Original Papers

• 1.

  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
  Journal of Bioscience and Bioengineering. Volume 129,Issue 5, 581-587.

• 2.

  Yutaka Umakoshi, Yosuke Nakano, Kosuke Fukuda, Kenichi Watanabe, Izuru Miyawaki, Eiichiro Fukusaki
  Automatic switching valve system to minimize variation of liquid chromatography-tandem mass spectrometry-based chiral amino acid profiling
  Journal of bioscience and bioengineering. Volume 129, Issue 6, 773-779.

• 3.

  Benedikt Heyman, Hannah Tulke, Sastia Prama Putri, Eiichiro Fukusaki, Jochen Büchs
  Online monitoring of the respiratory quotient reveals metabolic phases during microaerobic 2,3‐butanediol production with Bacillus licheniformis
  Engineering in Life Sciences. Volume 20, Issue 3-4, 133-144.

• 4.

  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, 296-301.

• 5.

  Elan Hernadi, Eti Rohaeti, Mohamad Rafi, Wulan Tri Wahyuni, Sastia Prama Putri, Eiichiro Fukusaki
  HPLC fingerprinting coupled with linear discriminant analysis for the detection of adulteration in Orthosiphon aristatus
  Journal of Liquid Chromatography & Related Technologies. 42 (15-16), 513-520.

• 6.

  Sastia Prama Putri, Tomoya Irifune, Eiichiro Fukusaki
  GC/MS based metabolite profiling of Indonesian specialty coffee from different species and geographical origin
  Metabolomics. 15 (10), 126 (2019).

• 7.

  Nakamura M, Moritsuna M, Yuda K, Fujimura S, Sugiura Y, Shimma S, Nishimoto K, Nishikawa T, Suematsu M, Ogawa S, Higashi T.
  Quantitative MALDI-MS/MS Assay for Serum Cortisol Through Charged Derivatization
  J Pharm Biomed Anal. 178, 112912. Epub 2019.

• 8.

  Shimma S, Sagawa T.
  Microscopy and Mass Spectrometry Imaging Reveals the Distributions of Curcumin Species in Dried Turmeric Root
  J Agric Food Chem. 67 (34), 9652 (2019)

• 9.

  Birthe Halmschlag, Xenia Steurer, Sastia P Putri, Eiichiro Fukusaki, Lars M Blank
  Tailor-made poly-γ-glutamic acid production
  Metabolic engineering. 55, 239-248 (2019).

• 10.

  Tomohiko Fukuda, Kiyofumi Takamatsu, Takeshi Bamba, Eiichiro Fukusaki
  Gas chromatography-mass spectrometry metabolomics-based prediction of potato tuber sprouting during long-term storage
  Journal of bioscience and bioengineering. 128 (2), 249-254 (2019).

• 11.

  Emi Takeo, Yuki Sugiura, Tatsuki Uemura, Koshiro Nishimoto, Masanori Yasuda, Eiji Sugiyama, Sumio Ohtsuki, Tatsuya Higashi, Tetsuo Nishikawa, Makoto Suematsu, Eiichiro Fukusaki, Shuichi Shimma
  Tandem mass spectrometry imaging reveals distinct accumulation patterns of steroid structural isomers in human adrenal glands
  Analytical chemistry. 91 (14), 8918-8925 (2019).

• 12.

  Miho Sakai, Yoshihiro Hayakawa, Yasuhiro Funada, Takashi Ando, Eiichiro Fukusaki, Takeshi Bamba
  Development of a practical online supercritical fluid extraction–supercritical fluid chromatography/mass spectrometry system with an integrated split-flow method
  Journal of Chromatography A. 1592, 161-172 (2019).

• 13.

  Anjaritha AR Parijadi, Sobir Ridwani, Fenny M Dwivany, Sastia P Putri, Eiichiro Fukusaki
  A metabolomics-based approach for the evaluation of off-tree ripening conditions and different postharvest treatments in mangosteen (Garcinia mangostana)
  Metabolomics. 15 (5), 73 (2019).

• 14.

  Yosuke Nakano, Moyu Taniguchi, Eiichiro Fukusaki
  High-sensitive liquid chromatography-tandem mass spectrometry-based chiral metabolic profiling focusing on amino acids and related metabolites
  Journal of bioscience and bioengineering. 127 (4), 520-527 (2019).

• 15.

  Katsuaki Nitta, Walter A Laviña, Sammy Pontrelli, James C Liao, Sastia P Putri, Eiichiro Fukusaki
  Metabolome analysis revealed the knockout of glyoxylate shunt as an effective strategy for improvement of 1-butanol production in transgenic Escherichia coli
  Journal of bioscience and bioengineering. 127 (3), 301-308 (2019).

• 16.

  Moyu Taniguchi, Asako Shimotori, Eiichiro Fukusaki
  Enantioselective Amino Acid Profile Improves Metabolomics-based Sensory Prediction of Japanese Sake
  Food Science and Technology Research. 25 (6), 775-784 (2019).

• 17.

  Takahiro Ogawa, Ken-Ichi Kusumoto, Eiichiro Fukusaki
  Construction of a Prediction Model for Taste of Miso (Japanese Fermented Soybean Paste) Using Metabolic Profiling and Quantitative Descriptive Analyses
  Food Science and Technology Research. 25 (6), 871-877 (2019).

• 18.

  Filemon Jalu Nusantara Putra, Sastia Prama Putri, Eiichiro Fukusaki
  Metabolomics-based profiling of three terminal alkene-producing Jeotgalicoccus spp. during different growth phase
  Journal of bioscience and bioengineering. 127 (1), 52-58 (2019).

Reviews

• 1.

  Britt SR Claes, Emi Takeo, Eiichiro Fukusaki, Shuichi Shimma, Ron MA Heeren
  Imaging isomers on a biological surface: A review
  Mass Spectrometry 8 (1), A0078-A0078 (2019)

• 2.

  Nakano Y, Taniguchi M, Umakoshi Y, Watai D, Fukusaki E.
  High-Throughput LC-MS/MS Method for Chiral Amino Acid Analysis Without Derivatization.
  Methods Mol Biol. 2019;2030:253-261. doi: 10.1007/978-1-4939-9639-1_19.

Original Papers

• 1.

  Horiguchi, I., Suzuki, I., Morimura, T. and Sakai, Y.
  An orbital shaking culture of mammalian cells in O-shaped vessels for the production of uniform aggregates.
  J. Vis. Exp. e57922.

• 2.

  Shuzui, E., Kim, M.-H. and Kino-oka, M.
  Anomalous cell migration triggers a switch to deviation from the undifferentiated state in colonies of human induced pluripotent stems on feeder layers.
  J. Biosci. Bioeng. 127, 246-255.

• 3.

  Kim, M.-H., Takeuchi, K. and Kino-oka, M.
  Role of cell-secreted extracellular matrix formation in aggregate formation and stability of human induced pluripotent stem cells in suspension culture.
  J. Biosci. Bioeng. 127, 372-380.

• 4.

  Nguyen, T.N.T., Sasaki, K. and Kino-oka, M.
  Elucidation of human induced pluripotent stem cell behaviors in colonies based on a kinetic model.
  J. Biosci. Bioeng. 127, 625-632.

• 5.

  Shuzui, E., Kim, M.-H., Azuma, K., Fujinaga, Y. and Kino-oka, M.
  Maintenance of an undifferentiated state of human-induced pluripotent stem cells through botulinum hemagglutinin-mediated regulation of cell behavior.
  J. Biosci. Bioeng. 127, 744-751.

• 6.

  Chang, C., Kim, M.-H., Agung, E., Senda, S. and Kino-oka, M.
  Effect of migratory behaviors on human induced pluripotent stem cell colony formation on different extracellular matrix proteins.
  Regen. Ther. 10, 27-35.

• 7.

  Oki, Y., Kirita, K., Ohta, S., Ohba, S., Horiguchi, I., Sakai, Y. and Ito, T.
  Switching of cell proliferation/differentiation in thiol-maleimide clickable microcapsules triggered by in situ conjugation of biomimetic peptides.
  Biomacromolecules 20, 2350-2359.

• 8.

  Koaykul, C., Kim, M.-H., Kawahara, Y., Yuge, L. and Kino-oka, M.
  Alterations in nuclear lamina and the cytoskeleton of bone marrow-derived human mesenchymal stem cells cultured under simulated microgravity conditions.
  Stem Cells Dev. 28, 1167-1176.

• 9.

  Kino-oka, M., Mizutani, M. and Medcalf N.
  Cell manufacturability.
  Cell & Gene Therapy Insights 5, 1347-1359.

• 10.

  Koaykul, C., Kim, M.-H., Kawahara, Y., Yuge, L. and Kino-oka, M.
  Maintenance of neurogenic differentiation potential in passaged bone marrow-derived human mesenchymal stem cells under simulated microgravity conditions.
  Stem Cells Dev. 28, 1552–1561.

• 11.

  Kato, Y., Matsumoto, T. and Kino-oka, M.
  Effect of liquid flow by pipetting during medium change on deformation of hiPSC aggregates.
  Regen. Ther. 12, 20-26.

• 12.

  Ogawa, Y., Mizutani, M., Okamoto, R., Kitajima H., Ezoe, S. and Kino-oka, M.
  Understanding the formation and behaviors of droplets toward consideration of changeover during cell manufacturing.
  Regen. Ther. 12, 36-42.

• 13.

  Torizal, FG., Horiguchi, I., Kimura, K. and Sakai, Y.
  Size-Dependent Hepatic Differentiation of Human Induced Pluripotent Stem Cells Spheroid in Suspension Culture.
  Regen. Ther. 12, 66-73.

• 14.

  Ibuki, M., Horiguchi, I. and Sakai, Y.
  A novel tool for suspension culture of human induced pluripotent stem cells: Lysophospholipids as a cell aggregation regulator.
  Regen. Ther. 12, 74-82.

• 15.

  Sekimoto, A., Kanemaru, Y., Okano Y., Kanie, K., Kato, R. and Kino-oka, M.
  Numerical investigation of particle dispersion in the preprocessing stage for a static cell cultivation.
  Regen. Ther. 12, 83-87.

• 16.

  Galvanauskas, V., Simutis, R., Nath, C.S. and Kino-oka, M.
  Kinetic modeling of human induced pluripotent stem cell expansion in suspension culture.
  Regen. Ther. 12, 88-93.

• 17.

  Suigyama, H., Shiokaramatsu, M. and Kino-oka, M.
  A distribution-based approach for determining lot sizes in the filling of human-induced pluripotent stem cells.
  Regen. Ther. 12, 94-101.

• 18.

  Mizutani, M., Terunuma, H., Samejima, H., Ashiba, K. and Kino-oka, M.
  Variation in the manufacturing reproducibility of autologous cell-based products depending on raw material shipment conditions.
  Regen. Ther. 12, 102-107

Original Papers

• 1.

  Yamamoto, K., Ishibashi, O., Sugiura, K., Ubatani, M., Sakaguchi, M., Nakatsuji, M., Shimamoto, S., Noda, M., Uchiyama, S., Fukutomi, Y., Nishimura, S. and Inui, T.
  Crystal structure of the dog allergen Can f 6 and structure-based implications of its cross-reactivity with the cat allergen Fel d 4.
  Sci Rep. 9(1):1503.

• 2.

  Matsui, T., Kamata, S., Ishii, K., Maruno, T., Ghanem, N., Uchiyama, S., Kato, K., Suzuki,A., Oda-Ueda ,N., Ogawa, T. and Tanaka, Y.
  SDS-induced oligomerization of Lys49-phospholipase A2 from snake venom.
  Sci Rep. 9(1):2330.

• 3.

  Yoneda, S., Niederleitner, B., Wiggenhorn, M., Koga, H., Totoki, S., Krayukhina, E., Friess, W. and Uchiyama, S.
  Quantitative laser diffraction (qLD) for a quantification of protein aggregates – comparison with resonant mass measurement, nano-particle tracking, flow imaging and light obscuration.
  J. Pharm. Sci. 108, 755-762.

• 4.

  Harazono, A., Shibata, H., Kiyoshi, M., Muto, T., Fukuda, J., Torisu, T., Saitoh, S., Nishimura, H., Uchiyama, S. and Ishii-Watabe, A.
  Interlaboratory comparison about feasibility of insoluble particulate matter test for injections with reduced test volume in light obscuration method.
  Biologicals 57, 46-49.

• 5.

  Krayukhina, E., Yokoyama, M., Kakuhou Hayashihara, K., Maruno, T., Noda M., Watanabe, H., Uchihashi, T. and Uchiyama, S.
  An assessment of the ability of submicron- and micron-size silicone oil droplets in dropped pre-fillable syringes to invoke early- and late-stage immune responses.
  J. Pharm. Sci. 108, 2278-2287.

• 6.

  Noda, M., Ishii, K., Yamauchi, M., Oyama, H., Tadokoro, T., Maenaka, K., Torisu, T. and Uchiyama, S.
  Identification of IgG1 Aggregation Initiation Region by Hydrogen/Deuterium Mass Spectrometry.
  J. Pharm. Sci. 108, 2323-2333.

• 7.

  Zhan, Y.-Y., Kojima, T., Ishii, K., Takahashi, S., Haketa, Y., Maeda, H., Uchiyama, S. and Hiraoka, S.
  SpectrometryTemperature-Controlled Repeatable Scrambling and Induced-fit Self-Sorting of Building Blocks Between Cubic Assemblies.
  Nature Communications 2019; 10: 1440.

• 8.

  Sekiguchi, T., Satoh, T., Kurimoto, E., Song, C., Kozai, T., Watanabe, H., Ishii, K., Yagi, H., Yanaka, S., Uchiyama, S., Uchihashi, T., Murata, K. and Kato, K.
  Mutational and Combinatorial Control of Self-Assembling and Disassembling of Human Proteasome α. Subunits.
  Int J Mol Sci. 20(9) pii: E2308.

• 9.

  Yunoki, Y., Ishii, K., Yagi-Utsumi, M., Murakami, R., Uchiyama, S., Yagi, H. and Kato,K.
  ATP hydrolysis by KaiC promotes its KaiA binding in the cyanobacterial circadian clock system.
  Life Sci Alliance. 2(3). pii: e201900368.

• 10.

  Yogo, R., Yamaguchi, Y., Watanabe, H., Yagi, H., Satoh T., Nakanishi, M., Onitsukam M., Omasam, T., Shimada, M., Maruno, T., Torisu, T., Watanabe, S., Hig,o D., Uchihashi, T., Yanaka, S., Uchiyama, S. and Kato, K.
  The Fab portion of immunoglobulin G contributes to its binding to Fcγ receptor III.
  Sci Rep. 9(1):11957.

• 11.

  Fujikawa, A., Sugawara, H., Tanga, N., Ishii, K., Kuboyama, K., Uchiyama, S., Suzuki, R. and Noda, M.
  A head-to-toe dimerization has physiological relevance for ligand-induced inactivation of protein tyrosine receptor type Z.
  J Biol Chem. 294(41):14953-14965.

• 12.

  Muraki, N., Ishii, K., Uchiyama, S., Itoh, SG., Okumura, H. and Aono, S.
  Structural characterization of HypX responsible for CO biosynthesis in the maturation of NiFe-hydrogenase.
  Commun Biol. 2:385.

• 13.

  Sugiyama, M., Fukaya, T., Moon JY., Ishida, K., Matsushita, A., Kim, SY. and Yeo, SH.
  Analysis and enhancement of the ethanol resistance of Pichia kudriavzevii N77-4, a strain newly isolated from the Korean traditional fermentation starter Nuruk, for improved fermentation performance.
  J Phys: Conf Ser. 1282: 012062.

Reviews

• 1.

  Wakayama, R., Uchiyama, S. and Hall D.
  Ionic liquids and protein folding-old tricks for new solvents.
  Biophys Rev. 11,209-225

Original Papers

• 1.

  Religia, P., Kato, Y., Fukushima, E. O., Matsuura, T., Muranaka, T., and Watanabe, H.
  Atrazine exposed phytoplankton causes the production of non-viable offspring on Daphnia magna.
  Mar Environ Res 145, 177-183

• 2.

  Okamura, K., Matsushita, S., Kato, Y., Watanabe, H., Matsui, A., Oka, T., and Matsuura, T.
  In vitro synthesis of the human calcium transporter Letm1 within cell-sized liposomes and investigation of its lipid dependency.
  J Biosci Bioeng 127, 544-548

• 3.

  Ogawa, M., Uyeda, A., Harada, K., Sato, Y., Kato, Y., Watanabe, H., Honda, K., and Matsuura, T.
  Class III polyphosphate kinase 2 enzymes catalyze the pyrophosphorylation of adenosine-5'-monophosphate.
  ChemBioChem 20, 2961-2967

• 4.

  Noba, K., Ishikawa, M., Uyeda, A., Watanabe, T., Hohsaka, T., Yoshimoto, S., Matsuura, T., and Hori, K.
  Bottom-up creation of an artificial cell covered with the adhesive bacterionanofiber protein AtaA.
  J Am Chem Soc 141, 19058-19066

• 5.

  Dwidar, M., Seike, Y., Kobori, S., Whitaker, C., Matsuura, T., and Yokobayashi, Y.
  Programmable artificial cells using histamine-responsive synthetic riboswitch.
  J Am Chem Soc 141, 11103-11114

• 6.

  Cabalzar, A. P., Fields, P. D., Kato, Y., Watanabe, H., and Ebert, D.
  Parasite-mediated selection in a natural metapopulation of Daphnia magna.
  Mol Ecol 28, 4770-4785

Original Papers

• 1.

  Munakata R., Takemura T., Tatsumi K., Moriyoshi E., Yanagihara K., Sugiyama A., Suzuki H., Seki H., Muranaka H., Kawano N., Yoshimatsu K., Kawahara N., Grosjean J., Bourgaud F., Hehn A., Yazaki K.
  Isolation of Artemisia capillaris membrane-bound di-prenyltransferase for phenylpropanoids and redesign of artepillin C in yeast.
  Communications Biol., 2: 384.

• 2.

  Vo N.N., Nomura Y, Muranaka T., Fukushima E.O.
  Structure-activity relationships of pentacyclic triterpenoids as inhibitors of cyclooxygenase and lipoxygenase enzymes.
  J. Nat. Prod., 82, 3311–3320.

• 3.

  Fanani M.Z., Fukushima E.O., Sawai S., Tang J., Ishimori M., Sudo H., Ohyama K., Seki H., Saito K., Muranaka T.
  Molecular basis of C-30 product regioselectivity of legume oxidases involved in high-value triterpenoid biosynthesis.
  Front. Plant Sci., 10: 1520.

• 4.

  Yasumoto S., Umemoto N., Lee H.J., Nakayasu M., Sawai S., Sakuma T., Yamamoto T., Mizutani M., Saito K., Muranaka T.
  Efficient genome engineering using Platinum TALEN in potato.
  Plant Biotechnol., 36, 167–173.

• 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.

• 6.

  Srisawat P., Fukushima E.O., Yasumoto S., Robertlee J., Suzuki H., Seki H., Muranaka T.
  Identification of oxidosqualene cyclases from the medicinal legume tree Bauhinia forficata: a step toward discovering preponderant α‐amyrin‐producing activity.
  New Phytol., 224, 352–366.

• 7.

  Muangphrom P., Misaki M., Suzuki M., Shimomura M., Suzuki H., Seki H., Muranaka T.
  Identification and characterization of (+)-α-bisabolol and 7-epi-silphiperfol-5-ene synthases from Artemisia abrotanum.
  Phytochemistry, 164, 144–153.

• 8.

  Nomura M., Seki H., Suzuki T., Ohyama K., Mizutani M., Kaku T., Tamura K., Ono E., Horikawa M., Sudo H., Hayashi H., Saito K., Muranaka T.
  Functional specialization of UDP‐glycosyltransferase 73P12 in licorice to produce a sweet triterpenoid saponin, glycyrrhizin.
  Plant J., 99, 1127–1143.

Original Papers

• 1.

  Kaneyoshi, K., Uchiyama, K., Onitsuka, M., Yamano-Adachi, N., Koga, Y. and Omasa, T.
  Analysis of intracellular IgG secretion in Chinese hamster ovary cells to improve IgG production.
  J. Biosci. Bioeng., 127, 1, 107-113.

• 2.

  Kaneyoshi, K., Yamano-Adachi, N., Koga, Y., Uchiyama, K., and Omasa, T.
  Analysis of the immunoglobulin G (IgG) secretion efficiency in recombinant Chinese hamster ovary (CHO) cells by using Citrine-fusion IgG.
  Cytotechnology, 71, 1, 193-207.

• 3.

  Kaneyoshi, K., Kuroda, K., Uchiyama, K., Onitsuka, M., Yamano-Adachi, N., Koga, Y. and Omasa, T.
  Secretion analysis of intracellular “difficult-to-express” immunoglobulin G (IgG) in Chinese hamster ovary (CHO) cells.
  Cytotechnology, 71, 1, 305-316.

• 4.

  Koga, Y., Konishi, K., Kobayashi, A., Kanaya, S. and Takano, K.
  Anaerobic glycerol-3-phosphate dehydrogenase complex from hyperthermophilic archaeon Thermococcus kodakarensis KOD1.
  J. Biosci. Bioeng., 127, 6, 679-685.

• 5.

  Onitsuka, M., Kadoya, Y. and Omasa, T.
  Secretory leakage of IgG1 aggregates from recombinant Chinese hamster ovary cells.
  J. Biosci. Bioeng., 127, 6, 752-757.

• 6.

  Yogo, R., Yamaguchi, Y., Watanabe, H., Yagi, H., Satoh, T., Nakanishi, M., Onitsuka, M., Omasa, T., Shimada, M., Maruno, T., Torisu, T., Watanabe, S., Higo, D., Uchihashi, T., Yanaka, S., Uchiyama, S. and Kato, K.
  The Fab portion of immunoglobulin G contributes to its binding to Fcγ receptor III.
  Sci. Rep., 9, 11957.

Original Papers

• 1.

  Ohashi, H., Ohashi, T., Misaki, R. and Fujiyama, K.
  Arabidopsis thaliana α1,2-l-fucosyltransferase catalyzes the transfer of l-galactose to xyloglucan oligosaccharides
  FEBS Lett. 593, 187-194.

• 2.

  Tsai, Y.Y., Ohashi, T., Wu, C.C., Bataa, D., Misaki, R., Limtong, S. and Fujiyama, K.
  Delta-9 fatty acid desaturase overexpression enhanced lipid production and oleic acid content in Rhodosporidium toruloides for preferable yeast lipid production
  J Biosci Bioeng. 127, 430-440.

• 3.

  Flores, R.J.D., Ohashi, T., Sakai, K., Gonoi, T., Kawasaki, H. and Fujiyama, K.
  The neutral N-linked glycans of the Basidiomycetous yeasts Pseudozyma antarctica and Malassezia furfur (Subphylum Ustilaginomycotina)
  J Gen Appl Microbiol. 65, 53-63.

• 4.

  Arofatullah, N.A., Kabirun, S., Fujiyama, K. and Widianto, D.
  Molecular identification and in vitro propagation of arbuscular mycorrhiza from tea plant rhizosphere
  Curr. Res. Environ. Appl. Mycol. 9, 92–102.

• 5.

  Bunsangiam, S., Sakpuntoon, V., Srisuk, N., Ohashi, T., Fujiyama, K. and Limtong, S.
  Biosynthetic pathway of indole-3-acetic acid in Basidiomycetous yeast Rhodosporidiobolus fluvialis
  Mycobiology 47, 292-300.

• 6.

  Matsuura, H., Ujiie, K., Duyen, T.T.M., Izutsu, K., Fujiyama, K., Maeda, S., Harada, K. and Hirata, K.
  Development of a paper-Based luminescence bioassay for therapeutic monitoring of aminoglycosides: a proof-of-concept study.
  Appl. Biochem. Biotechnol. 189, 798-809.

Reviews

• 1.

  Fujiyama, K.
  ‘Plant and Glycan’, in Taniguchi, N., et al. (eds.) Glycoscience: Basic Science to Applications.
  Singapore: Springer, pp. 114-115.

Original Papers

• 1.

  Honda, K., Ono, T., Okano, K., Miyake, R., Dekishima, Y., Kawabata, H.
  Expression of engineered carbonyl reductase from Ogataea minuta in Rhodococcus opacus and its application to whole-cell bioconversion in anhydrous solvents.
  J. Biosci. Bioeng. 127, 145-149.

• 2.

  Taniguchi, H., Imura, M., Okano, K., Honda, K.
  Developing a single strain for in vitro salvage synthesis of NAD+ at high temperatures and its potential for bioconversion.
  Microb. Cell Fact. 18, 75.

• 3.

  Hanatani, Y., Imura, M., Taniguchi, H., Okano, K., Toya, Y., Iwakiri, R., Honda, K.
  In vitro production of cysteine from glucose.
  Appl. Microbiol. Biotechnol. 103, 8009–8019.

• 4.

  Ogawa, M., Uyeda, A., Harada, K., Sato, Y., Kato, Y., Watanabe, H., Honda, K., Matsuura, T.
  Class III polyphosphate kinase 2 enzymes catalyze the pyrophosphorylation of adenosine-5′-monophosphate.
  ChemBioChem 20,2961-2967.

• 5.

  Ueda, S., Ikeda, H., Namba, T., Ikejiri, Y., Nihimoto, Y., Arai, M., Nihira, T., Kitani, S.
  Identification of biosynthetic genes for the β-carboline alkaloid kitasetaline and production of the fluorinated derivatives by heterologous expression.
  J. Ind. Microbiol. Biotechnol. 46,739-750.

Original Papers

• 1.

  Inagaki, S., Agetsuma, M., Ohara, S., Iijima, T., Yokota, H., Wazawa, T., Arai, Y. and Nagai, T.
  Imaging local brain activity of multiple freely moving mice sharing the same environment.
  Sci. Rep. 9, 7460.

• 2.

  Farhana, I., Hossain, M.N., Suzuki, K., Matsuda, T. and Nagai, T.
  Genetically Encoded Fluorescence/Bioluminescence Bimodal Indicators for Ca2+ Imaging.
  ACS Sens. 4, 1825-1834.

• 3.

  Shinoda, H., Lu, Kai., Nakashima, R., Wazawa, T., Noguchi, K., Matsuda, T. and Nagai, T.
  Acid-Tolerant Reversibly Switchable Green Fluorescent Protein for Super-resolution Imaging under Acidic Conditions.
  Cell Chem. Biol. 26, 1469-1479.

• 4.

  Oketani, R., Suda, H., Uegaki, K., Kubo, T., Matsuda, T., Yamanaka, M., Arai, Y., Smith, N., Nagai, T. and Fujita, K.
  Visible-wavelength two-photon excitation microscopy with multifocus scanning for volumetric live-cell imaging.
  J Biomed Opt. 25, 014502.

Reviews

• 1.

  Lu, K., Vu, C.Q., Matsuda, T. and Nagai, T.
  Fluorescent protein-based indicators for functional super-resolution imaging of biomolecular activities in living cells.
  Int. J. Mol. Sci. 20, 5784.

Original Papers

• 1.

  Schuller, J.M., Birrell, J.A., Tanaka, H., Konuma, T., Wulfhorst, H., Cox, N., Schuller, S.K., Thiemann, J., Lubitz, W., Sétif, P., Ikegami, T., Engel, B.D., Kurisu, G. and Nowaczyk, M.M.
  Structural adaptations of photosynthetic complex I enable ferredoxin-dependent electron transfer.
  Science. 363, 257-260.

• 2.

  Grabsztunowicz, M., Mulo, P., Baymann, F., Mutoh, R., Kurisu, G., Sétif, P., Beyer, P. and Krieger-Liszkay, A.
  Electron transport pathways in isolated chromoplasts from Narcissus pseudonarcissus L.
  Plant J. 99, 245-25.

• 3.

  Nagamura, R., Fukuda, M., Kawamoto, A., Matoba, K., Dohmae, N., Ishitani, R., Takagi, J. and Nureki. O.
  Structural basis for oligomerization of the prokaryotic peptide transporter PepTSo2.
  Acta Crst F. 75, 348-358.

• 4.

  Sugiura, K., Tanaka, H., Kurisu, G., Wakabayashi, K. and Hisabori, T.
  Multicolor Redox Sensor Proteins Can Visualize Redox Changes in Various Compartments of the Living Cell.
  Biochim Biophys Acta Gen Subj. 1863, 1098-1107.

• 5.

  Berengut, FJ., Berengut, CJ., Doye, PKJ., Presern, D., Kawamoto, A., Ruan, J., Wainwright, JM. and Lee, KL.
  Design and synthesis of pleated DNA origami nanotubes with adjustable diameters.
  Nucleic Acids Res. 47, 11963-11975.

• 6.

  Nishikawa, SM., Nakane, D., Toyonaga, T., Kawamoto, A., Kato, T., Namba, K. and Miyata, M.
  Refined mechanism of Mycoplasma mobile gliding based on structure, ATPase activity, and sialic acid binding of machinery.
  mBio. 10, e02846-19.

Reviews

• 1.

  Minamino, T., Kawamoto, A., Kinoshita, M. and Namba, K.
  Molecular organization and assembly of the export apparatus of flagellar type III secretion system.
  Springer. 1-17.

Original Papers

• 1.

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

• 2.

  Tokuyama, K., Toya, Y., Matsuda, F., Cress, B.F., Koffas, M.A.G. and Shimizu, H.
  Magnesium starvation improves production of malonyl-CoA-derived metabolites in Escherichia coli.
  Metab. Eng. 52, 215–223.

• 3.

  Nishiguchi, H., Hiasa, N., Uebayashi, K., Liao, J., Shimizu, H. and Matsuda, F.
  Transomics data-driven, ensemble kinetic modeling for system-level understanding and engineering of the cyanobacteria central metabolism.
  Metab. Eng. 52, 273–283.

• 4.

  Kamiura, R., Toya, Y., Matsuda, F. and Shimizu, H.
  Theophylline-inducible riboswitch accurately regulates protein expression at low level in Escherichia coli.
  Biotechnol. Lett. 41, 743–751.

• 5.

  Maruyama, M., Nishiguchi, H., Toyoshima, M., Okahashi, N., Matsuda, F. and Shimizu, H.
  Time-resolved analysis of short term metabolic adaptation at dark transition in Synechocystis sp. PCC 6803.
  J. Biosci. Bioeng. 128, 4, 424-428.

• 6.

  Ueda, K., Mizuuchi, R., Matsuda, F. and Ichihashi, N.
  A fusion method to develop an expanded artificial genomic RNA replicable by Qβ replicase.
  ChemBioChem 20, 2331-2335.

• 7.

  Kamiura, R., Matsuda, F. and Ichihashi, N.
  Survival of membrane-damaged Escherichia coli in a cytosol-mimicking solution.
  J. Biosci. Bioeng. 128, 558–563.

• 8.

  Okahashi, N., Kawana, S., Iida, J., Shimizu, H. and Matsuda, F.
  Fragmentation of Dicarboxylic and Tricarboxylic Acids in the Krebs Cycle Using GC-EI-MS and GC-EI-MS/MS.
  Mass Spectrom. 8, A0073, 1-21.

• 9.

  Izumi, Y., Matsuda, F., Hirayama, A., Ikeda, K., Kita, Y., Horie, K., Saigusa, D., Saito, K., Sawada, Y., Nakanishi, H., Okahashi, N., Takahashi, M., Nakao, M., Hata, K., Hoshi, Y., Morihara, M., Tanabe, K., Bamba, T. and Oda, Y.
  Inter-laboratory comparison of metabolite measurements for metabolomics data integration.
  Metabolites, 9, 257, 1-12.

Original Papers

• 1.

  Kamata, K., Toya, Y., and Shimizu, H.
  Effect of precise control of flux ratio between the glycolytic pathways on mevalonate production in Escherichia coli.
  Biotechnology and Bioengineering. 116(5), 1080-1088.

• 2.

  Nishiguchi, H., Hiasa, N., Uebayashi, K., Liao. J,, Shimizu, H., and Matsuda, F.
  Transomics data-driven, ensemble kinetic modeling for system-level understanding and engineering of the cyanobacteria central metabolism.
  Metabolic Engineering. 52, 273-283.

• 3.

  Kamiura, R., Toya, Y., Matsuda, F., and Shimizu, H.
  Theophylline-inducible riboswitch accurately regulates protein expression at low level in Escherichia coli.
  Biotechnology Letters. 41, 743–751.

• 4.

  Maruyama, M., Nishiguchi, H., Toyohima, M., Okahashi, N., Matsuda, F., and Shinizu, H.
  Time-resolved analysis of short term metabolic adaptation at dark transition in Synechocystis sp. PCC6803.
  Journal of Bioscience Bioengineering.128(4), 424-428.

• 5.

  Kitamura, S., Toya, Y., and Shimizu, H.
  13C-Metabolic Flux Analysis Reveals Effect of Phenol on Central Carbon Metabolism in Escherichia coli.
  Frontiers in Microbiology. 10,1010.

• 6.

  Tandar S. T., Senoo, S., Toya, Y., and Shimizu, H.
  Optogenetic switch for controlling the central metabolic flux of Escherichia coli.
  Metabolic Engineering. 55, 68-75.

• 7.

  Tokuyama, K., Toya, Y., and Shimizu, H.
  Prediction of rate‐limiting reactions for growth‐associated production using a constraint‐based approach.
  Biotechnology Journal. 1800431

• 8.

  Adachi, S., Tanaka, Y., Miyagi, A., Kashima, M., Tezuka, A., Toya, Y., Kobayashi, S., Ohkubo, S., Shimizu, H., Kawai-Yamada, M., Sage, R.F., Nagano, A., and Yamori, W.
  High-yielding rice Takanari has superior photosynthetic response under fluctuating light to a commercial rice Koshihikari.
  Journal of Experimental Botany. 70(19), 5287–5297.

• 9.

  Okahashi, N. Kawana, S., Iida, J., Shimizu, H., Matsuda, F.
  Fragmentation of dicarboxylic and tricarboxylic acids in the Krebs cycle using GC-EI-MS and GC-EI-MS/MS.
  Mass Spectrometory, A0073.

• 10.

  Hanatani, Y., Imura, M., Taniguchi, H., Okano,K., Toya, Y., Iwakiri, R., and Honda, K.
  In vitro production of cysteine from glucose.
  Applied Microbiology and Biotechnology, 103 (19). 8009–8019.

• 11.

  Senoo, S., Tandar., S. T., Kitamura, S., Toya, Y., and Shimizu, H.
  Light-inducible flux control of triosephosphate isomerase on glycolysis in Escherichia coli.
  Biotechnology and Bioengineering. 116(12), 3292-3300.

• 12.

  Morita, K., Matsuda, F., Okamoto, K., Ishii, J., Kondo, A., and Shimizu, H.
  Repression of mitochondrial metabolism for cytosolic pyruvate-derived chemical production in Saccharomyces cerevisiae.
  Microbial Cell Factories. 18(1), 177.