13C-metabolic flux analysis of respiratory chain disrupted strain ΔndhF1 of Synechocystis sp. PCC 6803

Keisuke Wada, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu

Applied Biochemistry and Biotechnology　2025/01/15　Research paper (scientific journal)

Yamadazyma thunbergiae sp. nov., a novel yeast species associated with Bengal clock vines and soil in Okinawa, Japan.

Taisuke Seike, Hiroki Takekata, Natsue Sakata, Chikara Furusawa, Fumio Matsuda

International journal of systematic and evolutionary microbiology　Vol. 74　No. 10　2024/10　Research paper (scientific journal)

Identification of TPI1 As a potential therapeutic target in pancreatic cancer with dependency of TP53 mutation using multi-omics analysis.

Tomoaki Toyoda, Nami Miura, Shingo Kato, Takeshi Masuda, Ryuji Ohashi, Akira Matsushita, Fumio Matsuda, Sumio Ohtsuki, Akira Katakura, Kazufumi Honda

Cancer science　Vol. 115　No. 11　p. 3622-3635　2024/09/11

13C-metabolic flux analysis reveals metabolic rewiring in HL-60 neutrophil-like cells through differentiation and immune stimulation

Takeo Taniguchi, Nobuyuki Okahashi, Fumio Matsuda

Metabolic Engineering Communications　Vol. 18　p. e00239-e00239　2024/05　Research paper (scientific journal)

Metabolome analysis of metabolic burden in Escherichia coli caused by overexpression of green fluorescent protein and delta-rhodopsin

Chinatsu Matsuyama, Taisuke Seike, Nobuyuki Okahashi, Teppei Niide, Kiyotaka Y. Hara, Yoko Hirono-Hara, Jun Ishii, Hiroshi Shimizu, Yoshihiro Toya, Fumio Matsuda

Journal of Bioscience and Bioengineering　Vol. 137　No. 3　p. 187-194　2024/03　Research paper (scientific journal)

Data Processing of Product Ion Spectra: Methods to Control False Discovery Rate in Compound Search Results for Untargeted Metabolomics.

Fumio Matsuda

Mass spectrometry (Tokyo, Japan)　Vol. 13　No. 1　2024　Research paper (scientific journal)

Data Processing of Product Ion Spectra: Redundancy of Product Ion Spectra of Small Molecules in Data-Dependent Acquisition Dataset

Fumio Matsuda

Mass Spectrometry　Vol. 12　No. 1　p. A0138-A0138　2023/12/08　Research paper (scientific journal)

Development of 13C-Metabolic Flux Analysis for HL-60 Neutrophil-like Cell Using GC-MS

Takeo Taniguchi, Nobuyuki Okahashi, Fumio Matsuda

Journal of the Mass Spectrometry Society of Japan　Vol. 71　No. 4　p. 155-159　2023/12/01

Improved 2,3-Butanediol Production Rate of Metabolically Engineered Saccharomyces cerevisiae by Deletion of RIM15 and Activation of Pyruvate Consumption Pathway

Masahiko Sugimura, Taisuke Seike, Nobuyuki Okahashi, Yoshihiro Izumi, Takeshi Bamba, Jun Ishii, Fumio Matsuda

International Journal of Molecular Sciences　Vol. 24　No. 22　p. 16378-16378　2023/11/15　Research paper (scientific journal)

Lipidome and metabolome analyses reveal metabolic alterations associated with MCF-7 apoptosis upon 4-hydroxytamoxifen treatment

Kazuki Nishimoto, Nobuyuki Okahashi, Masaharu Maruyama, Yoshihiro Izumi, Kohta Nakatani, Yuki Ito, Junko Iida, Takeshi Bamba, Fumio Matsuda

Scientific Reports　Vol. 13　No. 1　p. 18549-18549　2023/10/29　Research paper (scientific journal)

Improvement of ethanol and 2,3-butanediol production in Saccharomyces cerevisiae by ATP wasting

Futa Yatabe, Taisuke Seike, Nobuyuki Okahashi, Jun Ishii, Fumio Matsuda

Microbial Cell Factories　Vol. 22　No. 1　2023/10/08　Research paper (scientific journal)

Comprehensive analysis of the composition of the major phospholipids during the asexual life cycle of the filamentous fungus Aspergillus nidulans

Ryo Iwama, Nobuyuki Okahashi, Tetsuki Suzawa, Chuner Yang, Fumio Matsuda, Hiroyuki Horiuchi

Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids　p. 159379-159379　2023/08　Research paper (scientific journal)

Effects of n-butanol production on metabolism and the photosystem in Synecococcus elongatus PCC 7942 based on metabolic flux and target proteome analyses.

Keisuke Wada, Kiyoka Uebayashi, Yoshihiro Toya, Sastia Prama Putri, Fumio Matsuda, Eiichiro Fukusaki, James C Liao, Hiroshi Shimizu

The Journal of general and applied microbiology　2023/03/20　Research paper (scientific journal)

Wickerhamiella bidentis sp. nov., a novel yeast species isolated from flowers and insects in Japan.

Taisuke Seike, Hiroki Takekata, Yui Uchida, Natsue Sakata, Chikara Furusawa, Fumio Matsuda

International journal of systematic and evolutionary microbiology　Vol. 73　No. 3　2023/03　Research paper (scientific journal)

Simple and Rapid Non-ribosomal Peptide Synthetase Gene Assembly Using the SEAM–OGAB Method

Varada Jagadeesh, Takanobu Yoshida, Misugi Uraji, Nobuyuki Okahashi, Fumio Matsuda, Christopher J. Vavricka, Kenji Tsuge, Akihiko Kondo

ACS Synthetic Biology　2022/12/23　Research paper (scientific journal)

Data Processing of Product Ion Spectra: Quality Improvement by Averaging Multiple Similar Spectra of Small Molecules

Fumio Matsuda, Shuka Komori, Yuki Yamada, Daiki Hara, Nobuyuki Okahashi

Mass Spectrometry　Vol. 11　No. 1　p. A0106-A0106　2022/12/15　Research paper (scientific journal)

<sup>13</sup>C-tracer Analysis of Phospholipids by LC-QTOF/MS

Yuki Yamada, Keita Murakami, Nobuyuki Okahashi, Atsuhiko Toyama, Junko Iida, Fumio Matsuda

Journal of the Mass Spectrometry Society of Japan　Vol. 70　No. 4　p. 241-244　2022/12/01　Research paper (scientific journal)

Lipidome variation of industrial Saccharomyces cerevisiae strains analyzed by LC-QTOF/MS-based untargeted lipidomics

Shuka Komori, Nobuyuki Okahashi, Junko Iida, Fumio Matsuda

Journal of Bioscience and Bioengineering　2022/12　Research paper (scientific journal)

Conversion of Mevalonate to Isoprenol Using Light Energy in Escherichia coli without Consuming Sugars for ATP Supply.

Mikoto Sano, Ryo Tanaka, Kentaro Kamata, Yoko Hirono-Hara, Jun Ishii, Fumio Matsuda, Kiyotaka Y Hara, Hiroshi Shimizu, Yoshihiro Toya

ACS synthetic biology　Vol. 11　No. 12　p. 3966-3972　2022/11/28　Research paper (scientific journal)

Evolutionary approach for improved proton pumping activity of heterologous rhodopsin expressed in Escherichia coli.

Kensuke Otsuka, Taisuke Seike, Yoshihiro Toya, Jun Ishii, Yoko Hirono-Hara, Kiyotaka Y Hara, Fumio Matsuda

Journal of bioscience and bioengineering　Vol. 134　No. 6　p. 484-490　2022/09/25　Research paper (scientific journal)

13C metabolic flux analysis clarifies distinct metabolic phenotypes of cancer cell spheroid mimicking tumor hypoxia.

Shingo Noguchi, Kenichi Wakita, Fumio Matsuda, Hiroshi Shimizu

Metabolic engineering　Vol. 73　p. 192-200　2022/07/31　Research paper (scientific journal)

Isotope Calculation Gadgets: A Series of Software for Isotope-Tracing Experiments in Garuda Platform

Nobuyuki Okahashi, Yuki Yamada, Junko Iida, Fumio Matsuda

Metabolites　Vol. 12　No. 7　p. 646-646　2022/07/14　Research paper (scientific journal)

Constitutive expression of the global regulator AbrB restores the growth defect of a genome-reduced Bacillus subtilis strain and improves its metabolite production.

Junya Yamamoto, Onuma Chumsakul, Yoshihiro Toya, Takuya Morimoto, Shenghao Liu, Kenta Masuda, Yasushi Kageyama, Takashi Hirasawa, Fumio Matsuda, Naotake Ogasawara, Hiroshi Shimizu, Ken-Ichi Yoshida, Taku Oshima, Shu Ishikawa

DNA research : an international journal for rapid publication of reports on genes and genomes　Vol. 29　No. 3　2022/05/27　Research paper (scientific journal)

Metabolomics-based phenotypic screens for evaluation of drug synergy via direct-infusion mass spectrometry.

Xiyuan Lu, G Lavender Hackman, Achinto Saha, Atul Singh Rathore, Meghan Collins, Chelsea Friedman, S Stephen Yi, Fumio Matsuda, John DiGiovanni, Alessia Lodi, Stefano Tiziani

iScience　Vol. 25　No. 5　p. 104221-104221　2022/05/20　Research paper (scientific journal)

Optogenetic reprogramming of carbon metabolism using light-powering microbial proton pump systems.

Yoshihiro Toya, Yoko Hirono-Hara, Hidenobu Hirayama, Kentaro Kamata, Ryo Tanaka, Mikoto Sano, Sayaka Kitamura, Kensuke Otsuka, Rei Abe-Yoshizumi, Satoshi P Tsunoda, Hiroshi Kikukawa, Hideki Kandori, Hiroshi Shimizu, Fumio Matsuda, Jun Ishii, Kiyotaka Y Hara

Metabolic engineering　Vol. 72　p. 227-236　2022/03/26

Improvement of 2,3-butanediol production by dCas9 gene expression system in Saccharomyces cerevisiae.

Keisuke Morita, Taisuke Seike, Jun Ishii, Fumio Matsuda, Hiroshi Shimizu

Journal of bioscience and bioengineering　Vol. 133　No. 3　p. 208-212　2022/03　Research paper (scientific journal)

Data science-based modeling of the lysine fermentation process

Seibutsu-kogaku Kaishi　Vol. 100　No. 2　p. 80-80　2022/02/25

Automated Recommendation of Research Keywords from PubMed That Suggest the Molecular Mechanism Associated with Biomarker Metabolites.

Shinji Kanazawa, Satoshi Shimizu, Shigeki Kajihara, Norio Mukai, Junko Iida, Fumio Matsuda

Metabolites　Vol. 12　No. 2　2022/02/01　Research paper (scientific journal)

Comparative Evaluation of Plasma Metabolomic Data from Multiple Laboratories.

Shin Nishiumi, Yoshihiro Izumi, Akiyoshi Hirayama, Masatomo Takahashi, Motonao Nakao, Kosuke Hata, Daisuke Saigusa, Eiji Hishinuma, Naomi Matsukawa, Suzumi M Tokuoka, Yoshihiro Kita, Fumie Hamano, Nobuyuki Okahashi, Kazutaka Ikeda, Hiroki Nakanishi, Kosuke Saito, Masami Yokota Hirai, Masaru Yoshida, Yoshiya Oda, Fumio Matsuda, Takeshi Bamba

Metabolites　Vol. 12　No. 2　2022/02/01　Research paper (scientific journal)

mfapy: An open-source Python package for 13C-based metabolic flux analysis.

Fumio Matsuda, Kousuke Maeda, Takeo Taniguchi, Yuya Kondo, Futa Yatabe, Nobuyuki Okahashi, Hiroshi Shimizu

Metabolic engineering communications　Vol. 13　2021/12

Defective cytokinin signaling reprograms lipid and flavonoid gene-to-metabolite networks to mitigate high salinity in Arabidopsis.

Mostafa Abdelrahman, Rie Nishiyama, Cuong Duy Tran, Miyako Kusano, Ryo Nakabayashi, Yozo Okazaki, Fumio Matsuda, Ricardo A Chávez Montes, Mohammad Golam Mostofa, Weiqiang Li, Yasuko Watanabe, Atsushi Fukushima, Maho Tanaka, Motoaki Seki, Kazuki Saito, Luis Herrera-Estrella, Lam-Son Phan Tran

Proceedings of the National Academy of Sciences of the United States of America　Vol. 118　No. 48　2021/11/30　Research paper (scientific journal)

Increased carvone production in Escherichia coli by balancing limonene conversion enzyme expression via targeted quantification concatamer proteome analysis.

Erika Yoshida, Motoki Kojima, Munenori Suzuki, Fumio Matsuda, Kazutaka Shimbo, Akiko Onuki, Yousuke Nishio, Yoshihiro Usuda, Akihiko Kondo, Jun Ishii

Scientific reports　Vol. 11　No. 1　p. 22126-22126　2021/11/11　Research paper (scientific journal)

Proteome analysis of response to different spectral light irradiation in Synechocystis sp. PCC 6803.

Masakazu Toyoshima, Masumi Sakata, Yoshifumi Ueno, Yoshihiro Toya, Fumio Matsuda, Seiji Akimoto, Hiroshi Shimizu

Journal of proteomics　Vol. 246　p. 104306-104306　2021/08/30　Research paper (scientific journal)

Synthetic production of prenylated naringenins in yeast using promiscuous microbial prenyltransferases.

Shota Isogai, Nobuyuki Okahashi, Ririka Asama, Tomomi Nakamura, Tomohisa Hasunuma, Fumio Matsuda, Jun Ishii, Akihiko Kondo

Metabolic engineering communications　Vol. 12　2021/06　Research paper (scientific journal)

Comparative 13 C-metabolic flux analysis indicate elevation of ATP regeneration, carbon dioxide, and heat production in industrial Saccharomyces cerevisiae strains.

Futa Yatabe, Nobuyuki Okahashi, Taisuke Seike, Fumio Matsuda

Biotechnology journal　Vol. 17　No. 3　2021/05/13　Research paper (scientific journal)

Soft-sensor development for monitoring the lysine fermentation process.

Kento Tokuyama, Yoshiki Shimodaira, Yohei Kodama, Ryuzo Matsui, Yasuhiro Kusunose, Shunsuke Fukushima, Hiroaki Nakai, Yuichiro Tsuji, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu

Journal of bioscience and bioengineering　Vol. 132　No. 2　p. 183-189　2021/05/03　Research paper (scientific journal)

Treatment of RB1-intact hepatocellular carcinoma with CDK4/6 inhibitor combination therapy.

Jindan Sheng, Susumu Kohno, Nobuhiro Okada, Nobuyuki Okahashi, Kana Teranishi, Fumio Matsuda, Hiroshi Shimizu, Paing Linn, Naoko Nagatani, Minako Yamamura, Kenichi Harada, Shin-Ichi Horike, Hiroshi Inoue, Seiji Yano, Sharad Kumar, Shunsuke Kitajima, Itsuki Ajioka, Chiaki Takahashi

Hepatology (Baltimore, Md.)　Vol. 74　No. 4　p. 1971-1993　2021/04/30　Research paper (scientific journal)

Elevated Sporulation Efficiency in Fission Yeast Schizosaccharomyces japonicus Strains Isolated from Drosophila.

Taisuke Seike, Natsue Sakata, Fumio Matsuda, Chikara Furusawa

Journal of fungi (Basel, Switzerland)　Vol. 7　No. 5　2021/04/29　Research paper (scientific journal)

Random Transfer of Ogataea polymorpha Genes into Saccharomyces cerevisiae Reveals a Complex Background of Heat Tolerance.

Taisuke Seike, Yuki Narazaki, Yoshinobu Kaneko, Hiroshi Shimizu, Fumio Matsuda

Journal of fungi (Basel, Switzerland)　Vol. 7　No. 4　2021/04/15　Research paper (scientific journal)

Analyses of Lipid A Diversity in Gram-Negative Intestinal Bacteria Using Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry.

Nobuyuki Okahashi, Masahiro Ueda, Fumio Matsuda, Makoto Arita

Metabolites　Vol. 11　No. 4　2021/03/26　Research paper (scientific journal)

Seed-coat protective neolignans are produced by the dirigent protein AtDP1 and the laccase AtLAC5 in Arabidopsis.

Keiko Yonekura-Sakakibara, Masaomi Yamamura, Fumio Matsuda, Eiichiro Ono, Ryo Nakabayashi, Satoko Sugawara, Tetsuya Mori, Yuki Tobimatsu, Toshiaki Umezawa, Kazuki Saito

The Plant cell　Vol. 33　No. 1　p. 129-152　2021/03/22　Research paper (scientific journal)

Mutations in hik26 and slr1916 lead to high-light stress tolerance in Synechocystis sp. PCC6803.

Katsunori Yoshikawa, Kenichi Ogawa, Yoshihiro Toya, Seiji Akimoto, Fumio Matsuda, Hiroshi Shimizu

Communications biology　Vol. 4　No. 1　p. 343-343　2021/03/16　Research paper (scientific journal)

Fake metabolomics chromatogram generation for facilitating deep learning of peak-picking neural networks.

Shinji Kanazawa, Akira Noda, Arisa Ito, Kyoko Hashimoto, Akihiro Kunisawa, Tsuyoshi Nakanishi, Shigeki Kajihara, Norio Mukai, Junko Iida, Eiichiro Fukusaki, Fumio Matsuda

Journal of bioscience and bioengineering　Vol. 131　No. 2　p. 207-212　2021/02　Research paper (scientific journal)

Novel allosteric inhibition of phosphoribulokinase identified by ensemble kinetic modeling of Synechocystis sp. PCC 6803 metabolism.

Hiroki Nishiguchi, James Liao, Hiroshi Shimizu, Fumio Matsuda

Metabolic engineering communications　Vol. 11　2020/12　Research paper (scientific journal)

Data science-based modeling of the lysine fermentation process.

Kento Tokuyama, Yoshiki Shimodaira, Takahiro Terawaki, Yasuhiro Kusunose, Hiroaki Nakai, Yuichiro Tsuji, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu

Journal of bioscience and bioengineering　Vol. 130　No. 4　p. 409-415　2020/10　Research paper (scientific journal)

Assessment of Protein Content and Phosphorylation Level in Synechocystis sp. PCC 6803 under Various Growth Conditions Using Quantitative Phosphoproteomic Analysis.

Masakazu Toyoshima, Yuma Tokumaru, Fumio Matsuda, Hiroshi Shimizu

Molecules (Basel, Switzerland)　Vol. 25　No. 16　2020/08/06　Research paper (scientific journal)

Direct and quantitative analysis of altered metabolic flux distributions and cellular ATP production pathway in fumarate hydratase-diminished cells.

Shingo Noguchi, Hirokazu Ishikawa, Kenichi Wakita, Fumio Matsuda, Hiroshi Shimizu

Scientific reports　Vol. 10　No. 1　p. 13065-13065　2020/08/03　Research paper (scientific journal)

Effects of mutations of GID protein-coding genes on malate production and enzyme expression profiles in Saccharomyces cerevisiae.

Hiroaki Negoro, Kengo Matsumura, Fumio Matsuda, Hiroshi Shimizu, Yoji Hata, Hiroki Ishida

Applied microbiology and biotechnology　Vol. 104　No. 11　p. 4971-4983　2020/06　Research paper (scientific journal)

Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of Arabidopsis thaliana

Ratklao Siriwach, Fumio Matsuda, Kentaro Yano, Masami Yokota Hirai

Metabolites　Vol. 10　No. 4　p. 159-159　2020/04/18　Research paper (scientific journal)

Computational data mining method for isotopomer analysis in the quantitative assessment of metabolic reprogramming

Fumio Matsuda, Kousuke Maeda, Nobuyuki Okahashi

Scientific Reports　Vol. 10　No. 1　2020/01　Research paper (scientific journal)

Comparison of metabolic profiles of yeasts based on the difference of the Crabtree positive and negative.

Makoto Imura, Katsuaki Nitta, Ryo Iwakiri, Fumio Matsuda, Hiroshi Shimizu, Eiichiro Fukusaki

Journal of bioscience and bioengineering　Vol. 129　No. 1　p. 52-58　2020/01　Research paper (scientific journal)

Corrigendum: A Fusion Method to Develop an Expanded Artificial Genomic RNA Replicable by Qβ Replicase.

Kensuke Ueda, Ryo Mizuuchi, Fumio Matsuda, Norikazu Ichihashi

Chembiochem : a European journal of chemical biology　Vol. 20　No. 23　p. 2968-2968　2019/12/02

Survival of membrane-damaged Escherichia coli in a cytosol-mimicking solution

Rikuto Kamiura, Fumio Matsuda, Norikazu Ichihashi

Journal of Bioscience and Bioengineering　Vol. 128　No. 5　p. 558-563　2019/11　Research paper (scientific journal)

Inter-Laboratory Comparison of Metabolite Measurements for Metabolomics Data Integration

Yoshihiro Izumi, Fumio Matsuda, Akiyoshi Hirayama, Kazutaka Ikeda, Yoshihiro Kita, Kanta Horie, Daisuke Saigusa, Kosuke Saito, Yuji Sawada, Hiroki Nakanishi, Nobuyuki Okahashi, Masatomo Takahashi, Motonao Nakao, Kosuke Hata, Yutaro Hoshi, Motohiko Morihara, Kazuhiro Tanabe, Takeshi Bamba, Yoshiya Oda

Metabolites　Vol. 9　No. 11　p. 257-257　2019/10/31　Research paper (scientific journal)

Repression of mitochondrial metabolism for cytosolic pyruvate-derived chemical production in Saccharomyces cerevisiae.

Keisuke Morita, Fumio Matsuda, Koji Okamoto, Jun Ishii, Akihiko Kondo, Hiroshi Shimizu

Microbial cell factories　Vol. 18　No. 1　p. 177-177　2019/10/15

Time-resolved analysis of short term metabolic adaptation at dark transition in Synechocystis sp. PCC 6803

Masaharu Maruyama, Hiroki Nishiguchi, Masakazu Toyoshima, Nobuyuki Okahashi, Fumio Matsuda, Hiroshi Shimizu

Journal of Bioscience and Bioengineering　Vol. 128　No. 4　p. 424-428　2019/10　Research paper (scientific journal)

A Fusion Method to Develop an Expanded Artificial Genomic RNA Replicable by Qβ Replicase

Kensuke Ueda, Ryo Mizuuchi, Fumio Matsuda, Norikazu Ichihashi

ChemBioChem　Vol. 20　No. 18　p. 2331-2335　2019/09/16　Research paper (scientific journal)

クラブトリー陽性および陰性の差異に基づく酵母代謝のプロファイルの比較

井村 誠, 新田 克章, 岩切 亮, 松田 史生, 清水 浩, 福崎 英一郎

日本生物工学会大会講演要旨集　Vol. 2019年　p. 179-179　2019/08

Theophylline-inducible riboswitch accurately regulates protein expression at low level in Escherichia coli.

Rikuto Kamiura, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu

Biotechnology letters　Vol. 41　No. 6-7　p. 743-751　2019/07　Research paper (scientific journal)

代謝工学におけるバイオインフォマティクスの利用

戸谷吉博, 松田史生

生物工学誌　Vol. 97　No. 5　p. 261-264　2019/05

Transomics data-driven, ensemble kinetic modeling for system-level understanding and engineering of the cyanobacteria central metabolism

Hiroki Nishiguchi, Natsuki Hiasa, Kiyoka Uebayashi, James Liao, Hiroshi Shimizu, Fumio Matsuda

Metabolic Engineering　Vol. 52　p. 273-283　2019/03　Research paper (scientific journal)

Magnesium starvation improves production of malonyl-CoA-derived metabolites in Escherichia coli.

Kento Tokuyama, Yoshihiro Toya, Fumio Matsuda, Brady F Cress, Mattheos A G Koffas, Hiroshi Shimizu

Metabolic engineering　Vol. 52　p. 215-223　2019/03　Research paper (scientific journal)

Fragmentation of Dicarboxylic and Tricarboxylic Acids in the Krebs Cycle Using GC-EI-MS and GC-EI-MS/MS.

Nobuyuki Okahashi, Shuichi Kawana, Junko Iida, Hiroshi Shimizu, Fumio Matsuda

Mass spectrometry (Tokyo, Japan)　Vol. 8　No. 1　2019　Research paper (scientific journal)

Sugar phosphate analysis with baseline separation and soft ionization by gas chromatography-negative chemical ionization-mass spectrometry improves flux estimation of bidirectional reactions in cancer cells

Nobuyuki Okahashi, Kousuke Maeda, Shuichi Kawana, Junko Iida, Hiroshi Shimizu, Fumio Matsuda

Metabolic Engineering　Vol. 51　p. 43-49　2019/01　Research paper (scientific journal)

Editorial overview: Recent progress in analytical technologies for design-build-test-learn cycle in biotechnology.

Hiroshi Shimizu, Fumio Matsuda

Current opinion in biotechnology　Vol. 54　p. 145-147　2018/12

Targeted proteome analysis of microalgae under high-light conditions by optimized protein extraction of photosynthetic organisms

Masakazu Toyoshima, Masumi Sakata, Kazuki Ohnishi, Yuma Tokumaru, Yusuke Kato, Ryutaro Tokutsu, Wataru Sakamoto, Jun Minagawa, Fumio Matsuda, Hiroshi Shimizu

Journal of Bioscience and Bioengineering　Vol. 127　No. 3　p. 394-402　2018/09　Research paper (scientific journal)

Metabolic flux of the oxidative pentose phosphate pathway under low light conditions in Synechocystis sp. PCC 6803

Kentaro Ueda, Tsubasa Nakajima, Katsunori Yoshikawa, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu

Journal of Bioscience and Bioengineering　Vol. 126　No. 1　p. 38-43　2018/07/01　Research paper (scientific journal)

Molecular Components of Arabidopsis Intact Vacuoles Clarified with Metabolomic and Proteomic Analyses.

Miwa Ohnishi, Aya Anegawa, Yuko Sugiyama, Kazuo Harada, Akira Oikawa, Yasumune Nakayama, Fumio Matsuda, Yukiko Nakamura, Ryosuke Sasaki, Chizuko Shichijo, Patrick G Hatcher, Hidehiro Fukaki, Shigehiko Kanaya, Koh Aoki, Mami Yamazaki, Eiichiro Fukusaki, Kazuki Saito, Tetsuro Mimura

Plant & cell physiology　Vol. 59　No. 7　p. 1353-1362　2018/07/01

Comparative analysis of fermentation and enzyme expression profiles among industrial Saccharomyces cerevisiae strains

Kiyoka Uebayashi, Hiroshi Shimizu, Fumio Matsuda

Applied Microbiology and Biotechnology　p. 1-11　2018/06/07　Research paper (scientific journal)

Transcriptome analysis of the cyanobacterium Synechocystis sp. PCC 6803 and mechanisms of photoinhibition tolerance under extreme high light conditions.

Ogawa K, Yoshikawa K, Matsuda F, Toya Y, Shimizu H

Journal of bioscience and bioengineering　Vol. 126　No. 5　p. 596-602　2018/06　Research paper (scientific journal)

Application of adaptive laboratory evolution to overcome a flux limitation in an Escherichia coli production strain

Kento Tokuyama, Yoshihiro Toya, Takaaki Horinouchi, Chikara Furusawa, Fumio Matsuda, Hiroshi Shimizu

Biotechnology and Bioengineering　Vol. 115　No. 6　p. 1542-1551　2018/06/01　Research paper (scientific journal)

A pyruvate carbon flux tugging strategy for increasing 2,3-butanediol production and reducing ethanol subgeneration in the yeast Saccharomyces cerevisiae

Jun Ishii, Keisuke Morita, Kengo Ida, Hiroko Kato, Shohei Kinoshita, Shoko Hataya, Hiroshi Shimizu, Akihiko Kondo, Fumio Matsuda

Biotechnology for Biofuels　No. 11　2018/06　Research paper (scientific journal)

¹³C-metabolic flux analysis of ethanol-assimilating Saccharomyces cerevisiae for S-adenosyl-L-methionine production.

Hayakawa K, Matsuda F, Shimizu H

Microbial cell factories　Vol. 17　No. 1　2018/05　Research paper (scientific journal)

Metabolic engineering of mevalonate-producing Escherichia coli strains based on thermodynamic analysis

Hikaru Nagai, Ami Masuda, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu

Metabolic Engineering　Vol. 47　p. 1-9　2018/05/01　Research paper (scientific journal)

Expression of Saccharomyces cerevisiae cDNAs to enhance the growth of non-ethanol-producing S. cerevisiae strains lacking pyruvate decarboxylases

Yuki Narazaki, Yuta Nomura, Keisuke Morita, Hiroshi Shimizu, Fumio Matsuda

Journal of Bioscience and Bioengineering　2018　Research paper (scientific journal)

Mass Spectrometry-Based Method to Study Inhibitor-Induced Metabolic Redirection in the Central Metabolism of Cancer Cells.

Chie Araki, Nobuyuki Okahashi, Kousuke Maeda, Hiroshi Shimizu, Fumio Matsuda

Mass spectrometry (Tokyo, Japan)　Vol. 7　No. 1　2018

Comparative Targeted Proteomics of the Central Metabolism and Photosystems in SigE mutant strains of synechocystis sp. PCC 6803

Yuma Tokumaru, Kiyoka Uebayashi, Masakazu Toyoshima, Takashi Osanai, Fumio Matsuda, Hiroshi Shimizu

Molecules　Vol. 23　No. 5　2018　Research paper (scientific journal)

A Highly Specific Genome-Wide Association Study Integrated with Transcriptome Data Reveals the Contribution of Copy Number Variations to Specialized Metabolites in Arabidopsis thaliana Accessions

Kazumasa Shirai, Fumio Matsuda, Ryo Nakabayashi, Masanori Okamoto, Maho Tanaka, Akihiro Fujimoto, Minami Shimizu, Kazuo Shinozaki, Motoaki Seki, Kazuki Saito, Kousuke Hanada

Molecular Biology and Evolution　Vol. 34　No. 12　p. 3111-3122　2017/12/01　Research paper (scientific journal)

Learning from quantitative data to understand central carbon metabolism

Fumio Matsuda, Yoshihiro Toya, Hiroshi Shimizu

Biotechnology Advances　Vol. 35　No. 8　p. 971-980　2017/12/01

Metabolic engineering of isopropyl alcohol-producing Escherichia coli strains with C-13-metabolic flux analysis

Nobuyuki Okahashi, Fumio Matsuda, Katsunori Yoshikawa, Tomokazu Shirai, Yoshiko Matsumoto, Mitsufumi Wada, Hiroshi Shimizu

BIOTECHNOLOGY AND BIOENGINEERING　Vol. 114　No. 12　p. 2782-2793　2017/12　Research paper (scientific journal)

Metabolic engineering of Synechococcus elongatus PCC 7942 for improvement of 1,3-propanediol and glycerol production based on in silico simulation of metabolic flux distribution

Yasutaka Hirokawa, Shingo Matsuo, Hiroyuki Hamada, Fumio Matsuda, Taizo Hanai

Microbial Cell Factories　Vol. 16　No. 1　2017/11/25　Research paper (scientific journal)

The RB-IL-6 axis controls self-renewal and endocrine therapy resistance by fine-tuning mitochondrial activity.

S Kitajima, A Yoshida, S Kohno, F Li, S Suzuki, N Nagatani, Y Nishimoto, N Sasaki, H Muranaka, Y Wan, T C Thai, N Okahashi, F Matsuda, H Shimizu, T Nishiuchi, Y Suzuki, K Tominaga, N Gotoh, M Suzuki, M E Ewen, D A Barbie, O Hirose, T Tanaka, C Takahashi

Oncogene　Vol. 36　No. 36　p. 5145-5157　2017/09/07　Research paper (scientific journal)

Heterologous expression of bacterial phosphoenol pyruvate carboxylase and Entner-Doudoroff pathway in Saccharomyces cerevisiae for improvement of isobutanol production

Keisuke Morita, Yuta Nomura, Jun Ishii, Fumio Matsuda, Akihiko Kondo, Hiroshi Shimizu

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 124　No. 3　p. 263-270　2017/09　Research paper (scientific journal)

Erratum: Acetate-mediated novel survival strategy against drought in plants (Nature Plants (2017) 3 (17097) DOI: 10.1038/nplants.2017.97)

Jong-Myong Kim, Taiko Kim To, Akihiro Matsui, Keitaro Tanoi, Natsuko I. Kobayashi, Fumio Matsuda, Yoshiki Habu, Daisuke Ogawa, Takuya Sakamoto, Sachihiro Matsunaga, Khurram Bashir, Sultana Rasheed, Marina Ando, Hiroko Takeda, Kanako Kawaura, Miyako Kusano, Atsushi Fukushima, Takaho A. Endo, Takashi Kuromori, Junko Ishida, Taeko Morosawa, Maho Tanaka, Chieko Torii, Yumiko Takebayashi, Hitoshi Sakakibara, Yasunari Ogihara, Kazuki Saito, Kazuo Shinozaki, Alessandra Devoto, Motoaki Seki

Nature Plants　Vol. 3　2017/07/17　Research paper (scientific journal)

Acetate-mediated novel survival strategy against drought in plants

Jong-Myong Kim, Taiko Kim To, Akihiro Matsui, Keitaro Tanoi, Natsuko I. Kobayashi, Fumio Matsuda, Yoshiki Habu, Daisuke Ogawa, Takuya Sakamoto, Sachihiro Matsunaga, Khurram Bashir, Sultana Rasheed, Marina Ando, Hiroko Takeda, Kanako Kawaura, Miyako Kusano, Atsushi Fukushima, Takaho A. Endo, Takashi Kuromori, Junko Ishida, Taeko Morosawa, Maho Tanaka, Chieko Torii, Yumiko Takebayashi, Hitoshi Sakakibara, Yasunari Ogihara, Kazuki Saito, Kazuo Shinozaki, Alessandra Devoto, Motoaki Seki

Nature Plants　Vol. 3　No. 7　2017/06/26　Research paper (scientific journal)

Synthetic metabolic bypass for a metabolic toggle switch enhances acetyl-CoA supply for isopropanol production by Escherichia coli

Yuki Soma, Taiki Yamaji, Fumio Matsuda, Taizo Hanai

Journal of Bioscience and Bioengineering　Vol. 123　No. 5　p. 625-633　2017/05/01　Research paper (scientific journal)

Metabolic Flux Analysis of the Synechocystis sp. PCC 6803 Delta nrtABCD Mutant Reveals a Mechanism for Metabolic Adaptation to Nitrogen-Limited Conditions (vol 58, pg 537, 2017)

Tsubasa Nakajima, Katsunori Yoshikawa, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu

PLANT AND CELL PHYSIOLOGY　Vol. 58　No. 5　p. 976-976　2017/05

Metabolic Flux Analysis of the Synechocystis sp PCC 6803 Delta nrtABCD Mutant Reveals a Mechanism for Metabolic Adaptation to Nitrogen-Limited Conditions

Tsubasa Nakajima, Katsunori Yoshikawa, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu

PLANT AND CELL PHYSIOLOGY　Vol. 58　No. 3　p. 537-545　2017/03　Research paper (scientific journal)

Prediction of Hopeless Peptides Unlikely to be Selected for Targeted Proteome Analysis.

Matsuda F, Tomita A, Shimizu H

Mass spectrometry (Tokyo, Japan)　Vol. 6　No. 1　2017/02

Targeted proteome analysis of single-gene deletion strains of Saccharomyces cerevisiae lacking enzymes in the central carbon metabolism

Fumio Matsuda, Syohei Kinoshita, Shunsuke Nishino, Atsumi Tomita, Hiroshi Shimizu

PLOS ONE　Vol. 12　No. 2　2017/02　Research paper (scientific journal)

C-13-metabolic flux analysis for mevalonate-producing strain of Escherichia coli

Keisuke Wada, Yoshihiro Toya, Satomi Banno, Katsunori Yoshikawa, Fumio Matsuda, Hiroshi Shimizu

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 123　No. 2　p. 177-182　2017/02　Research paper (scientific journal)

Omics-integrated approach for metabolic state analysis of microbial processes

Hiroshi Shimizu, Chikara Furusawa, Takashi Hirasawa, Katsunori Yoshikawa, Yoshihiro Toya, Tomokazu Shirai, Fumio Matsuda

Applied Bioengineering: Innovations and Future Directions　p. 213-236　2017/01/01　Part of collection (book)

Rewiring of embryonic glucose metabolism via suppression of PFK-1 and aldolase during mouse chorioallantoic branching.

Hidenobu Miyazawa, Yoshifumi Yamaguchi, Yuki Sugiura, Kurara Honda, Koki Kondo, Fumio Matsuda, Takehiro Yamamoto, Makoto Suematsu, Masayuki Miura

Development (Cambridge, England)　Vol. 144　No. 1　p. 63-73　2017/01/01　Research paper (scientific journal)

Lipoprotein profiling methodology based on determination of apolipoprotein concentration.

Hiroaki Takeda, Yoshihiro Izumi, Atsumi Tomita, Tomonari Koike, Masashi Shiomi, Eiichiro Fukusaki, Fumio Matsuda, Takeshi Bamba

Bioanalysis　Vol. 9　No. 1　p. 9-19　2017/01

Differences in glucose yield of residues from among varieties of rice, wheat, and sorghum after dilute acid pretreatment

Hiroshi Teramura, Kengo Sasaki, Hideo Kawaguchi, Fumio Matsuda, Jun Kikuchi, Tomokazu Shirai, Takashi Sazuka, Masanori Yamasaki, Shigeo Takumi, Chiaki Ogino, Akihiko Kondo

Bioscience, Biotechnology and Biochemistry　Vol. 81　No. 8　p. 1650-1656　2017　Research paper (scientific journal)

Metabolic Adaptation to Nutritional Stress in Human Colorectal Cancer.

Masaaki Miyo, Masamitsu Konno, Naohiro Nishida, Toshinori Sueda, Kozo Noguchi, Hidetoshi Matsui, Hugh Colvin, Koichi Kawamoto, Jun Koseki, Naotsugu Haraguchi, Junichi Nishimura, Taishi Hata, Noriko Gotoh, Fumio Matsuda, Taroh Satoh, Tsunekazu Mizushima, Hiroshi Shimizu, Yuichiro Doki, Masaki Mori, Hideshi Ishii

Scientific reports　Vol. 6　p. 38415-38415　2016/12/07

Investigation of useful carbon tracers for ¹³C-metabolic flux analysis of Escherichia coli by considering five experimentally determined flux distributions

Kousuke Maeda, Nobuyuki Okahashi, Yoshihiro Toya, Fumio Matsuda, Hiroshi Shimizu

Metabolic Engineering Communications　Vol. 3　p. 187-195　2016/12/01　Research paper (scientific journal)

Positive effects of proline addition on the central metabolism of wild-type and lactic acid-producing Saccharomyces cerevisiae strains

Riyanto Heru Nugroho, Katsunori Yoshikawa, Fumio Matsuda, Hiroshi Shimizu

BIOPROCESS AND BIOSYSTEMS ENGINEERING　Vol. 39　No. 11　p. 1711-1716　2016/11　Research paper (scientific journal)

GC-MS/MS survey of collision-induced dissociation of tert-butyldimethylsilyl-derivatized amino acids and its application to C-13-metabolic flux analysis of Escherichia coli central metabolism

Nobuyuki Okahashi, Shuichi Kawana, Junko Iida, Hiroshi Shimizu, Fumio Matsuda

ANALYTICAL AND BIOANALYTICAL CHEMISTRY　Vol. 408　No. 22　p. 6133-6140　2016/09　Research paper (scientific journal)

Toward the complete utilization of rice straw: Methane fermentation and lignin recovery by a combinational process involving mechanical milling, supporting material and nanofiltration

Kengo Sasaki, Mami Okamoto, Tomokazu Shirai, Yota Tsuge, Ayami Fujino, Daisuke Sasaki, Masahiko Morita, Fumio Matsuda, Jun Kikuchi, Akihiko Kondo

BIORESOURCE TECHNOLOGY　Vol. 216　p. 830-837　2016/09　Research paper (scientific journal)

Regular expressions of MS/MS spectra for partial annotation of metabolite features

Fumio Matsuda

Metabolomics　Vol. 12　No. 7　2016/07/01　Research paper (scientific journal)

Overexpressing enzymes of the Ehrlich pathway and deleting genes of the competing pathway in Saccharomyces cerevisiae for increasing 2-phenylethanol production from glucose

Li Shen, Yuya Nishimura, Fumio Matsuda, Jun Ishii, Akihiko Kondo

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 122　No. 1　p. 34-39　2016/07　Research paper (scientific journal)

Metabolome analysis of Saccharomyces cerevisiae and optimization of culture medium for S-adenosyl-L-methionine production

Kenshi Hayakawa, Fumio Matsuda, Hiroshi Shimizu

AMB EXPRESS　Vol. 6　No. 1　2016/06　Research paper (scientific journal)

Organosolv pretreatment of sorghum bagasse using a low concentration of hydrophobic solvents such as 1-butanol or 1-pentanol

Hiroshi Teramura, Kengo Sasaki, Tomoko Oshima, Fumio Matsuda, Mami Okamoto, Tomokazu Shirai, Hideo Kawaguchi, Chiaki Ogino, Ko Hirano, Takashi Sazuka, Hidemi Kitano, Jun Kikuchi, Akihiko Kondo

BIOTECHNOLOGY FOR BIOFUELS　Vol. 9　2016/02　Research paper (scientific journal)

Metabolic characterization of cultured mammalian cells by mass balance analysis, tracer labeling experiments and computer-aided simulations

Nobuyuki Okahashi, Susumu Kohno, Shunsuke Kitajima, Fumio Matsuda, Chiaki Takahashi, Hiroshi Shimizu

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 120　No. 6　p. 725-731　2015/12　Research paper (scientific journal)

C-13-metabolic flux analysis in S-adenosyl-L-methionine production by Saccharomyces cerevisiae

Kenshi Hayakawa, Shuichi Kajihata, Fumio Matsuda, Hiroshi Shimizu

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 120　No. 5　p. 532-538　2015/11　Research paper (scientific journal)

Absolute quantitation of glycolytic intermediates reveals thermodynamic shifts in Saccharomyces cerevisiae strains lacking PFK1 or ZWF1 genes

Shunsuke Nishino, Nobuyuki Okahashi, Fumio Matsuda, Hiroshi Shimizu

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 120　No. 3　p. 280-286　2015/09　Research paper (scientific journal)

C-13-based metabolic flux analysis of Saccharomyces cerevisiae with a reduced Crabtree effect

Shuichi Kajihata, Fumio Matsuda, Mika Yoshimi, Kenshi Hayakawa, Chikara Furusawa, Akihisa Kanda, Hiroshi Shimizu

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 120　No. 2　p. 140-144　2015/08　Research paper (scientific journal)

Precipitate obtained following membrane separation of hydrothermally pretreated rice straw liquid revealed by 2D NMR to have high lignin content

Kengo Sasaki, Mami Okamoto, Tomokazu Shirai, Yota Tsuge, Hiroshi Teramura, Daisuke Sasaki, Hideo Kawaguchi, Tomohisa Hasunuma, Chiaki Ogino, Fumio Matsuda, Jun Kikuchi, Akihiko Kondo

BIOTECHNOLOGY FOR BIOFUELS　Vol. 8　2015/06　Research paper (scientific journal)

Changes in Lignin and Polysaccharide Components in 13 Cultivars of Rice Straw following Dilute Acid Pretreatment as Studied by Solution-State 2D H-1-C-13 NMR

Hiroshi Teramura, Kengo Sasaki, Tomoko Oshima, Shimpei Aikawa, Fumio Matsuda, Mami Okamoto, Tomokazu Shirai, Hideo Kawaguchi, Chiaki Ogino, Masanori Yamasaki, Jun Kikuchi, Akihiko Kondo

PLOS ONE　Vol. 10　No. 6　2015/06　Research paper (scientific journal)

Evaluation of Brachypodium distachyon L-Tyrosine Decarboxylase Using L-Tyrosine Over-Producing Saccharomyces cerevisiae

Shuhei Noda, Tomokazu Shirai, Keiichi Mochida, Fumio Matsuda, Sachiko Oyama, Mami Okamoto, Akihiko Kondo

PLOS ONE　Vol. 10　No. 5　2015/05　Research paper (scientific journal)

Eliminating the isoleucine biosynthetic pathway to reduce competitive carbon outflow during isobutanol production by Saccharomyces cerevisiae

Kengo Ida, Jun Ishii, Fumio Matsuda, Takashi Kondo, Akihiko Kondo

MICROBIAL CELL FACTORIES　Vol. 14　2015/04　Research paper (scientific journal)

Nano-scale liquid chromatography coupled to tandem mass spectrometry using the multiple reaction monitoring mode based quantitative platform for analyzing multiple enzymes associated with central metabolic pathways of Saccharomyces cerevisiae using ultra fast mass spectrometry

Fumio Matsuda, Tairo Ogura, Atsumi Tomita, Ichiro Hirano, Hiroshi Shimizu

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 119　No. 1　p. 117-120　2015/01　Research paper (scientific journal)

Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism

Matsuda Fumio, Nakabayashi Ryo, Yang Zhigang, Okazaki Yozo, Yonemaru Jun-ichi, Ebana Kaworu, Yano Masahiro, Saito Kazuki

Plant Journal　Vol. 81　No. 1　p. 13-23　2015

Tyramine biosynthesis from glucose using Brachypodium distachyon tyrosine decarboxylase expressing Saccharomyces cerevisiae

Shuhei Noda, Tomokazu Shirai, Keiichi Mochida, Sachiko Oyama, Mami Okamoto, Fumio Matsuda, Kondo Akihiko

JOURNAL OF BIOTECHNOLOGY　Vol. 185　p. S102-S102　2014/09　Research paper (scientific journal)

Integrated Metabolic Flux and Omics Analysis of Synechocystis sp PCC 6803 under Mixotrophic and Photoheterotrophic Conditions

Tsubasa Nakajima, Shuichi Kajihata, Katsunori Yoshikawa, Fumio Matsuda, Chikara Furusawa, Takashi Hirasawa, Hiroshi Shimizu

PLANT AND CELL PHYSIOLOGY　Vol. 55　No. 9　p. 1605-1612　2014/09　Research paper (scientific journal)

Three gene expression vector sets for concurrently expressing multiple genes in Saccharomyces cerevisiae

Jun Ishii, Takashi Kondo, Harumi Makino, Akira Ogura, Fumio Matsuda, Akihiko Kondo

FEMS YEAST RESEARCH　Vol. 14　No. 3　p. 399-411　2014/05　Research paper (scientific journal)

Increased biomass production and glycogen accumulation in apcE gene deleted Synechocystis sp PCC 6803

Ancy Joseph, Shimpei Aikawa, Kengo Sasaki, Fumio Matsuda, Tomohisa Hasunuma, Akihiko Kondo

AMB EXPRESS　Vol. 4　2014/03　Research paper (scientific journal)

Enhancement of oxidative and drought tolerance in Arabidopsis by overaccumulation of antioxidant flavonoids.

Ryo Nakabayashi, Keiko Yonekura-Sakakibara, Kaoru Urano, Makoto Suzuki, Yutaka Yamada, Tomoko Nishizawa, Fumio Matsuda, Mikiko Kojima, Hitoshi Sakakibara, Kazuo Shinozaki, Anthony J Michael, Takayuki Tohge, Mami Yamazaki, Kazuki Saito

The Plant journal : for cell and molecular biology　Vol. 77　No. 3　p. 367-79　2014/02　Research paper (scientific journal)

Rre37 stimulates accumulation of 2-oxoglutarate and glycogen under nitrogen starvation in Synechocystis sp PCC 6803

Joseph Ancy, Aikawa Shimpei, Sasaki Kengo, Teramura Hiroshi, Hasunuma Tomohisa, Matsuda Fumio, Osanai Takashi, Hirai Masami Yokota, Kondo Akihiko

FEBS LETTERS　Vol. 588　No. 3　p. 466-471　2014/01/31

OpenMebius: An Open Source Software for Isotopically Nonstationary C-13-Based Metabolic Flux Analysis

Shuichi Kajihata, Chikara Furusawa, Fumio Matsuda, Hiroshi Shimizu

BIOMED RESEARCH INTERNATIONAL　2014　Research paper (scientific journal)

Rre37 stimulates accumulation of 2-oxoglutarate and glycogen under nitrogen starvation in Synechocystis sp PCC 6803

Ancy Joseph, Shimpei Aikawa, Kengo Sasaki, Hiroshi Teramura, Tomohisa Hasunuma, Fumio Matsuda, Takashi Osanai, Masami Yokota Hirai, Akihiko Kondo

FEBS LETTERS　Vol. 588　No. 3　p. 466-471　2014/01　Research paper (scientific journal)

Production of indole alkaloids by metabolic engineering of the tryptophan pathway in rice

Joseph G. Dubouzet, Fumio Matsuda, Atsushi Ishihara, Hisashi Miyagawa, Kyo Wakasa

Plant Biotechnology Journal　Vol. 11　No. 9　p. 1103-1111　2013/12　Research paper (scientific journal)

Glucose content in the liquid hydrolysate after dilute acid pretreatment is affected by the starch content in rice straw

Hiroshi Teramura, Tomoko Oshima, Fumio Matsuda, Kengo Sasaki, Chiaki Ogino, Masanori Yamasaki, Akihiko Kondo

BIORESOURCE TECHNOLOGY　Vol. 149　p. 520-524　2013/12　Research paper (scientific journal)

Increased isobutanol production in Saccharomyces cerevisiae by eliminating competing pathways and resolving cofactor imbalance

Fumio Matsuda, Jun Ishii, Takashi Kondo, Kengo Ida, Hironori Tezuka, Akihiko Kondo

MICROBIAL CELL FACTORIES　Vol. 12　2013/12　Research paper (scientific journal)

Metabolic pathway engineering of yeast Saccharomyces cerevisiae for isobutanol production

Jun Ishii, Fumio Matsuda, Akihiko Kondo

YEAST　Vol. 30　p. 210-210　2013/09

Method for Assessing the Statistical Significance of Mass Spectral Similarities Using Basic Local Alignment Search Tool Statistics

Fumio Matsuda, Hiroshi Tsugawa, Eiichiro Fukusaki

ANALYTICAL CHEMISTRY　Vol. 85　No. 17　p. 8291-8297　2013/09　Research paper (scientific journal)

Evaluation of control mechanisms for Saccharomyces cerevisiae central metabolic pathway using metabolic analysis of single-gene deletion mutants

Shuhei Noda, Tomokazu Shirai, Fumio Matsuda, Mami Okamoto, Akihiko Kondo

YEAST　Vol. 30　p. 170-170　2013/09

Cocktail delta-integration of xylose assimilation genes for efficient ethanol production from xylose in Saccharomyces cerevisiae

Hiroko Kato, Fumio Matsuda, Ryosuke Yamada, Kento Nagata, Tomokazu Shirai, Tomohisa Hasunuma, Akihiko Kondo

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 116　No. 3　p. 333-336　2013/09　Research paper (scientific journal)

Aqueous size-exclusion chromatographic method for the quantification of cyanobacterial native glycogen

Yoshihiro Izumi, Shimpei Aikawa, Fumio Matsuda, Tomohisa Hasunuma, Akihiko Kondo

Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences　Vol. 930　p. 90-97　2013/07/01　Research paper (scientific journal)

Regulation of central carbon metabolism in Saccharomyces cerevisiae by metabolic inhibitors

Fumio Matsuda, Tomokazu Shirai, Jun Ishii, Akihiko Kondo

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 116　No. 1　p. 59-64　2013/07　Research paper (scientific journal)

Direct conversion of Spirulina to ethanol without pretreatment or enzymatic hydrolysis processes

Shimpei Aikawa, Ancy Joseph, Ryosuke Yamada, Yoshihiro Izumi, Takahiro Yamagishi, Fumio Matsuda, Hiroshi Kawai, Jo-Shu Chang, Tomohisa Hasunuma, Akihiko Kondo

ENERGY & ENVIRONMENTAL SCIENCE　Vol. 6　No. 6　p. 1844-1849　2013/06　Research paper (scientific journal)

Display of active beta-glucosidase on the surface of Schizosaccharomyces pombe cells using novel anchor proteins

Tsutomu Tanaka, Sayoko Matsumoto, Mari Yamada, Ryosuke Yamada, Fumio Matsuda, Akihiko Kondo

Applied Microbiology and Biotechnology　Vol. 97　No. 10　p. 4343-4352　2013/05　Research paper (scientific journal)

Utilization of Lactic Acid Bacterial Genes in Synechocystis sp PCC 6803 in the Production of Lactic Acid

Ancy Joseph, Shimpei Aikawa, Kengo Sasaki, Yota Tsuge, Fumio Matsuda, Tsutomu Tanaka, Akihiko Kondo

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　Vol. 77　No. 5　p. 966-970　2013/05　Research paper (scientific journal)

Integrative Analysis of Secondary Metabolism and Transcript Regulation in Arabidopsis Thaliana

Fumio Matsuda, Kazuki Saito

The Handbook of Plant Metabolomics　p. 175-195　2013/04/12　Part of collection (book)

Evaluation of control mechanisms for Saccharomyces cerevisiae central metabolic reactions using metabolome data of eight single-gene deletion mutants

Tomokazu Shirai, Fumio Matsuda, Mami Okamoto, Akihiko Kondo

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　Vol. 97　No. 8　p. 3569-3577　2013/04　Research paper (scientific journal)

PRIMe Update: Innovative content for plant metabolomics and integration of gene expression and metabolite accumulation

Tetsuya Sakurai, Yutaka Yamada, Yuji Sawada, Fumio Matsuda, Kenji Akiyama, Kazuo Shinozaki, Masami Yokota Hirai, Kazuki Saito

Plant and Cell Physiology　Vol. 54　No. 2　2013/02　Research paper (scientific journal)

Implementation of a transhydrogenase-like shunt to counter redox imbalance during xylose fermentation in Saccharomyces cerevisiae

Hiroyuki Suga, Fumio Matsuda, Tomohisa Hasunuma, Jun Ishii, Akihiko Kondo

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　Vol. 97　No. 4　p. 1669-1678　2013/02　Research paper (scientific journal)

Ability of a perfluoropolymer membrane to tolerate by-products of ethanol fermentation broth from dilute acid-pretreated rice straw

Kengo Sasaki, Fumio Matsuda, Tomohisa Hasunuma, Chiaki Ogino, Masakatsu Urairi, Kazuhito Yoshida, Akihiko Kondo

Biochemical Engineering Journal　Vol. 70　p. 135-139　2013/01/15　Research paper (scientific journal)

メタボローム–QTL解析を用いた玄米代謝物組成にかかわる自然変異の探索:コメ品質の遺伝的な差をメタボローム分析で探索する

松田 史生, 岡咲 洋三, 斉藤 和季

化学と生物　Vol. 51　No. 12　p. 792-794　2013

Development of microbial cell factories for bio-refinery through synthetic bioengineering

Akihiko Kondo, Jun Ishii, Kiyotaka Y. Hara, Tomohisa Hasunuma, Fumio Matsuda

JOURNAL OF BIOTECHNOLOGY　Vol. 163　No. 2　p. 204-216　2013/01　Research paper (scientific journal)

Changes in primary and secondary metabolite levels in response to gene targeting-mediated site-directed mutagenesis of the anthranilate synthase gene in rice

Hiroaki Saika, Akira Oikawa, Ryo Nakabayashi, Fumio Matsuda, Kazuki Saito, Seiichi Toki

Metabolites　Vol. 2　No. 4　p. 1123-1138　2012/12/18　Research paper (scientific journal)

RIKEN tandem mass spectral database (ReSpect) for phytochemicals: A plant-specific MS/MS-based data resource and database

Yuji Sawada, Ryo Nakabayashi, Yutaka Yamada, Makoto Suzuki, Muneo Sato, Akane Sakata, Kenji Akiyama, Tetsuya Sakurai, Fumio Matsuda, Toshio Aoki, Masami Yokota Hirai, Kazuki Saito

Phytochemistry　Vol. 82　p. 38-45　2012/10　Research paper (scientific journal)

Design of superior cell factories for a sustainable biorefinery by synthetic bioengineering

Tomohisa Hasunuma, Fumio Matsuda, Akihiko Kondo

Systems Metabolic Engineering　Vol. 9789400745346　p. 329-348　2012/08/01　Part of collection (book)

Genetic engineering to enhance the Ehrlich pathway and alter carbon flux for increased isobutanol production from glucose by Saccharomyces cerevisiae

Takashi Kondo, Hironori Tezuka, Jun Ishii, Fumio Matsuda, Chiaki Ogino, Akihiko Kondo

Journal of Biotechnology　Vol. 159　No. 1-2　p. 32-37　2012/05/31　Research paper (scientific journal)

Dissection of genotype-phenotype associations in rice grains using metabolome quantitative trait loci analysis

Fumio Matsuda, Yozo Okazaki, Akira Oikawa, Miyako Kusano, Ryo Nakabayashi, Jun Kikuchi, Jun-Ichi Yonemaru, Kaworu Ebana, Masahiro Yano, Kazuki Saito

Plant Journal　Vol. 70　No. 4　p. 624-636　2012/05

Widely targeted metabolic profiling analysis of yeast central metabolites

Hiroko Kato, Yoshihiro Izumi, Tomohisa Hasunuma, Fumio Matsuda, Akihiko Kondo

JOURNAL OF BIOSCIENCE AND BIOENGINEERING　Vol. 113　No. 5　p. 665-673　2012/05　Research paper (scientific journal)

Synergistic enhancement of glycogen production in Arthrospira platensis by optimization of light intensity and nitrate supply

Shimpei Aikawa, Yoshihiro Izumi, Fumio Matsuda, Tomohisa Hasunuma, Jo-Shu Chang, Akihiko Kondo

BIORESOURCE TECHNOLOGY　Vol. 108　p. 211-215　2012/03　Research paper (scientific journal)

Coupled transcript-metabolite profiling: Towards systems biology approaches to unravel regulation of seed secondary metabolism

Thierry Joët, Eleanore T. Wurtzel, Fumio Matsuda, Kazuki Saito, Stéphane Dussert

Seed Development: OMICS Technologies Toward Improvement of Seed Quality and Crop Yield: OMICS in Seed Biology　p. 367-385　2012/01/01　Part of collection (book)

Two glycosyltransferases involved in anthocyanin modification delineated by transcriptome independent component analysis in Arabidopsis thaliana

Keiko Yonekura-Sakakibara, Atsushi Fukushima, Ryo Nakabayashi, Kousuke Hanada, Fumio Matsuda, Satoko Sugawara, Eri Inoue, Takashi Kuromori, Takuya Ito, Kazuo Shinozaki, Bunyapa Wangwattana, Mami Yamazaki, Kazuki Saito

Plant Journal　Vol. 69　No. 1　p. 154-167　2012/01　Research paper (scientific journal)

Construction of an artificial pathway for isobutanol biosynthesis in the cytosol of saccharomyces cerevisiae

Fumio Matsuda, Takashi Kondo, Kengo Ida, Hironori Tezuka, Jun Ishii, Akihiko Kondo

Bioscience, Biotechnology and Biochemistry　Vol. 76　No. 11　p. 2139-2141　2012　Research paper (scientific journal)

Effects of freeze-drying of samples on metabolite levels in metabolome analyses

Akira Oikawa, Takao Otsuka, Yusuke Jikumaru, Shinjiro Yamaguchi, Fumio Matsuda, Ryo Nakabayashi, Tadashi Takashina, Kanji Isuzugawa, Kazuki Saito, Katsuhiro Shiratake

Journal of Separation Science　Vol. 34　No. 24　p. 3561-3567　2011/12　Research paper (scientific journal)

Comparative Profiling Analysis of Central Metabolites in Euglena gracilis under Various Cultivation Conditions

Fumio Matsuda, Masahiro Hayashi, Akihiko Kondo

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　Vol. 75　No. 11　p. 2253-2256　2011/11　Research paper (scientific journal)

Exploring molecular backgrounds of quality traits in rice by predictive models based on high-coverage metabolomics

Henning Redestig, Miyako Kusano, Kaworu Ebana, Makoto Kobayashi, Akira Oikawa, Yozo Okazaki, Fumio Matsuda, Masanori Arita, Naoko Fujita, Kazuki Saito

BMC Systems Biology　Vol. 5　2011/10/28　Research paper (scientific journal)

Metabolomics of a single vacuole reveals metabolic dynamism in an alga Chara australis

Akira Oikawa, Fumio Matsuda, Munehiro Kikuyama, Tetsuro Mimura, Kazuki Saito

Plant Physiology　Vol. 157　No. 2　p. 544-551　2011/10　Research paper (scientific journal)

Repeated-batch fermentation of lignocellulosic hydrolysate to ethanol using a hybrid Saccharomyces cerevisiae strain metabolically engineered for tolerance to acetic and formic acids

Tomoya Sanda, Tomohisa Hasunuma, Fumio Matsuda, Akihiko Kondo

BIORESOURCE TECHNOLOGY　Vol. 102　No. 17　p. 7917-7924　2011/09　Research paper (scientific journal)

Engineering strategy of yeast metabolism for higher alcohol production

Fumio Matsuda, Chikara Furusawa, Takashi Kondo, Jun Ishii, Hiroshi Shimizu, Akihiko Kondo

MICROBIAL CELL FACTORIES　Vol. 10　2011/09　Research paper (scientific journal)

Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity

Fumio Matsuda, Ryo Nakabayashi, Yuji Sawada, Makoto Suzuki, Masami Y. Hirai, Shigehiko Kanaya, Kazuki Saito

Frontiers in Plant Science　Vol. 2　2011/08/22　Research paper (scientific journal)

Enzymatic glutathione production using metabolically engineered Saccharomyces cerevisiae as a whole-cell biocatalyst

Hideyo Yoshida, Kiyotaka Y. Hara, Kentaro Kiriyama, Hideki Nakayama, Fumiyoshi Okazaki, Fumio Matsuda, Chiaki Ogino, Hideki Fukuda, Akihiko Kondo

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　Vol. 91　No. 4　p. 1001-1006　2011/08　Research paper (scientific journal)

Variation in Biomass Properties among Rice Diverse Cultivars

Fumio Matsuda, Masanori Yamasaki, Tomohisa Hasunuma, Chiaki Ogino, Akihiko Kondo

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　Vol. 75　No. 8　p. 1603-1605　2011/08　Research paper (scientific journal)

Metabolomics reveals comprehensive reprogramming involving two independent metabolic responses of Arabidopsis to UV-B light

Miyako Kusano, Takayuki Tohge, Atsushi Fukushima, Makoto Kobayashi, Naomi Hayashi, Hitomi Otsuki, Youichi Kondou, Hiroto Goto, Mika Kawashima, Fumio Matsuda, Rie Niida, Minami Matsui, Kazuki Saito, Alisdair R. Fernie

Plant Journal　Vol. 67　No. 2　p. 354-369　2011/07　Research paper (scientific journal)

Application of gene targeting to designed mutation breeding of high-tryptophan rice

Hiroaki Saika, Akira Oikawa, Fumio Matsuda, Haruko Onodera, Kazuki Saito, Seiichi Toki

Plant Physiology　Vol. 156　No. 3　p. 1269-1277　2011/07　Research paper (scientific journal)

Efficient fermentation of xylose to ethanol at high formic acid concentrations by metabolically engineered Saccharomyces cerevisiae

Tomohisa Hasunuma, Kyung-mo Sung, Tomoya Sanda, Kazuya Yoshimura, Fumio Matsuda, Akihiko Kondo

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY　Vol. 90　No. 3　p. 997-1004　2011/05　Research paper (scientific journal)

Metabolomics in Plant Biotechnology

Yozo Okazaki, Akira Oikawa, Miyako Kusano, Fumio Matsuda, Kazuki Saito

Plant Metabolism and Biotechnology　p. 373-388　2011/03/28　Part of collection (book)

Covering chemical diversity of genetically-modified tomatoes using metabolomics for objective substantial equivalence assessment

Miyako Kusano, Henning Redestig, Tadayoshi Hirai, Akira Oikawa, Fumio Matsuda, Atsushi Fukushima, Masanori Arita, Shin Watanabe, Megumu Yano, Kyoko Hiwasa-Tanase, Hiroshi Ezura, Kazuki Saito

PLoS ONE　Vol. 6　No. 2　2011　Research paper (scientific journal)

Metabolomics for functional genomics, systems biology, and biotechnology

Kazuki Saito, Fumio Matsuda

Annual Review of Plant Biology　Vol. 61　p. 463-489　2010/06/02　Research paper (scientific journal)

Metabolic profiling and cytological analysis of proanthocyanidins in immature seeds of Arabidopsis thaliana flavonoid accumulation mutants

Satoshi Kitamura, Fumio Matsuda, Takayuki Tohge, Keiko Yonekura-Sakakibara, Mami Yamazaki, Kazuki Saito, Issay Narumi

PLANT JOURNAL　Vol. 62　No. 4　p. 549-559　2010/05　Research paper (scientific journal)

Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis

Henning Redestig, Miyako Kusano, Atsushi Fukushima, Fumio Matsuda, Kazuki Saito, Masanori Arita

BMC Bioinformatics　Vol. 11　2010/04/29　Research paper (scientific journal)

AtMetExpress development: A phytochemical atlas of Arabidopsis development

Fumio Matsuda, Masami Y. Hirai, Eriko Sasaki, Kenji Akiyama, Keiko Yonekura-Sakakibara, Nicholas J. Provart, Tetsuya Sakurai, Yukihisa Shimada, Kazuki Saito

Plant Physiology　Vol. 152　No. 2　p. 566-578　2010/02　Research paper (scientific journal)

The effect of double over-expressions of two MYB genes on gene expression and flavonoid accumulation in Arabidopsis

Nakabayashi Ryo, Yonekura-Sakakibara Keiko, Matsuda Fumio, Tohge Takayuki, Kitajima Mariko, Takayama Hiromitsu, Yamazaki Mami, Saito Kazuki

Plant and Cell Physiology Supplement　Vol. 2010　p. 0868-0868　2010

MassBank: A public repository for sharing mass spectral data for life sciences

Hisayuki Horai, Masanori Arita, Shigehiko Kanaya, Yoshito Nihei, Tasuku Ikeda, Kazuhiro Suwa, Yuya Ojima, Kenichi Tanaka, Satoshi Tanaka, Ken Aoshima, Yoshiya Oda, Yuji Kakazu, Miyako Kusano, Takayuki Tohge, Fumio Matsuda, Yuji Sawada, Masami Yokota Hirai, Hiroki Nakanishi, Kazutaka Ikeda, Naoshige Akimoto, Takashi Maoka, Hiroki Takahashi, Takeshi Ara, Nozomu Sakurai, Hideyuki Suzuki, Daisuke Shibata, Steffen Neumann, Takashi Iida, Ken Tanaka, Kimito Funatsu, Fumito Matsuura, Tomoyoshi Soga, Ryo Taguchi, Kazuki Saito, Takaaki Nishioka

Journal of Mass Spectrometry　Vol. 45　No. 7　p. 703-714　2010　Research paper (scientific journal)

Metabolic profiling analysis of genetically modified rice seedlings that overproduce tryptophan reveals the occurrence of its inter-tissue translocation

Fumio Matsuda, Atsushi Ishihara, Kojiro Takanashi, Keiko Morino, Haruna Miyazawa, Kyo Wakasa, Hisashi Miyagawa

Plant Biotechnology　Vol. 27　No. 1　p. 17-27　2010　Research paper (scientific journal)

Expression of bacterial tyrosine ammonia-lyase creates a novel p-coumaric acid pathway in the biosynthesis of phenylpropanoids in Arabidopsis

Yasutaka Nishiyama, Choong-Soo Yun, Fumio Matsuda, Tadamasa Sasaki, Kazuki Saito, Yuzuru Tozawa

Planta　Vol. 232　No. 1　p. 209-218　2010　Research paper (scientific journal)

Evaluation of amino acid content and nutritional quality of transgenic soybean seeds with high-level tryptophan accumulation

Masao Ishimoto, Shaikh M. Rahman, Moemen S. Hanafy, Mutasim M. Khalafalla, Hany A. El-Shemy, Yumi Nakamoto, Yoichi Kita, Kojiro Takanashi, Fumio Matsuda, Yoshihiro Murano, Tomoko Funabashi, Hisashi Miyagawa, Kyo Wakasa

Molecular Breeding　Vol. 25　No. 2　p. 313-326　2010/01　Research paper (scientific journal)

Members of the LBD Family of Transcription Factors Repress Anthocyanin Synthesis and Affect Additional Nitrogen Responses in Arabidopsis

Grit Rubin, Takayuki Tohge, Fumio Matsuda, Kazuki Saito, Wolf-Ruediger Scheible

PLANT CELL　Vol. 21　No. 11　p. 3567-3584　2009/11

Assessment of metabolome annotation quality: A method for evaluating the false discovery rate of elemental composition searches

Fumio Matsuda, Yoko Shinbo, Akira Oikawa, Masami Yokota Hirai, Oliver Flehn, Shigehiko Kanaya, Kazuki Saito

PLoS ONE　Vol. 4　No. 10　2009/10/16　Research paper (scientific journal)

A Chloroplastic UDP-Glucose Pyrophosphorylase from Arabidopsis Is the Committed Enzyme for the First Step of Sulfolipid Biosynthesis

Okazaki Yozo, Shimojima Mie, Sawada Yuji, Toyooka Kiminori, Narisawa Tomoko, Mochida Keiichi, Tanaka Hironori, Matsuda Fumio, Hirai Akiko, Hirai Masami Yokota, Ohta Hiroyuki, Saito Kazuki

PLANT CELL　Vol. 21　No. 3　p. 892-909　2009/03　Research paper (scientific journal)

MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites

Fumio Matsuda, Keiko Yonekura-Sakakibara, Rie Niida, Takashi Kuromori, Kazuo Shinozaki, Kazuki Saito

Plant Journal　Vol. 57　No. 3　p. 555-577　2009/02　Research paper (scientific journal)

Functional Identification of a Novel Anthocyanin Glycosyltransferase Gene in Arabidopsis

Yonekura-Sakakibara Keiko, Inoue Eri, Matsuda Fumio, Wangwattana Bunyapa, Yamazaki Mami, Saito Kazuki

Plant and Cell Physiology Supplement　Vol. 2009　p. 0326-0326　2009

Visualization of metabolite identifier information

Matsuda Fumio, Redestig Henning, Sawada Yuji, Shinbo Yoko, Hirai Masami Yokota, Kanaya Shigehiko, Saito Kazuki

Plant Biotechnology　Vol. 26　No. 5　p. 479-483　2009

Rice metabolomics

Akira Oikawa, Fumio Matsuda, Miyako Kusano, Yozo Okazaki, Kazuki Saito

Rice　Vol. 1　No. 1　p. 63-71　2008/09

Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis

Keiko Yonekura-Sakakibara, Takayuki Tohge, Fumio Matsuda, Ryo Nakabayashi, Hiromitsu Takayama, Rie Niida, Akiko Watanabe-Takahashi, Eri Inoue, Kazuki Saito

Plant Cell　Vol. 20　No. 8　p. 2160-2176　2008/08　Research paper (scientific journal)

Mutation of a rice gene encoding a phenylalanine biosynthetic enzyme results in accumulation of phenylalanine and tryptophan

Tetsuya Yamada, Fumio Matsuda, Koji Kasai, Shuichi Fukuoka, Keisuke Kitamura, Yuzuru Tozawa, Hisashi Miyagawa, Kyo Wakasa

Plant Cell　Vol. 20　No. 5　p. 1316-1329　2008/05　Research paper (scientific journal)

The tryptophan pathway is involved in the defense responses of rice against pathogenic infection via serotonin production

Atsushi Ishihara, Yumi Hashimoto, Chihiro Tanaka, Joseph G. Dubouzet, Takahito Nakao, Fumio Matsuda, Takaaki Nishioka, Hisashi Miyagawa, Kyo Wakasa

Plant Journal　Vol. 54　No. 3　p. 481-495　2008/05　Research paper (scientific journal)

Present Status of Metabolome Analysis and Future Perspective : 2. Data Processing Technologies

MATSUDA Fumio, OIKAWA Akira, KUSANO Miyako, KIKUCHI Jun, SAITO Kazuki

化学と生物　Vol. 45　No. 12　p. 834-842　2007/12/01

Present Status of Metabolome Analysis and Future Perspective : 1. Sample Preparation, Measurement Technologies

MATSUDA Fumio, OIKAWA Akira, KUSANO Miyako, KIKUCHI Jun, SAITO Kazuki

化学と生物　Vol. 45　No. 11　p. 754-760　2007/11/01

Integrated metabolomic and transcriptomic analyses of high-tryptophan rice expressing a mutant anthranilate synthase alpha subunit

Joseph G. Dubouzet, Atsushi Ishihara, Fumio Matsuda, Hisashi Miyagawa, Hiroyoshi Iwata, Kyo Wakasa

Journal of Experimental Botany　Vol. 58　No. 12　p. 3309-3321　2007/10　Research paper (scientific journal)

Metabolomics for metabolically manipulated plants: Effects of tryptophan overproduction

Atsushi Ishihara, Fumio Matsuda, Hisashi Miyagawa, Kyo Wakasa

Metabolomics　Vol. 3　No. 3　p. 319-334　2007/09　Research paper (scientific journal)

Metabolic flux analysis in plants using dynamic labeling technique: Application to tryptophan biosynthesis in cultured rice cells

Fumio Matsuda, Kyo Wakasa, Hisashi Miyagawa

Phytochemistry　Vol. 68　No. 16-18　p. 2290-2301　2007/08　Research paper (scientific journal)

【最新プロテオミクス・メタボロミクス 質量分析の基礎からバイオ医薬への応用】 メタボローム解析 マススペクトロメトリーによる植物メタボローム解析

草野 都, 峠 隆之, 松田 史生, 岡咲 洋三, 及川 彰, 斉藤 和季

細胞工学　Vol. 別冊　No. プロテオミクス・メタボロミクス　p. 146-156　2007/07

Estimation of metabolic fluxes, expression levels and metabolite dynamics of a secondary metabolic pathway in potato using label pulse-feeding experiments combined with kinetic network modelling and simulation

Elmar Heinzle, Fumio Matsuda, Hisashi Miyagawa, Kyo Wakasa, Takaaki Nishioka

Plant Journal　Vol. 50　No. 1　p. 176-187　2007/04　Research paper (scientific journal)

High-level tryptophan accumulation in seeds of transgenic rice and its limited effects on agronomic traits and seed metabolite profile

Kyo Wakasa, Hisakazu Hasegawa, Hiroshi Nemoto, Fumio Matsuda, Haruna Miyazawa, Yuzuru Tozawa, Keiko Morino, Akira Komatsu, Tetsuya Yamada, Teruhiko Terakawa, Hisashi Miyagawa

Journal of Experimental Botany　Vol. 57　No. 12　p. 3069-3078　2006/09　Research paper (scientific journal)

Characterization of tryptophan-overproducing potato transgenic for a mutant rice anthranilate synthase α-subunit gene (OASA1D)

Fumio Matsuda, Tetsuya Yamada, Haruna Miyazawa, Hisashi Miyagawa, Kyo Wakasa

Planta　Vol. 222　No. 3　p. 535-545　2005/10　Research paper (scientific journal)

Quantification of indole-3-acetic acid and amino acid conjugates in rice by liquid chromatography-electrospray ionization-tandem mass spectrometry

Fumio Matsuda, Haruna Miyazawa, Kyo Wakasa, Hisashi Miyagawa

Bioscience, Biotechnology and Biochemistry　Vol. 69　No. 4　p. 778-783　2005/04　Research paper (scientific journal)

Metabolic flux analysis of the phenylpropanoid pathway in elicitor-treated potato tuber tissue

Fumio Matsuda, Keiko Morino, Rieko Ano, Masaki Kuzawa, Kyo Wakasa, Hisashi Miyagawa

Plant and Cell Physiology　Vol. 46　No. 3　p. 454-466　2005/03　Research paper (scientific journal)

Metabolic profiling of tryptophan-overproducing rice calli that express a feedback-insensitive α subunit of anthranilate synthase

Keiko Morino, Fumio Matsuda, Haruna Miyazawa, Akiko Sukegawa, Hisashi Miyagawa, Kyo Wakasa

Plant and Cell Physiology　Vol. 46　No. 3　p. 514-521　2005/03　Research paper (scientific journal)

In vitro biosynthesis of volicitin in Spodoptera litura

Naoko Yoshinaga, Nobuyoshi Morigaki, Fumio Matsuda, Ritsuo Nishida, Naoki Mori

Insect Biochemistry and Molecular Biology　Vol. 35　No. 2　p. 175-184　2005/02　Research paper (scientific journal)

Metabolism of avenanthramide phytoalexins in oats

Yozo Okazaki, Taishi Isobe, Yoichi Iwata, Tetsuya Matsukawa, Fumio Matsuda, Hisashi Miyagawa, Atsushi Ishihara, Takaaki Nishioka, Hajime Iwamura

Plant Journal　Vol. 39　No. 4　p. 560-572　2004/08　Research paper (scientific journal)

Determination of potato glycoalkaloids using high-pressure liquid chromatography-electrospray ionisation/mass spectrometry

Fumio Matsuda, Keiko Morino, Haruna Miyazawa, Masahiro Miyashita, Hisashi Miyagawa

Phytochemical Analysis　Vol. 15　No. 2　p. 121-124　2004/03　Research paper (scientific journal)

Metabolic flux analysis of the phenylpropanoid pathway in wound-healing potato tuber tissue using stable isotope-labeled tracer and LC-MS spectroscopy

F Matsuda, K Morino, M Miyashita, H Miyagawa

PLANT AND CELL PHYSIOLOGY　Vol. 44　No. 5　p. 510-517　2003/05　Research paper (scientific journal)

Metabolic flux analysis of phenylpropanoid pathway in wound-healing potato tuber tissue

F Matsuda, H Miyagawa

PLANT AND CELL PHYSIOLOGY　Vol. 44　p. S192-S192　2003

Involvement of reactive oxygen species in the induction of (S)-N-p-coumaroyloctopamine accumulation by beta-1,3-glucooligosaccharide elicitors in potato tuber tissues

F Matsuda, H Miyagawa, T Ueno

ZEITSCHRIFT FUR NATURFORSCHUNG C-A JOURNAL OF BIOSCIENCES　Vol. 56　No. 3-4　p. 228-234　2001/03　Research paper (scientific journal)

beta-1,3-glucooligosaccharide induced activation of four enzymes responsible for N-p-coumaroyloctopamine biosynthesis in potato (Solanum tuberosum cv.) tuber tissue

F Matsuda, H Miyagawa, T Ueno

ZEITSCHRIFT FUR NATURFORSCHUNG SECTION C-A JOURNAL OF BIOSCIENCES　Vol. 55　No. 5-6　p. 373-382　2000/05　Research paper (scientific journal)

Absolute structure of N-p-coumaroyloctopamine in elicitor-treated potato tuber tissue

F Matsuda, H Miyagawa, T Ueno

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY　Vol. 64　No. 3　p. 625-627　2000/03　Research paper (scientific journal)

Molecular Breeding of a Tryptophan-Fortified Rice via Homologous Recombination-Mediated Gene Targeting Based on Protein Engineering

Hiroaki Saika, Akira Oikawa, Fumio Matsuda, Haruko Onodera, Kazuki Saito, Senichi Toki

IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-ANIMAL　Vol. 46　p. S158-S159　1970/01