Original Paper

Nobukazu Mae, Yoshio Makino, Seiichi Oshita, Yoshinori Kawagoe, Atsushi Tanaka, Koh Aoki, Atsushi Kurabayashi, Takashi Akihiro, Kazuhito Akama, Satoshi Koike, Mariko Takayama, Chiaki Matsukura, Hiroshi Ezura (2012) Accumulation mechanism of γ-aminobutyric acid in tomatoes (Solanum lycopersicum L.) under low O2 with and without CO2. J. Agric. Food Chem. Accepted on Dec 22, 2011. 

Max Itkin, Ilana Rogachev, Noam Alkan, Tally Rosenberg, Sergey Malitsky, Laura Masini, Sagit Meir, Yoko Iijima, Koh Aoki, Ric de Vos, Dov Prusky, Saul Burdman, Jules Beekwider, Asaph Aharoni (2011) GLYCOALKALOID METABOLISM 1 is Required for Steroidal Alkaloid Glycosylation and Prevention of Phytotoxicity in Tomato. Plant Cell, 2011 Dec 16. [Epub ahead of print]. PMID: 22180624. Full text

 Takeshi Saito, Tohru Ariizumi, Yoshihiro Okabe, Erika Asamizu, Kyoko Hiwasa-Tanase1, Naoya Fukuda, Tsuyoshi Mizoguchi, Yukiko Yamazaki, Koh Aoki, and Hiroshi Ezura (2011) TOMATOMA: A Novel Tomato Mutant Database Distributing Micro-Tom Mutant Collections. Plant Cell Physiol., 52: 289-296. Full text

 Tohru Ariizumi, Koh Aoki, Hiroshi Ezura (2011) Systematic development of tomato bioresource in Japan. Interdisciplinary Bio Central, 3: article No. 1, pp. 1-6. Full text

 Anna Nakashima, Yoko Iijima, Koh Aoki, Daisuke Shibata, Koichi Sugimoto, Junji Takabayashi, and Kenji Matsui (2011) Monogalactosyl diacylglycerol is a substrate for lipoxygenase: its implications for oxylipin formation directly from lipids. Journal of Plant Interactions, 6: 93-97.

 Nozomu Sakurai, Takeshi Ara, Yoshiyuki Ogata, Ryosuke Sano, Takashi Ohno, Kenjiro Sugiyama, Atsushi Hiruta, Kiyoshi Yamazaki, Kentaro Yano, Koh Aoki, Asaph Aharoni, Kazuki Hamada, Koji Yokoyama, Shingo Kawamura, Hirofumi Otsuka, Toshiaki Tokimatsu, Minoru Kanehisa, Hideyuki Suzuki, Kazuki Saito, Daisuke Shibata (2011) KaPPA-View4: A metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data. Nucleic Acids Res. 39: D677-684. PDF

 Young-Il Kim, Shizuka Hirai, Haruya Takahashi, Tsuyoshi Goto, Chie Ohyane, Taneaki Tsugane, Chiaki Konishi, Takashi Fujii, Shuji Inai, Yoko Iijima, Koh Aoki, Daisuke Shibata, Nobuyuki Takahashi, Teruo Kawada (2010) 9-oxo-10(E),12(E)-octadecadienoic acid derived from tomato is a potent peroxisome proliferator-activated receptor α agonist to decrease triglyceride accumulation in mouse primary hepatocytes. Mol. Nutr. Food Res., 55: 585-593.

 Y.-G. Yin, T. Tomonaga, Y. Iijima, K. Aoki, D. Shibata, H. Ashihara, S. Nishimura, H. Ezura and C. Matsukura (2010) Metabolic alterations in organic acid and gamma-amino butyric acid in developing tomato (Solanum lycopersicum L.) fruits. Plant Cell Physiol., 51: 1300-1314. Full text

 Koh Aoki*, Kentaro Yano, Ayako Suzuki, Shingo Kawamura, Nozomu Sakurai, Kunihiro Suda, Atsushi Kurabayashi, Tatsuya Suzuki, Taneaki Tsugane, Manabu Watanabe, Kazuhide Ooga, Maiko Torii, Takanori Narita, Tadasu Shin-i, Yuji Kohara, Naoki Yamamoto, Hideki Takahashi, Yuichiro Watanabe, Mayumi Egusa, Motoichiro Kodama, Yuki Ichinose, Mari Kikuchi, Sumire Fukushima, Akiko Okabe, Tsutomu Arie, Yuko Sato, Katsumi Yazawa, Shinobu Satoh, Toshikazu Omura, Hiroshi Ezura and Daisuke Shibata (2010) Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics. BMC Genomics, 11:210, PMID 20350329 (KA and KY contributed equally.) Full text PDF

 Takumi Ogawa, Takeshi Ara, Koh Aoki, Hideyuki Suzuki, Daisuke Shibata (2010) Transient increase in salicylic acid and its glucose conjugates after wounding in Arabidopsis leaves. Plant Biotechnol., 27: 205-209. PDF

 Soichi Ozaki, Yoshiyuki Ogata, Kunihiro Suda, Atsushi Kurabayashi, Tatsuya Suzuki, Naoki Yamamoto, Yoko Iijima, Taneaki Tsugane, Takashi Fujii, Chiaki Konishi, Shuji Inai, Somnuk Bunsupa, Mami Yamazaki, Daisuke Shibata, and Koh Aoki* (2010) Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module. DNA Res. 17: 105-116. PMID: 20130013 Full text PDF

 Takeshi Ara, Nozomu Sakurai, Yoshie Tange, Yoshihiko Morishita, Hideyuki Suzuki, Koh Aoki, Kazuki Saito, Daisuke Shibata (2009) Improvement of the quantitative differential metabolome pipeline for gas chromatography-mass spectrometry data by automated reliable peak selection. Plant Biotechnol., 26: 445-449. PDF

 Yoshiyuki Ogata, Nozomu Sakurai, Hideyuki Suzuki, Koh Aoki, Kazuki Saito, Daisuke Shibata (2009) The prediction of local modular structures in a co-expression network based on gene expression datasets. Genome Informatics. 23: 117-127. PDF

 Yoko Iijima, Yukio Fujiwara, Takeaki Tokita, Tsuyoshi Ikeda, Toshihiro Nohara, Koh Aoki*, Daisuke Shibata (2009) Involvement of ethylene in the accumulation of esculeoside A during fruit ripening of tomato (Solanum lycopersicum). J. Agric. Food Chem., 57: 3247-3252. PDF

 Kentaro Yano, Koh Aoki, Hideyuki Suzuki, Daisuke Shibata (2009) DAGViz: a directed acyclic graph browser that supports analysis of Gene Ontology annotation Plant Biotechnol. 26: 9-13. PDF

 Yoko Iijima, Koh Aoki* (2009) Application of metabolomics to improve tomato fruit productivity and quality. J. Japan. Soc. Hort. Sci., 78: 14-22. PDF

 Yoshiyuki Ogata, Nozomu Sakurai, Koh Aoki, Hideyuki Suzuki, Koei Okazaki, Kazuki Saito, Daisuke Shibata (2009) KAGIANA: An Excel-based tool for retrieving summary information on Arabidopsis genes. Plant Cell Physiol., 50: 173-177. PDF

 Ryosuke Sano, Yoshiyuki Ogata, Hideyuki Suzuki, Yoichi Ogawa, Tomoko Dansako, Nozomu Sakurai, Koei Okazaki, Koh Aoki, Kazuki Saito, Daisuke Shibata (2008) Over-expression of transcription associated factor genes co-expressed with genes of the mevalonate pathway, upstream of isoprenoid biosynthesis, in Arabidopsis cultured cells. Plant Biotechnol., 25: 583-587.

 Ryosuke Sano, Hideyuki Suzuki, Yoichi Ogawa, Tomoko Dansako, Nozomu Sakurai, Koei Okazaki, Koh Aoki, Kazuki Saito, Daisuke Shibata (2008) Suppression of carotenoid synthesis in transgenic Arabidopsis plants over-expressing the AHL29/SOB3 gene. Plant Biotechnol., 25: 573-577.

 Takashi Akihiro, Satoshi Koike, Ryoji Tani, Takehiro Tominaga, Shin Watanabe, Yoko Iijima, Koh Aoki, Daisuke Shibata, Hiroshi Ashihara, Chiaki Matsukura, Kazuhito Akama, Tatsuhito Fujimura, Hiroshi Ezura (2008) Biochemical mechanism on GABA accumulation during fruit development in tomato. Plant Cell Physiol., 49: 1378-1389.

21 Yukiko Nakamura, Shigehiko Kanaya, Nozomu Sakurai, Yoko Iijima, Koh Aoki, Koei Okazaki, Hideyuki Suzuki, Masahiko Kitayama, Daisuke Shibata (2008) A tool for high-throughput prediction of molecular formulas and identification of isotopic peaks from large-scale mass spectrometry data. Plant Biotechnology 25: 377-380.

22 Chiaki Matsukura, Koh Aoki, Naoya Fukuda, Tsuyoshi Mizoguchi, Erika Asamizu, T Saito, Daisuke Shibata, Hiroshi Ezura (2008) Comprehensive resources for tomato functional genomics based on the miniature model tomato Micro-Tom. Current Genomics, 9: .436-443.

23 Yoichi Ogawa, Hideyuki Suzuki, Nozomu Sakurai, Koh Aoki, Kazuki Saito and Daisuke Shibata (2008) Cryopreservation and metabolic profiling analysis of Arabidopsis T87 suspension-cultured cells. Cryo Letters, 29: 427-436.

24 Hideki Goda, Eriko Sasaki, Kenji Akiyama, Akiko Maruyama-Nakashita, Kazumi Nakabayashi, Weigiang Li, Mikihiro Ogawa, Yukika Yamauchi, Jeremy Preston, Koh Aoki, Takatoshi Kiba, Suguru Takatsuto, Shozo Fujioka, Tadao Asami, Takeshi Nakano, Hisashi Kato, Takeshi Mizuno, Hitoshi Sakakibara, Shinjiro Yamaguchi, Eiji Nambara, Yuji Kamiya, Hideki Takahashi, Masami Yokota Hirai, Tetsuya Sakurai, Kazuo Shinozaki, Kazuki Saito, Shigeo Yoshida, Yukihisa Shimada. (2008) The AtGenExpress hormone- and chemical-treatment data set: Experimental design, data evaluation, model data analysis, and data access. Plant J., 55: 526-542.

25 Yoko Iijima, Yukiko Nakamura, Yoshiyuki Ogata, Ken’ichi Tanaka, Nozomu Sakurai, Kunihiro Suda, Tatsuya Suzuki, Hideyuki Suzuki, Koei Okazaki, Shigehiko Kanaya, Koh Aoki*, Daisuke Shibata. (2008) Metabolite annotations based on the integration of mass spectral information. Plant J., 54: 949-962. (*Corresponding author).

26 Yoichi Ogawa, Tomoko Dansako, Kentaro Yano, Nozomu Sakurai, Hideyuki Suzuki, Koh Aoki, Masaaki Noji, Kazuki Saito, Daisuke Shibata (2008) Efficient and high-throughput vector construction and Agrobacterium-mediated transformation of Arabidopsis thaliana suspension-cultured cells for functional genomics. Plant Cell Physiol., 49: 242-250.

27 Yukio Fujiwara, Naoko Kiyota, Masaharu Hori, Sayaka Matsushita, Yoko Iijima, Koh Aoki, Daisuke Shibata, Motohiro Takeya, Tsuyoshi Ikeda, Toshihiro Nohara, Ryoji Nagai (2007) Esculeogenin A, a New Tomato Sapogenol, Ameliorates Hyperlipidemia and Atherosclerosis in ApoE-Deficient Mice by Inhibiting ACAT. Arterioscler Thromb. Vasc. Biol. 27: 2400-2406.

28 Yoko Iijima, Kunihiro Suda, Tatsuya Suzuki, Koh Aoki*, Daisuke Shibata (2008) Metabolite profiling of chalcones and flavanones in tomato fruit. J. Japan Soc. Hortic. Sci., 77: 94-102. (*Corresponding author).

29 Hideyuki Suzuki, Ryosuke Sasaki, Yoshiyuki Ogata, Yukiko Nakamura, Nozomu Sakurai, Mariko Kitajima, Hiromitsu Takayama, Shigehiko Kanaya, Koh Aoki*, Daisuke Shibata, Kazuki Saito* (2008) Metabolic profiling of flavonoids in Lotus japonicus using liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry. Phytochemistry, 69: 99-111. (*Corresponding author).

30 Masami Yokota Hirai, Kenjiro Sugiyama, Yuji Sawada, Takayuki Tohge, Takeshi Obayashi, Akane Suzuki, Ryoichi Araki, Nozomu Sakurai, Hideyuki Suzuki, Koh Aoki, Hideki Goda, Osamu Ishizaki Nishizawa, Daisuke Shibata, Kazuki Saito (2007) Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosysnthesis. Proc. Natl. Acad. Sci. U.S.A. 104: 6478-6483.

31 Koh Aoki, Yoshiyuki Ogata, Daisuke Shibata (2007) Approaches for extracting practical information from gene coexpression networks in plant biology. Plant Cell Physiol. 48: 381-390.

32 Koh Aoki, Kentaro Yano, Nozomu Sakurai, Daisuke Shibata, Taneaki Tsugane, Manabu Watanabe, Yong-Gen Yin, Chiaki Matsukura (2007) Expression-based approach toward functional characterization of tomato genes that have no or weak similarity to Arabidopsis genes. Acta Hortic. 745: 457-464.

33 Shin Watanabe, Tsuyoshi Mizoguchi, Koh Aoki, Yasutaka Kubo, Hitoshi Mori, Shunsuke Imanishi, Yukiko Yamazaki, Daisuke Shibata, Hiroshi Ezura (2007) Ethylmethanesulfonate (EMS) mutagenesis of Solanum lycopersicum cv. Micro-Tom for large-scale mutant screens. Plant Biotechnology, 24: 33-38.

34 Toshikazu Omura, Shin Watanabe, Yoko Iijima, Koh Aoki, Daisuke Shibata, and Hiroshi Ezura (2007)  Molecular and genetic characterization of transgenic tomato expressing 3-hydroxy-3-methylglutaryl coenzyme A reductase. Plant Biotechnology, 24: 107-116.

35 Kentaro Yano, Koh Aoki, Daisuke Shibata (2007) Genomic database for tomato. Plant Biotechnology 24: 17-26.

36 Kentaro Yano, Taneaki Tsugane, Manabu Watanabe, Fumi Maeda, Koh Aoki, Daisuke Shibata (2006) Non-biased distribution of the tomato genes that have no counterpart in Arabidopsis thaliana in expression patterns during fruit ripening. Plant Biotechnology 23: 199-202

37 KentaroYano, Manabu Watanabe, Naoki Yamamoto, Taneaki Tsugane, Koh Aoki, Nozomu Sakurai, Daisuke Shibata (2006) MiBASEA database of a miniature tomato cultivar Micro-Tom. Plant Biotechnology 23: 195-198

38 Koh Aoki, Nobuo Suzui, Shu Fujimaki, Keiko Yonekura-Sakakibara, Naoshi Dohmae, Koji Takio, Toru Fujiwara, Hiroaki Hayashi, Tomoyuki Yamaya, Hitoshi Sakakibara (2005) Destination-selective long-distance movement of phloem proteins. Plant Cell 17: 1801-1814

39 Takatoshi Kiba, Koh Aoki, Hitoshi Sakakibara, Takeshi Mizuno (2004) A novel class of Arabidopsis response regulator genes, the ectopic expression of which results in phenocopy of the wol cytokinin-receptor deficient mutant. Plant&Cell Physiol. 45: 1063-1077

40 Kentaro Takei, Nanae Ueda, Koh Aoki, Takashi Kuromori, Takashi Hirayama, Kazuo Shinozaki, Tomoyuki Yamaya, Hitoshi Sakakibara (2004) AtIPT3 is a key determinant of nitrate-dependent cytokinin biosynthesis in Arabidopsis. Plant & Cell Physiol. 45:1053-1062

41 Matthieu Denoual, Koh Aoki, Agnes Mita-Tixier and Hiroyuki Fujita (2003) A MICROFLUIDIC DEVICE FOR LONG-TERM STUDY OF INDIVIDUAL CELLS. Micro Total Analysis System 2003, Volume 1, pp531-534, Eds; Northrup, M.A., Jensen, K.F., Jed Harrison, D. MESA monographs

42 Yasuharu Asakura, Takeshi Hagino, Yukinori Ohta, Koh Aoki, Keiko Yonekura-Sakakibara, Atsushi Deji, Tomoyuki Yamaya, Tatsuo Sugiyama and Hitoshi Sakakibara (2003) Molecular characterization of His-Asp phosphorelay signaling factors in maize leaves: Implications of the signal divergence by cytokinin-inducible response regulators in the cytosol and the nuclei. Plant Mol. Biol. 52: 331-341

43 Koh Aoki, Friedrich Kragler, Beatriz Xoconostle-Cazares, William J. Lucas (2002) A subclass of plant heat shock cognate 70 chaperones carries a motif that facilitates trafficking through plasmodesmata. Proc. Natl. Acad. Sci. USA 99: 16342-16347

44 Bambang Sugiharto, Netty Ermawati, Hitoshi Mori, Koh Aoki, Keiko Yonekura-Sakakibara, Tomoyuki Yamaya, Tatsuo Sugiyama, Hotoshi Sakakibara (2002) Identification and characterization of a gene encoding drought-inducible protein localizing in the bundle sheath cell of sugarcane. Plant Cell Physiol. 43: 350-354

45 Byung-Chun Yoo, Koh Aoki, Yu Xiang, Leslie R. Campbell, Richard J. Hull, Beatriz Xoconostle-Cazares, Jan Monzer, Jung-Youn Lee, Diane E. Ullman, William J. Lucas (2000) Characterization of Cucurbita maxima phloem serpin-1 (CmPS-1): a developmentally regulated elastase inhibitor. J. Biol. Chem. 275: 35122-35128

46 Koh Aoki, Miyuki Yamamoto, Keishiro Wada (1998) Photosynthetic and heterotrophic ferredoxin isoproteins are colocalized in fruit plastids of tomato. Plant Physiol. 118: 439-449

47 Koh Aoki and Keishiro Wada (1996) Temporal and spatial distribution of ferredoxin isoproteins in tomato fruit. Plant Physiol. 112: 651-657

48 Kaeko Kamide, Harumi Sakai, Koh Aoki, Yukika Sanada, Keishiro Wada, Laura S. Green, Biohon C. Yee, Bob B. Buchanan (1995) Amino acid sequences of ferredoxin isoproteins from different organs of tomato plant (Lycopersicon esculentum Mill.). Photosynthesis Research, 46: 301-308

49 Eiki Momotani, Kou Aoki, Hideo Tsuji (1991) Effect of benzyladenine on diurnal changes in DNA content per chloroplast and chloroplast replication in intact bean leaves. J. Exp. Bot. 42: 1287-1293

 

Book

Mireille Faurobert, Yoko Iijima, Koh Aoki* 2009, Proteomics and Metabolomics. In : Liedel, B., Slade, A., Hurst, S., Labate, J., Stommel, J.(ed) Tomato. In the series on Genomics of Fruits and Vegetable Crops. Science Publishers, Enfield, New Hampshire : in press (*corresponding editor)

Koh Aoki(2009)Dictionary of Plant genome Science. Ed. by Komamine A, Saito K., Tabata S., Fujimura T., Machida Y., Mii M. Asakura Shoten.

Koh Aoki, Yoko Iijima (2007) Metabolomics. Tomato. In: Kole C (ed) Genome Mapping and Molecular Breeding in Plants. Springer, Berlin, Heidelberg, New York: pp79-84.