Publications by authors named "Soichi Kojima"

99Publications

Imaging of the ex vivo transglutaminase activity in liver macrophages of sepsis mice.

Anal Biochem 2020 05 3;597:113654. Epub 2020 Mar 3.

Liver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ab.2020.113654DOI Listing
May 2020

Prevention of arachidonic acid-induced liver injury by controlling oxidative stress-mediated transglutaminase activation with garlic extracts.

Exp Ther Med 2020 Feb 27;19(2):1522-1527. Epub 2019 Dec 27.

Liver Cancer Prevention Research Unit, RIKEN Center for Integrative Medical Sciences, Wako, Saitama 351-0198, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3892/etm.2019.8384DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6966192PMC
February 2020

Lipid desaturation-associated endoplasmic reticulum stress regulates MYCN gene expression in hepatocellular carcinoma cells.

Cell Death Dis 2020 01 27;11(1):66. Epub 2020 Jan 27.

Liver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41419-020-2257-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6985230PMC
January 2020

Anti-interleukin-6 receptor antibody treatment ameliorates postoperative adhesion formation.

Sci Rep 2019 11 26;9(1):17558. Epub 2019 Nov 26.

Department of Surgery, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-019-54175-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879753PMC
November 2019

Fungal NOX is an essential factor for induction of TG2 in human hepatocytes.

Med Mycol 2020 Jul;58(5):679-689

School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/mmy/myz105DOI Listing
July 2020

Development of an anti-hepatitis B virus (HBV) agent through the structure-activity relationship of the interferon-like small compound CDM-3008.

Bioorg Med Chem 2019 02 5;27(3):470-478. Epub 2018 Dec 5.

Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S09680896183154
Publisher Site
http://dx.doi.org/10.1016/j.bmc.2018.11.039DOI Listing
February 2019

The urea transporter DUR3 contributes to rice production under nitrogen-deficient and field conditions.

Physiol Plant 2019 Sep 9;167(1):75-89. Epub 2019 Jan 9.

Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/ppl.12872DOI Listing
September 2019

Arachidonic acid suppresses hepatic cell growth through ROS-mediated activation of transglutaminase.

FEBS Open Bio 2018 Oct 11;8(10):1703-1710. Epub 2018 Sep 11.

Liver Cancer Prevention Research Unit RIKEN Center for Integrative Medical Sciences Wako Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/2211-5463.12511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168684PMC
October 2018

Prevention of acute liver injury by suppressing plasma kallikrein-dependent activation of latent TGF-β.

Biochem Biophys Res Commun 2018 10 12;504(4):857-864. Epub 2018 Sep 12.

Liver Cancer Prevention Research Unit, RIKEN Center for Integrative Medical Sciences, Saitama, Japan; Graduate School of Medical & Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbrc.2018.09.026DOI Listing
October 2018

Reply to Yoshida: Liver cancer stem cells: Identification and lipid metabolic reprogramming.

Proc Natl Acad Sci U S A 2018 07 25;115(28):E6390-E6391. Epub 2018 Jun 25.

Liver Cancer Prevention Research Unit, RIKEN Center for Integrative Medical Sciences, Wako, Saitama 351-0198, Japan;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1808740115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048540PMC
July 2018

Outgrowth of Rice Tillers Requires Availability of Glutamine in the Basal Portions of Shoots.

Rice (N Y) 2018 May 9;11(1):31. Epub 2018 May 9.

Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki-Aza, Aoba-ku, Sendai, 980-8572, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12284-018-0225-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5943206PMC
May 2018

Glycosylation controls cooperative PECAM-VEGFR2-β3 integrin functions at the endothelial surface for tumor angiogenesis.

Oncogene 2018 08 2;37(31):4287-4299. Epub 2018 May 2.

Disease Glycomics Team, Systems Glycobiology Research Group, RIKEN, Saitama, 351-0198, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41388-018-0271-7DOI Listing
August 2018

Cytosolic Glutamine Synthetase Isozymes Play Redundant Roles in Ammonium Assimilation Under Low-Ammonium Conditions in Roots of Arabidopsis thaliana.

Plant Cell Physiol 2018 Mar;59(3):601-613

Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Sendai, 980-0845 Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/pcp/pcy014DOI Listing
March 2018

Lack of ACTPK1, an STY kinase, enhances ammonium uptake and use, and promotes growth of rice seedlings under sufficient external ammonium.

Plant J 2018 03 17;93(6):992-1006. Epub 2018 Feb 17.

Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi, 981-8555, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/tpj.13824DOI Listing
March 2018

Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes.

EBioMedicine 2017 Oct 12;24:257-266. Epub 2017 Sep 12.

Micro-Signaling Regulation Technology Unit, RIKEN Center for Life Science Technologies, Wako, Saitama 3510198, Japan; Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo 1058461, Japan. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ebiom.2017.09.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5652006PMC
October 2017

FANTOM5 CAGE profiles of human and mouse samples.

Authors:
Shuhei Noguchi Takahiro Arakawa Shiro Fukuda Masaaki Furuno Akira Hasegawa Fumi Hori Sachi Ishikawa-Kato Kaoru Kaida Ai Kaiho Mutsumi Kanamori-Katayama Tsugumi Kawashima Miki Kojima Atsutaka Kubosaki Ri-Ichiroh Manabe Mitsuyoshi Murata Sayaka Nagao-Sato Kenichi Nakazato Noriko Ninomiya Hiromi Nishiyori-Sueki Shohei Noma Eri Saijyo Akiko Saka Mizuho Sakai Christophe Simon Naoko Suzuki Michihira Tagami Shoko Watanabe Shigehiro Yoshida Peter Arner Richard A Axton Magda Babina J Kenneth Baillie Timothy C Barnett Anthony G Beckhouse Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher Ailsa J Carlisle Hans C Clevers Carrie A Davis Michael Detmar Taeko Dohi Albert S B Edge Matthias Edinger Anna Ehrlund Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Afsaneh Eslami Michela Fagiolini Lynsey Fairbairn Mary C Farach-Carson Geoffrey J Faulkner Carmelo Ferrai Malcolm E Fisher Lesley M Forrester Rie Fujita Jun-Ichi Furusawa Teunis B Geijtenbeek Thomas Gingeras Daniel Goldowitz Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Yuki Hasegawa Meenhard Herlyn Peter Heutink Kelly J Hitchens David A Hume Tomokatsu Ikawa Yuri Ishizu Chieko Kai Hiroshi Kawamoto Yuki I Kawamura Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura Sarah Klein S Peter Klinken Alan J Knox Soichi Kojima Haruhiko Koseki Shigeo Koyasu Weonju Lee Andreas Lennartsson Alan Mackay-Sim Niklas Mejhert Yosuke Mizuno Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Kelly J Morris Hozumi Motohashi Christine L Mummery Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Tadasuke Nozaki Soichi Ogishima Naganari Ohkura Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Robert Passier Margaret Patrikakis Ana Pombo Swati Pradhan-Bhatt Xian-Yang Qin Michael Rehli Patrizia Rizzu Sugata Roy Antti Sajantila Shimon Sakaguchi Hiroki Sato Hironori Satoh Suzana Savvi Alka Saxena Christian Schmidl Claudio Schneider Gundula G Schulze-Tanzil Anita Schwegmann Guojun Sheng Jay W Shin Daisuke Sugiyama Takaaki Sugiyama Kim M Summers Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Andru Tomoiu Hiroo Toyoda Marc van de Wetering Linda M van den Berg Roberto Verardo Dipti Vijayan Christine A Wells Louise N Winteringham Ernst Wolvetang Yoko Yamaguchi Masayuki Yamamoto Chiyo Yanagi-Mizuochi Misako Yoneda Yohei Yonekura Peter G Zhang Silvia Zucchelli Imad Abugessaisa Erik Arner Jayson Harshbarger Atsushi Kondo Timo Lassmann Marina Lizio Serkan Sahin Thierry Sengstag Jessica Severin Hisashi Shimoji Masanori Suzuki Harukazu Suzuki Jun Kawai Naoto Kondo Masayoshi Itoh Carsten O Daub Takeya Kasukawa Hideya Kawaji Piero Carninci Alistair R R Forrest Yoshihide Hayashizaki

Sci Data 2017 08 29;4:170112. Epub 2017 Aug 29.

RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/sdata.2017.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5574368PMC
August 2017

Plasma Kallikrein-Dependent Transforming Growth Factor-β Activation in Patients With Chronic Pancreatitis and Pancreatic Cancer.

Pancreas 2017 03;46(3):e20-e22

Micro-Signaling Regulation Technology Unit, RIKEN Center for Life Science Technologies, Wako, Japan; Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Endoscopy, Nagoya University Hospital, Nagoya, Japan; Micro-Signaling Regulation Technology Unit, RIKEN Center for Life Science Technologies, Wako, Japan; Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan; Micro-Signaling Regulation Technology Unit, RIKEN Center for Life Science Technologies, Wako, Japan

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1097/MPA.0000000000000736DOI Listing
March 2017

The chimeric repressor for the GATA4 transcription factor improves tolerance to nitrogen deficiency in .

Plant Biotechnol (Tokyo) 2017 16;34(3):151-158. Epub 2017 Sep 16.

Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.5511/plantbiotechnology.17.0727aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6565994PMC
September 2017

Contributions of two cytosolic glutamine synthetase isozymes to ammonium assimilation in Arabidopsis roots.

J Exp Bot 2017 01;68(3):613-625

Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/jxb/erw454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5441914PMC
January 2017

Phenosafranin inhibits nuclear localization of transglutaminase 2 without affecting its transamidase activity.

Amino Acids 2017 03 24;49(3):483-488. Epub 2016 Sep 24.

Micro-Signaling Regulation Technology Unit, RIKEN Center for Life Science Technologies, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00726-016-2337-6DOI Listing
March 2017

In vivo imaging of advanced glycation end products (AGEs) of albumin: first observations of significantly reduced clearance and liver deposition properties in mice.

Org Biomol Chem 2016 Jun;14(24):5755-60

Biofunctional Synthetic Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan. and Biofunctional Chemistry Laboratory, A. Butlerov Institute of Chemistry, Kazan Federal University, 18 Kremlyovskaya Street, Kazan 420008, Russia and Japan Science and Technology Agency-PRESTO, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1039/c6ob00098cDOI Listing
June 2016

Metabolome Analyses Uncovered a Novel Inhibitory Effect of Acyclic Retinoid on Aberrant Lipogenesis in a Mouse Diethylnitrosamine-Induced Hepatic Tumorigenesis Model.

Cancer Prev Res (Phila) 2016 Mar 7;9(3):205-14. Epub 2016 Jan 7.

Micro-Signaling Regulation Technology Unit, RIKEN Center for Life Science Technologies, Saitama, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/1940-6207.CAPR-15-0326DOI Listing
March 2016

Growth Properties and Biomass Production in the Hybrid C4 Crop Sorghum bicolor.

Plant Cell Physiol 2016 May 27;57(5):944-52. Epub 2015 Oct 27.

Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai, 981-8555 Japan CREST, JST, Gobancho, Chiyoda-ku, Tokyo, 102-0076 Japan

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/pcp/pcv158DOI Listing
May 2016

Carboxylic Derivatives of Vitamin K2 Inhibit Hepatocellular Carcinoma Cell Growth through Caspase/Transglutaminase-Related Signaling Pathways.

J Nutr Sci Vitaminol (Tokyo) 2015 ;61(4):285-90

Micro-Signaling Regulation Technology Unit, RIKEN Center for Life Science Technologies.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3177/jnsv.61.285DOI Listing
July 2016

L(59) TGF-β LAP degradation products serve as a promising blood biomarker for liver fibrogenesis in mice.

Fibrogenesis Tissue Repair 2015 15;8:17. Epub 2015 Sep 15.

Micro-Signaling Regulation Technology Unit, RIKEN Center for Life Science Technologies, Wako, Saitama 351-0918 Japan.

View Article

Download full-text PDF

Source
http://www.fibrogenesis.com/content/8/1/17
Publisher Site
http://dx.doi.org/10.1186/s13069-015-0034-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570586PMC
September 2015

A candidate factor that interacts with RF2, a restorer of fertility of Lead rice-type cytoplasmic male sterility in rice.

Rice (N Y) 2014 Dec 7;7(1):21. Epub 2014 Oct 7.

Graduate School of Agricultural Science, Tohoku University, Sendai, 981-8555, Japan,

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12284-014-0021-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4884035PMC
December 2014

Hepatic fibrosis and angiogenesis after bile duct ligation are endogenously expressed vasohibin-1 independent.

Biochem Biophys Res Commun 2015 Jul 27;463(3):384-8. Epub 2015 May 27.

Micro-Signaling Regulation Technology Unit, RIKEN Center for Life Science Technologies, Saitama, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbrc.2015.05.074DOI Listing
July 2015

Eicosapentaenoic acid ameliorates non-alcoholic steatohepatitis in a novel mouse model using melanocortin 4 receptor-deficient mice.

PLoS One 2015 27;10(3):e0121528. Epub 2015 Mar 27.

Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan; Japan Science and Technology Agency, CREST, Tokyo, Japan.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121528PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4376873PMC
March 2016

Autophagy supports biomass production and nitrogen use efficiency at the vegetative stage in rice.

Plant Physiol 2015 May 18;168(1):60-73. Epub 2015 Mar 18.

Department of Applied Plant Science, Graduate School of Agricultural Sciences, Tohoku University, Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan (S.W, Y.H., K.Ka., S.K., T.Y., A.M., H.I.); Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai 980-8577, Japan (M.I.);Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aramaki, Aoba-ku, Sendai 980-8578, Japan (M.I.); School of Bioscience and Biotechnology, Tokyo University of Technology, Hachioji, Tokyo 192-0982, Japan (T.K.);Department of Applied Biological Science (T.K., S.H., K.Ku.), and Research Institute for Science and Technology (T.K., K.Ku.), Tokyo University of Science, Noda, Chiba 278-8510, Japan; andCREST, Japan Science and Technology Agency, Chiyoda-ku, Tokyo 102-0076, Japan (A.M.)

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1104/pp.15.00242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424030PMC
May 2015

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.

Authors:
Erik Arner Carsten O Daub Kristoffer Vitting-Seerup Robin Andersson Berit Lilje Finn Drabløs Andreas Lennartsson Michelle Rönnerblad Olga Hrydziuszko Morana Vitezic Tom C Freeman Ahmad M N Alhendi Peter Arner Richard Axton J Kenneth Baillie Anthony Beckhouse Beatrice Bodega James Briggs Frank Brombacher Margaret Davis Michael Detmar Anna Ehrlund Mitsuhiro Endoh Afsaneh Eslami Michela Fagiolini Lynsey Fairbairn Geoffrey J Faulkner Carmelo Ferrai Malcolm E Fisher Lesley Forrester Daniel Goldowitz Reto Guler Thomas Ha Mitsuko Hara Meenhard Herlyn Tomokatsu Ikawa Chieko Kai Hiroshi Kawamoto Levon M Khachigian S Peter Klinken Soichi Kojima Haruhiko Koseki Sarah Klein Niklas Mejhert Ken Miyaguchi Yosuke Mizuno Mitsuru Morimoto Kelly J Morris Christine Mummery Yutaka Nakachi Soichi Ogishima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry Ovchinnikov Robert Passier Margaret Patrikakis Ana Pombo Xian-Yang Qin Sugata Roy Hiroki Sato Suzana Savvi Alka Saxena Anita Schwegmann Daisuke Sugiyama Rolf Swoboda Hiroshi Tanaka Andru Tomoiu Louise N Winteringham Ernst Wolvetang Chiyo Yanagi-Mizuochi Misako Yoneda Susan Zabierowski Peter Zhang Imad Abugessaisa Nicolas Bertin Alexander D Diehl Shiro Fukuda Masaaki Furuno Jayson Harshbarger Akira Hasegawa Fumi Hori Sachi Ishikawa-Kato Yuri Ishizu Masayoshi Itoh Tsugumi Kawashima Miki Kojima Naoto Kondo Marina Lizio Terrence F Meehan Christopher J Mungall Mitsuyoshi Murata Hiromi Nishiyori-Sueki Serkan Sahin Sayaka Nagao-Sato Jessica Severin Michiel J L de Hoon Jun Kawai Takeya Kasukawa Timo Lassmann Harukazu Suzuki Hideya Kawaji Kim M Summers Christine Wells David A Hume Alistair R R Forrest Albin Sandelin Piero Carninci Yoshihide Hayashizaki

Science 2015 Feb 12;347(6225):1010-4. Epub 2015 Feb 12.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1259418DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681433PMC
February 2015

Asparagine synthetase1, but not asparagine synthetase2, is responsible for the biosynthesis of asparagine following the supply of ammonium to rice roots.

Plant Cell Physiol 2015 Apr 28;56(4):769-78. Epub 2015 Jan 28.

Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, 981-8555 Japan

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/pcp/pcv005DOI Listing
April 2015

Urea retranslocation from senescing Arabidopsis leaves is promoted by DUR3-mediated urea retrieval from leaf apoplast.

Plant J 2015 Feb 5;81(3):377-87. Epub 2015 Jan 5.

Department of Physiology & Cell Biology, Leibniz-Institute of Plant Genetics and Crop Plant Research, Corrensstr 3, D-06466, Gatersleben, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/tpj.12740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4329417PMC
February 2015

Potential associations between perihepatic lymph node enlargement and liver fibrosis, hepatocellular injury or hepatocarcinogenesis in chronic hepatitis B virus infection.

Hepatol Res 2015 Apr 16;45(4):397-404. Epub 2014 Jun 16.

Department of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/hepr.12361DOI Listing
April 2015

A promoter-level mammalian expression atlas.

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

Nature 2014 Mar;507(7493):462-70

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature13182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748PMC
March 2014

NADH-dependent glutamate synthase plays a crucial role in assimilating ammonium in the Arabidopsis root.

Physiol Plant 2014 Sep 2;152(1):138-51. Epub 2014 Apr 2.

Graduate School of Agricultural Science, Tohoku University, Sendai, 9818555, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/ppl.12177DOI Listing
September 2014

CLE-CLAVATA1 peptide-receptor signaling module regulates the expansion of plant root systems in a nitrogen-dependent manner.

Proc Natl Acad Sci U S A 2014 Feb 21;111(5):2029-34. Epub 2014 Jan 21.

Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1319953111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3918772PMC
February 2014

Neovessel formation promotes liver fibrosis via providing latent transforming growth factor-β.

Biochem Biophys Res Commun 2014 Jan 19;443(3):950-6. Epub 2013 Dec 19.

Micro-signaling Regulation Technology Unit, RIKEN Center for Life Science Technologies, Wako, Saitama 351-0198, Japan. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbrc.2013.12.074DOI Listing
January 2014

HCV NS3 protease enhances liver fibrosis via binding to and activating TGF-β type I receptor.

Sci Rep 2013 Nov 22;3:3243. Epub 2013 Nov 22.

1] Micro-signaling Regulation Technology Unit, RIKEN Center for Life Science Technologies, Saitama 351-0198, Japan [2] Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Kanagawa 223-8522, Japan [3] Drug Discovery Laboratory, Wakunaga Pharmaceutical Co., Ltd., Hiroshima 739-1195, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep03243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3837337PMC
November 2013

Pituitary adenylate cyclase-activating polypeptide type 1 receptor (PAC1) gene is suppressed by transglutaminase 2 activation.

J Biol Chem 2013 Nov 17;288(45):32720-30. Epub 2013 Sep 17.

From the Department of Pharmacology, Graduate School of Medical and Dental Sciences, University of Kagoshima, Kagoshima 890-8544, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1074/jbc.M113.452706DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820906PMC
November 2013

Variations in both TG1 and TG2 isozyme-specific in situ activities and protein expressions during mouse embryonic development.

J Histochem Cytochem 2013 Nov 29;61(11):793-801. Epub 2013 Jul 29.

Graduate School of Bioagricultural Sciences (MI), Nagoya University, Nagoya, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1369/0022155413501676DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3808576PMC
November 2013

Cytosolic glutamine synthetase1;2 is responsible for the primary assimilation of ammonium in rice roots.

Plant Cell Physiol 2013 Jun 18;54(6):934-43. Epub 2013 Mar 18.

Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, 981-8555 Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/pcp/pct046DOI Listing
June 2013

Regulation of transglutaminase-mediated hepatic cell death in alcoholic steatohepatitis and non-alcoholic steatohepatitis.

J Gastroenterol Hepatol 2012 Mar;27 Suppl 2:52-7

Molecular Ligand Biology Research Team, Chemical Genomics Research Group, Chemical Biology Department, RIKEN Advanced Science Institute, Saitama, Japan.

View Article

Download full-text PDF

Source
http://doi.wiley.com/10.1111/j.1440-1746.2011.07009.x
Publisher Site
http://dx.doi.org/10.1111/j.1440-1746.2011.07009.xDOI Listing
March 2012

New insights into the functions and localization of nuclear transglutaminase 2.

FEBS J 2011 Dec 21;278(24):4756-67. Epub 2011 Nov 21.

Chemical Biology Department, RIKEN Advanced Science Institute, Wako, Saitama, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1742-4658.2011.08409.xDOI Listing
December 2011

Free fatty acids induce transglutaminase 2-dependent apoptosis in hepatocytes via ER stress-stimulated PERK pathways.

J Cell Physiol 2012 Mar;227(3):1130-7

Chemical Biology Department, RIKEN Advanced Science Institute, Wako, Saitama, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/jcp.22833DOI Listing
March 2012

Hepatitis C virus RNA replication in human stellate cells regulates gene expression of extracellular matrix-related molecules.

Biochem Biophys Res Commun 2011 Apr 1;407(1):135-40. Epub 2011 Mar 1.

Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbrc.2011.02.125DOI Listing
April 2011

Dual induction of caspase 3- and transglutaminase-dependent apoptosis by acyclic retinoid in hepatocellular carcinoma cells.

Mol Cancer 2011 Jan 9;10. Epub 2011 Jan 9.

Molecular Ligand Biology Research Team, Chemical Genomics Research Group, Chemical Biology Department, RIKEN Advanced Science Institute, Wako, Saitama 351-0198, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1476-4598-10-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024303PMC
January 2011

Brain infarction correlates more closely with acrolein than with reactive oxygen species.

Biochem Biophys Res Commun 2011 Jan 25;404(4):1044-9. Epub 2010 Dec 25.

Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbrc.2010.12.107DOI Listing
January 2011

Ammonium triggers lateral root branching in Arabidopsis in an AMMONIUM TRANSPORTER1;3-dependent manner.

Plant Cell 2010 Nov 30;22(11):3621-33. Epub 2010 Nov 30.

Molecular Plant Nutrition, University of Hohenheim, D-70593 Stuttgart, Germany.

View Article

Download full-text PDF

Source
http://www.plantcell.org/cgi/doi/10.1105/tpc.110.076216
Publisher Site
http://dx.doi.org/10.1105/tpc.110.076216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3015122PMC
November 2010

In situ detection of active transglutaminases for keratinocyte type (TGase 1) and tissue type (TGase 2) using fluorescence-labeled highly reactive substrate peptides.

J Histochem Cytochem 2011 Feb;59(2):180-7

Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1369/jhc.2010.957225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3201132PMC
February 2011

Spliceostatin A blocks angiogenesis by inhibiting global gene expression including VEGF.

Cancer Sci 2010 Nov;101(11):2483-9

Chemical Genetics Laboratory Molecular Ligand Biology Research Team, Chemical Genomics Research Group, RIKEN Advanced Science Institute, Wako, Saitama, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1349-7006.2010.01686.xDOI Listing
November 2010

Transcriptional regulation of cannabinoid receptor-1 expression in the liver by retinoic acid acting via retinoic acid receptor-gamma.

J Biol Chem 2010 Jun 21;285(25):19002-11. Epub 2010 Apr 21.

Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland 20892-9413, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1074/jbc.M109.068460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885177PMC
June 2010

Recent advances in understanding the roles of transglutaminase 2 in alcoholic steatohepatitis.

Cell Biol Int 2010 Feb 22;34(3):325-34. Epub 2010 Feb 22.

Molecular Ligand Biology Research Team, Chemical Genomics Research Group, Chemical Biology Department, RIKEN Advanced Science Institute, 21 Hirosawa, Wako, Saitama 3510198, Japan.

View Article

Download full-text PDF

Source
http://doi.wiley.com/10.1042/CBI20090130
Publisher Site
http://dx.doi.org/10.1042/CBI20090130DOI Listing
February 2010

Induction of cross-linking and silencing of Sp1 by transglutaminase during liver injury in ASH and NASH via different ER stress pathways.

Dig Dis 2010 27;28(6):715-21. Epub 2011 Apr 27.

Molecular Ligand Biology Research Team, Chemical Genomics Research Group, Chemical Biology Department, RIKEN Advanced Science Institute, Wako, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1159/000324278DOI Listing
August 2011

Acyclic retinoid inhibits angiogenesis by suppressing the MAPK pathway.

Lab Invest 2010 Jan 19;90(1):52-60. Epub 2009 Oct 19.

Molecular Ligand Biology Research Team, Chemical Genomics Research Group, Chemical Biology Department, RIKEN Advanced Science Institute, Saitama 351-0198, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/labinvest.2009.110DOI Listing
January 2010

Role of transglutaminase 2 in liver injury via cross-linking and silencing of transcription factor Sp1.

Gastroenterology 2009 May 14;136(5):1783-95.e10. Epub 2009 Jan 14.

Molecular Ligand Biology Research Team, Chemical Genomics Research Group, Chemical Biology Department, RIKEN Advanced Science Institute, Wako, Saitama, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1053/j.gastro.2009.01.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4960455PMC
May 2009

Mechanism of inhibition of tumor angiogenesis by beta-hydroxyisovalerylshikonin.

Cancer Sci 2009 Feb;100(2):269-77

Molecular Ligand Biology Research Team, Chemical Genomics Research Group, Chemical Biology Department, RIKEN Advanced Science Institute, 2-1 Hiroshima, Wako, Saitama, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1349-7006.2008.01049.xDOI Listing
February 2009

AtAMT1;4, a pollen-specific high-affinity ammonium transporter of the plasma membrane in Arabidopsis.

Plant Cell Physiol 2009 Jan 10;50(1):13-25. Epub 2008 Dec 10.

Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Beijing, PR China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/pcp/pcn186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638712PMC
January 2009

Azaspirene, a fungal product, inhibits angiogenesis by blocking Raf-1 activation.

Cancer Sci 2008 Sep 10;99(9):1853-8. Epub 2008 Jul 10.

Antibiotics Laboratory, Advanced Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1349-7006.2008.00890.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687096PMC
September 2008

Plasminogen N-terminal activation peptide modulates the activity of angiostatin-related peptides on endothelial cell proliferation and migration.

Biochem Biophys Res Commun 2008 May 21;369(2):635-40. Epub 2008 Feb 21.

Department of Chemistry, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.

View Article

Download full-text PDF

Source
http://linkinghub.elsevier.com/retrieve/pii/S0006291X0800326
Publisher Site
http://dx.doi.org/10.1016/j.bbrc.2008.02.050DOI Listing
May 2008

Inhibition of tumor angiogenesis by targeting endothelial surface ATP synthase with sangivamycin.

Jpn J Clin Oncol 2007 Nov 23;37(11):867-73. Epub 2007 Oct 23.

Molecular Cellular Pathology Research Unit, RIKEN, Wako, Saitama 351-0198, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/jjco/hym115DOI Listing
November 2007

Phosphorylated retinoid X receptor alpha loses its heterodimeric activity with retinoic acid receptor beta.

Cancer Sci 2007 Dec 28;98(12):1868-74. Epub 2007 Sep 28.

Department of Medicine, Gifu University Graduate School of Medicine, Gifu, 501-1194, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1349-7006.2007.00621.xDOI Listing
December 2007

AtDUR3 represents the major transporter for high-affinity urea transport across the plasma membrane of nitrogen-deficient Arabidopsis roots.

Plant J 2007 Oct 2;52(1):30-40. Epub 2007 Aug 2.

Molecular Plant Nutrition, Institute for Plant Nutrition, University of Hohenheim, D-70593 Stuttgart, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1365-313X.2007.03223.xDOI Listing
October 2007

Increased Rubisco content in transgenic rice transformed with the 'sense' rbcS gene.

Plant Cell Physiol 2007 Apr 22;48(4):626-37. Epub 2007 Mar 22.

Department of Applied Plant Science, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai 981-8555, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/pcp/pcm035DOI Listing
April 2007

17beta-estradiol induces IL-1alpha gene expression in rheumatoid fibroblast-like synovial cells through estrogen receptor alpha (ERalpha) and augmentation of transcriptional activity of Sp1 by dissociating histone deacetylase 2 from ERalpha.

J Immunol 2007 Mar;178(5):3059-66

Department of Molecular Health Sciences, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4049/jimmunol.178.5.3059DOI Listing
March 2007

Zonal differences in gallium-67 uptakes between perivenous versus periportal regions of rat liver following carbon tetrachloride treatment.

Hepatol Res 2006 Oct 14;36(2):78-85. Epub 2006 Aug 14.

Department of Radiopharmacy, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi 981-8558, Japan.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.hepres.2006.07.006DOI Listing
October 2006