Research Topics
Genomes and Genes | Tomoyoshi SogaSummaryAffiliation: Keio University Country: Japan Publications
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Publications
Capillary electrophoresis method for the analysis of inorganic anions, organic acids, amino acids, nucleotides, carbohydrates and other anionic compoundsT Soga
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
Electrophoresis 22:3418-25. 2001..This method is simple and universal for anion analysis, and could be readily applied to the simultaneous determination of anionic compounds. In this work, it was used to identify and quantify important anions in sea urchin and sake...- Differential metabolomics reveals ophthalmic acid as an oxidative stress biomarker indicating hepatic glutathione consumptionTomoyoshi Soga
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0017, Japan
J Biol Chem 281:16768-76. 2006..Our method can thus pinpoint specific metabolite changes and provide insights into the perturbation of metabolic pathways on a large scale and serve as a powerful new tool for discovering low molecular weight biomarkers... 
Serum metabolomics reveals γ-glutamyl dipeptides as biomarkers for discrimination among different forms of liver diseaseTomoyoshi Soga
Institute for Advanced Biosciences, Keio University, Tsuruoka 997 0052, Japan
J Hepatol 55:896-905. 2011..We applied a metabolome profiling approach to serum samples obtained from patients with different liver diseases, to discover noninvasive and reliable biomarkers for rapid-screening diagnosis of liver diseases...- Metabolomic profiling of anionic metabolites by capillary electrophoresis mass spectrometryTomoyoshi Soga
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0052, Japan
Anal Chem 81:6165-74. 2009..8 and 24 fmol) at a signal-to-noise ratio of 3. This method is quantitative, sensitive, and robust, and its utility was demonstrated by the analysis of the metabolites in the central metabolic pathways extracted from mouse liver... - Analysis of nucleotides by pressure-assisted capillary electrophoresis-mass spectrometry using silanol mask techniqueTomoyoshi Soga
Institute for Advanced Biosciences, Keio University, Kakuganji, Tsuruoka, Yamagata 997 0052, Japan
J Chromatogr A 1159:125-33. 2007..The methodology was used to suggest that pfkA is the main functional enzyme... - Qualitative and quantitative analysis of amino acids by capillary electrophoresis-electrospray ionization-tandem mass spectrometryTomoyoshi Soga
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
Electrophoresis 25:1964-72. 2004..The power of the method was demonstrated by analyzing amino acids in human urine... - Quantitative metabolome analysis using capillary electrophoresis mass spectrometryTomoyoshi Soga
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0017, Japan
J Proteome Res 2:488-94. 2003..subtilis sporulation... - Pressure-assisted capillary electrophoresis electrospray ionization mass spectrometry for analysis of multivalent anionsTomoyoshi Soga
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0017, Japan
Anal Chem 74:6224-9. 2002..The utility of the method was demonstrated by analysis of citrate isomers, nucleotides, dinucleotides, and CoA compounds extracted from Bacillus subtilis cells... - Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometryTomoyoshi Soga
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
Anal Chem 74:2233-9. 2002..This method was applied to the comprehensive analysis of metabolic intermediates extracted from Bacillus subtilis, and 27 anionic metabolites could be directly detected and quantified... 
Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolismKenji Nakahigashi
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0017, Japan
Mol Syst Biol 5:306. 2009..The emergence of an alternative pathway not requiring any changes in gene expression, but rather relying on the accumulation of an intermediate metabolite may be a novel mechanism mediating the robustness of these metabolic networks...- Time-resolved metabolomics reveals metabolic modulation in rice foliageShigeru Sato
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
BMC Syst Biol 2:51. 2008..However, the results were unsatisfactory and effective data-mining techniques that apply appropriate comprehensive datasets are needed... - P-BOSS: a new filtering method for treasure hunting in metabolomicsMineo Morohashi
Human Metabolome Technologies, Inc, Yamagata 997 0052, Japan
J Chromatogr A 1159:142-8. 2007..As the result, P-BOSS showed remarkably superior performance, reducing 65% of all peaks, while leaving significant peaks... - Multiple high-throughput analyses monitor the response of E. coli to perturbationsNobuyoshi Ishii
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0017, Japan
Science 316:593-7. 2007..coli actively regulated enzyme levels to maintain a stable metabolic state in response to changes in growth rate. E. coli thus seems to use complementary strategies that result in a metabolic network robust against perturbations... - Direct measurement of isotopomer of intracellular metabolites using capillary electrophoresis time-of-flight mass spectrometry for efficient metabolic flux analysisYoshihiro Toya
Institute for Advanced Biosciences, Keio University, 403 1 Nipponkoku, Daihoji, Tsuruoka, Yamagata 997 0017, Japan
J Chromatogr A 1159:134-41. 2007..However, our CE-TOFMS method facilitates high-throughput flux analysis without requiring complicated sample preparation such as hydrolysis of proteins and derivatization of amino acids... - Disruption of HIF-1α in hepatocytes impairs glucose metabolism in diet-induced obesity miceDaigo Ochiai
Department of Obstetrics and Gynecology, School of Medicine, Keio University, Japan
Biochem Biophys Res Commun 415:445-9. 2011..These findings suggest that HIF-1 in hepatocytes plays protective roles against the progression of diabetes mellitus... - Prediction of liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome using artificial neural networksKosaku Shinoda
Human Metabolome Technologies, Inc, Tsuruoka, Yamagata 997-0052, Japan
J Proteome Res 5:3312-7. 2006..Our approach is useful for the proteome-wide characterization of peptides and the identification of unknown peptide peaks obtained in proteome analysis... - 13C-metabolic flux analysis for batch culture of Escherichia coli and its Pyk and Pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolitesYoshihiro Toya
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
Biotechnol Prog 26:975-92. 2010..Furthermore, ATP production was the primary objective function in the Pgi mutant. This study demonstrates how cells adjust their metabolism in response to environmental changes and/or genetic perturbations in the batch cultivation... - In silico modeling and metabolome analysis of long-stored erythrocytes to improve blood storage methodsTaiko Nishino
Institute for Advanced Biosciences, Keio University, 403 1, Daihoji, Tsuruoka, Yamagata 997 0017, Japan
J Biotechnol 144:212-23. 2009..Alterations in the metabolic intermediate concentrations after long storage were qualitatively predicted by the model. Finally, through further systematic analysis, we also discuss the usability of our model... - Depiction of metabolome changes in histidine-starved Escherichia coli by CE-TOFMSYoshiaki Ohashi
Human Metabolome Technologies, Inc, Tsuruoka, Yamagata 997 0052, Japan
Mol Biosyst 4:135-47. 2008..Simultaneously, disciplined responses were observed in the glycolysis, tricarboxylic acid cycle, and amino acid and nucleotide biosynthesis pathways as regulated by amino acid starvation... - Metabolomics approach for enzyme discoveryNatsumi Saito
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997 0017 Japan
J Proteome Res 5:1979-87. 2006..Our approach should be broadly applicable and useful for enzyme discovery in any system... - Changes in the charged metabolite and sugar profiles of pasteurized and unpasteurized Japanese sake with storageMasahiro Sugimoto
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
J Agric Food Chem 60:2586-93. 2012..Rather than stabilizing the sake metabolite profile during storage, pasteurization results in characteristic changes compared to unpasteurized sake... 
MathDAMP: a package for differential analysis of metabolite profilesRichard Baran
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0017, Japan
BMC Bioinformatics 7:530. 2006..The task remains difficult, given the datasets' size, complexity, and common shifts in migration (elution/retention) times between samples analyzed by hyphenated mass spectrometry methods...- Metabolomic profiles and sensory attributes of edamame under various storage duration and temperature conditionsMasahiro Sugimoto
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
J Agric Food Chem 58:8418-25. 2010..In particular, changes in amino acid levels were related to sensory attributes. The downstream metabolites of shikimate as well as phospholipids and gamma-aminobutyric acid increased with increasing storage temperatures... - Visualization of three-way comparisons of omics dataRichard Baran
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0017, Japan
BMC Bioinformatics 8:72. 2007..However, the current color-codings limit the visualizations to single datasets or pairwise comparisons... - GTP-dependent RNA 3'-terminal phosphate cyclase from the hyperthermophilic archaeon Pyrococcus furiosusAsako Sato
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
Genes Cells 16:1190-9. 2011..furiosus). The possible roles of Pf-Rtc and the importance of terminal phosphate structures in RNA are discussed... - Capillary electrophoresis-mass spectrometry for metabolomicsTomoyoshi Soga
Institute for Advanced Biosciences, Keio University and Human Metabolome Technologies Inc, Yamagata, Japan
Methods Mol Biol 358:129-37. 2007..This chapter highlights detailed practical procedures for using this technology... - Metabolite profiling reveals YihU as a novel hydroxybutyrate dehydrogenase for alternative succinic semialdehyde metabolism in Escherichia coliNatsumi Saito
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997 0017, Japan
J Biol Chem 284:16442-51. 2009..These findings suggest that YihU is a novel gamma-hydroxybutyrate dehydrogenase involved in the metabolism of succinic semialdehyde, and other potentially toxic intermediates that may accumulate under stress conditions in E. coli... - Unveiling cellular biochemical reactions via metabolomics-driven approachesNatsumi Saito
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0017, Japan
Curr Opin Microbiol 13:358-62. 2010.... - Prediction of metabolite identity from accurate mass, migration time prediction and isotopic pattern information in CE-TOFMS dataMasahiro Sugimoto
Institute for Advanced Biosciences, Keio University, Yamagata, Japan
Electrophoresis 31:2311-8. 2010..9% of the peaks were assigned metabolite names by matching with the standard library alone, the proportion increased to 52.2%. The proposed methodology increases the value of metabolomic data sets obtained from CE-TOFMS profiling... - Model-based definition of population heterogeneity and its effects on metabolism in sporulating Bacillus subtilisMineo Morohashi
Human Metabolome Technologies, Inc, Tsuruoka, Yamagata 997 0052, Japan
J Biochem 142:183-91. 2007..The results imply that careful consideration must be made in the interpretation of data obtained from cells yielding population heterogeneity... - Large-scale prediction of cationic metabolite identity and migration time in capillary electrophoresis mass spectrometry using artificial neural networksMasahiro Sugimoto
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
Anal Chem 77:78-84. 2005..0% of cases. We suggest that this approach can be used for the prediction of the migration time of any cation and that it represents a powerful method for the identification of uncharacterized CE-MS peaks in metabolome analysis... - Metabolomic anatomy of an animal model revealing homeostatic imbalances in dyslipidaemiaTakushi Ooga
Human Metabolome Technologies, Inc, 246 2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997 0052, Japan
Mol Biosyst 7:1217-23. 2011..These changes were considered to be due to the pleiotropic action of statin, including antioxidant effects, rather than its main inhibitory action on cholesterol biosynthesis... - Quantitative metabolome profiling of colon and stomach cancer microenvironment by capillary electrophoresis time-of-flight mass spectrometryAkiyoshi Hirayama
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan and National Cancer Center Hospital East, Kashiwa, Chiba, Japan
Cancer Res 69:4918-25. 2009.... - Hypotaurine is an Energy-Saving Hepatoprotective Compound against Ischemia-Reperfusion Injury of the Rat LiverTadayuki Sakuragawa
Department of Biochemistry and Integrative Medical Biology, School of Medicine, Keio University, Tokyo 160 8582, Japan
J Clin Biochem Nutr 46:126-34. 2010..These results suggest that taurine serves as a surrogate marker for ischemia-reperfusion indicating effectiveness of hypotaurine as an energy-saving hepatoprotective amino acid... - HybGFS: a hybrid method for genome-fingerprint scanningKosaku Shinoda
Human Metabolome Technologies, Inc, Tsuruoka, Yamagata, 997 0052, Japan
BMC Bioinformatics 7:479. 2006..Thus, there is a need for novel high-throughput protein-identification methods that are independent of existing predefined protein databases... - Application of capillary electrophoresis-mass spectrometry to synthetic in vitro glycolysis studiesAya Itoh
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
Electrophoresis 25:1996-2002. 2004..This approach is likely useful for the synthesis of natural products requiring complex sequential biocatalytic reactions... - Microelectrospray interface with coaxial sheath flow for high-resolution capillary electrophoresis/mass spectrometry separationMasahiko Hashimoto
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0017, Japan
Rapid Commun Mass Spectrom 21:3579-84. 2007..The interface also provides higher separation qualities and improved detection sensitivities compared with a conventional ion spray (IS) interface... - Roles of hemoglobin Allostery in hypoxia-induced metabolic alterations in erythrocytes: simulation and its verification by metabolome analysisAyako Kinoshita
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0017, Japan
J Biol Chem 282:10731-41. 2007..These results suggest that Hb allostery in erythrocytes serves as an O(2)-sensing trigger that drives glycolytic acceleration to stabilize intracellular energetics and promote the ability to release O(2) from the cells... - Polymer entrapment in polymerized silicate for preparing highly stable capillary coatings for CE and CE-MSMaria Rowena N Monton
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0017, Japan
Anal Chem 79:7838-44. 2007..Thus, two novel types of highly stable coated capillaries, one with anodic EOF and the other cathodic, were developed... - Metabolome analysis by capillary electrophoresis-mass spectrometryMaria Rowena N Monton
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0017, Japan
J Chromatogr A 1168:237-46; discussion 236. 2007..It also discusses how some of the key features of CE-MS were exploited in selected metabolomic applications... - Cystathionine beta-synthase as a carbon monoxide-sensitive regulator of bile excretionTsunehiro Shintani
Department of Biochemistry and Integrative Medical Biology, Department of Surgery, School of Medicine, Keio University, Tokyo, Japan
Hepatology 49:141-50. 2009.... - Metabolic profiling reveals new serum biomarkers for differentiating diabetic nephropathyAkiyoshi Hirayama
Institute for Advanced Biosciences, Keio University, 246 2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997 0052, Japan
Anal Bioanal Chem 404:3101-9. 2012..Combination of serum metabolomics with multivariate analyses enabled accurate discrimination of DN patients. The results suggest that capillary electrophoresis-mass spectrometry based metabolome analysis could be used for DN diagnosis... - Metabolomic profiling rationalized pyruvate efficacy in cybrid cells harboring MELAS mitochondrial DNA mutationsKenjiro Kami
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0017, Japan Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252 8520, Japan
Mitochondrion 12:644-53. 2012.... - Amino acid analysis by capillary electrophoresis-mass spectrometryAkiyoshi Hirayama
Institute for Advanced Biosciences, Keio University, Kakuganji, Tsuruoka, Yamagata, Japan
Methods Mol Biol 828:77-82. 2012..This method is simple, rapid, and selective and could be readily applied to the analysis of free amino acids in various samples... - Correlation between sensory evaluation scores of Japanese sake and metabolome profilesMasahiro Sugimoto
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0052, Japan
J Agric Food Chem 58:374-83. 2010..The methodology demonstrated here carries great potential for predicting the relevant parameters and quantitative relationships between charged metabolites and sensory evaluation in Japanese refined sake... - Metabolomic identification of the target of the filopodia protrusion inhibitor glucopiericidin AMitsuhiro Kitagawa
Department of Biosciences and Informatics, Keio University, Kohokuku, Yokohama, Kanagawa, Japan
Chem Biol 17:989-98. 2010..Our results represent a challenge of molecular target identification using metabolomic analysis... - MMMDB: Mouse Multiple Tissue Metabolome DatabaseMasahiro Sugimoto
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0017, Japan
Nucleic Acids Res 40:D809-14. 2012..Thus, MMMDB allows newly measured data to be compared with the other data in the database. MMMDB is available at: http://mmmdb.iab.keio.ac.jp... - Simultaneous determination of the main metabolites in rice leaves using capillary electrophoresis mass spectrometry and capillary electrophoresis diode array detectionShigeru Sato
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
Plant J 40:151-63. 2004.... - Sheathless capillary electrophoresis-mass spectrometry with a high-sensitivity porous sprayer for cationic metabolome analysisAkiyoshi Hirayama
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0052, Japan
Analyst 137:5026-33. 2012..More than 180 successive runs could be conducted without any problems, and only the BGE needed to be changed... - Positive autoregulation delays the expression phase of mammalian clock gene Per2Yukino Ogawa
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
PLoS ONE 6:e18663. 2011..These results indicate that the Per2 positive feedback regulation is a significant factor responsible for generating the phase difference between Per1 and Per2 gene expression... - HIF-1alpha is necessary to support gluconeogenesis during liver regenerationToshihide Tajima
Department of Obstetrics and Gynecology, Keio University, Shinjuku ku, Tokyo, Japan
Biochem Biophys Res Commun 387:789-94. 2009..In conclusion, these findings provide evidence for roles of HIF-1alpha in the regulation of gluconeogenesis under liver regeneration... - Biochemical and functional characterization of novel NADH kinase in the enteric protozoan parasite Entamoeba histolyticaGhulam Jeelani
Department of Parasitology, National Institute of Infectious Diseases, 1 23 1 Toyama, Shinjuku, Tokyo 162 8640, Japan Department of Biochemistry and Integrative Medical Biology, School of Medicine, Keio University, Shinjuku, Tokyo 160 8582, Japan
Biochimie 95:309-19. 2013..These data, together with the essentially of NAD(H) kinase gene, underscore its significance as an NADP(H)-producing enzyme in this organism, and should help in designing of drugs targeting this enzyme... - A yeast metabolite extraction protocol optimised for time-series analysesKalesh Sasidharan
Institute for Advanced Biosciences, Keio University, Nipponkoku 403 1, Daihouji, Tsuruoka City, Yamagata, Japan
PLoS ONE 7:e44283. 2012..Cell weight, number and size distribution was used to calculate metabolites to an attomol/cell level. We apply this method to samples obtained from the respiratory oscillation that occurs when yeast are grown continuously... - MassBank: a public repository for sharing mass spectral data for life sciencesHisayuki Horai
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0035, Japan
J Mass Spectrom 45:703-14. 2010..6. Thus, MassBank is useful for the identification of chemical compounds and the publication of experimental data... - Evaluation of metabolic alteration in transgenic rice overexpressing dihydroflavonol-4-reductaseHideyuki Takahashi
Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
Ann Bot (Lond) 98:819-25. 2006..CONCLUSIONS: The overexpression of YK1 (DFR) was associated with slight changes in the amounts of several metabolites analysed in whole plants, whilst glutathione derivatives were substantially increased in suspension-cultured cells... - [Metabolomics: system for genome interacting with environments through chemical substances]Takaaki Nishioka
Tanpakushitsu Kakusan Koso 50:2198-203. 2005 - Conductivity detection in capillary zone electrophoresis: inspection by PeakMasterMichal Jaros
Faculty of Science, Charles University, CZ-128 040 Prague 2, Czech Republic
Electrophoresis 26:1948-53. 2005..It is shown that the terms direct and indirect conductivity detection are misleading and should not be used... - [Analytical system for metabolomics]Hideyuki Suzuki
Tanpakushitsu Kakusan Koso 49:1893-9. 2004 - Development of bottom-fermenting saccharomyces strains that produce high SO2 levels, using integrated metabolome and transcriptome analysisSatoshi Yoshida
Central Laboratories for Frontier Technology, Kirin Holdings Co, Ltd, 1 13 5 Fukuura Kanazawa ku, Yokohama shi, Kanagawa 236 0004, Japan
Appl Environ Microbiol 74:2787-96. 2008..One promising mutant produced much higher levels of SO(2) than the parent but produced parental levels of H(2)S...