Original Papers

• 1.

  Matsumoto M, Kunisawa A, Hattori T, Kawana S, Kitada Y, Tamada H, Kawano S, Hayakawa Y, Iida J, Fukusaki E.
  Free D-amino acids produced by commensal bacteria in the colonic lumen.
  Sci Rep. 2018 Dec 17;8(1):17915.

• 2.

  Konya Y, Taniguchi M, Furuno M, Nakano Y, Tanaka N, Fukusaki E.
  Mechanistic study on the high-selectivity enantioseparation of amino acids using a chiral crown ether-bonded stationary phase and acidic, highly organic mobile phase by liquid chromatography/time-of-flight mass spectrometry.
  J Chromatogr A. 2018 Nov 30;1578:35-44.

• 3.

  K Yamamoto, A Amalia, SP Putri, E Fukusaki, FM Dwivany
  Expression Analysis of 1-aminocyclopropane-1-carboxylic Acid Oxidase Genes in Chitosan-Coated Banana
  HAYATI Journal of Biosciences 25 (1), 18-24

• 4.

  Pontrelli S, Fricke RCB, Teoh ST, Laviña WA, Putri SP, Fitz-Gibbon S, Chung M, Pellegrini M, Fukusaki E, Liao JC.
  Metabolic repair through emergence of new pathways in Escherichia coli.
  Nat Chem Biol. 2018 Nov;14(11):1005-1009.

• 5.

  Pontrelli S, Fricke RCB, Sakurai SSM, Putri SP, Fitz-Gibbon S, Chung M, Wu HY, Chen YJ, Pellegrini M, Fukusaki E, Liao JC.
  Directed strain evolution restructures metabolism for 1-butanol production in minimal media.
  Metab Eng. 2018 Aug 11;49:153-163.

• 6.

  Enomoto Y, An PN, Yamaguchi M, Fukusaki E, Shimma S.
  Mass spectrometric imaging of GABA in the Drosophila melanogaster adult head.
  Anal Sci. 2018 Sep 10;34(9):1055-1059.

• 7.

  Takahashi M, Izumi Y, Iwahashi F, Nakayama Y, Iwakoshi M, Nakao M, Yamato S, Fukusaki E, Bamba T.
  Highly Accurate Detection and Identification Methodology of Xenobiotic Metabolites Using Stable Isotope Labeling, Data Mining Techniques, and Time-Dependent Profiling Based on LC/HRMS/MS.
  Anal Chem. 2018 Aug 7;90(15):9068-9076.

• 8.

  Fathima AM, Chuang D, Laviña WA, Liao J, Putri SP, Fukusaki E.
  Iterative cycle of widely targeted metabolic profiling for the improvement of 1-butanol titer and productivity in Synechococcus elongatus.
  Biotechnol Biofuels. 2018 Jul 9;11:188.

• 9.

  Sastia Prama Putri, Yasumune Nakayama, Claire Shen, Shingo Noguchi, Katsuaki Nitta, Takeshi Bamba, Sammy Pontrelli, James Liao, Eiichiro Fukusaki
  Identifying metabolic elements that contribute to productivity of 1-propanol bioproduction using metabolomic analysis
  Metabolomics 14 (7), 96

• 10.

  Ohtsu S, Yamaguchi M, Nishiwaki H, Fukusaki E, Shimma S.
  Development of a visualization method for imidacloprid in Drosophila melanogaster via imaging mass spectrometry.
  Anal Sci. 2018 Sep 10;34(9):991-996.

• 11.

  Miyoshi K, Enomoto Y, Fukusaki E, Shimma S.
  Visualization of Asparaptine in Asparagus (Asparagus officinalis) using MALDI-IMS.
  Anal Sci. 2018 Sep 10;34(9):997-1001.

• 12.

  Nagao H, Nishizawa H, Tanaka Y, Fukata T, Mizushima T, Furuno M, Bamba T, Tsushima Y, Fujishima Y, Kita S, Funahashi T, Maeda N, Mori M, Fukusaki E, Shimomura I.
  Hypoxanthine Secretion from Human Adipose Tissue and its Increase in Hypoxia.
  Obesity (Silver Spring). 2018 Jul;26(7):1168-1178.

• 13.

  Kadar AD, Aditiawati P, Astawan M, Putri SP, Fukusaki E.
  Gas chromatography coupled with mass spectrometry-based metabolomics for the classification of tempe from different regions and production processes in Indonesia.
  J Biosci Bioeng. 2018 Sep;126(3):411-416.

• 14.

  Imura M, Iwakiri R, Bamba T, Fukusaki E.
  Metabolomics approach to reduce the Crabtree effect in continuous culture of Saccharomyces cerevisiae.
  J Biosci Bioeng. 2018 Aug;126(2):183-188.

• 15.

  Obata Y, Kita S, Koyama Y, Fukuda S, Takeda H, Takahashi M, Fujishima Y, Nagao H, Masuda S, Tanaka Y, Nakamura Y, Nishizawa H, Funahashi T, Ranscht B, Izumi Y, Bamba T, Fukusaki E, Hanayama R, Shimada S, Maeda N, Shimomura I.
  Adiponectin/T-cadherin system enhances exosome biogenesis and decreases cellular ceramides by exosomal release.
  JCI Insight. 2018 Apr 19;3(8). pii: 99680.

• 16.

  Ohnishi M, Anegawa A, Sugiyama Y, Harada K, Oikawa A, Nakayama Y, Matsuda F, Nakamura Y, Sasaki R, Shichijo C, Hatcher PG, Fukaki H, Kanaya S, Aoki K, Yamazaki M, Fukusaki E, Saito K, Mimura T.
  Molecular Components of Arabidopsis Intact Vacuoles Clarified with Metabolomic and Proteomic Analyses.
  Plant Cell Physiol. 2018 Jul 1;59(7):1353-1362.

• 17.

  Harada R, Yuzuki M, Ito K, Shiga K, Bamba T, Fukusaki E.
  Microbe participation in aroma production during soy sauce fermentation.
  J Biosci Bioeng. 2018 Jan 20. pii: S1389-1723(17)31003-4.

• 18.

  Takeuchi Y, Nakayama Y, Fukusaki E, Irino Y.
  Glutamate production from ammonia via glutamate dehydrogenase 2 activity supports cancer cell proliferation under glutamine depletion.
  Biochem Biophys Res Commun. 2018 Jan 1;495(1):761-767.

• 19.

  Parijadi AAR, Putri SP, Ridwani S, Dwivany FM, Fukusaki E.
  Metabolic profiling of Garcinia mangostana (mangosteen) based on ripening stages.
  J Biosci Bioeng. 2018 Feb;125(2):238-244.

• 20.

  Hatanaka H, Mitsunaga H, Fukusaki E.
  Inhibition of Saccharomyces cerevisiae growth by simultaneous uptake of glucose and maltose.
  J Biosci Bioeng. 2018 Jan;125(1):52-58.

Original Papers

• 1.

  Kim, M.-H., Matsubara, Y., Fujinaga, Y. and Kino-oka, M.
  A simple and robust method for culturing human induced pluripotent stem cells in an undifferentiated state using botulinum haemagglutinin.
  Biotechnol. J. Vol.13, 1700384.

• 2.

  Kagihiro, M., Fukumori, K., Aoki, T., Ungkulpasvich, U., Mizutani, M., Viravaidya-Pasuwat, K. and Kino-oka, M.
  Kinetic analysis of cell decay during the filling process:application to lot size determination in manufacturing systems for human induced pluripotent and mesenchymal stem cells.
  Biochem. Eng. J. Vol.131, pp.31–38

• 3.

  Wongin, S., Waikakul, S., Chotiyarnwong, P., Siriwatwechakul, W., Kino-oka, M., Kim, M.-H. and Viravaidya-Pasuwat, K.
  Maintenance of human chondrogenic phenotype on a dendrimer-immobilized surface for an application of cell sheet engineering.
  BMC Biotechnology. Vol.18, article 14

• 4.

  Nurhayati, R.,W., Ojima, Y., Dohda, T. and Kino-oka M.
  Large-scale culture of a megakaryocytic progenitor cell line with a single-use bioreactor system.
  Biotechnol. Prog. Vol.34, pp.362–369

• 5.

  C, Nath, S, Tokura, T., Kim, M.-H. and Kino-oka, M.
  Botulinum hemagglutinin–mediated in situ break–up of human induced pluripotent stem cell aggregates for high–density suspension culture.
  Biotechnol. Bioeng. Vol.115, pp.910-920.

• 6.

  Yamamoto, T., Yano M., Okano, Y. and Kino-oka, M.
  Numerical investigation for the movement of cell colonies in bioreactors: stirring and orbital shaking tanks.
  J. Chem. Eng. Jpn. Vol.51, pp. 423–430

• 7.

  Kato, Y., Kim, M.-H. and Kino-oka M.
  Comparison of growth kinetics between static and dynamic cultures of human induced pluripotent stem cells.
  J. Biosci. Bioeng. Vol.125, pp. 736–740

• 8.

  Kikuchi, T., Kino-oka, M., Wada M., Kobayashi, T., Kato M, Takeda, S., Kubo, H., Ogawa T., Sunayama, H., Tanimoto, K., Mizutani, M., Shimizu, T. and Okano T.
  A Novel, flexible and automated manufacturing facility for cell-based health care products: tissue factory.
  Regenerative Therapy. Vol.9 pp.89-99

• 9.

  Chihara, R., Kitajima, H., Ogawa, Y., Nakamura, H., Tsutsui, S., Mizutani, M., Kino-oka, M. and Ezoe, S.
  Effects of residual H2O2 on the growth of MSCs after decontamination.
  Regenerative Therapy. Vol.9, pp.111-115

Reviews

• 1.

  Kim, M.-H. and Kino-oka, M.
  Bioprocessing strategies for pluripotent stem cells based on waddington's epigenetic landscape.
  Trends Biotechnol. Vol.36, pp.89-104.

Original Papers

• 1.

  Kinoshita, M., Furukawa, Y., Uchiyama, S., Imada, K., Namba, K., Minamino, T.
  Insight into adaptive remodeling of the rotor ring complex of the bacterial flagellar motor.
  Biochem. Biophys. Res. Comm. 496, 12-17.

• 2.

  Kim, R., Kanamaru, S., Mikawa, T., Prevost, C., Ishii, K., Ito, K., Uchiyama, S., Oda, M., Iwasaki, H., Kim, S. K., Takahashi, M.
  RecA requires two molecules of Mg2+ ions for its optimal strand exchange activity in vitro.
  Nucleic Acids Research, 46, 2548-2559.

• 3.

  Zhan, Y., Ogata, K., Kojima, T., Koide, T., Ishii, K., Mashiko, T., Tachikawa, M., Uchiyama, S., Hiraoka, S.
  Hyperthermostable Cube-shaped Assembly in Water.
  Communications Chemistry, 1, Article number: 14.

• 4.

  Maruno, T., Watanabe, H., Yoneda, S., Uchihashi, T., Adachi S., Arai, K., Sawaguchi, T., Uchiyama, S.
  Sweeping of adsorbed therapeutic protein on prefillable syringes promotes micron aggregate generation.
  J. Pharm. Sci., 107, 1521-1529.

• 5.

  Shinozaki, N., Hashimoto, R., Noda, M., Uchiyama, S.
  Physicochemical improvement of rabbit derived single-domain antibodies by substitutions with amino acids conserved in camelid antibodies.
  J. Biosci. Bioeng., 125, 654-661.

• 6.

  Uchihashi T, Watanabe YH, Nakazaki Y, Yamasaki T, Watanabe T, Maruno T, Ishii K, Uchiyama S, Song C, Murata K, Iino R, Ando T.
  Dynamic structural states of ClpB involved in its disaggregation function.
  Nature Communications, 9, Article number: 2147.

• 7.

  Kashida, H., Hattori, Y., Tazoe, K., Inoue, T., Nishikawa, K., Ishii, K., Uchiyama, S., Yamashita, H., Abe, M., Kamiya, Y., Asanuma, H.
  Bifacial nucleobases for hexaplex formation in aqueous solution.
  J. Am. Chem. Soc., 40, 8456–8462

• 8.

  Numoto, N., Kamiya, N., Bekker, G. J., Yamagami, Y., Inaba, S., Ishii, K., Uchiyama, S., Kawai, F., Ito, N., Oda, M.
  Structural Dynamics of PET-degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-bound States Elucidates Ca2+ Driven Catalytic Cycles.
  Biochemistry.,57,5289-5300.

• 9.

  Sasano Y, Sakata T, Okusaki S, Sugiyama M, Kaneko Y, Harashima S.
  Genetic analysis of suppressor mutants of a pho84 disruptant in the search for genes involved in intracellular inorganic phosphate sensing in Saccharomyces cerevisiae.
  Genes Genet. Syst. 93, 199-207.

• 10.

  Sugiyama M, Baek SY, Takashima S, Miyashita N, Ishida K, Mun JY, Yeo SH.
  Overexpression of PkINO1 improves ethanol resistance of Pichia kudriavzevii N77-4 isolated from the Korean traditional fermentation starter nuruk.
  J. Biosci. Bioeng. 126, 682-689.

Reviews

• 1.

  Ishii, K., Zhou, M, and Uchiyama S.
  Native mass spectrometry for understanding dynamic protein complex
  BBA General subjects, 1862, 275-286.

• 2.

  Uchiyama S., Noda M., and Krayukhina E.
  Sedimentation velocity analytical ultracentrifugation for characterization of therapeutic antibodies
  Biophy. Rev. 10, 259-269.

Original Papers

• 1.

  Uyeda A, Watanabe T, Hohsaka T, Matsuura T
  Different protein localizations on the inner and outer leaflet of cell-sized liposomes using cell-free protein synthesis
  Synth Biol 3(1), ysy006.

• 2.

  Torner K, Nakanishi T, Matsuura T, Kato Y, Watanabe H
  Genomic integration and ligand-dependent activation of the human estrogen receptor alpha in the crustacean Daphnia magna
  PLoS One 13(6):e0198023.

• 3.

  Rivetti C, Campos B, Pina B, Raldua D, Kato Y, Watanabe H, Barata C
  Tryptophan hydroxylase (TRH) loss of function mutations induce growth and behavioral defects in Daphnia magna
  Sci Rep 8(1):1518.

• 4.

  Matsuura T, Hosoda K, Shimizu Y
  Robustness of a reconstituted Escherichia coli protein translation system analyzed by computational modeling
  ACS Synth Biol 7(8):1964-1972.

• 5.

  Kato Y, Perez CAG, Mohamad Ishak NS, Nong QD, Sudo Y, Matsuura T, Wada T, Watanabe H
  A 5' UTR-overlapping LncRNA activates the male-determining gene doublesex1 in the Crustacean Daphnia magna.
  Curr Biol 28(11):1811-1817 e1814.

• 6.

  Iwamoto M, Elfaramawy MA, Yamatake M, Matsuura T, Oiki S
  Concurrent in vitro synthesis and functional detection of nascent activity of the KcsA Channel under a membrane potential
  ACS Synth Biol 7(4):1004-1011

• 7.

  Ismail NIB, Kato Y, Matsuura T, Watanabe H
  Generation of white-eyed Daphnia magna mutants lacking scarlet function.
  PLoS One 13(11):e0205609.

• 8.

  Elfaramawy MA, Fujii S, Uyeda A, Osaki T, Takeuchi S, Kato Y, Watanabe H, Matsuura T
  Quantitative analysis of cell-free synthesized membrane proteins at the stabilized droplet interface bilayer
  Chem Commun 54(86):12226-12229.

• 9.

  Callens M, Watanabe H, Kato Y, Miura J, Decaestecker E
  Microbiota inoculum composition affects holobiont assembly and host growth in Daphnia.
  Microbiome 6(1):56

• 10.

  Adhitama N, Matsuura T, Kato Y, Watanabe H
  Monitoring ecdysteroid activities using genetically encoded reporter gene in Daphnia magna
  Mar Environ Res 140:375-381.

Original Papers

• 1.

  Wagatsuma T, Maejima E, Watanabe T, Toyomasu T, Kuroda M, Muranaka T, Ohyama K, Ishikawa A, Usui M, Hossain Khan S, Maruyama H, Tawaraya K, Kobayashi Y, Koyama H.
  Dark conditions enhance aluminum tolerance in several rice cultivars via multiple modulations of membrane sterols.
  Journal of Experimental Botany. 69, 567-577.

• 2.

  Tamura K, Yoshida K, Hiraoka Y, Sakaguchi, D, Chikugo A, Mochida K, Kojoma M, Mitsuda N, Saito K, Muranaka T, Seki H.
  The basic helix-loop-helix transcription factor GubHLH3 positively regulates soyasaponin biosynthetic genes in Glycyrrhiza uralensis.
  Plant and Cell Physiology. 59, 783-796.

• 3.

  Yano R, Takagi K, Tochigi S, Fujisawa Y, Nomura Y, Tsuchinaga H, Takahashi Y, Takada Y, Kaga A, Anai T, Tsukamoto C, Seki H, Muranaka T, Ishimoto M.
  Isolation and characterization of the soybean Sg-3 gene that is involved in genetic variation in sugar chain composition at the C-3 position in soyasaponins.
  Plant and Cell Physiology. 59, 797-810.

• 4.

  Robertlee J, Kobayashi K, Tang J, Suzuki M, Muranaka T.
  Evidence that the Arabidopsis thaliana 3-hydroxy-3-methylglutaryl-CoA reductase 1 is phosphorylated at Ser577 in planta.
  Plant Biotechnology. 35, 1-7.

• 5.

  Muangphrom P, Seki H, Matsumoto S, Nishiwaki M, Fukushima EO, Muranaka T.
  Identification and characterization of a novel sesquiterpene synthase, 4-amorphen-11-ol synthase, from Artemisia maritima.
  Plant Biotechnology. 35, 113-121.

• 6.

  Suzuki H, Fukushima E.O, Umemoto N, Ohyama K, Seki H, Muranaka T.
  Comparative analysis of CYP716A subfamily enzymes for the heterologous production of C-28 oxidized triterpenoids in transgenic yeast.
  Plant Biotechnology. 35, 131-139.

• 7.

  Nakayasu M, Akiyama R, Lee H.J, Osakabe K, Osakabe Y, Watanabe B, Sugimoto Y, Umemoto N, Saito K, Muranaka T, Mizutani M.
  Generation of α-solanine-free hairy roots of potato by CRISPR/Cas9 mediated genome editing of the St16DOX gene.
  Plant Physiology and Biochemistry. 131, 70-77.

• 8.

  Kusano H, Ohnuma M, Mutsuro-Aoki H, Asahi T, Ichinosawa D, Onodera H, Asano K, Noda T, Horie T, Fukumoto K, Kihara M, Teramura H, Yazaki K, Umemoto N, Muranaka T, Shimada H.
  Establishment of a modified CRISPR/Cas9 system with increased mutagenesis frequency using the translational enhancer dMac3 and multiple guide RNAs in potato.
  Scientific Reports. 8, 13753.

• 9.

  Takagi K, Yano R, Tochigi S, Fujisawa Y, Tsuchinaga H, Takahashi Y, Takada Y, Kaga A, Anai T, Tsukamoto C, Seki H, Muranaka T, Ishimoto M.
  Genetic and functional characterization of Sg-4 glycosyltransferase involved in the formation of sugar chain structure at the C-3 position of soybean saponins.
  Phytochemistry. 156, 96-105.

• 10.

  Nakamura M, Tran ML, Le QL, Suzuki H, Nguyen CM, Vu HG, Tamura K, Nguyen VT, Suzuki H, Misaki R, Muranaka T, Ninh KB, Fujiyama K, Seki H.
  Transcriptome sequencing and identification of cytochrome P450 monooxygenases involved in the biosynthesis of maslinic acid and corosolic acid in Avicennia marina.
  Plant Biotechnology. 35, 341-348.

Reviews

• 1.

  Seki H, Tamura K, Muranaka T.
  Plant-derived isoprenoid sweeteners: recent progress in biosynthetic gene discovery and perspectives on microbial production.
  Bioscience, Biotechnology, and Biochemistry. 82，927-934.

Original Papers

• 1.

  Ohtake H, Okano K, Kunisada M, Takano H, Toda M
  Simple technology for recycling phosphate from wastewater to farmland in rural areas.
  AMBIO. 47(Suppl. 1), S83-S92.

• 2.

  Ihling N, Bittner N, Diederichs S, Schelden M, Korona A, Höfler GT, Fulton A, Jaeger KE, Honda K, Ohtake H, Büchs J
  Online measurement of the respiratory activityin shake flasks enables the identification of cultivation phases and patternsindicating recombinant protein production in various Escherichia coli host strains.
  Biotechnol. Prog. 34, 315-327.

• 3.

  Okano K, Uematsu G, Hama S, Tanaka T, Noda H, Kondo A, Honda K
  Metabolic engineering of Lactobacillus plantarum for direct L-lactic acid from raw corn starch.
  Biotechnol. J. 13, 1700517.

• 4.

  Rafi M, Handayani F, Darusman LK, Rohaeti E, Wahyu Y, Sulistiyani, Honda K, Putri SP
  A combination of simultaneous quantification of fourtriterpenes and fingerprint analysis using HPLC for rapid identificationof Centella asiatica from its related plants and classification based on cultivation ages.
  Ind. Crops Prod. 122, 93-97.

Reviews

• 1.

  Okano K, Honda K, Taniguchi H, Kondo A
  De novo design of biosynthetic pathways for bacterial production of bulk chemicals and biofuels.
  FEMS Microbiol. Lett.，365，fny215.

Original Papers

• 1.

  Onitsuka M, Kinoshita Y, Nishizawa A, Tsutsui T, Omasa T.
  Enhanced IgG1 production by overexpression of nuclear factor kappa B inhibitor zeta (NFKBIZ) in Chinese hamster ovary cells.
  Cytotechnology. 70,675-685.

• 2.

  Yamano N, Omasa T.
  EGCG improves recombinant protein productivity in Chinese hamster ovary cell cultures via cell proliferation control.
  Cytotechnology. 70,1697-1706.

• 3.

  Kamachi Y, Omasa T.
  Development of hyper osmotic resistant CHO host cells for enhanced antibody production.
  Journal of Bioscience and Bioengineering.125,470-478.

• 4.

  Nakashima Y, Miyagi-Shiohira C, Noguchi H, Omasa T.
  Atorvastatin inhibits the HIF1α-PPAR axis, which is essential for maintaining the function of human induced pluripotent stem cells.
  Molecular Therapy. 26,1715-1734.

• 5.

  Kimura S, Omasa T.
  Genome sequence comparison between Chinese hamster ovary (CHO) DG44 cells and mouse using end sequences of CHO BAC clones based on BAC-FISH results.
  Cytotechnology.70,1399-1407.

• 6.

  Nakashima Y, Miyagi-Shiohira C, Noguchi H, Omasa T.
  The healing effect of human milk fat globule-EGF factor 8 protein (MFG-E8) in a rat model of Parkinson’s disease.
  Brain Science.8,E167.

Original Papers

• 1.

  Flores RJD, Ohashi T, Sakai K, Gonoi T, Kawasaki H, Fujiyama K.
  The neutral N-linked glycans of the Basidiomycetous yeasts Pseudozyma antarctica and Malassezia furfur (Subphylum Ustilaginomycotina).
  J Gen Appl Microbiol. doi: 10.2323/jgam.2018.05.003. [Epub ahead of print]

• 2.

  Wu CC, Tsai YY, Ohashi T, Misaki R, Limtong S, Fujiyama K.
  Isolation of a thermotolerant Rhodosporidium toruloides DMKU3-TK16 mutant and its fatty acid profile at high temperature.
  FEMS Microbiol Lett. 365, doi: 10.1093/femsle/fny203.

• 3.

  Priyambada SA, Misaki R, Okamoto T, Ohashi T, Ueda K, Matsuura Y, Fujiyama K.
  St6gal1 knockdown alters HBV life cycle in HepAD38 cells.
  Biochem Biophys Res Commun. 503, 1841-1847.

• 4.

  Naphatsamon U, Ohashi T, Misaki R, Fujiyama K.
  The Production of Human β-Glucocerebrosidase in Nicotiana benthamiana Root Culture.
  Int J Mol Sci. 19, doi: 10.3390/ijms19071972.

• 5.

  Roychowdhury S, Oh YJ, Kajiura H, Hamorsky KT, Fujiyama K, Matoba N.
  Hydroponic Treatment of Nicotiana benthamiana with Kifunensine Modifies the N-glycans of Recombinant Glycoprotein Antigens to Predominantly Man9 High-Mannose Type upon Transient Overexpression.
  Front Plant Sci. 9, doi: 10.3389/fpls.2018.00062.

• 6.

  Thi Sam N, Misaki R, Ohashi T, Fujiyama K.
  Enhancement of glycosylation by stable co-expression of two sialylation-related enzymes on Chinese hamster ovary cells.
  J Biosci Bioeng. 126, 102-110.

• 7.

  Suganuma M, Nomura T, Higa Y, Kataoka Y, Funaguma S, Okazaki H, Suzuki T, Fujiyama K, Sezutsu H, Tatematsu KI, Tamura T.
  N-glycan sialylation in a silkworm-baculovirus expression system.
  J Biosci Bioeng. 126, 9-14.

• 8.

  Polburee P, Ohashi T, Tsai YY, Sumyai T, Lertwattanasakul N, Limtong S, Fujiyama K.
  Molecular cloning and overexpression of DGA1, an acyl-CoA-dependent diacylglycerol acyltransferase, in the oleaginous yeast Rhodosporidiobolus fluvialis DMKU-RK253.
  Microbiology. 164, 1-10.

Original Papers

• 1.

  Ueda S, Kitani S, Namba T, Arai M, Ikeda H, and Nihira T.
  Engineered production of kitasetalic acid, a new tetrahydro-β-carboline with the ability to suppress glucose-regulated protein synthesis.
  J Antibiot (Tokyo). 71, 854-861.

• 2.

  Kitani S, Yoshida M, Boonlucksanawong O, Panbangred W, Anuegoonpipat A, Kurosu T, Ikuta K, Igarashi Y, and Nihira T.
  Cystargamide B, a cyclic lipodepsipeptide with protease inhibitory activity from Streptomyces sp.
  J Antibiot (Tokyo). 71, 662-666.

• 3.

  Nguyen TB, Kitani S, Shimma S, and Nihira T.
  Butenolides from Streptomyces albus J1074 act as external signals to stimulate avermectin production in Streptomyces avermitilis.
  Appl Environ Microbiol. 84, e02791-17.

• 4.

  Suroto DA, Kitani S, Arai M, Ikeda H, and Nihira T.
  Characterization of the biosynthetic gene cluster for cryptic phthoxazolin A in Streptomyces avermitilis.
  PLoS One. 13:e0190973.

• 5.

  Pait IGU, Kitani S, Roslan FW, Ulanova D, Arai M, Ikeda H, and Nihira T.
  Discovery of a new diol-containing polyketide by heterologous expression of a silent biosynthetic gene cluster from Streptomyces lavendulae FRI-5.
  J Ind Microbiol Biotechnol. 45, 77-87.

• 6.

  Kitani S, Ueguchi T, Igarashi Y, Leetanasaksakul K, Thamchaipenet A, and Nihira T.
  Rakicidin F, a new antibacterial cyclic depsipeptide from a marine sponge-derived Streptomyces sp.
  J Antibiot (Tokyo). 71, 139-141.

• 7.

  Nguyen HN, Ishidoh KI, Kinoshita H, Nihira T.
  Targeted cloning of a large gene cluster from Lecanicillium genome by Cre/loxP based method.
  J Microbiol Methods. 150, 47-54.

Original Papers

• 1.

  Nezu A, Morita T, Nagai T and Tanimura A.
  Simultaneous monitoring of Ca2+ responses and salivary secretion in live animals reveals a threshold intracellular Ca2+ concentration for salivation.
  The Physiological Society, 104, 61-69.

• 2.

  Arai Y, Takauchi H, Ogami Y, Fujiwara S, Nakano M, Matsuda T and Nagai T.
  Spontaneously blinking fluorescent protein for simple single laser super-resolution live cell imaging.
  ACS Chemical Biology, 13, 1938-1943.

• 3.

  Komatsu N, Terai K, Imanishi A, Kamioka Y, Sumiyama K, Jin T, Okada Y, Nagai T and Matsuda M.
  A platform of BRET-FRET hybrid biosensors for optogenetics, chemical screening, and in vivo imaging.
  Scientific Reports, 8, 8984.

• 4.

  Sato R, Kawashima R, Mai Duy Luu T, Nakano M, Nagai T and Masuda S.
  Significance of PGR5-dependent cyclic electron flow for optimizing the rate of ATP synthesis and consumption in Arabidopsis chloroplasts.
  Photosynthesis Research, 139, 359-365.

• 5.

  Suzuki K, Onishi T, Nakada C, Takei S, J. Daniels M, Nakano M, Matsuda T and Nagai T.
  Uninterrupted monitoring of drug effects in human-induced pluripotent stem cell-derived cardiomyocytes with bioluminescence Ca2+ microscopy.
  BMC Research Notes, 11, 313.

• 6.

  Riani Y D, Matsuda T, Takemoto K, Nagai T.
  Green monomeric photosensitizing fluorescent protein for photo-inducible protein inactivation and cell ablation.
  BMC Biol, 16, 50.

• 7.

  Hara-Kuge S, Nishihara T, Matsuda T, Kitazono T, Teramoto T, Nagai T and Ishihara T.
  An improved inverse-type Ca2+ indicator can detect putative neuronal inhibition in Caenorhabditis elegans by increasing signal intensity upon Ca2+ decrease.
  PLoS ONE, 13, e0194707.

• 8.

  Nadim H, Suzuki K, Iwano M, Matsuda T and Nagai T.
  Bioluminescent low-affinity Ca2+ indicator for ER with multicolor calcium imaging in single living cells.
  ACS Chemical Biology, 13, 1862-1871.

• 9.

  Ohta Y, Furuta T, Nagai T and Horikawa K.
  Red fluorescent cAMP indicator with increased affinity and expanded dynamic range.
  Sci. Rep., 8, 1866.

• 10.

  Wazawa T, Arai Y, Kawahara Y, Takauchi H, Washio T, and Nagai T.
  Highly biocompatible super-resolution fluorescence imaging using the fast photoswitching fluorescent protein Kohinoor and SPoD-ExPAN with Lp-regularized image reconstruction.
  Microscopy, 67, 89-98.

• 11.

  Kushida Y, Arai Y, Shimono K, and Nagai T.
  Biomimetic chemical sensing by fluorescence signals using a virus-like particle-based platform.
  ACS Sensors, 3, 87-92.

• 12.

  Maeshima K, Matsuda T, Shindo Y, Imamura H, Tamura S, Imai R, Kawakami S, Nagashima R, Soga T, Noji H, Oka K and Nagai T.
  A transient rise in free Mg2+ ions released from ATP-Mg by its hydrolysis contributes to mitotic chromosome condensation.
  Current Biology, 28, 444-451.

• 13.

  Shinoda H, Ma Y, Nakashima R, Sakurai K, Matsuda T, Nagai T.
  Acid-tolerant monomeric GFP from Olindias formosa.
  Cell Chemical Biology, 25, 330-338.

Reviews

• 1.

  Shinoda H, Michael S and Nagai T.
  Fluorescent proteins for investigating biological events in acidic environments.
  International Journal of Molecular Science, 19, 1548.

Original Papers

• 1.

  Ueda, K., Nakajima, T., Yoshikawa, K., Toya, Y., Matsuda, F. and Shimizu, H.
  Metabolic flux of the oxidative pentose phosphate pathway under low light conditions in Synechocystis sp. PCC 6803.
  J. Biosci. Bioeng. 126, 38-43.

• 2.

  Tokuyama, K., Toya, Y., Horinouchi, T., Furusawa, C., Matsuda, F. and Shimizu, H.
  Application of adaptive laboratory evolution to overcome a flux limitation in an Escherichia coli production strain.
  Biotechnol. Bioeng. 115, 1542-1551.

• 3.

  Nagai, H., Masuda, A., Toya, Y., Matsuda, F. and Shimizu, H.
  Metabolic engineering of mevalonate-producing Escherichia coli strains based on thermodynamic analysis.
  Metab. Eng. 47, 1-9.

• 4.

  Narazaki, Y., Nomura, Y., Morita, K., Shimizu, H. and Matsuda, F.
  Expression of Saccharomyces cerevisiae cDNAs to enhance the growth of non-ethanol-producing S. cerevisiae strains lacking pyruvate decarboxylases.
  J. Biosci. Bioeng. 126, 317-321.

• 5.

  Araki, C., Okahashi, N., Maeda, K., Shimizu, H. and Matsuda, F.
  Mass Spectrometry-Based Method to Study Inhibitor-Induced Metabolic Redirection in the Central Metabolism of Cancer Cells.
  Mass Spectrom. 7, A0067, 1-9.

• 6.

  Tokumaru, Y., Uebayashi, K., Toyoshima, M., Osanai, T., Matsuda, F. and Shimizu, H.
  Comparative Targeted Proteomics of the Central Metabolism and Photosystems in SigE mutant strains of synechocystis sp. PCC 6803.
  Molecules 23. 1051, 1-14.

• 7.

  Tsuji, G., Sunami, T. and Ichihashi, N.
  Production of giant unilamellar vesicles by the water-in-oil emulsion-transfer method without high internal concentrations of sugars.
  J. Biosci. Bioeng. 126, 4, 540-545.

• 8.

  Hayakawa, K., Matsuda, F. and Shimizu, H.
  13C-metabolic flux analysis of ethanol-assimilating Saccharomyces cerevisiae for S-adenosyl-l-methionine production.
  Microb. Cell Fact. 17, 1-13.

• 9.

  Uebayashi, K., Shimizu, H. and Matsuda, F.
  Comparative analysis of fermentation and enzyme expression profiles among industrial Saccharomyces cerevisiae strains.
  Appl. Microbiol. and Biotechnol. 102, 7071-7081.

• 10.

  Ogawa, K., Yoshikawa, K., Matsuda, F., Toya, Y. and Shimizu, H.
  Transcriptome analysis of the cyanobacterium Synechocystis sp. PCC 6803 and mechanisms of photoinhibition tolerance under extreme high light conditions.
  J. Biosci. Bioeng. 126, 5, 596-602.

• 11.

  Ishii, J., Morita, K., Ida, K., Kato, H., Kinoshita, S., Hataya, S., Shimizu, H., Kondo, A. and Matsuda, F.
  A pyruvate carbon flux tugging strategy for increasing 2,3-butanediol production and reducing ethanol subgeneration in the yeast Saccharomyces cerevisiae.
  Biotechnol. Biofuels 11, 1, 1-21.

• 12.

  Ohnishi, M., Anegawa, A., Sugiyama, Y., Harada, K., Oikawa, A., Nakayama, Y., Matsuda, F., Nakamura, Y., Sasaki, R., Shichijo, C., Hatcher, P.G., Fukaki, H., Kanaya, S., Aoki, K., Yamazaki, M., Fukusaki, E., Saito, K. and Mimura, T.
  Molecular components of arabidopsis intact vacuoles clarified with metabolomic and proteomic analyses.
  Plant Cell Physiol. 59, 1353-1362.

• 13.

  Okahashi, N., Maeda, K., Kawana, S., Iida, J., Shimizu, H. and Matsuda, F.
  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.
  Metab. Eng. 51, 43-49.

Original Papers

• 1.

  Tokuyama K, Toya Y, Matsuda F, Cress BF, Koffas MAG, Shimizu H.
  Magnesium starvation improves production of malonyl-CoA-derived metabolites in Escherichia coli.
  Metabolic Engineering. 52, 215-223.

• 2.

  Toyoshima M, Sakata M, Ohnishi K, Tokumaru Y, Kato Y, Tokutsu R, Sakamoto W, Minagawa J, Matsuda F, Shimizu H.
  Targeted proteome analysis of microalgae under high-light conditions by optimized protein extraction of photosynthetic organisms.
  Journal of Bioscience and Bioengineering. 127, 394-402.

• 3.

  Okahashi N, Maeda K, Kawana S, Iida J, Shimizu H, Matsuda F.
  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.
  Metabolic Engineering. 51, 43-49.

• 4.

  Maruyama Y, Toya Y, Kurokawa H, Fukano Y, Sato A, Umemura H, Yamada K, Iwasaki H, Tobori N, Shimizu H.
  Characterization of oil-producing yeast Lipomyces starkeyi on glycerol carbon source based on metabolomics and 13C-labeling.
  Applied Microbiology and Biotechnology. 102, 8909-8920.

• 5.

  Ishii J, Morita K, Ida K, Kato H, Kinoshita S, Hataya S, Shimizu H, Kondo A, Matsuda F.
  A pyruvate carbon flux tugging strategy for increasing 2,3-butanediol production and reducing ethanol subgeneration in the yeast Saccharomyces cerevisiae.
  Biotechnology for Biofuels. 11, 180.

• 6.

  Ogawa K, Yoshikawa K, Matsuda F, Toya Y, Shimizu H.
  Transcriptome analysis of the cyanobacterium Synechocystis sp. PCC 6803 and mechanisms of photoinhibition tolerance under extreme high light conditions.
  Journal of bioscience and bioengineering. 126, 596-602.

• 7.

  Uebayashi K, Shimizu H, Matsuda F.
  Comparative analysis of fermentation and enzyme expression profiles among industrial Saccharomyces cerevisiae strains.
  Applied Microbiology and Biotechnology. 102, 7071-7081.

• 8.

  Hayakawa K, Matsuda F, Shimizu H.
  13C-metabolic flux analysis of ethanol-assimilating Saccharomyces cerevisiae for S-adenosyl-L-methionine production.
  Microbial Cell Factories. 17, 82.

• 9.

  Tokumaru Y, Uebayashi K, Toyoshima M, Osanai T, Matsuda F, Shimizu H.
  Comparative targeted proteomics of the central metabolism and the photosystems in the SigE mutant Strains of Synechocystis sp. PCC 6803.
  Molecules. 23, 1051.

• 10.

  Araki C, Okahashi N, Maeda K, Shimizu H, Matsuda F.
  Mass spectrometry-based method to study inhibitor-induced metabolic redirection in the central metabolism of cancer cells.
  Mass Spectrometry. 7, A0067.

• 11.

  Narazaki Y, Nomura Y, Morita K, Shimizu H, Matsuda F.
  Expression of Saccharomyces cerevisiae cDNAs to enhance the growth of non-ethanol-producing S. cerevisiae strains lacking pyruvate decarboxylases.
  Journal of bioscience and bioengineering. 126, 317-321.

• 12.

  Nagai H, Masuda A, Toya Y, Matsuda F, Shimizu H.
  Metabolic engineering of a mevalonate-producing Escherichia coli strain based on thermodynamic analysis.
  Metabolic Engineering. 47, 1-9.

• 13.

  Tokuyama K, Toya Y, Horinouchi T, Furusawa C, Matsuda F, Shimizu H.
  Application of adaptive laboratory evolution to overcome a flux limitation in an Escherichia coli production strain.
  Biotechnology and bioengineering. 115, 1542-1551.

• 14.

  Ueda K, Nakajima T, Yoshikawa K, Toya Y, Matsuda F, Shimizu H.
  Metabolic flux of the oxidative pentose phosphate pathway under low light conditions in Synechocystis sp. PCC 6803.
  Journal of bioscience and bioengineering. 126, 38-43.

• 15.

  Hirasawa T, Saito M, Yoshikawa K, Furusawa C, Shmizu H.
  Integrated analysis of transcriptome and metabolome of Corynebacterium glutamicum during penicillin-induced glutamic acid production.
  Biotechnology journal. 13, e1700612.

Reviews

• 1.

  Shimizu H, Matsuda F.
  Editorial overview: Recent progress in analytical technologies for design-build-test-learn cycle in biotechnology.
  Current Opinion in Biotechnology. 54, 145-147.