Tomokazu Shirai

Tomokazu Shirai

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Tomokazu Shirai

Tomokazu Shirai

Publications by authors named "Tomokazu Shirai"

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Construction of a Model Culture System of Human Colonic Microbiota to Detect Decreased Lachnospiraceae Abundance and Butyrogenesis in the Feces of Ulcerative Colitis Patients.

Biotechnol J 2019 Feb 21:e1800555. Epub 2019 Feb 21.

Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.

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http://dx.doi.org/10.1002/biot.201800555DOI Listing
February 2019

Designing artificial metabolic pathways, construction of target enzymes, and analysis of their function.

Curr Opin Biotechnol 2018 12 20;54:41-44. Epub 2018 Feb 20.

Biomass Engineering Research Division, Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.copbio.2018.01.021DOI Listing
December 2018

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

Biotechnol Bioeng 2017 12 17;114(12):2782-2793. Epub 2017 Aug 17.

Department of Bioinfomatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan.

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http://doi.wiley.com/10.1002/bit.26390
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http://dx.doi.org/10.1002/bit.26390DOI Listing
December 2017

Engineering a synthetic pathway for maleate in Escherichia coli.

Nat Commun 2017 10 27;8(1):1153. Epub 2017 Oct 27.

Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1038/s41467-017-01233-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5658364PMC
October 2017

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

Biosci Biotechnol Biochem 2017 Aug 16;81(8):1650-1656. Epub 2017 Jun 16.

a Graduate School of Science, Technology and Innovation, Kobe University , Kobe , Japan.

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http://dx.doi.org/10.1080/09168451.2017.1336922DOI Listing
August 2017

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

Bioresour Technol 2016 Sep 11;216:830-7. Epub 2016 Jun 11.

Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501, Japan; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.biortech.2016.06.029DOI Listing
September 2016

Anionic metabolite biosynthesis enhanced by potassium under dark, anaerobic conditions in cyanobacteria.

Sci Rep 2016 08 31;6:32354. Epub 2016 Aug 31.

School of Agriculture, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan.

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http://dx.doi.org/10.1038/srep32354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5006033PMC
August 2016

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

PLoS One 2015 17;10(6):e0128417. Epub 2015 Jun 17.

Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Rokkodaicho, Nada-ku, Kobe, Hyogo, Japan; RIKEN Biomass Engineering Program, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0128417PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4470627PMC
March 2016

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

PLoS One 2015 21;10(5):e0125488. Epub 2015 May 21.

Biomass Engineering Program, RIKEN, Yokohama, Kanagawa, Japan; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0125488PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4440718PMC
February 2016

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

Biotechnol Biofuels 2016 2;9:27. Epub 2016 Feb 2.

Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Hyogo Kobe, 657-8501 Japan ; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Kanagawa Yokohama, 230-0045 Japan.

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http://dx.doi.org/10.1186/s13068-016-0427-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4736640PMC
February 2016

Metabolic design of a platform Escherichia coli strain producing various chorismate derivatives.

Metab Eng 2016 Jan 3;33:119-129. Epub 2015 Dec 3.

Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.ymben.2015.11.007DOI Listing
January 2016

Designing intracellular metabolism for production of target compounds by introducing a heterologous metabolic reaction based on a Synechosystis sp. 6803 genome-scale model.

Microb Cell Fact 2016 Jan 18;15:13. Epub 2016 Jan 18.

RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1186/s12934-016-0416-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4717628PMC
January 2016

Alteration of cyanobacterial sugar and amino acid metabolism by overexpression hik8, encoding a KaiC-associated histidine kinase.

Environ Microbiol 2015 Jul 27;17(7):2430-40. Epub 2015 Jan 27.

RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1111/1462-2920.12715DOI Listing
July 2015

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

Biotechnol Biofuels 2015 18;8:88. Epub 2015 Jun 18.

RIKEN Biomass Engineering Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan ; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, Hyogo 657-8501 Japan.

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http://dx.doi.org/10.1186/s13068-015-0273-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4476084PMC
June 2015

Molecular mechanisms and metabolic engineering of glutamate overproduction in Corynebacterium glutamicum.

Subcell Biochem 2012 ;64:261-81

Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan.

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http://dx.doi.org/10.1007/978-94-007-5055-5_13DOI Listing
September 2014

Capillary electrophoresis-mass spectrometry reveals the distribution of carbon metabolites during nitrogen starvation in Synechocystis sp. PCC 6803.

Environ Microbiol 2014 Feb 25;16(2):512-24. Epub 2013 Jun 25.

RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.

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http://dx.doi.org/10.1111/1462-2920.12170DOI Listing
February 2014

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

J Biosci Bioeng 2013 Sep 4;116(3):333-6. Epub 2013 May 4.

Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan.

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http://dx.doi.org/10.1016/j.jbiosc.2013.03.020DOI Listing
September 2013

Regulation of central carbon metabolism in Saccharomyces cerevisiae by metabolic inhibitors.

J Biosci Bioeng 2013 Jul 26;116(1):59-64. Epub 2013 Feb 26.

Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan.

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http://dx.doi.org/10.1016/j.jbiosc.2013.01.018DOI Listing
July 2013

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

Appl Microbiol Biotechnol 2013 Apr 7;97(8):3569-77. Epub 2012 Dec 7.

Biomass Engineering Program, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1007/s00253-012-4597-8DOI Listing
April 2013

Investigating the effects of perturbations to pgi and eno gene expression on central carbon metabolism in Escherichia coli using (13)C metabolic flux analysis.

Microb Cell Fact 2012 Jun 21;11:87. Epub 2012 Jun 21.

Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1186/1475-2859-11-87DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3778843PMC
June 2012

Evaluating (13)C enrichment data of free amino acids for precise metabolic flux analysis.

Biotechnol J 2011 Nov;6(11):1377-87

Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan.

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http://dx.doi.org/10.1002/biot.201000446DOI Listing
November 2011

Identification of a gene encoding a transporter essential for utilization of C4 dicarboxylates in Corynebacterium glutamicum.

Appl Environ Microbiol 2008 Sep 27;74(17):5290-6. Epub 2008 Jun 27.

Research Institute of Innovative Technology for the Earth, 9-2 Kizugawadai, Kizugawa, Kyoto 619-0292, Japan.

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http://dx.doi.org/10.1128/AEM.00832-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2546659PMC
September 2008

Group 2 sigma factor SigB of Corynebacterium glutamicum positively regulates glucose metabolism under conditions of oxygen deprivation.

Appl Environ Microbiol 2008 Aug 20;74(16):5146-52. Epub 2008 Jun 20.

Research Institute of Innovative Technology for the Earth, 9-2 Kizugawadai, Kizugawa, Kyoto 619-0292, Japan.

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http://dx.doi.org/10.1128/AEM.00944-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2519270PMC
August 2008

Distinct roles of two anaplerotic pathways in glutamate production induced by biotin limitation in Corynebacterium glutamicum.

J Biosci Bioeng 2008 Jul;106(1):51-8

Department of Bioengineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan.

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http://dx.doi.org/10.1263/jbb.106.51DOI Listing
July 2008

Precise metabolic flux analysis of coryneform bacteria by gas chromatography-mass spectrometry and verification by nuclear magnetic resonance.

J Biosci Bioeng 2006 Nov;102(5):413-24

Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1263/jbb.102.413DOI Listing
November 2006

Comparative study of flux redistribution of metabolic pathway in glutamate production by two coryneform bacteria.

Metab Eng 2005 Mar;7(2):59-69

Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.

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http://dx.doi.org/10.1016/j.ymben.2004.10.001DOI Listing
March 2005