Original Papers

• 1.

  Adinda P Wisman, Yoshihiro Tamada, Shuji Hirohata, Katsuya Gomi, Eiichiro Fukusaki, Shuichi Shimma
  Mapping haze-komi on rice koji grains using β-glucuronidase expressing Aspergillus oryzae and mass spectrometry imaging
  Journal of Bioscience and Bioengineering, Volume 129, Issue 3, March 2020, Pages 296-301.

• 2.

  Siska Septiana, Nancy Dewi Yuliana, Boy Muchlis Bachtiar, Sastia Prama Putri, Eiichiro Fukusaki, Walter Alvarez Laviña, Christofora Hanny Wijaya
  Metabolomics approach for determining potential metabolites correlated with sensory attributes of Melaleuca cajuputi essential oil, a promising flavor ingredient
  J Biosci Bioeng. 2020 May;129(5):581-587.

• 3.

  Omori K, Katakami N, Arakawa S, Yamamoto Y, Ninomiya H, Takahara M, Matsuoka TA, Tsugawa H, Furuno M, Bamba T, Fukusaki E, Shimomura I.
  Identification of Plasma Inositol and Indoxyl Sulfate as Novel Biomarker Candidates for Atherosclerosis in Patients with Type 2 Diabetes. -Findings from Metabolome Analysis Using GC/MS
  J Atheroscler Thromb. 2020 Oct 1;27(10):1053-1067. doi: 10.5551/jat.52506.

• 4.

  Kawai M, Harada R, Yoda N, Yamasaki-Yashiki S, Fukusaki E, Katakura Y.
  Suppression of lactate production by using sucrose as a carbon source in lactic acid bacteria
  J Biosci Bioeng. 2020 Jan;129(1):47-51.

• 5.

  Halmschlag B, Hoffmann K, Hanke R, Putri SP, Fukusaki E, Büchs J, Blank LM.
  Comparison of Isomerase and Weimberg Pathway for γ-PGA Production From Xylose by Engineered Bacillus subtilis
  Front Bioeng Biotechnol. 2020 Jan 21;7:476.

• 6.

  Halmschlag B, Putri SP, Fukusaki E, Blank LM.
  Identification of Key Metabolites in Poly-γ-Glutamic Acid Production by Tuning γ-PGA Synthetase Expression
  Front Bioeng Biotechnol. 2020 Jan 30;8:38.

• 7.

  Imura M, Nitta K, Iwakiri R, Matsuda F, Shimizu H, Fukusaki E.
  Comparison of metabolic profiles of yeasts based on the difference of the Crabtree positive and negative
  J Biosci Bioeng. 2020 Jan;129(1):52-58.

• 8.

  Fathima AM, Laviña WA, Putri SP, Fukusaki E.
  Accumulation of sugars and nucleosides in response to high salt and butanol stress in 1-butanol producing Synechococcus elongatus
  J Biosci Bioeng. 2020 Feb;129(2):177-183.

• 9.

  Dwivany FM, Nugrahapraja H, Fukusaki E, Putri SP, Novianti C, Radjasa SK, Fauziah T, Nirmala Sari LD.
  Dataset of Cavendish banana transcriptome in response to chitosan coating application
  Data Brief. 2020 Feb 26;29:105337.

• 10.

  Jantrapirom S, Enomoto Y, Karinchai J, Yamaguchi M, Yoshida H, Fukusaki E, Shimma S, Yamaguchi M.
  The depletion of ubiquilin in Drosophila melanogaster disturbs neurochemical regulation to drive activity and behavioral deficits
  Sci Rep. 2020 Mar 30;10(1):5689.

• 11.

  Ikram MMM, Ridwani S, Putri SP, Fukusaki E.
  GC-MS Based Metabolite Profiling to Monitor Ripening-Specific Metabolites in Pineapple ( Ananas comosus)
  Metabolites. 2020 Mar 31;10(4):134.

• 12.

  Yamana T, Taniguchi M, Nakahara T, Ito Y, Okochi N, Putri SP, Fukusaki E.
  Component Profiling of Soy-Sauce-Like Seasoning Produced from Different Raw Materials
  Metabolites. 2020 Apr 1;10(4):137.

• 13.

  Taniguchi M, Takao Y, Kawasaki H, Yamada T, Fukusaki E.
  Profiling of taste-related compounds during the fermentation of Japanese sake brewed with or without a traditional seed mash (kimoto)
  J Biosci Bioeng. 2020 Jul;130(1):63-70.

• 14.

  Suantika G, Situmorang ML, Saputra FI, Putri SLE, Putri SP, Aditiawati P, Fukusaki E.
  Metabolite profiling of whiteleg shrimp Litopenaeus vannamei from super-intensive culture in closed aquaculture systems: a recirculating aquaculture system and a hybrid zero water discharge-recirculating aquaculture system
  Metabolomics. 2020 Apr 10;16(4):49.

• 15.

  Aditiawati P, Astuti DI, Kriswantoro JA, Khanza SM, Kamarisima, Irifune T, Amalia F, Fukusaki E, Putri SP.
  GC/MS-based metabolic profiling for the evaluation of solid state fermentation to improve quality of Arabica coffee beans
  Metabolomics. 2020 Apr 23;16(5):57. doi: 10.1007/s11306-020-01678-y.

• 16.

  Laviña WA, Sakurai SSM, Pontrelli S, Putri SP, Fukusaki E.
  Metabolomics Analysis Reveals Global Metabolic Changes in the Evolved E. coli Strain with Improved Growth and 1-Butanol Production in Minimal Medium
  Metabolites. 2020 May 13;10(5):192.

• 17.

  Katakami N, Omori K, Taya N, Arakawa S, Takahara M, Matsuoka TA, Tsugawa H, Furuno M, Bamba T, Fukusaki E, Shimomura I.
  Plasma metabolites associated with arterial stiffness in patients with type 2 diabetes
  Cardiovasc Diabetol. 2020 Jun 11;19(1):75.

• 18.

  Halmschlag B, Putri SP, Fukusaki E, Blank LM.
  Poly-γ-glutamic acid production by Bacillus subtilis 168 using glucose as the sole carbon source: A metabolomic analysis
  J Biosci Bioeng. 2020 Sep;130(3):272-282.

• 19.

  Yoshikawa K, Furuno M, Tanaka N, Fukusaki E.
  Fast enantiomeric separation of amino acids using liquid chromatography/mass spectrometry on a chiral crown ether stationary phase
  J Biosci Bioeng. 2020 Oct;130(4):437-442.

• 20.

  Fukuda T, Takamatsu K, Bamba T, Fukusaki E.
  Potato tuber metabolomics-based prediction of chip color quality and application using gas chromatography/flame ionization detector
  Biosci Biotechnol Biochem. 2020 Nov;84(11):2193-2198.

• 21.

  Ohshima K, Nojima S, Tahara S, Kurashige M, Kawasaki K, Hori Y, Taniguchi M, Umakoshi Y, Okuzaki D, Wada N, Ikeda JI, Fukusaki E, Morii E.
  Serine racemase enhances growth of colorectal cancer by producing pyruvate from serine
  Nat Metab. 2020 Jan;2(1):81-96.

• 22.

  Takeo E, Fukusaki E, Shimma S.
  Mass Spectrometric Enzyme Histochemistry Method Developed for Visualizing In Situ Cholinesterase Activity in Mus musculus and Drosophila melanogaster
  Anal Chem. 2020 Sep 15;92(18):12379-12386.

• 23.

  Kadar AD, Astawan M, Putri SP, Fukusaki E.
  Metabolomics-Based Study of the Effect of Raw Materials to the End Product of Tempe-An Indonesian Fermented Soybean
  Metabolites. 2020 Sep 11;10(9):367.

• 24.

  Putri Wisman A, Tamada Y, Hirohata S, Fukusaki E, Shimma S.
  Metabolic Visualization Reveals the Distinct Distribution of Sugars and Amino Acids in Rice Koji
  Mass Spectrom (Tokyo). 2020;9(1):A0089.

• 25.

  Nojima Y, Takeda Y, Maeda Y, Bamba T, Fukusaki E, Itoh MN, Mizuguchi K, Kumanogoh A.
  Metabolomic analysis of fibrotic mice combined with public RNA-Seq human lung data reveal potential diagnostic biomarker candidates for lung fibrosis
  FEBS Open Bio. 2020 Sep 22;10(11):2427-36.

• 26.

  Kanazawa S, Noda A, Ito A, Hashimoto K, Kunisawa A, Nakanishi T, Kajihara S, Mukai N, Iida J, Fukusaki E, Matsuda F.
  Fake metabolomics chromatogram generation for facilitating deep learning of peak-picking neural networks
  J Biosci Bioeng. 2021 Feb;131(2):207-212.

• 27.

  Nitta K, Carratore FD, Breitling R, Takano E, Putri SP, Fukusaki E.
  Multi-Omics Analysis of the Effect of cAMP on Actinorhodin Production in Streptomyces coelicolor
  Front Bioeng Biotechnol. 2020 Nov 5;8:595552.

• 28.

  Dissook S, Putri SP, Fukusaki E.
  Metabolomic Analysis of Response to Nitrogen-Limiting Conditions in Yarrowia spp
  Metabolites. 2020 Dec 29;11(1):E16.

Original Papers

• 1.

  Thummarati, P. and Kino-oka, M.
  Effect of Co-culturing Fibroblasts in Human Skeletal Muscle Cell Sheet on Angiogenic Cytokine Balance and Angiogenesis.
  Front. Bioeng. Biotechnol. 8, 578140.

• 2.

  Sugiyama, H., Shiokaramatsu, M., Kagihiro, M., Fukumori, K., Horiguchi, I., Kino-oka, M.
  Apoptosis-Based Method for Determining Lot Sizes in the Filling of Human-Induced Pluripotent Stem Cells.
  J. Tissue Eng. Regen. Med. 14(11), 1641-1651

• 3.

  Ayuningtyas, FD., Kim, M.-H., Kino-oka, M.
  Muscle Lineage Switching by Migratory Behaviour-Driven Epigenetic Modifications of Human Mesenchymal Stem Cells on a Dendrimer-Immobilized Surface.
  Acta Biomater. 106, 170-180.

• 4.

  Hashida, A., Uemura, T., Kino-oka, M.
  Kinetics on Aggregate Behaviors of Human Induced Pluripotent Stem Cells in Static Suspension and Rotating Flow Cultures.
  J. Biosci. Bioeng. 127, 625-632.

• 5.

  Kagihiro, M., Fukumori ,K., Horiguchi, I., Kim, M.-H. and Kino-oka, M.
  Suppression of Time-Dependent Decay by Controlling the Redox Balance of Human Induced Pluripotent Stem Cells Suspended in a Cryopreservation Solution.
  Biochem. Eng. J., Vol.155, 107465 (2020)

• 6.

  Baba, K., Sasaki, K., Morita, M., Tanaka, T., Teranishi, Y., Ogasawara, T., Oie, Y., Kusumi, I., Inoie, M., Hata, K., Quantock, A., Kino-oka, M., Nishida, K.
  Cell Jamming, Stratification and p63 Expression in Cultivated Human Corneal Epithelial Cell Sheets.
  Sci. Rep, Vol.10, N0.9282(2020).

• 7.

  Hayashi, Y., Horiguchi, I., Kino-oka, M., Sugiyama, H.
  Slow Freezing Process Design for Human Induced Pluripotent Stem Cells by Modeling Intracontainer Variation.
  Computers and Chemical Engineering,　Vol.132, 106597 (2019)

Reviews

• 1.

  Kim M.-H. and Kino-oka M.
  Designing a Blueprint for Next-Generation Stem Cell Bioprocessing Development.
  Biotechnol. Bioeng. Vol.117, No.3, pp.832-843 (2020)

• 2.

  Kim M.-H. and Kino-oka M.
  Bioengineering Considerations for a Nurturing Way to Enhance Scalable Expansion of Human Pluripotent Stem Cells.
  Biotechnol. J., Vol. 15, No. 4, 1900314 (2020)

Original Papers

• 1.

  Krayukhina, E., Fukuhara, A., & Uchiyama, S.
  Assessment of the Injection Performance of a Tapered Needle for Use in Prefilled Biopharmaceutical Products.
  Journal of pharmaceutical sciences, 109(1), 515–523.

• 2.

  Oyama, H., Koga, H., Tadokoro, T., Maenaka, K., Shiota, A., Yokoyama, M., Noda, M., Torisu, T., & Uchiyama, S.
  Relation of Colloidal and Conformational Stabilities to Aggregate Formation in a Monoclonal Antibody..
  Journal of pharmaceutical sciences, 109(1), 308–315.

• 3.

  Gambe-Gilbuena, A., Shibano, Y., Krayukhina, E., Torisu, T., & Uchiyama, S.
  Automatic Identification of the Stress Sources of Protein Aggregates Using Flow Imaging Microscopy Images.
  Journal of pharmaceutical sciences, 109(1), 614–623.

• 4.

  Yagi-Utsumi, M., Sikdar, A., Song, C., Park, J., Inoue, R., Watanabe, H., Burton-Smith, R. N., Kozai, T., Suzuki, T., Kodama, A., Ishii, K., Yagi, H., Satoh, T., Uchiyama, S., Uchihashi, T., Joo, K., Lee, J., Sugiyama, M., Murata, K., & Kato, K.
  Supramolecular tholos-like architecture constituted by archaeal proteins without functional annotation.
  Scientific reports, 10(1), 1540.

• 5.

  Dwivany, F. M., Syam, F., Nugrahapraja, H., Radjasa, O. K., Moeis, M. R., & Uchiyama, S.
  Dataset of microbial community structure in alcohol sprayed banana associated with ripening process.
  Data in brief, 29, 105216.

• 6.

  Miyahara, Y., Shintani, K., Hayashihara-Kakuhou, K., Zukawa, T., Morita, Y., Nakazawa, T., Yoshida, T., Ohkubo, T., & Uchiyama, S.
  Effect of UVC Irradiation on the Oxidation of Histidine in Monoclonal Antibodies.
  Scientific reports, 10(1), 6333.

• 7.

  Imamura, A., Okada, T., Mase, H., Otani, T., Kobayashi, T., Tamura, M., Kubata, B. K., Inoue, K., Rambo, R. P., Uchiyama, S., Ishii, K., Nishimura, S., & Inui, T.
  Allosteric regulation accompanied by oligomeric state changes of Trypanosoma brucei GMP reductase through cystathionine-β-synthase domain.
  Nature communications, 11(1), 1837.

• 8.

  Kamiya, Y., Sato, F., Murayama, K., Kodama, A., Uchiyama, S., & Asanuma, H.
  Incorporation of Pseudo-complementary Bases 2,6-Diaminopurine and 2-Thiouracil into Serinol Nucleic Acid (SNA) to Promote SNA/RNA Hybridization.
  Chemistry, an Asian journal, 15(8), 1266–1271.

• 9.

  Maruno, T., Ohkubo, T., & Uchiyama, S.
  Stirring rate affects thermodynamics and unfolding kinetics in isothermal titration calorimetry.
  Journal of biochemistry, 168(1), 53–62.

Reviews

• 1.

  Ishii-Watabe, A., Shibata, H., Suetomo, H., Ikeda, Y., Telikepalli, S., Kiyoshi, M., Hayashi, Y., Muto, T., Tanaka, Y., Ueda, S., Iwura, T., Saitoh, S., Aoyama, M., Harazono, A., Hyuga, M., Goda, Y., Torisu, T., & Uchiyama, S.
  Recent Achievements and Current Interests in Research on the Characterization and Quality Control of Biopharmaceuticals in Japan.
  Journal of pharmaceutical sciences, 109(5), 1652–1661.

• 2.

  Yanaka, S., & Uchiyama, S.
  Current status and issues of protein solution biophysics-Session 1SDP.
  Biophysical reviews, 12(2), 263–264.

Original Papers

• 1.

  Lee, JS., Kim, DH., Choi, BS., Kato, Y., Watanabe, H. and Lee, JS.
  Complete mitochondrial genome of the freshwater water flea Daphnia magna NIES strain (Cladocera, Daphniidae): Rearrangement of two ribosomal RNA genes.
  Mitochondrial DNA Part B, 5, 1822-1823.

• 2.

  Sangkuanun, T., Wichienchot, S., Kato, Y., Watanabe, H. and Peerakietkhajorn, S.
  Oligosaccharides derived from dragon fruit modulate gut microbiota, reduce oxidative stress and stimulate toll-pathway related gene expression in freshwater crustacean Daphnia magna.
  Fish Shellfish Immunol. 103, 126-134.

• 3.

  Nong, QD., Matsuura, T., Kato, Y., and Watanabe, H.
  Two Doublesex1 mutants revealed a tunable gene network underlying intersexuality in Daphnia magna.
  PLoS ONE 15, e0238256.

• 4.

  Adhitama, N., Kato, Y., Matsuura, T., and Watanabe, H.
  Roles of and cross-talk between ecdysteroid and sesquiterpenoid pathways in embryogenesis of branchiopod crustacean Daphnia magna.
  PLoS ONE 15, e0239893.

• 5.

  Nguyen, ND., Matsuura, T., Kato, Y., and Watanabe, H.
  Caloric restriction upregulates the expression of DNMT3.1, lacking the conserved catalytic domain, in Daphnia magna.
  Genesis 8, e23396.

• 6.

  Arao, T., Kato, Y., Nong, QD., Yamamoto, H., Watanabe, H., Matsuura, T., Tatarazako, N., Tani, K., Okamoto, A., Matsumoto, T. and Watanabe, H.
  Production of genome-edited Daphnia for heavy metal detection by fluorescence.
  Sci. Rep. 10, 21490.

• 7.

  Ismail, NIB., Kato, Y., Matsuura, T., Gómez-Canela, C., Barata, C. and Watanabe, H.
  Reduction of histamine and enhanced spinning behavior of Daphnia magna caused by scarlet mutant.
  Genesis 9, e23403.

• 8.

  Zhan, X., Ohtsuki, H., Makino, W., Kato, Y., Watanabe, H. and Urabe, J.
  Variations in effects of ectosymbiotic microbes on the growth rates among different species and genotypes of Daphnia fed different algal diets.
  Ecol. Res. 36, 303-312

Original Papers

• 1.

  Okazawa, A., Wakabayashi, T., Muranaka, T., Sugimoto, Y. and Ohta, D.
  The effect of nojirimycin on the transcriptome of germinating Orobanche minor seeds.
  J. Pestic. Sci., 45, 230-237.

• 2.

  Chung, S.Y., Seki, H., Fujisawa, Y., Shimoda, Y., Hiraga, S., Nomura, Y., Saito, K., Ishimoto, M. and Muranaka, T.
  A cellulose synthase-derived enzyme catalyses 3-O-glucuronosylation in saponin biosynthesis.
  Nat. Commun., 11, 5664.

• 3.

  Yasumoto, S., Sawai, S., Lee, H.J., Mizutani, M., Saito, K., Umemoto, N. and Muranaka, T.
  Targeted genome editing in tetraploid potato through transient TALEN expression by Agrobacterium infection.
  Plant Biotechnol., 37, 205–211.

• 4.

  Srisawat, P., Yasumoto, S., Fukushima, E.O., Robertlee, J., Seki, H. and Muranaka, T.
  Production of the bioactive plant-derived triterpenoid morolic acid in engineered Saccharomyces cerevisiae.
  Biotechnol. Bioeng., 117: 2198–2208.

• 5.

  Suzuki H., Fukushima E.O., Shimizu Y., Seki H., Fujisawa Y., Ishimoto M., Osakabe K., Osakabe Y., Muranaka T.
  Lotus japonicus triterpenoid profile and characterization of the CYP716A51 and LjCYP93E1 genes involved in their biosynthesis in planta.
  Plant Cell Physiol., 60: 2496-2509.

Preface

• 1.

  Tabei, Y. and Muranaka, T.
  Preface to the special issue “Technology in tissue culture toward horizon of plant biotechnology”.
  Biophysics and Physicobiology, 17, 98-99.

Original Papers

• 1.

  Yamano-Adachi N., Arishima, R., Puriwat, S., Omasa T.
  Establishment of fast-growing serum-free immortalised cells from Chinese hamster lung tissues for biopharmaceutical production
  Scientific Reports 10, 17612 (12 pages) (2020) DOI: 10.1038/s41598-020-74735-0

• 2.

  Yamano-Adachi N., Ogata N., Tanaka S., Onitsuka M., Omasa T.
  Characterization of Chinese hamster ovary cells with disparate chromosome numbers: reduction of the amount of mRNA relative to total protein
  J. Biosci. Bioeng. 129, 121-128 (2020) doi: 10.1016/j.jbiosc.2019.06.012.

• 3.

  Samy A., Kaneyoshi, K., Omasa T.
  Improvement of intracellular traffic system by overexpression of KDEL receptor 1 in antibody‐producing CHO cells
  Biotechnology J., 15, e1900352 (9 pages) (2020) doi:10.1002/biot.201900352.

• 4.

  Asano, R., Hosokawa,K., Taki, S., Konno, S., Shimomura, I., Ogata, H., Okada, M., Arai,K., Onitsuka, M., Omasa, T., Nakanishi, T., Umetsu, M., Kumagai, I.
  Build-up functionalization of anti-EGFR × anti-CD3 bispecific diabodies by integrating high　affinity mutants and functional molecular formats
  Scientific Reports 10, 4913 (8 pages) (2020) DOI: 10.1038/s41598-020-61840-3

• 5.

  Kido, M., Idogaki, H., Nishikawa, K., Motoishi, K., Omasa T.
  Screening of new cell cycle suppressive compounds from marine-derived microorganisms in Chinese hamster ovary cells
  J. Biosci. Bioeng. 130, 106-113 (2020) DOI:10.1016/j.jbiosc.2020.03.001

• 6.

  Doi, T., Kajihara, H., Chuman, Y., Kuwae, K., Kaminagayoshi, T., Omasa T.
  Development of a scale-up strategy for CHO cell culture processes using the kLa ratio as a direct indicator of gas stripping conditions
  Biotechnology Prog., 36, e3000 (12 page) (2020) DOI: 10.1002/btpr.3000

• 7.

  Kido, M., Idogaki, H., Nishikawa, K., Omasa T.
  Low-concentration staurosporine improves recombinant antibody productivity in Chinese hamster ovary cells without inducing cell death
  J. Biosci. Bioeng., 130, 525-532 (2020) DOI: 10.1016/j.jbiosc.2020.07.005./p>

• 8.

  Komatsu,K., Kumon, K., Arita, M., Onitsuka, M., Omasa, T., Yohda M.
  Effect of the disulfide isomerase PDIa4 on the antibody production of CHO cells
  J. Biosci. Bioeng., 130, 637-643 (2020) DOI: 10.1016/j.jbiosc.2020.08.001

• 9.

  Hokao, R., Matsumura, H., Katsumi, R., Angkawidjaja, C., Takano, K., Kanaya, S., Koga, Y.
  Affinity shift of ATP upon glycerol binding to a glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakarensis KOD1
  J. Biosci. Bioeng., 129, 657-663 (2020) https://doi.org/10.1016/j.jbiosc.2019.12.008

• 10.

  Sakudo, A., Imanishi, Y., Hirata, A., Koga, Y., Shintani, H.
  Effect of nitrogen gas plasma generated by a fast-pulsed power supply using a static induction thyristor on scrapie prion
  Pathogens, 9, 819 (2020) https://doi.org/10.3390/pathogens9100819

Original Papers

• 1.

  Nguyen, T.S., Misaki, R., Ohashi, T., Fujiyama, K.
  Enhancement of sialylation in rIgG in glyco-engineered Chinese hamster ovary cells.
  Cytotechnology 72, 343-355.

• 2.

  Matsumura, T., Amatsu, S., Misaki, R., Yutani, M., Anariwa, D., Kohda, T., Fujiyama, K., Ikuta, K., Fujinaga, Y.
  Fully Human Monoclonal Antibodies Effectively Neutralizing Botulinum Neurotoxin Serotype B.
  Toxins 12, 302.

• 3.

  Wongwisansri, S., Promdonkoy, P., Likhitrattanapisal, S., Harnpichanchai, P., Fujiyama, K., Kaneko, Y., Eurwilaichitr, L., Ingsrisawang. S., Tanapongpipat, S.
  Mating-type switching and mating-type gene array expression in the methylotrophic yeast Ogataea thermomethanolica TBRC656
  Microbiol. Res. 232,126372.

• 4.

  Kajiura, H., Nakamura, Y., Nishimura, M., Ohashi, T., Misaki, R., Fujiyama, K.
  Characterization of Bombyx mori N-acetylglucosaminyltransferase II splicing variants
  Biochem. Biophys. Res. Commun. 529, 404-410.

• 5.

  Ohashi, T., Fujisawa, Y., Hayes, M.R., Misaki, R., Pietruszka, J., Fujiyama, K.
  Transglycosylation toward naringenin-7-O-glucoside using an N180H mutant of Coprinopsis cinerea endo-β-N-acetylglucosaminidase.
  Biochem. Biophys. Res. Commun. 530, 155-159.

• 6.

  Arifin, M., Budiman, C., Fujiyama, K., Arief, I.I.
  Kinetic and Thermodynamic Study of Plantaricin IIA-1A5, a Bacteriocin Produced by Indonesian Probiotic Lactobacillus plantarum IIA-1A5
  Protein Pept. Lett. 28, 680-686

• 7.

  Wachananawat, B., Kuroha, T., Takenaka, Y., Kajiura, H., Naramoto, S., Yokoyama, R., Ishizaki, K., Nishitani, K., Ishimizu, T.
  Diversity of Pectin Rhamnogalacturonan I Rhamnosyltransferases in Glycosyltransferase Family 106
  Front Plant Sci. 11, 997.

Original Papers

• 1.

  Okano, K., Zhu, Q., and Honda, K.
  In vitro reconstitution of non-phosphorylative Entner–Doudoroff pathway for lactate production.
  J. Biosci. Bioeng. 129, 269-275.

• 2.

  Sato, Y., Okano, K., Kimura, H., and Honda, K.
  TEMPURA: Database of growth TEMPeratures of Usual and RAre prokaryotes.
  Microbes Environ. 35, ME20074.

• 3.

  Okano, K., Sato, Y., Inoue, S., Kawakami, S., Kitani, S. and Honda, K.
  Enhancement of S-adenosylmethionine-dependent methylation by integrating methanol metabolism with 5-methyltetrahydrofolate formation in Escherichia coli.
  Catalysts 10, 1001.

Original Papers

• 1.

  Araki, S., Nakano, M., Tsugane, M., Sunaga, F., Hattori, M., Nagai, T. and Suzuki, H.
  A simple microfluidic device for live-imaging of the vertical section of epithelial cells.
  Analyst, 145, 667-674.

• 2.

  Kuboki, T., Ebata, H., Matsuda, T., Arai, Y., Nagai, T. and Kidoaki, S.
  Hierarchical development of motile polarity in durotactic cells just crossing an elasticity boundary.
  Cell Structure and Function, 45, 33-43.

• 3.

  Hossain, M.N., Ishida, R., Hattori, M., Matsuda, T. and Nagai, T.
  Bioluminescent Ratiometric Indicator for Analysis of Water Hardness in Household Water.
  Sensors, 20, 3164.

• 4.

  Nakamura, S., Shigeyama, S., Minami, S., Shima, T., Akayama, S., Matsuda, T., Esposito, A., Napolitano, G., Kuma, A., Namba-Hamano, T., Nakamura, J., Yamamoto, K., Sasai, M., Tokumura, A., Miyamoto, M., Oe, Y., Fujita, T., Terawaki, S., Takahashi, A., Hamasaki, M., Yamamoto, M., Okada, Y., Komatsu, M., Nagai, T., Takabatake, Y., Xu, H., Isaka, Y., Ballabio, A. and Yoshimori, T.
  LC3 lipidation is essential for TFEB activation during the lysosomal damage response to kidney injury.
  Nature Cell Biology, 22, 1252–1263.

• 5.

  Harada, T., Sada, R., Osugi, Y., Matsumoto, S., Matsuda, T., Hayashi Nishino, M., Nagai, T., Harada, A. and Kikuchi, A.
  Palmitoylated CKAP4 regulates mitochondrial functions through an interaction with VDAC2 at ER-mitochondria contact sites.
  Journal of Cell Science, 133, jcs249045.

• 6.

  Hattori, M., Shirane, S., Matsuda, T., Nagayama, K. and Nagai, T.
  Smartphone-based portable bioluminescence imaging system enabling observation at various scales from whole mouse body to organelle.
  Sensors, 20, 7166.

Reviews

• 1.

  Nagai, T., Chikuma, S. and Hanaoka, K.
  Detection of singularity in immunity and cancer by novel imaging techniques.
  Biophysics and Physicobiology, 17, 98-99.

• 2.

  Wazawa, T., Washio, T. and Nagai, T.
  Highly Biocompatible Super-resolution Imaging: SPoD-OnSPAN.
  Single Molecule Microscopy, Yamamoto, N. & Okada, Y. Eds., Neuromethods, 229-244.

Original Papers

• 1.

  Takei, T., Ando, T., Takao, T., Ohnishi, Y., Kurisu, G., Iwaoka, M., and Hojo, H.
  Chemical synthesis of ferredoxin with 4 selenocysteine residues using a segment condensation method.
  Chem. Commun. (Camb). 56, 14239-14242.

• 2.

  Juniar, L., Tanaka, H., Yoshida, K., Hisabori, T., and Kurisu, G.
  Structural basis for thioredoxin isoform-based fine-tuning of ferredoxin-thioredoxin reductase activity.
  Protein. Sci. 29, 2538-2545.

• 3.

  Mizuno, H., Hoshino, J., So, M., Kogure, Y., Fujii, T., Ubara, Y., Takaichi, K., Nakaniwa, T., Tanaka, H., Kurisu, G., Kametani, F., Nakagawa, M., Yoshinaga, T., Sekijima, Y., Higuchi, K., Goto, Y., and Yazaki, M.
  Dialysis-related amyloidosis associated with a novel β 2-microglobulin variant.
  Amyloid. 2, 1-8.

• 4.

  Fujieda, N., Umakoshi, K., Ochi, Y., Nishikawa, Y., Yanagisawa, S., Kubo, M., Kurisu, G., and Itoh, S.
  Copper-Oxygen Dynamics in the Tyrosinase Mechanism.
  Angew. Chem. Int. Ed. Engl. 59, 13385-13390.

• 5.

  Kondo, T., Mutoh, R., Tabe, H., Kurisu, G., Oh-Oka, H., Fujiyoshi, S., and Matsushita, M.
  Cryogenic Single-Molecule Spectroscopy of the Primary Electron Acceptor in the Photosynthetic Reaction Center.
  J. Phys. Chem. Lett. 11, 3980-3986.

• 6.

  Ohnishi, Y., Muraki, N., Kiyota, D., Okumura, H., Baba, S., Kawano, Y., Kumasaka, T., Tanaka, H., and Kurisu, G.
  X-ray dose-dependent structural changes of the [2Fe-2S] ferredoxin from Chlamydomonas reinhardtii.
  J. Biochem. 167, 549-555.

• 7.

  Yamamoto, H., Mizoguchi, T., Tsukatani, Y., Tamiaki, H., Kurisu, G., and Fujita, Y.
  Chlorophyllide a oxidoreductase Preferentially Catalyzes 8-Vinyl Reduction over B-Ring Reduction of 8-Vinyl Chlorophyllide a in the Late Steps of Bacteriochlorophyll Biosynthesis.
  Chembiochem. 21, 1760-1766.

• 8.

  Fujieda, N., Ichihashi, H., Yuasa, M., Nishikawa, Y., Kurisu, G., and Itoh, S.
  Cupin Variants as a Macromolecular Ligand Library for Stereoselective Michael Addition of Nitroalkanes.
  Angew. Chem. Int. Ed. Engl. 59, 7717-7720.

• 9.

  Toda, A., Nishikawa, Y., Tanaka, H., Yagi, T., and Kurisu, G.
  The complex of outer-arm dynein light chain-1 and the microtubule-binding domain of the γ heavy chain shows how axonemal dynein tunes ciliary beating.
  J. Biol. Chem. 295, 3982-3989.

• 10.

  Hanson BS, Iida S, Read DJ, Harlen OG, Kurisu G, Nakamura H, and Harris SA.
  Continuum mechanical parameterisation of cytoplasmic dynein from atomistic simulation.
  Methods. S1046-2023, 30244-0.

• 11.

  Schuller, JM., Saura, P., Thiemann, J., Schuller, SK., Gamiz-Hernandez, AP., Kurisu, G., Nowaczyk, MM., and Kaila, VRI.
  Redox-coupled proton pumping drives carbon concentration in the photosynthetic complex I.
  Nat. Commun. 11, 494.

• 12.

  Charoenwattanasatien, R., Zinzius, K., Scholz, M., Wicke, S., Tanaka, H., Brandenburg, JS., Marchetti, GM., Ikegami, T., Matsumoto, T., Oda, T., Sato, M., Hippler, M., and Kurisu, G.
  Calcium sensing via EF-hand 4 enables thioredoxin activity in the sensor-responder protein calredoxin in the green alga Chlamydomonas reinhardtii.
  J. Biol. Chem. 295(1), 170-180.

• 13.

  Vizarraga, D., Kawamoto, A., Matsumoto, U., Illanes, R., Perez-Luque, R., Martin, J., Mazzolini, R., Bierge, P., Pich, O., Espasa, M., Sanfeliu, I., Esperalba, J., Fernandez-Huerta, M., Scheffer, M., Pinyol, J., Frangakis, A., Lluch-Senar, M., Mori, S., Shibayama, K., Kenri, T., Kato, T., Namba, K., Fita, I., Miyata, M. and Aparicio, D.
  Immunodominat proteins P1 and P40/P90 from human pathogen Mycoplasma pneumoniae.
  Nat. Commun. 11, 5188.

• 14.

  †Yamada, T., †Yoshida, T., †Kawamoto, A., Mitsuoka, K., Iwasaki, K. and Tsuge, H. (†equal contribution)
  Cryo-EM structures reveal translocational unfolding in the clostridial binary iota toxin complex.
  Nat. Struct & Mol. Biol. 27(3), 288-296.

• 15.

  Terashima, H., Tatsumi, C., Kawamoto, A., Namba, K., Minamino, T. and Imada, K.
  In Vitro autonomous construction of the flagellar axial structure in inverted membrane vesicles.
  Biomolecules. 10(1), 126.

• 16.

  Terashima, H., Hirano, K., Inoue, Y., Tokano, T., Kawamoto, A., Kato, T., Yamaguchi, E., Namba, K., Uchihashi, T., Kojima, S. and Homma, M.
  Assembly mechanism of a supramolecular MS-ring complex to initiate bacterial flagellar biogenesis in Vibrio Species.
  J. Bacteriol. 202(16), e00236-20.

• 17.

  Hakamada, K., Nakamura, M., Midorikawa, R., Shinohara, K., Noguchi, K., Nagaoka, H., Takashima, E., Morishima, K., Inoue, R., Sugiyama, M., Kawamoto, A. and Yohda, M.
  PV1 protein from Plasmodium falciparum exhibits chaperone-like functions and cooperates with HSP100s.
  Int. J. Mol. Sci. 21(22), 8616.

• 18.

  Kawamoto, A.
  In situ structural analysis of Leptospira spp. by electron cryotomography.
  Methods. Mol. Biol. Leptospira spp., 131-138.

Original Papers

• 1.

  Imura, M., Nitta, K., Iwakiri, R., Matsuda, F., Shimizu, H. and Fukusaki, E.
  Comparison of metabolic profiles of yeasts based on the difference of the Crabtree positive and negative.
  J. Biosci. Bioeng. 129, 52-58.

• 2.

  Matsuda, F., Maeda, K. and Okahashi, N.
  Computational data mining method for isotopomer analysis in the quantitative assessment of metabolic reprogramming.
  Sci. Rep. 10, 286.

• 3.

  Negoro, H., Matsumura, K., Matsuda, F., Shimizu, H., Hata, Y. and Ishida, H.
  Effects of mutations of GID protein-coding genes on malate production and enzyme expression profiles in Saccharomyces cerevisiae.
  Appl. Microbiol. Biotechnol. 104, 4971-4983.

• 4.

  Siriwach, R., Matsuda, F., Yano, K. and Hirai, M.-Y.
  Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of Arabidopsis thaliana.
  Metabolites. 10, 159.

• 5.

  Tsugawa, H., Ikeda, K., Takahashi, M., Satoh, A., Mori, Y., Uchino, H., Okahashi, N., Yamada, Y., Tada, I., Bonini, P., Higashi, Y., Okazaki, Y., Zhou, Z., Zhu, Z.-J., Koelmel, J., Cajka, T., Fiehn, O., Saito, K., Arita, M. and Arita, M.
  A lipidome atlas in MS-DIAL 4.
  Nat. Biotechnol. 38, 1159-1163.

• 6.

  Tokuyama, K., Shimodaira, Y., Terawaki, T., Kusunose, Y., Nakai, H., Tsuji, Y., Toya, Y., Matsuda, F. amd Shimizu, H.
  Data science-based modeling of the lysine fermentation process.
  J. Biosci. Bioeng. 130, 409-415.

• 7.

  Noguchi, S., Ishikawa, H., Wakita, K., Matsuda, F. and Shimizu, H.
  Direct and quantitative analysis of altered metabolic flux distributions and cellular ATP production pathway in fumarate hydratase-diminished cells.
  Sci. Rep. 10, 13065.

• 8.

  Toyoshima, M., Tokumaru, Y., Matsuda, F. and Shimizu, H.
  Assessment of protein content and phosphorylation level in Synechocystis sp. PCC 6803 under various growth conditions using quantitative phosphoproteomic analysis.
  Molecules. 25, 3582.

• 9.

  Kanazawa, S., Noda, A., Ito, A., Hashimoto, K., Kunisawa, A., Nakanishi, T., Kajihara, S., Mukai, N., Iida, J., Fukusaki, E. and Matsuda, F.
  Fake metabolomics chromatogram generation for facilitating deep learning of peak-picking neural networks.
  J. Biosci. Bioeng. 131, 207-212.

• 10.

  Nishiguchi, H., Liao, J., Shimizu, H. and Matsuda, F.
  Novel allosteric inhibition of phosphoribulokinase identified by ensemble kinetic modeling of Synechocystis sp. PCC 6803 metabolism.
  Metab. Eng. Commun. 11, e00153.

• 11.

  Yasuda, S., Okahashi, N., Tsugawa, H., Ogata, Y., Ikeda, K., Suda, W., Arai, H., Hattori, M. and Arita, M.
  Elucidation of gut microbiota-associated lipids using LC-MS/MS and 16S rRNA sequence analyses.
  iScience. 23, 101841.

Original Papers

• 1.

  Toyoshima, M., Tokumaru, Y., Matsuda F., and Shimizu, H.
  Assessment of protein content and phosphorylation level in Synechocystis sp. PCC 6803 under various growth conditions using quantitative phosphoproteomic analysis.
  Molecules, 25(16) 3582.

• 2.

  Noguchi, S., Ishikawa, H., Wakita, K., Matsuda, F., and Shimizu, H.
  Direct and quantitative analysis of altered metabolic flux distributions and cellular ATP production pathway in fumarate hydratase-diminished cells.
  Scientific Reports, 10, Article number 13065.

• 3.

  Tokuyama, K., Shimodaira, Y., Terawaki, T., Kusunose, Y., Nakai, H., Tsuji, Y., Toya, Y. Matsuda, F., and Shimizu, H.
  Data science-based modeling of the lysine fermentation process.
  Journal of Bioscience Bioengineering. 130(4), 409-415..

• 4.

  Nochino, N., Toya, Y., and Shimizu, H.
  Transcription factor ArcA is a flux sensor for the oxygen consumption rate in Escherichia coli..
  Biotechnology Journal. 15(6), 1900353.

• 5.

  Negoro, H., Matsumura, K., Matsuda, F., Shimizu, H., Hata, Y., and Ishida, H.
  Effects of mutations of GID protein-coding genes on malate production and enzyme expression profiles in Saccharomyces cerevisiae.
  Applied Microbiology Biotechnology. 104(11), 4971-4983.

• 6.

  Toyoshima, M., Toya, Y., and Shimizu, H.
  Flux balance analysis of cyanobacteria reveals selective use of photosynthetic electron transport components under different spectral light.
  Photosynthesis Research 143(1), 31-43 .

• 7.

  Nishiguchi, H., Liao, J. Shimizu, H., and Matsuda, F.
  Novel allosteric inhibition of phosphoribulokinase identified by ensemble kinetic modeling of Synechocystis sp. PCC 6803 metabolism.
  Metabolic Engineering Communications, e00153.

Reviews

• 1.

  Toya Y., and Shimizu, H.
  Flux controlling technology for central carbon metabolism for efficient microbial bio-production.
  Current Opinion in Biotechnology. 64, 169-174