartmentalization.” <i>Trends in Plant Science</i>. Cell Press, 2011. <a href=\"https://doi.org/10.1016/j.tplants.2011.05.002\">https://doi.org/10.1016/j.tplants.2011.05.002</a>."},"day":"01","intvolume":"        16","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2011","title":"Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization","date_created":"2018-12-11T12:01:21Z","date_published":"2011-09-01T00:00:00Z","oa_version":"None"},{"month":"10","date_updated":"2021-01-12T07:41:02Z","publication":"Developmental Cell","volume":21,"author":[{"first_name":"Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741","full_name":"Peter Marhavy","last_name":"Marhavy"},{"full_name":"Bielach, Agnieszka","last_name":"Bielach","first_name":"Agnieszka"},{"last_name":"Abas","full_name":"Abas, Lindy","first_name":"Lindy"},{"first_name":"Anas","last_name":"Abuzeineh","full_name":"Abuzeineh, Anas"},{"first_name":"Jérôme","last_name":"Duclercq","full_name":"Duclercq, Jérôme"},{"full_name":"Tanaka, Hirokazu","last_name":"Tanaka","first_name":"Hirokazu"},{"full_name":"Pařezová, Markéta","last_name":"Pařezová","first_name":"Markéta"},{"last_name":"Petrášek","full_name":"Petrášek, Jan","first_name":"Jan"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Jirí Friml"},{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková","full_name":"Eva Benková"}],"doi":"10.1016/j.devcel.2011.08.014","issue":"4","extern":1,"publisher":"Cell Press","page":"796 - 804","status":"public","citation":{"mla":"Marhavý, Peter, et al. “Cytokinin Modulates Endocytic Trafficking of PIN1 Auxin Efflux Carrier to Control Plant Organogenesis.” <i>Developmental Cell</i>, vol. 21, no. 4, Cell Press, 2011, pp. 796–804, doi:<a href=\"https://doi.org/10.1016/j.devcel.2011.08.014\">10.1016/j.devcel.2011.08.014</a>.","ieee":"P. Marhavý <i>et al.</i>, “Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis,” <i>Developmental Cell</i>, vol. 21, no. 4. Cell Press, pp. 796–804, 2011.","short":"P. Marhavý, A. Bielach, L. Abas, A. Abuzeineh, J. Duclercq, H. Tanaka, M. Pařezová, J. Petrášek, J. Friml, J. Kleine Vehn, E. Benková, Developmental Cell 21 (2011) 796–804.","apa":"Marhavý, P., Bielach, A., Abas, L., Abuzeineh, A., Duclercq, J., Tanaka, H., … Benková, E. (2011). Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2011.08.014\">https://doi.org/10.1016/j.devcel.2011.08.014</a>","ama":"Marhavý P, Bielach A, Abas L, et al. Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis. <i>Developmental Cell</i>. 2011;21(4):796-804. doi:<a href=\"https://doi.org/10.1016/j.devcel.2011.08.014\">10.1016/j.devcel.2011.08.014</a>","ista":"Marhavý P, Bielach A, Abas L, Abuzeineh A, Duclercq J, Tanaka H, Pařezová M, Petrášek J, Friml J, Kleine Vehn J, Benková E. 2011. Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis. Developmental Cell. 21(4), 796–804.","chicago":"Marhavý, Peter, Agnieszka Bielach, Lindy Abas, Anas Abuzeineh, Jérôme Duclercq, Hirokazu Tanaka, Markéta Pařezová, et al. “Cytokinin Modulates Endocytic Trafficking of PIN1 Auxin Efflux Carrier to Control Plant Organogenesis.” <i>Developmental Cell</i>. Cell Press, 2011. <a href=\"https://doi.org/10.1016/j.devcel.2011.08.014\">https://doi.org/10.1016/j.devcel.2011.08.014</a>."},"day":"18","publist_id":"3603","type":"journal_article","quality_controlled":0,"publication_status":"published","abstract":[{"text":"Cytokinin is an important regulator of plant growth and development. In Arabidopsis thaliana, the two-component phosphorelay mediated through a family of histidine kinases and response regulators is recognized as the principal cytokinin signal transduction mechanism activating the complex transcriptional response to control various developmental processes. Here, we identified an alternative mode of cytokinin action that uses endocytic trafficking as a means to direct plant organogenesis. This activity occurs downstream of known cytokinin receptors but through a branch of the cytokinin signaling pathway that does not involve transcriptional regulation. We show that cytokinin regulates endocytic recycling of the auxin efflux carrier PINFORMED1 (PIN1) by redirecting it for lytic degradation in vacuoles. Stimulation of the lytic PIN1 degradation is not a default effect for general downregulation of proteins from plasma membranes, but a specific mechanism to rapidly modulate the auxin distribution in cytokinin-mediated developmental processes.","lang":"eng"}],"_id":"3097","date_published":"2011-10-18T00:00:00Z","date_created":"2018-12-11T12:01:22Z","title":"Cytokinin modulates endocytic trafficking of PIN1 auxin efflux carrier to control plant organogenesis","year":"2011","intvolume":"        21"},{"year":"2011","intvolume":"         7","date_published":"2011-10-25T00:00:00Z","date_created":"2018-12-11T12:01:22Z","title":"Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane","type":"journal_article","publist_id":"3601","publication_status":"published","quality_controlled":0,"_id":"3098","abstract":[{"lang":"eng","text":"Cell polarity reflected by asymmetric distribution of proteins at the plasma membrane is a fundamental feature of unicellular and multicellular organisms. It remains conceptually unclear how cell polarity is kept in cell wall-encapsulated plant cells. We have used super-resolution and semi-quantitative live-cell imaging in combination with pharmacological, genetic, and computational approaches to reveal insights into the mechanism of cell polarity maintenance in Arabidopsis thaliana. We show that polar-competent PIN transporters for the phytohormone auxin are delivered to the center of polar domains by super-polar recycling. Within the plasma membrane, PINs are recruited into non-mobile membrane clusters and their lateral diffusion is dramatically reduced, which ensures longer polar retention. At the circumventing edges of the polar domain, spatially defined internalization of escaped cargos occurs by clathrin-dependent endocytosis. Computer simulations confirm that the combination of these processes provides a robust mechanism for polarity maintenance in plant cells. Moreover, our study suggests that the regulation of lateral diffusion and spatially defined endocytosis, but not super-polar exocytosis have primary importance for PIN polarity maintenance."}],"citation":{"ista":"Kleine Vehn J, Wabnik KT, Martinière A, Łangowski Ł, Willig K, Naramoto S, Leitner J, Tanaka H, Jakobs S, Robert S, Luschnig C, Govaerts W, Hell S, Runions J, Friml J. 2011. Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane. Molecular Systems Biology. 7.","ama":"Kleine Vehn J, Wabnik KT, Martinière A, et al. Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane. <i>Molecular Systems Biology</i>. 2011;7. doi:<a href=\"https://doi.org/10.1038/msb.2011.72\">10.1038/msb.2011.72</a>","chicago":"Kleine Vehn, Jürgen, Krzysztof T Wabnik, Alexandre Martinière, Łukasz Łangowski, Katrin Willig, Satoshi Naramoto, Johannes Leitner, et al. “Recycling, Clustering and Endocytosis Jointly Maintain PIN Auxin Carrier Polarity at the Plasma Membrane.” <i>Molecular Systems Biology</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/msb.2011.72\">https://doi.org/10.1038/msb.2011.72</a>.","short":"J. Kleine Vehn, K.T. Wabnik, A. Martinière, Ł. Łangowski, K. Willig, S. Naramoto, J. Leitner, H. Tanaka, S. Jakobs, S. Robert, C. Luschnig, W. Govaerts, S. Hell, J. Runions, J. Friml, Molecular Systems Biology 7 (2011).","ieee":"J. Kleine Vehn <i>et al.</i>, “Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane,” <i>Molecular Systems Biology</i>, vol. 7. Nature Publishing Group, 2011.","mla":"Kleine Vehn, Jürgen, et al. “Recycling, Clustering and Endocytosis Jointly Maintain PIN Auxin Carrier Polarity at the Plasma Membrane.” <i>Molecular Systems Biology</i>, vol. 7, Nature Publishing Group, 2011, doi:<a href=\"https://doi.org/10.1038/msb.2011.72\">10.1038/msb.2011.72</a>.","apa":"Kleine Vehn, J., Wabnik, K. T., Martinière, A., Łangowski, Ł., Willig, K., Naramoto, S., … Friml, J. (2011). Recycling, clustering and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane. <i>Molecular Systems Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/msb.2011.72\">https://doi.org/10.1038/msb.2011.72</a>"},"day":"25","publisher":"Nature Publishing Group","status":"public","extern":1,"doi":"10.1038/msb.2011.72","month":"10","publication":"Molecular Systems Biology","date_updated":"2021-01-12T07:41:02Z","author":[{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"full_name":"Krzysztof Wabnik","last_name":"Wabnik","orcid":"0000-0001-7263-0560","first_name":"Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Martinière","full_name":"Martinière, Alexandre","first_name":"Alexandre"},{"first_name":"Łukasz","last_name":"Łangowski","full_name":"Łangowski, Łukasz"},{"last_name":"Willig","full_name":"Willig, Katrin","first_name":"Katrin"},{"first_name":"Satoshi","full_name":"Naramoto, Satoshi","last_name":"Naramoto"},{"last_name":"Leitner","full_name":"Leitner, Johannes","first_name":"Johannes"},{"first_name":"Hirokazu","full_name":"Tanaka, Hirokazu","last_name":"Tanaka"},{"last_name":"Jakobs","full_name":"Jakobs, Stefan","first_name":"Stefan"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"full_name":"Luschnig, Christian","last_name":"Luschnig","first_name":"Christian"},{"first_name":"Willy","full_name":"Govaerts, Willy J","last_name":"Govaerts"},{"full_name":"Hell, Stefan W","last_name":"Hell","first_name":"Stefan"},{"first_name":"John","last_name":"Runions","full_name":"Runions, John"},{"full_name":"Jirí Friml","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"volume":7},{"doi":"10.1073/pnas.1108581108","month":"10","publication":"PNAS","date_updated":"2021-01-12T07:41:02Z","volume":108,"author":[{"last_name":"Drakakaki","full_name":"Drakakaki, Georgia","first_name":"Georgia"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"full_name":"Szatmári, Anna-Maria","last_name":"Szatmári","first_name":"Anna"},{"last_name":"Brown","full_name":"Brown, Michelle Q","first_name":"Michelle"},{"first_name":"Shingo","last_name":"Nagawa","full_name":"Nagawa, Shingo"},{"first_name":"Daniël","last_name":"Van Damme","full_name":"Van Damme, Daniël"},{"first_name":"Marylin","last_name":"Leonard","full_name":"Leonard, Marylin"},{"first_name":"Zhenbiao","full_name":"Yang, Zhenbiao","last_name":"Yang"},{"last_name":"Girke","full_name":"Girke, Thomas","first_name":"Thomas"},{"last_name":"Schmid","full_name":"Schmid, Sandra L","first_name":"Sandra"},{"last_name":"Russinova","full_name":"Russinova, Eugenia","first_name":"Eugenia"},{"full_name":"Jirí Friml","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"last_name":"Raikhel","full_name":"Raikhel, Natasha V","first_name":"Natasha"},{"full_name":"Hicks, Glen R","last_name":"Hicks","first_name":"Glen"}],"publisher":"National Academy of Sciences","status":"public","page":"17850 - 17855","issue":"43","extern":1,"publist_id":"3602","type":"journal_article","publication_status":"published","quality_controlled":0,"_id":"3099","abstract":[{"text":"Endomembrane trafficking relies on the coordination of a highly complex, dynamic network of intracellular vesicles. Understanding the network will require a dissection of cargo and vesicle dynamics at the cellular level in vivo. This is also a key to establishing a link between vesicular networks and their functional roles in development. We used a high-content intracellular screen to discover small molecules targeting endomembrane trafficking in vivo in a complex eukaryote, Arabidopsis thaliana. Tens of thousands of molecules were prescreened and a selected subset was interrogated against a panel of plasma membrane (PM) and other endomembrane compartment markers to identify molecules that altered vesicle trafficking. The extensive image dataset was transformed by a flexible algorithm into a marker-by-phenotype-by-treatment time matrix and revealed groups of molecules that induced similar subcellular fingerprints (clusters). This matrix provides a platform for a systems view of trafficking. Molecules from distinct clusters presented avenues and enabled an entry point to dissect recycling at the PM, vacuolar sorting, and cell-plate maturation. Bioactivity in human cells indicated the value of the approach to identifying small molecules that are active in diverse organisms for biology and drug discovery.","lang":"eng"}],"day":"25","citation":{"chicago":"Drakakaki, Georgia, Stéphanie Robert, Anna Szatmári, Michelle Brown, Shingo Nagawa, Daniël Van Damme, Marylin Leonard, et al. “Clusters of Bioactive Compounds Target Dynamic Endomembrane Networks in Vivo.” <i>PNAS</i>. National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1108581108\">https://doi.org/10.1073/pnas.1108581108</a>.","ista":"Drakakaki G, Robert S, Szatmári A, Brown M, Nagawa S, Van Damme D, Leonard M, Yang Z, Girke T, Schmid S, Russinova E, Friml J, Raikhel N, Hicks G. 2011. Clusters of bioactive compounds target dynamic endomembrane networks in vivo. PNAS. 108(43), 17850–17855.","ama":"Drakakaki G, Robert S, Szatmári A, et al. Clusters of bioactive compounds target dynamic endomembrane networks in vivo. <i>PNAS</i>. 2011;108(43):17850-17855. doi:<a href=\"https://doi.org/10.1073/pnas.1108581108\">10.1073/pnas.1108581108</a>","apa":"Drakakaki, G., Robert, S., Szatmári, A., Brown, M., Nagawa, S., Van Damme, D., … Hicks, G. (2011). Clusters of bioactive compounds target dynamic endomembrane networks in vivo. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1108581108\">https://doi.org/10.1073/pnas.1108581108</a>","ieee":"G. Drakakaki <i>et al.</i>, “Clusters of bioactive compounds target dynamic endomembrane networks in vivo,” <i>PNAS</i>, vol. 108, no. 43. National Academy of Sciences, pp. 17850–17855, 2011.","short":"G. Drakakaki, S. Robert, A. Szatmári, M. Brown, S. Nagawa, D. Van Damme, M. Leonard, Z. Yang, T. Girke, S. Schmid, E. Russinova, J. Friml, N. Raikhel, G. Hicks, PNAS 108 (2011) 17850–17855.","mla":"Drakakaki, Georgia, et al. “Clusters of Bioactive Compounds Target Dynamic Endomembrane Networks in Vivo.” <i>PNAS</i>, vol. 108, no. 43, National Academy of Sciences, 2011, pp. 17850–55, doi:<a href=\"https://doi.org/10.1073/pnas.1108581108\">10.1073/pnas.1108581108</a>."},"year":"2011","intvolume":"       108","date_published":"2011-10-25T00:00:00Z","title":"Clusters of bioactive compounds target dynamic endomembrane networks in vivo","date_created":"2018-12-11T12:01:23Z"},{"intvolume":"        30","year":"2011","date_published":"2011-08-17T00:00:00Z","title":"Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis ","date_created":"2018-12-11T12:01:23Z","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160660/"}],"_id":"3100","abstract":[{"text":"In multicellular organisms, morphogenesis relies on a strict coordination in time and space of cell proliferation and differentiation. In contrast to animals, plant development displays continuous organ formation and adaptive growth responses during their lifespan relying on a tight coordination of cell proliferation. How developmental signals interact with the plant cell-cycle machinery is largely unknown. Here, we characterize plant A2-type cyclins, a small gene family of mitotic cyclins, and show how they contribute to the fine-tuning of local proliferation during plant development. Moreover, the timely repression of CYCA2;3 expression in newly formed guard cells is shown to require the stomatal transcription factors FOUR LIPS/MYB124 and MYB88, providing a direct link between developmental programming and cell-cycle exit in plants. Thus, transcriptional downregulation of CYCA2s represents a critical mechanism to coordinate proliferation during plant development.","lang":"eng"}],"type":"journal_article","publist_id":"3600","publication_status":"published","quality_controlled":0,"citation":{"apa":"Vanneste, S., Coppens, F., Lee, E., Donner, T., Xie, Z., Van Isterdael, G., … Beeckman, T. (2011). Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis . <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2011.240\">https://doi.org/10.1038/emboj.2011.240</a>","mla":"Vanneste, Steffen, et al. “Developmental Regulation of CYCA2s Contributes to Tissue-Specific Proliferation in Arabidopsis .” <i>EMBO Journal</i>, vol. 30, no. 16, Wiley-Blackwell, 2011, pp. 3430–41, doi:<a href=\"https://doi.org/10.1038/emboj.2011.240\">10.1038/emboj.2011.240</a>.","ieee":"S. Vanneste <i>et al.</i>, “Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis ,” <i>EMBO Journal</i>, vol. 30, no. 16. Wiley-Blackwell, pp. 3430–3441, 2011.","short":"S. Vanneste, F. Coppens, E. Lee, T. Donner, Z. Xie, G. Van Isterdael, S. Dhondt, F. De Winter, B. De Rybel, M. Vuylsteke, L. De Veylder, J. Friml, D. Inzé, E. Grotewold, E. Scarpella, F. Sack, G. Beemster, T. Beeckman, EMBO Journal 30 (2011) 3430–3441.","chicago":"Vanneste, Steffen, Frederik Coppens, Eunkyoung Lee, Tyler Donner, Zidian Xie, Gert Van Isterdael, Stijn Dhondt, et al. “Developmental Regulation of CYCA2s Contributes to Tissue-Specific Proliferation in Arabidopsis .” <i>EMBO Journal</i>. Wiley-Blackwell, 2011. <a href=\"https://doi.org/10.1038/emboj.2011.240\">https://doi.org/10.1038/emboj.2011.240</a>.","ama":"Vanneste S, Coppens F, Lee E, et al. Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis . <i>EMBO Journal</i>. 2011;30(16):3430-3441. doi:<a href=\"https://doi.org/10.1038/emboj.2011.240\">10.1038/emboj.2011.240</a>","ista":"Vanneste S, Coppens F, Lee E, Donner T, Xie Z, Van Isterdael G, Dhondt S, De Winter F, De Rybel B, Vuylsteke M, De Veylder L, Friml J, Inzé D, Grotewold E, Scarpella E, Sack F, Beemster G, Beeckman T. 2011. Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis . EMBO Journal. 30(16), 3430–3441."},"day":"17","publisher":"Wiley-Blackwell","page":"3430 - 3441","status":"public","issue":"16","extern":1,"doi":"10.1038/emboj.2011.240","oa":1,"publication":"EMBO Journal","date_updated":"2021-01-12T07:41:04Z","volume":30,"author":[{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"first_name":"Frederik","last_name":"Coppens","full_name":"Coppens, Frederik"},{"first_name":"Eunkyoung","full_name":"Lee, EunKyoung","last_name":"Lee"},{"first_name":"Tyler","full_name":"Donner, Tyler J","last_name":"Donner"},{"first_name":"Zidian","full_name":"Xie, Zidian","last_name":"Xie"},{"first_name":"Gert","last_name":"Van Isterdael","full_name":"Van Isterdael, Gert"},{"last_name":"Dhondt","full_name":"Dhondt, Stijn","first_name":"Stijn"},{"full_name":"De Winter, Freya","last_name":"De Winter","first_name":"Freya"},{"first_name":"Bert","full_name":"De Rybel, Bert","last_name":"De Rybel"},{"first_name":"Marnik","full_name":"Vuylsteke, Marnik","last_name":"Vuylsteke"},{"last_name":"De Veylder","full_name":"De Veylder, Lieven","first_name":"Lieven"},{"full_name":"Jirí Friml","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Inzé","full_name":"Inzé, Dirk","first_name":"Dirk"},{"last_name":"Grotewold","full_name":"Grotewold, Erich","first_name":"Erich"},{"first_name":"Enrico","last_name":"Scarpella","full_name":"Scarpella, Enrico"},{"last_name":"Sack","full_name":"Sack, Fred","first_name":"Fred"},{"full_name":"Beemster, Gerrit T","last_name":"Beemster","first_name":"Gerrit"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"}],"month":"08"},{"doi":"10.1038/cr.2011.99","oa":1,"publication":"Cell Research","date_updated":"2021-01-12T07:41:04Z","volume":21,"author":[{"last_name":"Zwiewka","full_name":"Zwiewka, Marta","first_name":"Marta"},{"full_name":"Feraru, Elena","last_name":"Feraru","first_name":"Elena"},{"last_name":"Möller","full_name":"Möller, Barbara","first_name":"Barbara"},{"first_name":"Inhwan","last_name":"Hwang","full_name":"Hwang, Inhwan"},{"last_name":"Feraru","full_name":"Feraru, Mugurel I","first_name":"Mugurel"},{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"},{"full_name":"Jirí Friml","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"month":"01","publisher":"Nature Publishing Group","status":"public","page":"1711 - 1722","issue":"12","extern":1,"_id":"3101","abstract":[{"text":"Subcellular trafficking is required for a multitude of functions in eukaryotic cells. It involves regulation of cargo sorting, vesicle formation, trafficking and fusion processes at multiple levels. Adaptor protein (AP) complexes are key regulators of cargo sorting into vesicles in yeast and mammals but their existence and function in plants have not been demonstrated. Here we report the identification of the protein-affected trafficking 4 (pat4) mutant defective in the putative δ subunit of the AP-3 complex. pat4 and pat2, a mutant isolated from the same GFP imaging-based forward genetic screen that lacks a functional putative AP-3 β, as well as dominant negative AP-3 μ transgenic lines display undistinguishable phenotypes characterized by largely normal morphology and development, but strong intracellular accumulation of membrane proteins in aberrant vacuolar structures. All mutants are defective in morphology and function of lytic and protein storage vacuoles (PSVs) but show normal sorting of reserve proteins to PSVs. Immunoprecipitation experiments and genetic studies revealed tight functional and physical associations of putative AP-3 β and AP-3 δ subunits. Furthermore, both proteins are closely linked with putative AP-3 μ and σ subunits and several components of the clathrin and dynamin machineries. Taken together, these results demonstrate that AP complexes, similar to those in other eukaryotes, exist in plants, and that AP-3 plays a specific role in the regulation of biogenesis and function of vacuoles in plant cells. © 2011 IBCB, SIBS, CAS All rights reserved","lang":"eng"}],"type":"journal_article","publist_id":"3597","publication_status":"published","quality_controlled":0,"citation":{"mla":"Zwiewka, Marta, et al. “The AP 3 Adaptor Complex Is Required for Vacuolar Function in Arabidopsis.” <i>Cell Research</i>, vol. 21, no. 12, Nature Publishing Group, 2011, pp. 1711–22, doi:<a href=\"https://doi.org/10.1038/cr.2011.99\">10.1038/cr.2011.99</a>.","short":"M. Zwiewka, E. Feraru, B. Möller, I. Hwang, M. Feraru, J. Kleine Vehn, D. Weijers, J. Friml, Cell Research 21 (2011) 1711–1722.","ieee":"M. Zwiewka <i>et al.</i>, “The AP 3 adaptor complex is required for vacuolar function in Arabidopsis,” <i>Cell Research</i>, vol. 21, no. 12. Nature Publishing Group, pp. 1711–1722, 2011.","apa":"Zwiewka, M., Feraru, E., Möller, B., Hwang, I., Feraru, M., Kleine Vehn, J., … Friml, J. (2011). The AP 3 adaptor complex is required for vacuolar function in Arabidopsis. <i>Cell Research</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/cr.2011.99\">https://doi.org/10.1038/cr.2011.99</a>","ama":"Zwiewka M, Feraru E, Möller B, et al. The AP 3 adaptor complex is required for vacuolar function in Arabidopsis. <i>Cell Research</i>. 2011;21(12):1711-1722. doi:<a href=\"https://doi.org/10.1038/cr.2011.99\">10.1038/cr.2011.99</a>","ista":"Zwiewka M, Feraru E, Möller B, Hwang I, Feraru M, Kleine Vehn J, Weijers D, Friml J. 2011. The AP 3 adaptor complex is required for vacuolar function in Arabidopsis. Cell Research. 21(12), 1711–1722.","chicago":"Zwiewka, Marta, Elena Feraru, Barbara Möller, Inhwan Hwang, Mugurel Feraru, Jürgen Kleine Vehn, Dolf Weijers, and Jiří Friml. “The AP 3 Adaptor Complex Is Required for Vacuolar Function in Arabidopsis.” <i>Cell Research</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/cr.2011.99\">https://doi.org/10.1038/cr.2011.99</a>."},"day":"01","intvolume":"        21","year":"2011","date_published":"2011-01-01T00:00:00Z","title":"The AP 3 adaptor complex is required for vacuolar function in Arabidopsis","date_created":"2018-12-11T12:01:23Z","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357998/"}]},{"doi":"10.1105/tpc.111.088377","author":[{"last_name":"Berckmans","full_name":"Berckmans, Barbara","first_name":"Barbara"},{"full_name":"Vassileva, Valya","last_name":"Vassileva","first_name":"Valya"},{"first_name":"Stephan","last_name":"Schmid","full_name":"Schmid, Stephan P"},{"last_name":"Maes","full_name":"Maes, Sara","first_name":"Sara"},{"first_name":"Boris","last_name":"Parizot","full_name":"Parizot, Boris"},{"full_name":"Naramoto, Satoshi","last_name":"Naramoto","first_name":"Satoshi"},{"last_name":"Magyar","full_name":"Magyar, Zoltan","first_name":"Zoltan"},{"full_name":"Lessa Alvim Kamei, Claire","last_name":"Lessa Alvim Kamei","first_name":"Claire"},{"first_name":"Csaba","full_name":"Koncz, Csaba","last_name":"Koncz"},{"last_name":"Bögre","full_name":"Bögre, Laszlo","first_name":"Laszlo"},{"first_name":"Geert","last_name":"Persiau","full_name":"Persiau, Geert"},{"first_name":"Geert","full_name":"De Jaeger, Geert","last_name":"De Jaeger"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml","last_name":"Friml"},{"first_name":"Rüdiger","last_name":"Simon","full_name":"Simon, Rüdiger"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, Tom"},{"full_name":"de Veyldera, Lieven","last_name":"De Veyldera","first_name":"Lieven"}],"volume":23,"date_updated":"2021-01-12T07:41:04Z","publication":"Plant Cell","month":"10","page":"3671 - 3683","status":"public","publisher":"American Society of Plant Biologists","extern":1,"issue":"10","abstract":[{"lang":"eng","text":"Multicellular organisms depend on cell production, cell fate specification, and correct patterning to shape their adult body. In plants, auxin plays a prominent role in the timely coordination of these different cellular processes. A well-studied example is lateral root initiation, in which auxin triggers founder cell specification and cell cycle activation of xylem pole–positioned pericycle cells. Here, we report that the E2Fa transcription factor of Arabidopsis thaliana is an essential component that regulates the asymmetric cell division marking lateral root initiation. Moreover, we demonstrate that E2Fa expression is regulated by the LATERAL ORGAN BOUNDARY DOMAIN18/LATERAL ORGAN BOUNDARY DOMAIN33 (LBD18/LBD33) dimer that is, in turn, regulated by the auxin signaling pathway. LBD18/LBD33 mediates lateral root organogenesis through E2Fa transcriptional activation, whereas E2Fa expression under control of the LBD18 promoter eliminates the need for LBD18. Besides lateral root initiation, vascular patterning is disrupted in E2Fa knockout plants, similarly as it is affected in auxin signaling and lbd mutants, indicating that the transcriptional induction of E2Fa through LBDs represents a general mechanism for auxin-dependent cell cycle activation. Our data illustrate how a conserved mechanism driving cell cycle entry has been adapted evolutionarily to connect auxin signaling with control of processes determining plant architecture. "}],"_id":"3102","quality_controlled":0,"publication_status":"published","publist_id":"3598","type":"journal_article","day":"14","citation":{"ama":"Berckmans B, Vassileva V, Schmid S, et al. Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins. <i>Plant Cell</i>. 2011;23(10):3671-3683. doi:<a href=\"https://doi.org/10.1105/tpc.111.088377\">10.1105/tpc.111.088377</a>","ista":"Berckmans B, Vassileva V, Schmid S, Maes S, Parizot B, Naramoto S, Magyar Z, Lessa Alvim Kamei C, Koncz C, Bögre L, Persiau G, De Jaeger G, Friml J, Simon R, Beeckman T, De Veyldera L. 2011. Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins. Plant Cell. 23(10), 3671–3683.","chicago":"Berckmans, Barbara, Valya Vassileva, Stephan Schmid, Sara Maes, Boris Parizot, Satoshi Naramoto, Zoltan Magyar, et al. “Auxin Dependent Cell Cycle Reactivation through Transcriptional Regulation of Arabidopsis E2Fa by Lateral Organ Boundary Proteins.” <i>Plant Cell</i>. American Society of Plant Biologists, 2011. <a href=\"https://doi.org/10.1105/tpc.111.088377\">https://doi.org/10.1105/tpc.111.088377</a>.","mla":"Berckmans, Barbara, et al. “Auxin Dependent Cell Cycle Reactivation through Transcriptional Regulation of Arabidopsis E2Fa by Lateral Organ Boundary Proteins.” <i>Plant Cell</i>, vol. 23, no. 10, American Society of Plant Biologists, 2011, pp. 3671–83, doi:<a href=\"https://doi.org/10.1105/tpc.111.088377\">10.1105/tpc.111.088377</a>.","ieee":"B. Berckmans <i>et al.</i>, “Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins,” <i>Plant Cell</i>, vol. 23, no. 10. American Society of Plant Biologists, pp. 3671–3683, 2011.","short":"B. Berckmans, V. Vassileva, S. Schmid, S. Maes, B. Parizot, S. Naramoto, Z. Magyar, C. Lessa Alvim Kamei, C. Koncz, L. Bögre, G. Persiau, G. De Jaeger, J. Friml, R. Simon, T. Beeckman, L. De Veyldera, Plant Cell 23 (2011) 3671–3683.","apa":"Berckmans, B., Vassileva, V., Schmid, S., Maes, S., Parizot, B., Naramoto, S., … De Veyldera, L. (2011). Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.111.088377\">https://doi.org/10.1105/tpc.111.088377</a>"},"intvolume":"        23","year":"2011","title":"Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins","date_created":"2018-12-11T12:01:24Z","date_published":"2011-10-14T00:00:00Z"},{"year":"2011","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":"        14","oa_version":"None","date_published":"2011-12-01T00:00:00Z","date_created":"2018-12-11T12:01:24Z","title":"Clathrin-mediated endocytosis: The gateway into plant cells","publist_id":"3596","type":"journal_article","quality_controlled":"1","publication_status":"published","abstract":[{"text":"Endocytosis in plants has an essential role not only for basic cellular functions but also for growth and development, hormonal signaling and communication with the environment including nutrient delivery, toxin avoidance, and pathogen defense. The major endocytic mechanism in plants depends on the coat protein clathrin. It starts by clathrin-coated vesicle formation at the plasma membrane, where specific cargoes are recognized and packaged for internalization. Recently, genetic, biochemical and advanced microscopy studies provided initial insights into mechanisms and roles of clathrin-mediated endocytosis in plants. Here we summarize the present state of knowledge and compare mechanisms of clathrin-mediated endocytosis in plants with animal and yeast paradigms as well as review plant-specific regulations and roles of this process.","lang":"eng"}],"_id":"3103","language":[{"iso":"eng"}],"day":"01","citation":{"chicago":"Chen, Xu, Niloufer Irani, and Jiří Friml. “Clathrin-Mediated Endocytosis: The Gateway into Plant Cells.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.pbi.2011.08.006\">https://doi.org/10.1016/j.pbi.2011.08.006</a>.","ista":"Chen X, Irani N, Friml J. 2011. Clathrin-mediated endocytosis: The gateway into plant cells. Current Opinion in Plant Biology. 14(6), 674–682.","ama":"Chen X, Irani N, Friml J. Clathrin-mediated endocytosis: The gateway into plant cells. <i>Current Opinion in Plant Biology</i>. 2011;14(6):674-682. doi:<a href=\"https://doi.org/10.1016/j.pbi.2011.08.006\">10.1016/j.pbi.2011.08.006</a>","apa":"Chen, X., Irani, N., &#38; Friml, J. (2011). Clathrin-mediated endocytosis: The gateway into plant cells. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2011.08.006\">https://doi.org/10.1016/j.pbi.2011.08.006</a>","short":"X. Chen, N. Irani, J. Friml, Current Opinion in Plant Biology 14 (2011) 674–682.","ieee":"X. Chen, N. Irani, and J. Friml, “Clathrin-mediated endocytosis: The gateway into plant cells,” <i>Current Opinion in Plant Biology</i>, vol. 14, no. 6. Elsevier, pp. 674–682, 2011.","mla":"Chen, Xu, et al. “Clathrin-Mediated Endocytosis: The Gateway into Plant Cells.” <i>Current Opinion in Plant Biology</i>, vol. 14, no. 6, Elsevier, 2011, pp. 674–82, doi:<a href=\"https://doi.org/10.1016/j.pbi.2011.08.006\">10.1016/j.pbi.2011.08.006</a>."},"publisher":"Elsevier","status":"public","page":"674 - 682","issue":"6","extern":"1","doi":"10.1016/j.pbi.2011.08.006","month":"12","date_updated":"2021-01-12T07:41:05Z","publication":"Current Opinion in Plant Biology","author":[{"id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu","full_name":"Chen, Xu","last_name":"Chen"},{"full_name":"Irani, Niloufer","last_name":"Irani","first_name":"Niloufer"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"volume":14},{"abstract":[{"text":"Hippocampal sharp waves (SPWs) and associated fast (&quot;ripple&quot;) oscillations (SPW-Rs) in the CA1 region are among the most synchronous physiological patterns in the mammalian brain. Using two-dimensional arrays of electrodes for recording local field potentials and unit discharges in freely moving rats, we studied the emergence of ripple oscillations (140-220 Hz) and compared their origin and cellular-synaptic mechanisms with fast gamma oscillations (90-140 Hz). We show that (1) hippocampal SPW-Rs and fast gamma oscillations are quantitatively distinct patterns but involve the same networks and share similar mechanisms; (2) both the frequency and magnitude of fast oscillations are positively correlated with the magnitude of SPWs; (3) during both ripples and fast gamma oscillations the frequency of network oscillation is higher in CA1 than in CA3; and (4) the emergence of CA3 population bursts, a prerequisite for SPW-Rs, is biased by activity patterns in the dentate gyrus and entorhinal cortex, with the highest probability of ripples associated with an &quot;optimum&quot; level of dentate gamma power. We hypothesize that each hippocampal subnetwork possesses distinct resonant properties, tuned by the magnitude of the excitatory drive.","lang":"eng"}],"_id":"3138","type":"journal_article","publist_id":"3559","quality_controlled":0,"publication_status":"published","day":"08","citation":{"apa":"Sullivan, D., Csicsvari, J. L., Mizuseki, K., Montgomery, S., Diba, K., &#38; Buzsáki, G. (2011). Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.0294-11.2011\">https://doi.org/10.1523/JNEUROSCI.0294-11.2011</a>","mla":"Sullivan, David, et al. “Relationships between Hippocampal Sharp Waves Ripples and Fast Gamma Oscillation Influence of Dentate and Entorhinal Cortical Activity.” <i>Journal of Neuroscience</i>, vol. 31, no. 23, Society for Neuroscience, 2011, pp. 8605–16, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0294-11.2011\">10.1523/JNEUROSCI.0294-11.2011</a>.","short":"D. Sullivan, J.L. Csicsvari, K. Mizuseki, S. Montgomery, K. Diba, G. Buzsáki, Journal of Neuroscience 31 (2011) 8605–8616.","ieee":"D. Sullivan, J. L. Csicsvari, K. Mizuseki, S. Montgomery, K. Diba, and G. Buzsáki, “Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity,” <i>Journal of Neuroscience</i>, vol. 31, no. 23. Society for Neuroscience, pp. 8605–8616, 2011.","chicago":"Sullivan, David, Jozsef L Csicsvari, Kenji Mizuseki, Sean Montgomery, Kamran Diba, and György Buzsáki. “Relationships between Hippocampal Sharp Waves Ripples and Fast Gamma Oscillation Influence of Dentate and Entorhinal Cortical Activity.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2011. <a href=\"https://doi.org/10.1523/JNEUROSCI.0294-11.2011\">https://doi.org/10.1523/JNEUROSCI.0294-11.2011</a>.","ama":"Sullivan D, Csicsvari JL, Mizuseki K, Montgomery S, Diba K, Buzsáki G. Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity. <i>Journal of Neuroscience</i>. 2011;31(23):8605-8616. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0294-11.2011\">10.1523/JNEUROSCI.0294-11.2011</a>","ista":"Sullivan D, Csicsvari JL, Mizuseki K, Montgomery S, Diba K, Buzsáki G. 2011. Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity. Journal of Neuroscience. 31(23), 8605–8616."},"intvolume":"        31","year":"2011","date_published":"2011-06-08T00:00:00Z","date_created":"2018-12-11T12:01:36Z","title":"Relationships between hippocampal sharp waves ripples and fast gamma oscillation Influence of dentate and entorhinal cortical activity","doi":"10.1523/JNEUROSCI.0294-11.2011","date_updated":"2021-01-12T07:41:19Z","publication":"Journal of Neuroscience","volume":31,"author":[{"first_name":"David","full_name":"Sullivan, David W","last_name":"Sullivan"},{"full_name":"Jozsef Csicsvari","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","orcid":"0000-0002-5193-4036"},{"full_name":"Mizuseki, Kenji","last_name":"Mizuseki","first_name":"Kenji"},{"first_name":"Sean","last_name":"Montgomery","full_name":"Montgomery, Sean M"},{"first_name":"Kamran","full_name":"Diba, Kamran","last_name":"Diba"},{"first_name":"György","full_name":"Buzsáki, György","last_name":"Buzsáki"}],"month":"06","publisher":"Society for Neuroscience","status":"public","page":"8605 - 8616","issue":"23","extern":1},{"doi":"10.1073/pnas.1019507108","volume":108,"author":[{"full_name":"Tasic, Bosiljka","last_name":"Tasic","first_name":"Bosiljka"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Simon Hippenmeyer","last_name":"Hippenmeyer"},{"last_name":"Wang","full_name":"Wang, Charlene","first_name":"Charlene"},{"last_name":"Gamboa","full_name":"Gamboa, Matthew","first_name":"Matthew"},{"first_name":"Hui","full_name":"Zong, Hui","last_name":"Zong"},{"first_name":"Yanru","last_name":"Chen Tsai","full_name":"Chen-Tsai, Yanru"},{"full_name":"Luo, Liqun","last_name":"Luo","first_name":"Liqun"}],"publication":"PNAS","date_updated":"2021-01-12T07:41:22Z","month":"05","page":"7902 - 7907","status":"public","publisher":"National Academy of Sciences","extern":1,"issue":"19","abstract":[{"text":"Microinjection of recombinant DNA into zygotic pronuclei has been widely used for producing transgenic mice. However, with this method, the insertion site, integrity, and copy number of the transgene cannot be controlled. Here, we present an integrase-based approach to produce transgenic mice via pronuclear injection, whereby an intact single-copy transgene can be inserted into predetermined chromosomal loci with high efficiency (up to 40%), and faithfully transmitted through generations. We show that neighboring transgenic elements and bacterial DNA within the transgene cause profound silencing and expression variability of the transgenic marker. Removal of these undesirable elements leads to global high-level marker expression from transgenes driven by a ubiquitous promoter. We also obtained faithful marker expression from a tissue-specific promoter. The technique presented here will greatly facilitate murine transgenesis and precise structure/function dissection of mammalian gene function and regulation in vivo.","lang":"eng"}],"_id":"3145","publication_status":"published","quality_controlled":0,"type":"journal_article","publist_id":"3549","citation":{"mla":"Tasic, Bosiljka, et al. “Site Specific Integrase Mediated Transgenesis in Mice via Pronuclear Injection.” <i>PNAS</i>, vol. 108, no. 19, National Academy of Sciences, 2011, pp. 7902–07, doi:<a href=\"https://doi.org/10.1073/pnas.1019507108\">10.1073/pnas.1019507108</a>.","short":"B. Tasic, S. Hippenmeyer, C. Wang, M. Gamboa, H. Zong, Y. Chen Tsai, L. Luo, PNAS 108 (2011) 7902–7907.","ieee":"B. Tasic <i>et al.</i>, “Site specific integrase mediated transgenesis in mice via pronuclear injection,” <i>PNAS</i>, vol. 108, no. 19. National Academy of Sciences, pp. 7902–7907, 2011.","apa":"Tasic, B., Hippenmeyer, S., Wang, C., Gamboa, M., Zong, H., Chen Tsai, Y., &#38; Luo, L. (2011). Site specific integrase mediated transgenesis in mice via pronuclear injection. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1019507108\">https://doi.org/10.1073/pnas.1019507108</a>","ama":"Tasic B, Hippenmeyer S, Wang C, et al. Site specific integrase mediated transgenesis in mice via pronuclear injection. <i>PNAS</i>. 2011;108(19):7902-7907. doi:<a href=\"https://doi.org/10.1073/pnas.1019507108\">10.1073/pnas.1019507108</a>","ista":"Tasic B, Hippenmeyer S, Wang C, Gamboa M, Zong H, Chen Tsai Y, Luo L. 2011. Site specific integrase mediated transgenesis in mice via pronuclear injection. PNAS. 108(19), 7902–7907.","chicago":"Tasic, Bosiljka, Simon Hippenmeyer, Charlene Wang, Matthew Gamboa, Hui Zong, Yanru Chen Tsai, and Liqun Luo. “Site Specific Integrase Mediated Transgenesis in Mice via Pronuclear Injection.” <i>PNAS</i>. National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1019507108\">https://doi.org/10.1073/pnas.1019507108</a>."},"day":"10","intvolume":"       108","year":"2011","date_created":"2018-12-11T12:01:39Z","title":"Site specific integrase mediated transgenesis in mice via pronuclear injection","date_published":"2011-05-10T00:00:00Z"},{"extern":1,"issue":"2","page":"209 - 221","status":"public","publisher":"Cell Press","author":[{"last_name":"Liu","full_name":"Liu, Chong","first_name":"Chong"},{"last_name":"Sage","full_name":"Sage, Jonathan C","first_name":"Jonathan"},{"first_name":"Michael","full_name":"Miller, Michael R","last_name":"Miller"},{"first_name":"Roel","last_name":"Verhaak","full_name":"Verhaak, Roel G"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Simon Hippenmeyer"},{"full_name":"Vogel, Hannes","last_name":"Vogel","first_name":"Hannes"},{"last_name":"Foreman","full_name":"Foreman, Oded","first_name":"Oded"},{"last_name":"Bronson","full_name":"Bronson, Roderick T","first_name":"Roderick"},{"last_name":"Nishiyama","full_name":"Nishiyama, Akiko","first_name":"Akiko"},{"first_name":"Liqun","full_name":"Luo, Liqun","last_name":"Luo"},{"last_name":"Zong","full_name":"Zong, Hui","first_name":"Hui"}],"volume":146,"publication":"Cell","date_updated":"2021-01-12T07:41:23Z","month":"07","doi":"10.1016/j.cell.2011.06.014","date_created":"2018-12-11T12:01:40Z","title":"Mosaic analysis with double markers reveals tumor cell of origin in glioma","date_published":"2011-07-22T00:00:00Z","intvolume":"       146","year":"2011","day":"22","citation":{"apa":"Liu, C., Sage, J., Miller, M., Verhaak, R., Hippenmeyer, S., Vogel, H., … Zong, H. (2011). Mosaic analysis with double markers reveals tumor cell of origin in glioma. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2011.06.014\">https://doi.org/10.1016/j.cell.2011.06.014</a>","mla":"Liu, Chong, et al. “Mosaic Analysis with Double Markers Reveals Tumor Cell of Origin in Glioma.” <i>Cell</i>, vol. 146, no. 2, Cell Press, 2011, pp. 209–21, doi:<a href=\"https://doi.org/10.1016/j.cell.2011.06.014\">10.1016/j.cell.2011.06.014</a>.","short":"C. Liu, J. Sage, M. Miller, R. Verhaak, S. Hippenmeyer, H. Vogel, O. Foreman, R. Bronson, A. Nishiyama, L. Luo, H. Zong, Cell 146 (2011) 209–221.","ieee":"C. Liu <i>et al.</i>, “Mosaic analysis with double markers reveals tumor cell of origin in glioma,” <i>Cell</i>, vol. 146, no. 2. Cell Press, pp. 209–221, 2011.","chicago":"Liu, Chong, Jonathan Sage, Michael Miller, Roel Verhaak, Simon Hippenmeyer, Hannes Vogel, Oded Foreman, et al. “Mosaic Analysis with Double Markers Reveals Tumor Cell of Origin in Glioma.” <i>Cell</i>. Cell Press, 2011. <a href=\"https://doi.org/10.1016/j.cell.2011.06.014\">https://doi.org/10.1016/j.cell.2011.06.014</a>.","ama":"Liu C, Sage J, Miller M, et al. Mosaic analysis with double markers reveals tumor cell of origin in glioma. <i>Cell</i>. 2011;146(2):209-221. doi:<a href=\"https://doi.org/10.1016/j.cell.2011.06.014\">10.1016/j.cell.2011.06.014</a>","ista":"Liu C, Sage J, Miller M, Verhaak R, Hippenmeyer S, Vogel H, Foreman O, Bronson R, Nishiyama A, Luo L, Zong H. 2011. Mosaic analysis with double markers reveals tumor cell of origin in glioma. Cell. 146(2), 209–221."},"_id":"3147","abstract":[{"text":"Cancer cell of origin is difficult to identify by analyzing cells within terminal stage tumors, whose identity could be concealed by the acquired plasticity. Thus, an ideal approach to identify the cell of origin is to analyze proliferative abnormalities in distinct lineages prior to malignancy. Here, we use mosaic analysis with double markers (MADM) in mice to model gliomagenesis by initiating concurrent p53/Nf1 mutations sporadically in neural stem cells (NSCs). Surprisingly, MADM-based lineage tracing revealed significant aberrant growth prior to malignancy only in oligodendrocyte precursor cells (OPCs), but not in any other NSC-derived lineages or NSCs themselves. Upon tumor formation, phenotypic and transcriptome analyses of tumor cells revealed salient OPC features. Finally, introducing the same p53/Nf1 mutations directly into OPCs consistently led to gliomagenesis. Our findings suggest OPCs as the cell of origin in this model, even when initial mutations occur in NSCs, and highlight the importance of analyzing premalignant stages to identify the cancer cell of origin.","lang":"eng"}],"quality_controlled":0,"publication_status":"published","publist_id":"3548","type":"journal_article"},{"abstract":[{"text":"Regulated adhesion between cells and their environment is critical for normal cell migration. We have identified mutations in a gene encoding the Drosophila hydrogen peroxide (H2O2)-degrading enzyme Jafrac1, which lead to germ cell adhesion defects. During gastrulation, primordial germ cells (PGCs) associate tightly with the invaginating midgut primordium as it enters the embryo; however, in embryos from jafrac1 mutant mothers this association is disrupted, leaving some PGCs trailing on the outside of the embryo. We observed similar phenotypes in embryos from DE-cadherin/shotgun (shg) mutant mothers and were able to rescue the jafrac1 phenotype by increasing DE-cadherin levels. This and our biochemical evidence strongly suggest that Jafrac1-mediated reduction of H2O2 is required to maintain DE-cadherin protein levels in the early embryo. Our results present in vivo evidence of a peroxiredoxin regulating DE-cadherin-mediated adhesion.","lang":"eng"}],"_id":"3154","type":"journal_article","publist_id":"3541","publication_status":"published","quality_controlled":0,"citation":{"apa":"Degennaro, M., Hurd, T., Siekhaus, D. E., Biteau, B., Jasper, H., &#38; Lehmann, R. (2011). Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2010.12.007\">https://doi.org/10.1016/j.devcel.2010.12.007</a>","mla":"Degennaro, Matthew, et al. “Peroxiredoxin Stabilization of DE-Cadherin Promotes Primordial Germ Cell Adhesion.” <i>Developmental Cell</i>, vol. 20, no. 2, Cell Press, 2011, pp. 233–43, doi:<a href=\"https://doi.org/10.1016/j.devcel.2010.12.007\">10.1016/j.devcel.2010.12.007</a>.","ieee":"M. Degennaro, T. Hurd, D. E. Siekhaus, B. Biteau, H. Jasper, and R. Lehmann, “Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion,” <i>Developmental Cell</i>, vol. 20, no. 2. Cell Press, pp. 233–243, 2011.","short":"M. Degennaro, T. Hurd, D.E. Siekhaus, B. Biteau, H. Jasper, R. Lehmann, Developmental Cell 20 (2011) 233–243.","chicago":"Degennaro, Matthew, Thomas Hurd, Daria E Siekhaus, Benoit Biteau, Heinrich Jasper, and Ruth Lehmann. “Peroxiredoxin Stabilization of DE-Cadherin Promotes Primordial Germ Cell Adhesion.” <i>Developmental Cell</i>. Cell Press, 2011. <a href=\"https://doi.org/10.1016/j.devcel.2010.12.007\">https://doi.org/10.1016/j.devcel.2010.12.007</a>.","ama":"Degennaro M, Hurd T, Siekhaus DE, Biteau B, Jasper H, Lehmann R. Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion. <i>Developmental Cell</i>. 2011;20(2):233-243. doi:<a href=\"https://doi.org/10.1016/j.devcel.2010.12.007\">10.1016/j.devcel.2010.12.007</a>","ista":"Degennaro M, Hurd T, Siekhaus DE, Biteau B, Jasper H, Lehmann R. 2011. Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion. Developmental Cell. 20(2), 233–243."},"day":"15","intvolume":"        20","year":"2011","date_published":"2011-02-15T00:00:00Z","title":"Peroxiredoxin stabilization of DE-cadherin promotes primordial germ cell adhesion","date_created":"2018-12-11T12:01:42Z","doi":"10.1016/j.devcel.2010.12.007","date_updated":"2021-01-12T07:41:26Z","publication":"Developmental Cell","volume":20,"author":[{"last_name":"Degennaro","full_name":"DeGennaro, Matthew","first_name":"Matthew"},{"full_name":"Hurd, Thomas R","last_name":"Hurd","first_name":"Thomas"},{"full_name":"Daria Siekhaus","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"},{"first_name":"Benoit","last_name":"Biteau","full_name":"Biteau, Benoit"},{"first_name":"Heinrich","last_name":"Jasper","full_name":"Jasper, Heinrich"},{"first_name":"Ruth","full_name":"Lehmann, Ruth","last_name":"Lehmann"}],"month":"02","publisher":"Cell Press","page":"233 - 243","status":"public","issue":"2","extern":1},{"oa_version":"None","title":"Maximum margin multi-label structured prediction","date_created":"2018-12-11T12:01:45Z","date_published":"2011-12-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","citation":{"ama":"Lampert C. Maximum margin multi-label structured prediction. In: Neural Information Processing Systems Foundation; 2011.","ista":"Lampert C. 2011. Maximum margin multi-label structured prediction. NIPS: Neural Information Processing Systems.","chicago":"Lampert, Christoph. “Maximum Margin Multi-Label Structured Prediction.” Neural Information Processing Systems Foundation, 2011.","mla":"Lampert, Christoph. <i>Maximum Margin Multi-Label Structured Prediction</i>. Neural Information Processing Systems Foundation, 2011.","short":"C. Lampert, in:, Neural Information Processing Systems Foundation, 2011.","ieee":"C. Lampert, “Maximum margin multi-label structured prediction,” presented at the NIPS: Neural Information Processing Systems, Granada, Spain, 2011.","apa":"Lampert, C. (2011). Maximum margin multi-label structured prediction. Presented at the NIPS: Neural Information Processing Systems, Granada, Spain: Neural Information Processing Systems Foundation."},"day":"01","conference":{"name":"NIPS: Neural Information Processing Systems","start_date":"2011-12-12","end_date":"2011-12-14","location":"Granada, Spain"},"quality_controlled":"1","publication_status":"published","publist_id":"3522","type":"conference","language":[{"iso":"eng"}],"_id":"3163","abstract":[{"lang":"eng","text":"We study multi-label prediction for structured output sets, a problem that occurs, for example, in object detection in images, secondary structure prediction in computational biology, and graph matching with symmetries. Conventional multilabel classification techniques are typically not applicable in this situation, because they require explicit enumeration of the label set, which is infeasible in case of structured outputs. Relying on techniques originally designed for single-label structured prediction, in particular structured support vector machines, results in reduced prediction accuracy, or leads to infeasible optimization problems. In this work we derive a maximum-margin training formulation for multi-label structured prediction that remains computationally tractable while achieving high prediction accuracy. It also shares most beneficial properties with single-label maximum-margin approaches, in particular formulation as a convex optimization problem, efficient working set training, and PAC-Bayesian generalization bounds."}],"scopus_import":"1","related_material":{"record":[{"relation":"later_version","id":"3322","status":"public"}]},"status":"public","publisher":"Neural Information Processing Systems Foundation","article_processing_charge":"No","corr_author":"1","department":[{"_id":"ChLa"}],"month":"12","author":[{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph","last_name":"Lampert"}],"date_updated":"2025-06-03T11:47:47Z"},{"main_file_link":[{"url":"http://arxiv.org/pdf/1007.1229v3","open_access":"0"}],"title":"Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions","date_created":"2018-12-11T12:02:00Z","alternative_title":["LNCS"],"date_published":"2011-08-09T00:00:00Z","year":"2011","intvolume":"      6907","citation":{"short":"V. Kolmogorov, in:, Springer, 2011, pp. 400–411.","ieee":"V. Kolmogorov, “Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions,” presented at the MFCS: Mathematical Foundations of Computer Science, 2011, vol. 6907, pp. 400–411.","mla":"Kolmogorov, Vladimir. <i>Submodularity on a Tree: Unifying Submodularity on a Tree: Unifying L-Convex and Bisubmodular Functions Convex and Bisubmodular Functions</i>. Vol. 6907, Springer, 2011, pp. 400–11, doi:<a href=\"https://doi.org/10.1007/978-3-642-22993-0_37\">10.1007/978-3-642-22993-0_37</a>.","apa":"Kolmogorov, V. (2011). Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions (Vol. 6907, pp. 400–411). Presented at the MFCS: Mathematical Foundations of Computer Science, Springer. <a href=\"https://doi.org/10.1007/978-3-642-22993-0_37\">https://doi.org/10.1007/978-3-642-22993-0_37</a>","ista":"Kolmogorov V. 2011. Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 6907, 400–411.","ama":"Kolmogorov V. Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions. In: Vol 6907. Springer; 2011:400-411. doi:<a href=\"https://doi.org/10.1007/978-3-642-22993-0_37\">10.1007/978-3-642-22993-0_37</a>","chicago":"Kolmogorov, Vladimir. “Submodularity on a Tree: Unifying Submodularity on a Tree: Unifying L-Convex and Bisubmodular Functions Convex and Bisubmodular Functions,” 6907:400–411. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-22993-0_37\">https://doi.org/10.1007/978-3-642-22993-0_37</a>."},"day":"09","conference":{"name":"MFCS: Mathematical Foundations of Computer Science"},"quality_controlled":0,"publication_status":"published","type":"conference","publist_id":"3478","abstract":[{"text":"We introduce a new class of functions that can be minimized in polynomial time in the value oracle model. These are functions f satisfying f(x) + f(y) ≥ f(x ∏ y) + f(x ∐ y) where the domain of each variable x i corresponds to nodes of a rooted binary tree, and operations ∏,∐ are defined with respect to this tree. Special cases include previously studied L-convex and bisubmodular functions, which can be obtained with particular choices of trees. We present a polynomial-time algorithm for minimizing functions in the new class. It combines Murota's steepest descent algorithm for L-convex functions with bisubmodular minimization algorithms. ","lang":"eng"}],"_id":"3204","extern":1,"status":"public","page":"400 - 411","publisher":"Springer","month":"08","author":[{"full_name":"Vladimir Kolmogorov","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"}],"volume":6907,"date_updated":"2021-01-12T07:41:47Z","doi":"10.1007/978-3-642-22993-0_37"},{"status":"public","page":"113 - 120","publisher":"Omnipress","extern":1,"month":"01","author":[{"last_name":"Tarlow","full_name":"Tarlow, Daniel","first_name":"Daniel"},{"full_name":"Batra, Druv","last_name":"Batra","first_name":"Druv"},{"first_name":"Pushmeet","full_name":"Kohli, Pushmeet","last_name":"Kohli"},{"full_name":"Vladimir Kolmogorov","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"}],"date_updated":"2021-01-12T07:41:47Z","year":"2011","main_file_link":[{"url":"http://ttic.uchicago.edu/~dbatra/publications/assets/tbkk_icml11.pdf","open_access":"0"}],"title":"Dynamic tree block coordinate ascent","date_created":"2018-12-11T12:02:00Z","date_published":"2011-01-01T00:00:00Z","publication_status":"published","conference":{"name":"ICML: International Conference on Machine Learning"},"quality_controlled":0,"publist_id":"3475","type":"conference","abstract":[{"lang":"eng","text":"This paper proposes a novel Linear Programming (LP) based algorithm, called Dynamic Tree-Block Coordinate Ascent (DT-BCA), for performing maximum a posteriori (MAP) inference in probabilistic graphical models. Unlike traditional message passing algorithms, which operate uniformly on the whole factor graph, our method dynamically chooses regions of the factor graph on which to focus message-passing efforts. We propose two criteria for selecting regions, including an efficiently computable upper-bound on the increase in the objective possible by passing messages in any particular region. This bound is derived from the theory of primal-dual methods from combinatorial optimization, and the forest that maximizes the bounds can be chosen efficiently using a maximum-spanning-tree-like algorithm. Experimental results show that our dynamic schedules significantly speed up state-of-the-art LP-based message-passing algorithms on a wide variety of real-world problems."}],"_id":"3205","day":"01","citation":{"mla":"Tarlow, Daniel, et al. <i>Dynamic Tree Block Coordinate Ascent</i>. Omnipress, 2011, pp. 113–20.","ieee":"D. Tarlow, D. Batra, P. Kohli, and V. Kolmogorov, “Dynamic tree block coordinate ascent,” presented at the ICML: International Conference on Machine Learning, 2011, pp. 113–120.","short":"D. Tarlow, D. Batra, P. Kohli, V. Kolmogorov, in:, Omnipress, 2011, pp. 113–120.","apa":"Tarlow, D., Batra, D., Kohli, P., &#38; Kolmogorov, V. (2011). Dynamic tree block coordinate ascent (pp. 113–120). Presented at the ICML: International Conference on Machine Learning, Omnipress.","ama":"Tarlow D, Batra D, Kohli P, Kolmogorov V. Dynamic tree block coordinate ascent. In: Omnipress; 2011:113-120.","ista":"Tarlow D, Batra D, Kohli P, Kolmogorov V. 2011. Dynamic tree block coordinate ascent. ICML: International Conference on Machine Learning, 113–120.","chicago":"Tarlow, Daniel, Druv Batra, Pushmeet Kohli, and Vladimir Kolmogorov. “Dynamic Tree Block Coordinate Ascent,” 113–20. Omnipress, 2011."}},{"publisher":"IEEE","page":"1889 - 1896","status":"public","extern":1,"doi":"10.1109/CVPR.2011.5995361","date_updated":"2021-01-12T07:41:47Z","author":[{"full_name":"Osokin, Anton","last_name":"Osokin","first_name":"Anton"},{"last_name":"Vetrov","full_name":"Vetrov, Dmitry","first_name":"Dmitry"},{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov","last_name":"Kolmogorov"}],"month":"08","year":"2011","date_published":"2011-08-22T00:00:00Z","title":"Submodular decomposition framework for inference in associative Markov networks with global constraints","date_created":"2018-12-11T12:02:00Z","main_file_link":[{"open_access":"0","url":"http://arxiv.org/pdf/1103.1077v1"}],"abstract":[{"lang":"eng","text":"In this paper we address the problem of finding the most probable state of discrete Markov random field (MRF) with associative pairwise terms. Although of practical importance, this problem is known to be NP-hard in general. We propose a new type of MRF decomposition, submod-ular decomposition (SMD). Unlike existing decomposition approaches SMD decomposes the initial problem into sub-problems corresponding to a specific class label while preserving the graph structure of each subproblem. Such decomposition enables us to take into account several types of global constraints in an efficient manner. We study theoretical properties of the proposed approach and demonstrate its applicability on a number of problems."}],"_id":"3206","publist_id":"3476","type":"conference","conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"quality_controlled":0,"publication_status":"published","citation":{"chicago":"Osokin, Anton, Dmitry Vetrov, and Vladimir Kolmogorov. “Submodular Decomposition Framework for Inference in Associative Markov Networks with Global Constraints,” 1889–96. IEEE, 2011. <a href=\"https://doi.org/10.1109/CVPR.2011.5995361\">https://doi.org/10.1109/CVPR.2011.5995361</a>.","ama":"Osokin A, Vetrov D, Kolmogorov V. Submodular decomposition framework for inference in associative Markov networks with global constraints. In: IEEE; 2011:1889-1896. doi:<a href=\"https://doi.org/10.1109/CVPR.2011.5995361\">10.1109/CVPR.2011.5995361</a>","ista":"Osokin A, Vetrov D, Kolmogorov V. 2011. Submodular decomposition framework for inference in associative Markov networks with global constraints. CVPR: Computer Vision and Pattern Recognition, 1889–1896.","apa":"Osokin, A., Vetrov, D., &#38; Kolmogorov, V. (2011). Submodular decomposition framework for inference in associative Markov networks with global constraints (pp. 1889–1896). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. <a href=\"https://doi.org/10.1109/CVPR.2011.5995361\">https://doi.org/10.1109/CVPR.2011.5995361</a>","mla":"Osokin, Anton, et al. <i>Submodular Decomposition Framework for Inference in Associative Markov Networks with Global Constraints</i>. IEEE, 2011, pp. 1889–96, doi:<a href=\"https://doi.org/10.1109/CVPR.2011.5995361\">10.1109/CVPR.2011.5995361</a>.","short":"A. Osokin, D. Vetrov, V. Kolmogorov, in:, IEEE, 2011, pp. 1889–1896.","ieee":"A. Osokin, D. Vetrov, and V. Kolmogorov, “Submodular decomposition framework for inference in associative Markov networks with global constraints,” presented at the CVPR: Computer Vision and Pattern Recognition, 2011, pp. 1889–1896."},"day":"22"}]