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1. Organizing Scientific Competitions on the Semantic Web

Author

Shimoyama, Sayoko, Cox, Robert Sidney, III, Gifford, David, Toyoda, Tetsuro, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Decker, Hendrik, editor, Lhotská, Lenka, editor, Link, Sebastian, editor, Basl, Josef, editor, and Tjoa, A Min, editor

Published
2013
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2. Development of Linked Open Data for Bioresources

Author

Masuya, Hiroshi, Takatsuki, Terue, Makita, Yuko, Yoshida, Yuko, Mochizuki, Yoshiki, Kobayashi, Norio, Yoshiki, Atsushi, Nakamura, Yukio, Toyoda, Tetsuro, Obata, Yuichi, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Takeda, Hideaki, editor, Qu, Yuzhong, editor, Mizoguchi, Riichiro, editor, and Kitamura, Yoshinobu, editor

Published
2013
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6. MASCP Gator: An Aggregation Portal for the Visualization of Arabidopsis Proteomics Data

Author

Joshi, Hiren J., Hirsch-Hoffmann, Matthias, Baerenfaller, Katja, Gruissem, Wilhelm, Baginsky, Sacha, Schmidt, Robert, Schulze, Waltraud X., Sun, Qi, van Wijk, Klaas J., Egelhofer, Volker, Wienkoop, Stefanie, Weckwerth, Wolfram, Bruley, Christophe, Rolland, Norbert, Toyoda, Tetsuro, Nakagami, Hirofumi, Jones, Alexandra M., Briggs, Steven P., Castleden, Ian, Tanz, Sandra K., Millar, A. Harvey, and Heazlewood, Joshua L.

Published
2011

13. Murine induced pluripotent stem cells can be derived from and differentiate into natural killer T cells

Author

Watarai, Hiroshi, Fujii, Shin-ichiro, Yamada, Daisuke, Rybouchkin, Andrei, Sakata, Sakura, Nagata, Yuko, Iida-Kobayashi, Midori, Sekine-Kondo, Etsuko, Shimizu, Kanako, Shozaki, Yohei, Sharif, Jafar, Matsuda, Masashi, Mochiduki, Shinobu, Hasegawa, Takanori, Kitahara, Genta, Endo, Takaho A., Toyoda, Tetsuro, Ohara, Osamu, Harigaya, Ken-ichi, Koseki, Haruhiko, and Taniguchi, Masaru

Subjects
T cells -- Growth, Cell physiology -- Research -- Growth, Stem cells -- Growth -- Research, Cell differentiation -- Research -- Growth, Company growth, Health care industry
Abstract

NKT cells demonstrate antitumor activity when activated to produce Th1 cytokines by DCs loaded with α-galactosylceramide, the prototypic NKT cell-activating glycolipid antigen. However, most patients do not have sufficient numbers of NKT cells to induce an effective immune response in this context, indicating a need for a source of NKT cells that could be used to supplement the endogenous cell population. Induced pluripotent stem cells (iPSCs) hold tremendous potential for cell-replacement therapy, but whether it is possible to generate functionally competent NKT cells from iPSCs has not been rigorously assessed. In this study, we successfully derived iPSCs both from embryonic fibroblasts from mice harboring functional NKT cell-specific rearranged T cell receptor loci in the germline and from splenic NKT cells from WT adult mice. These iPSCs could be differentiated into NKT cells in vitro and secreted large amounts of the Th1 cytokine IFN-γ. Importantly, iPSC-derived NKT cells recapitulated the known adjuvant effects of natural NKT cells and suppressed tumor growth in vivo. These studies demonstrate the feasibility of expanding functionally competent NKT cells via an iPSC phase, an approach that may be adapted for NKT cell-targeted therapy in humans., Introduction NKT cells are characterized by their expression of an invariant TCR a chain encoded by Vα14-Jα18 in mice (1) and by Vα.24-Jα18 in humans (2), (3). NKT cells recognize [...]

Published
2010
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14. A promoter-level mammalian expression atlas

Author

Forrest, Alistair R. R., Kawaji, Hideya, Rehli, Michael, Kenneth Baillie, J., de Hoon, Michiel J. L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicolas, Jørgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Alam, Intikhab, Albanese, Davide, Altschuler, Gabriel M., Arakawa, Takahiro, Archer, John A. C., Arner, Peter, Babina, Magda, Rennie, Sarah, Balwierz, Piotr J., Beckhouse, Anthony G., Pradhan-Bhatt, Swati, Blake, Judith A., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Maxwell Burroughs, A., Califano, Andrea, Cannistraci, Carlo V., Carbajo, Daniel, Chen, Yun, Chierici, Marco, Ciani, Yari, Clevers, Hans C., Dalla, Emiliano, Davis, Carrie A., Detmar, Michael, Diehl, Alexander D., Dohi, Taeko, Drabløs, Finn, Edge, Albert S. B., Edinger, Matthias, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Fagiolini, Michela, Fairbairn, Lynsey, Fang, Hai, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander V., Fisher, Malcolm E., Frith, Martin C., Fujita, Rie, Fukuda, Shiro, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Jun-ichi, Geijtenbeek, Teunis B., Gibson, Andrew P., Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Harbers, Matthias, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Takehiro, Herlyn, Meenhard, Hitchens, Kelly J., Ho Sui, Shannan J., Hofmann, Oliver M., Hoof, Ilka, Hori, Fumi, Huminiecki, Lukasz, Iida, Kei, Ikawa, Tomokatsu, Jankovic, Boris R., Jia, Hui, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kaiho, Ai, Kajiyama, Kazuhiro, Kanamori-Katayama, Mutsumi, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Shintaro, Kato, Sachi, Kawaguchi, Shuji, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Peter Klinken, S., Knox, Alan J., Kojima, Miki, Kojima, Soichi, Kondo, Naoto, Koseki, Haruhiko, Koyasu, Shigeo, Krampitz, Sarah, Kubosaki, Atsutaka, Kwon, Andrew T., Laros, Jeroen F. J., Lee, Weonju, Lennartsson, Andreas, Li, Kang, Lilje, Berit, Lipovich, Leonard, Mackay-sim, Alan, Manabe, Ri-ichiroh, Mar, Jessica C., Marchand, Benoit, Mathelier, Anthony, Mejhert, Niklas, Meynert, Alison, Mizuno, Yosuke, de Lima Morais, David A., Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummery, Christine L., Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nakazato, Kenichi, van Nimwegen, Erik, Ninomiya, Noriko, Nishiyori, Hiromi, Noma, Shohei, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohmiya, Hiroko, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Pain, Arnab, Passier, Robert, Patrikakis, Margaret, Persson, Helena, Piazza, Silvano, Prendergast, James G. D., Rackham, Owen J. L., Ramilowski, Jordan A., Rashid, Mamoon, Ravasi, Timothy, Rizzu, Patrizia, Roncador, Marco, Roy, Sugata, Rye, Morten B., Saijyo, Eri, Sajantila, Antti, Saka, Akiko, Sakaguchi, Shimon, Sakai, Mizuho, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schneider, Claudio, Schultes, Erik A., Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sengstag, Thierry, Sheng, Guojun, Shimoji, Hisashi, Shimoni, Yishai, Shin, Jay W., Simon, Christophe, Sugiyama, Daisuke, Sugiyama, Takaaki, Suzuki, Masanori, Suzuki, Naoko, Swoboda, Rolf K., ’t Hoen, Peter A. C., Tagami, Michihira, Takahashi, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tatum, Zuotian, Thompson, Mark, Toyoda, Hiroo, Toyoda, Tetsuro, Valen, Eivind, van de Wetering, Marc, van den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Vorontsov, Ilya E., Wasserman, Wyeth W., Watanabe, Shoko, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Wood, Emily J., Yamaguchi, Yoko, Yamamoto, Masayuki, Yoneda, Misako, Yonekura, Yohei, Yoshida, Shigehiro, Zabierowski, Susan E., Zhang, Peter G., Zhao, Xiaobei, Zucchelli, Silvia, Summers, Kim M., Suzuki, Harukazu, Daub, Carsten O., Kawai, Jun, Heutink, Peter, Hide, Winston, Freeman, Tom C., Lenhard, Boris, Bajic, Vladimir B., Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin, Hume, David A., Carninci, Piero, and Hayashizaki, Yoshihide

Published
2014
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15. Current status of the multinational Arabidopsis community

Author

Parry, Geraint, Provart, Nicholas J., Brady, Siobhan M., Uzilday, Baris, Adams, Keith, Baginsky, Sacha, Bakker, Erica, Batley, Jacqui, Beale, Mike, Beilstein, Mark, Belkhadir, Youssef, Mendel, Gregor, Berardini, Tanya, Bergelson, Joy, Blanco?Herrera, Francisca, Brady, Siobhan, Braun, Hans?Peter, Briggs, Steve, Brownfield, Lynette, Cardarelli, Maura, Castellanos-Uribe, Marcos, Coruzzi, Gloria, Dassanayake, Maheshi, De Jaeger, Geert, Dilkes, Brian, Doherty, Colleen, Ecker, Joe, Edger, Pat, Edwards, David, El Kasmi, Farid, Eriksson, Maria, Exposito?Alonso, Moises, Falter?Braun, Pascal, Fernie, Alisdair, Ferro, Myriam, Fiehn, Oliver, Friesner, Joanna, Greenham, Katie, Guo, Yalong, Hamann, Thorsten, Hancock, Angela, Hauser, Marie?Theres, Heazlewood, Joshua, Ho, Cheng?Hsun, Huala, Eva, Hwang, Inhwan, Iuchi, Satoshi, Jaiswal, Pankaj, Jakobson, Liina, Jiang, Yunhe, Jiao, Yuling, Jones, Alexandra, Kadota, Yasuhiro, Khurana, Jitendra, Kliebenstein, Dan, Knee, Emma, Kobayashi, Masatomo, Koch, Marcus, Krouk, Gabriel, Larson, Tony, Last, Rob, Li, Song, Lurin, Claire, Lysak, Martin, Maere, Steven, Malinowski, Robert, Maumus, Florian, May, Sean, Mayer, Klaus, Mendoza?Cozatl, David, Mendoza?Poudereux, Isabel, Millar, Harvey, Mock, Hans?Peter, Mukhtar, Karolina, Mukhtar, Shahid, Murcha, Monika, Nakagami, Hirofumi, Nakamura, Yasukazu, Nicolov, Luke, Nikolau, Basil, Nowack, Moritz, Nunes?Nesi, Adriano, Palmgren, Michael, Patron, Nicola, Peck, Scott, Pedmale, Ullas, Perrot?Rechenmann, Catherine, Pieruschka, Roland, Pires, J. Chris, Provart, Nicholas, Reiser, Leonore, Rhee, Sue, Rigas, Stamatis, Rolland, Norbert, Romanowski, Andres, Savaldi?Goldstein, Sigal, Schmitz, Robert, Schulze, Waltraud, Seki, Motoaki, Shimizu, Kentaro K., Slotkin, Keith, Small, Ian, Somers, David, Sozzani, Rosangela, Spillane, Charles, Srinivasan, Ramamurthy, Taylor, Nicolas, Tello?Ruiz, Marcela?Karey, Thelen, Jay, Tohge, Takayuki, Town, Christopher, Toyoda, Tetsuro, Walley, Justin, Ware, Doreen, Weckwerth, Wolfram, Whitelegge, Julian, Wienkoop, Stefanie, Wright, Clay, Wrzaczek, Michael, Yamazaki, Misako, Yanovsky, Marcelo, Zhong, Xuehua, Peer, Yves, Wijk, Klaas, Gillhaussen, Philipp, and The Multinational Arabidopsis Steering Committee

Subjects
Arabidopsis thaliana, roadmap, collaboration, Research Network
Abstract

© 2020 The Authors. Plant Direct published by American Society of Plant Biologists and the Society for Experimental Biology and John Wiley & Sons Ltd The multinational Arabidopsis research community is highly collaborative and over the past thirty years these activities have been documented by the Multinational Arabidopsis Steering Committee (MASC). Here, we (a) highlight recent research advances made with the reference plant Arabidopsis thaliana; (b) provide summaries from recent reports submitted by MASC subcommittees, projects and resources associated with MASC and from MASC country representatives; and (c) initiate a call for ideas and foci for the “fourth decadal roadmap,” which will advise and coordinate the global activities of the Arabidopsis research community.

Published
2020

16. The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA

Author

Sharif, Jafar, Muto, Masahiro, Takebayashi, Shin-ichiro, Suetake, Isao, Iwamatsu, Akihiro, Endo, Takaho A., Shinga, Jun, Mizutani-Koseki, Yoko, Toyoda, Tetsuro, Okamura, Kunihiro, Tajima, Shoji, Mitsuya, Kohzoh, Okano, Masaki, and Koseki, Haruhiko

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

DNA methyltransferase (cytosine-5) 1 (Dnmt1) is the principal enzyme responsible for maintenance of CpG methylation and is essential for the regulation of gene expression, silencing of parasitic DNA elements, genomic [...]

Published
2007

18. Development of Linked Open Data for Bioresources

Author

Masuya, Hiroshi, primary, Takatsuki, Terue, additional, Makita, Yuko, additional, Yoshida, Yuko, additional, Mochizuki, Yoshiki, additional, Kobayashi, Norio, additional, Yoshiki, Atsushi, additional, Nakamura, Yukio, additional, Toyoda, Tetsuro, additional, and Obata, Yuichi, additional

Published
2013
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22. Arabidopsis Tiling Array Analysis to Identify the Stress-Responsive Genes

Author

Matsui, Akihiro, primary, Ishida, Junko, additional, Morosawa, Taeko, additional, Okamoto, Masanori, additional, Kim, Jong-Myong, additional, Kurihara, Yukio, additional, Kawashima, Makiko, additional, Tanaka, Maho, additional, To, Taiko Kim, additional, Nakaminami, Kentaro, additional, Kaminuma, Eli, additional, Endo, Takaho A., additional, Mochizuki, Yoshiki, additional, Kawaguchi, Shuji, additional, Kobayashi, Norio, additional, Shinozaki, Kazuo, additional, Toyoda, Tetsuro, additional, and Seki, Motoaki, additional

Published
2010
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28. The RIKEN integrated database of mammals

Author

Masuya, Hiroshi, Makita, Yuko, Kobayashi, Norio, Nishikata, Koro, Yoshida, Yuko, Mochizuki, Yoshiki, Doi, Koji, Takatsuki, Terue, Waki, Kazunori, Tanaka, Nobuhiko, Ishii, Manabu, Matsushima, Akihiro, Takahashi, Satoshi, Hijikata, Atsushi, Kozaki, Kouji, Furuichi, Teiichi, Kawaji, Hideya, Wakana, Shigeharu, Nakamura, Yukio, Yoshiki, Atsushi, Murata, Takehide, Fukami-Kobayashi, Kaoru, Mohan, Sujatha, Ohara, Osamu, Hayashizaki, Yoshihide, Mizoguchi, Riichiro, Obata, Yuichi, and Toyoda, Tetsuro

Published
2011
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50. Ligand-specific sequential regulation of transcription factors for differentiation of MCF-7 cells

Author

Toyoda Tetsuro, Yumoto Noriko, Nagashima Takeshi, Ide Kaori, Endo Takaho, Saeki Yuko, Suzuki Harukazu, Hayashizaki Yoshihide, Sakaki Yoshiyuki, and Okada-Hatakeyama Mariko

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Sharing a common ErbB/HER receptor signaling pathway, heregulin (HRG) induces differentiation of MCF-7 human breast cancer cells while epidermal growth factor (EGF) elicits proliferation. Although cell fates resulting from action of the aforementioned ligands completely different, the respective gene expression profiles in early transcription are qualitatively similar, suggesting that gene expression during late transcription, but not early transcription, may reflect ligand specificity. In this study, based on both the data from time-course quantitative real-time PCR on over 2,000 human transcription factors and microarray of all human genes, we identified a series of transcription factors which may control HRG-specific late transcription in MCF-7 cells. Results We predicted that four transcription factors including EGR4, FRA-1, FHL2, and DIPA should have responsibility of regulation in MCF-7 cell differentiation. Validation analysis suggested that one member of the activator protein 1 (AP-1) family, FOSL-1 (FRA-1 gene), appeared immediately following c-FOS expression, might be responsible for expression of transcription factor FHL2 through activation of the AP-1 complex. Furthermore, RNAi gene silencing of FOSL-1 and FHL2 resulted in increase of extracellular signal-regulated kinase (ERK) phosphorylation of which duration was sustained by HRG stimulation. Conclusion Our analysis indicated that a time-dependent transcriptional regulatory network including c-FOS, FRA-1, and FHL2 is vital in controlling the ERK signaling pathway through a negative feedback loop for MCF-7 cell differentiation.

Published
2009
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