Original Papers

• 1.

  Huang, H., Kawamata, T., Horie, T., Tsugawa, H., Nakayama, Y., Ohsumi, Y. and Fukusaki E.
  (2015) Bulk RNA degradation by nitrogen starvation-induced autophagy in yeast.
  EMBO J. 34, 154-168.

• 2.

  Ishibashi, M., Izumi, Y., Sakai, M., Ando, T., Fukusaki, E and Bamba, T.
  (2015) High-Throughput Simultaneous Analysis of Pesticides by Supercritical Fluid Chromatography Coupled with High-Resolution Mass Spectrometry.
  J. Agric. Food Chem. 63, 4457-4463.

• 3.

  Marfori, E., Kajiyama, S., Fukusaki, E. and Kobayashi, A.
  (2015) Lansioside D, a new triterpenoid glycoside antibiotic from the fruit peel of Lansium domesticum Correa.
  J. Pharmacogn. Phytochem. 3, 140-143.

• 4.

  Kakuta, S., Yamashita, T., Nishiumi, S., Yoshida, M., Fukusaki, E. and Bamba, T.
  (2015) Multi-Component Profiling of Trace Volatiles in Blood by Gas Chromatography/Mass Spectrometry with Dynamic Headspace Extraction.
  Mass Spectrom. 4, A0034

• 5.

  Tsugawa, H., Ohta, E., Izumi, Y., Ogiwara, A., Yukihira, D., Bamba, T., Fukusaki, E. and Arita M.
  (2015) MRM-DIFF: data processing strategy for differential analysis in large scale MRM-based lipidomics studies.
  Front. Genet. 5, 471, 1-15.

• 6.

  Wakabayashi, T., Joseph, B., Yasumoto, S., Akashi, T., Aoki, T., Harada, K., Muranaka, S., Bamba, T., Fukusaki, E., Takeuchi, Y., Yoneyama, K., Muranaka, T., Sugimoto, Y. and Okazawa, A.
  (2015) Planteose as a storage carbohydrate required for early stage of germination of Orobanche minor and its metabolism as a possible target for selective control.
  J. Exp. Bot. 66, 3085-3097.

• 7.

  Jumhawan, U., Putri, S.P., Yusianto, Bamba, T. and Fukusaki E.
  (2015) Application of gas chromatography/flame ionization detector-based metabolite fingerprinting for authentication of Asian palm civet coffee (Kopi Luwak).
  J Biosci. Bioeng. 120, 555-561.

• 8.

  Shimizu, R., Dempo, Y., Nakayama, Y., Nakamura S, Bamba T, Fukusaki E, Fukui T.
  (2015) New Insight into the Role of the Calvin Cycle: Reutilization of CO2 Emitted through Sugar Degradation.
  Sci Rep. 5, 11617.

• 9.

  Meissner, L., Kauffmann, K., Wengeler. T., Mitsunaga, H., Fukusaki, E. and Büchs, J.
  (2015) Influence of nitrogen source and pH value on undesired poly(γ-glutamic acid) formation of a protease producing Bacillus licheniformis strain.
  J. Ind. Microbiol. Biotechnol. 42, 1203-1215.

• 10.

  Takeda, H., Koike, T., Izumi, Y., Yamada, T., Yoshida, M., Shiomi, M., Fukusaki, E. and Bamba, T.
  (2015) Lipidomic analysis of plasma lipoprotein fractions in myocardial infarction-prone rabbits.
  J. Biosci. Bioeng. 120, 476-482.

• 11.

  Teoh, S. T., Putri, S., Mukai, Y., Bamba, T. and Fukusaki, E.
  (2015) A metabolomics-based strategy for identification of gene targets for phenotype improvement and its application to 1-butanol tolerance in Saccharomyces cerevisiae.
  Biotechnol. Biofuels. 8, 144, 1-14.

• 12.

  Kakuta, S., Nishiumi, S., Yoshida, M., Fukusaki, E. and Bamba, T.
  (2015) Profiling of volatile compounds in APCMin/+ mice blood by dynamic headspace extraction and gas chromatography/mass spectrometry.
  J. Chromatogr. B. 1003, 35–40.

• 13.

  Rahmen, N., Schlupp, C.D., Mitsunaga, H., Fulton, A., Aryani, T., Esch, L., Schaffrath, U., Fukuzaki, E., Jaeger, K. E. and Büchs, J.
  (2015) A particular silent codon exchange in a recombinant gene greatly influences host cell metabolic activity.
  Microb. Cell Fact. 14, 156, 1-14.

• 14.

  Shimma, S.
  (2015) Characterizations of Two-step Matrix Application Procedures for Imaging Mass Spectrometry.
  Mass Spectrum. Lett. 6, 21-25.

Original Papers

• 1.

  Ogawa, Y., Kim, MH. and Kino-oka, M.
  (2015) Changes in human mesenchymal stem cell behaviors on dendrimer-immobilized surfaces due to mediation of fibronectin adsorption and assembly.
  J. Biosci. Bioeng. 120, 709-714.

Original Papers

• 1.

  Poonperm, R., Takata, H., Hamano, T., Matsuda, A., Uchiyama, S., Hiraoka, Y. and Fukui, K.
  (2015) Chromosome scaffold is a double-stranded assembly of scaffold proteins.
  Sci. Rep. 5, 11916.

• 2.

  Equilibrina, I., Krayukhina E., Inoue, K., Ishikawa, Y., Kawamoto, A., Kato, T., Suetake, I., Tajima, S., Takata, H., Uchiyama, S. and Fukui, K.
  (2015) The role of phosphorylation of Histone H3 Serine 10 in chromosome condensation in vitro.
  Chromosome science 18, 9-14.

• 3.

  Kaneyoshi, K., Fukuda, S., Dwiranti, A., Kato, J., Otsuka, Y., Takata, H., Uchiyama, S., Ogawa, S. and Fukui, K.
  (2015) Effects of dehydration and drying steps on human chromosome interior revealed by focused ion beam/scanning electron microscopy (FIB/SEM).
  Chromosome Science 18, 23-28.

• 4.

  Robinson, I., Mohammed, Y., Schwenke, J., Estandarte, A., Zhang, F., Chen, B., Clark, J., Song, C., Nam, D., Joti, Y., Tono, K., Yabashi, M., Ratnasari, G., Kaneyoshi, K., Takata, H. and Fukui, K.
  (2015) Towards Single Particle Imaging of human chromosomes at SACLA.
  J. Phys. B: At. Mol. Opt. Phys. 48, 244007.

• 5.

  Krayukhina, E., Tsumoto, K., Uchiyama, S. and Fukui, K.
  (2015) Effects of syringe material and silicone oil lubrication on the stability of pharmaceutical proteins.
  J. Pharm. Sci. 104, 527-535.

• 6.

  Totoki, S., Yamamoto, G., Tsumoto, K., Uchiyama, S. and Fukui, K.
  (2015) Quantitative laser diffraction method for the assessment of protein subvisible particles.
  J. Pharm. Sci. 104, 618-626.

• 7.

  Volkin, D., Hershenson, S., Ho, R., Uchiyama, S., Winter, G. and Carpenter, J.
  (2015) Two Decades of Publishing Excellence in Pharmaceutical Biotechnology
  J. Pharm. Sci. 104, 290-300.

• 8.

  Han, W., Yamauchi, M., Hasegawa, U., Noda, M., Fukui, K., van der Vlies, Uchiyama, S. and Uyama, H.
  (2015) Pepsin immobilization on an aldehyde-modified polymethacrylate monolith and its application for protein analysis.
  J. Biosci. Bioeng. 119, 505-510.

• 9.

  Watanabe, K., Terakura, S., Martens, A.C., van Meerten, T., Uchiyama, S., Imai, M., Sakemura, R., Goto, Hanajiri, R., Imahashi, N., Shimada, K., Tomita, A., Kiyoi, H., Nishida, T., Naoe, T. and Murata, M.
  (2015) Target Antigen Density Governs the Efficacy of Anti–CD20-CD28-CD3 ζ Chimeric Antigen Receptor–Modified Effector CD8+ T Cells
  J. Immunol. 194, 911-920.

• 10.

  Ohto, U., Shibata, T., Tanji, H., Krayukhina, E., Uchiyama, S., Miyake, K. and Shimizu, T.
  (2015) Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9.
  Nature 520, 702-705.

• 11.

  Harada, S., Hiromori, Y., Nakamura, S., Kawahara, K., Fukakusa, S., Maruno, T., Noda, M., Uchiyama, S., Fukui, K., Nishikawa, J., Nagase, H., Kobayashi, Y., Yoshida, T., Ohkubo, T. and Nakanishi, T.
  (2015) Structural basis for PPARgamma transactivation by endocrine disrupting organotin compounds.
  Sci. Rep. 5, 8520.

• 12.

  Kita, S., Matsubara, H., Kasai, Y., Tamaoki, T., Okabe, Y., Fukuhara, H., Kamishikiryo, J., Krayukhina, E., Uchiyama, S., Ose, T., Kuroki, K. and Maenaka, K.
  (2015) Crystal structure of extracellular domain of human lectin-like transcript 1 (LLT1), the ligand for natural killer receptor-P1A.
  European Journal of Immunology 45, 1605-13.

• 13.

  Zhao, H., Uchiyama, S. and Schuck, P.
  (2015) A Multilaboratory Comparison of Calibration Accuracy and the Performance of External References in Analytical Ultracentrifugation.
  PLoS ONE 10, e0126420

• 14.

  Amano, M., Fukui, K. and Uchiyama, S.
  (2015) Suppression of methionine oxidation of a pharmaceutical antibody stored in a polymer-based syringe.
  J. Pharm. Sci.

• 15.

  Ishii, K., Enda, H., Noda, M., Kajino, M., Kim, A., Kurimoto, E., Sato, K., Nakano, A., Kobayashi, Y., Yagi., H., Uchiyama, S. and Kato, K.
  (2015) pH-dependent assembly and segregation of the coiled-coil segments of yeast putative cargo receptors Emp46p and Emp47p
  PLoS ONE 10, e0140287.

• 16.

  Yoshida, K., Tojoa ,K., Morib, M., Yamashita, K., Kitahara, S., Noda, M. and Uchiyama, S.
  (2015) Chemical mechanism of petal color development of Nemophila menziesii by a metalloanthocyanin, nemophilin.
  Tetrahedron 71, 9123-9130.

• 17.

  Uchiyama, S., Kawahara, K., Hosokawa, Y., Fukakusa, S., Oki, H., Nakamura, S., Kojima, Y., Noda, M., Takino, R., Miyahara, Y., Maruno, T., Kobayashi, Y., Ohkubo, T. and Fukui, K.
  (2015) Structural basis for dimer formation of human condensin SMC and its implications for single strand DNA recognition.
  J. Biol. Chem. 290, 29461-477.

• 18.

  Ishii, K., Noda, M., Yagi, H., Thammaporn, R., Seetaha, S.,
  Satoh, T., Kato, K. and Uchiyama, S.
  (2015) Disassembly of the self-assembled, double-ring structure of proteasome α7 homo-tetradecamer by α6.
  Sci. Rep. 5, 18167.

Original Papers

• 1.

  Uyeda, A., Watanabe, T., Kato, Y., Watanabe, H., Yomo, T., Hohsaka, T. and Matsuura, T.
  (2015) Liposome-Based in Vitro Evolution of Aminoacyl-tRNA Synthetase for Enhanced Pyrrolysine Derivative Incorporation.
  Chembiochem. 16, 1797-802.

• 2.

  Suzuki, A., Kato, Y., Matsuura, T. and Watanabe, H.
  (2015) Growth evaluation method by live imaging of Daphnia magna and its application to the estimation of an insect growth regulator.
  J. Appl. Toxicol. 35, 68-74.

• 3.

  Peerakietkhajorn, S., Tsukada, K., Kato, Y., Matsuura, T. and Watanabe, H.
  (2015) Symbiotic bacteria contribute to increasing the population size of a freshwater crustacean, Daphnia magna.
  Environ. Microbiol. Rep. 7, 364-72.

• 4.

  Peerakietkhajorn, S., Kato, Y., Kasalicky, V., Matsuura, T. and Watanabe, H.
  (2015) Betaproteobacteria Limnohabitans strains increase fecundity in the crustacean Daphnia magna: Symbiotic relationship between major bacterioplankton and zooplankton in freshwater ecosystem.
  Environ. Microbiol.

• 5.

  Nakanishi, T., Kato, Y., Matsuura, T. and Watanabe, H.
  (2015) TALEN-mediated homologous recombination in Daphnia magna.
  Sci. Rep. 5, 18312.

• 6.

  Naitou, A., Kato, Y., Nakanishi, T., Matsuura, T. and Watanabe, H.
  (2015) Heterodimeric TALENs induce targeted heritable mutations in the crustacean Daphnia magna.
  Biol. Open. 4, 364-9.

• 7.

  Fujii, S., Matsuura, T. and Yomo, T.
  (2015) In vitro directed evolution of alpha-hemolysin by liposome display.
  Biophysics. 11, 67-72.

• 8.

  Fujii, S., Matsuura, T. and Yomo, T.
  (2015) Membrane Curvature Affects the Formation of alpha-Hemolysin Nanopores.
  ACS Chem. Biol. 10, 1694-701.

Original Papers

• 1.

  Wakabayashi, T., Benesh, J., Yasumoto, S., Akashi, T., Aoki, T., Harada, K., Muranaka, S., Bamba, T., Fukusaki, E., Takeuchi, Y., Yoneyama, K., Muranaka, T., Sugimoto, Y. and Okazawa, A.
  (2015) Planteose as a storage carbohydrate required for early stage of germination of Orobanche minor and its metabolism as a possible target for selective control.
  J. Exp. Bot. 66, 3085-3097.

• 2.

  Khakimov, B., Kuzina-Poulsen, V., Erthmann, P.Ø., Fukushima, E.O., Augustin, J.M., Olsen, C.E., Scholtalbers, J., Volpin, H., Andersen, S.B., Hauser, T.P., Muranaka, T. and Bak, S. (2015) Identification and genome organization of saponin pathway genes from a wild crucifer, and their use for transient production of saponins in Nicotiana benthamiana.
  Plant J. 84, 478-490.

Reviews

• 1.

  Seki, H., Tamura, K. and Muranaka, T.
  (2015) P450s and UGTs: Key players in the structural diversity of triterpenoid saponins. Plant Cell Physiol. 56, 1463-1471.

Original Papers

• 1.

  Ninh, P.H., Honda, K., Sakai, T., Okano, K., and Ohtake, H.
  (2015) Assembly and multiple gene expression of thermophilic enzymes in Escherichia coli for in vitro metabolic engineering.
  Biotechnol. Bioeng. 112, 189-196.

• 2.

  Okano, K., Miyamaru, S., Kitao, A., Takano, H., Aketo, T., Toda, M., Honda, K., and Ohtake, H.
  (2015) Amorphous calcium silicate hydrates and their possible mechanism for recovering phosphate from waste water.
  Separ. Purif. Technol. 144, 63-69.

• 3.

  Diederichs, D., Linn, K., Luckgen, K., Klement, T., Grosch, J.H.,Honda, K., Ohtake, H., and Buchs, J.
  (2015) High-level production of　5S-hydroxyhexane-2-one by two thermostable oxidoreductases in awhole-cell catalytic approach.
  J. Mol. Cat. B: Enzym. 121, 37-44.

• 4.

  Pongtharangkul, T., Chuekitkumchorn, P., Suwanampa, N., Payongsri, P., Honda, K., Panbangred, W.
  (2015) Kinetic properties and stability of glucose dehydrogenase from Bacillus amyloliquefaciens SB5 and its potential for cofactor regeneration.
  AMB Express, 5, 68.

Reviews

• 1.

  Ohtake, H., Okano, K.
  (2015) Development and implementation of technologies for recycling phosphorus in secondary resources in Japan.
  Glob. Environ. Res. 19, 49-65.

Original Papers

• 1.

  Numamoto, M., Sasano, Y., Hirasaki, M., Sugiyama, M., Maekawa, H. and Harashima, S.
  (2015) The protein phosphatase Siw14 controls caffeine-induced nuclear localization and phosphorylation of Gln3 via the type 2A protein phosphatases Pph21 and Pph22 in Saccharomyces cerevisiae.
  J. Biochem. 157, 53-64.

• 2.

  Oda, S., Yurimoto, H., Nitta, N., Sasano, Y. and Sakai, Y.
  (2015) Molecular characterization of hap complex components responsible for methanol-inducible gene expression in the methylotrophic yeast Candida boidinii.
  Eukaryot. Cell 14, 278-285.

• 3.

  Sharmin, D., Sasano, Y., Sugiyama, M. and Harashima, S.
  (2015) Type 2C protein phosphatase Ptc6 participates in activation of the Slt2-mediated cell wall integrity pathway in Saccharomyces cerevisiae.
  J. Biosci. Bioeng. 119, 392-398.

• 4.

  Sasano, Y., Yamagishi, K., Tanikawa, M., Nakazawa, T., Sugiyama, M., Kaneko, Y. and Harashima, S.
  (2015) Stabilization of mini-chromosome segregation during mitotic growth by overexpression of YCR041W and its application to chromosome engineering in Saccharomyces cerevisiae.
  J. Biosci. Bioeng. 119, 526-531.

• 5.

  Numamoto, M., Tagami, S., Ueda, Y., Imabeppu, U., Sasano, Y, Hirasaki, M., Sugiyama, M., Maekawa, H. and Harashima, S.
  (2015) Nuclear localization domains of GATA activator Gln3 are required for transcription of target genes through dephosphorylation in Saccharomyces cerevisiae.
  J. Biosci. Bioeng. 120, 121-127.

• 6.

  Natesuntorn, W., Iwami, K., Matsubara, Y., Sasano, Y., Sugiyama, M., Kaneko,Y. and Harashima, S.
  (2015) Genome-wide construction of a series of designed segmental aneuploids in Saccharomyces cerevisiae.
  Sci. Rep. 5, 12510.

• 7.

  Hermansyah, Novia, Sugiyama, M. and Harashima, S.
  (2015) Candida tropicalis Isolated from Tuak, a North Sumatera-Indonesian Traditional Beverage, for Bioethanol Production.
  Microbiol. Biotechnol. Lett. 43, 241-248.

Reviews

• 1.

  Sugiyama, M., Sasano, Y. and Harashima, S.
  (2015) Adaptation mechanism of yeast to weak organic acid.
  Stress Biology of Yeasts and Fungi, Kitagaki, H. and Takagi, H. eds.
  Springer, 107-121.

Original Papers

• 1.

  Onitsuka, M. and Omasa, T.,
  (2015) Rapid evaluation of N-glycosylation status of antibodies with chemiluminescent lectin-binding assay.
  Journal of Bioscience and Bioengineering, 120, 1, 107-110.

• 2.

  Nakamura, T. and Omasa, T.
  (2015) Optimization of cell line development in the GS-CHO expression system using a high-throughput, single cell-based clone selection system.
  Journal of Bioscience and Bioengineering, 120, 3, 323-329.

• 3.

  Okumura, T., Masuda, K., Watanabe, K., Miyadai, K., Nonaka, K.,Yabuta, M. and Omasa, T.,
  (2015) Efficient enrichment of high-producing recombinant CHO cells for monoclonal antibody by flow cytometry.
  Journal of Bioscience and Bioengineering, 120, 3, 340-346.

• 4.

  Shirai, A., Onitsuka, M., Maseda, H., and Omasa, T.,
  (2015) Effect of polyphenols on reactive oxygen species production and cell growth of human dermal fibroblasts after irradiation with ultraviolet-A light.
  Biocontrol Science, 20, 1, 27-33.

• 5.

  Matsuyama, R., Tsutsui, T., Kyoung H., L., Onitsuka, M. and Omasa, T.,
  (2015), Improved gene amplification by cell-cycle engineering combined with the Cre-loxP system in Chinese hamster ovary cells
  Journal of Bioscience and Bioengineering, 120, 6, 701-708.

• 6.

  Ishii-Watabe, A., Hirose, A., Katori, N., Hashii, N., Arai, S., Awatsu, H., Eiza, A., Hara, Y., Hattori, H., Inoue, T., Isono, T., Iwakura, M., Kajihara, D., Kasahara, N., Matsuda, H., Murakami, S., Nakagawa, T., Okumura, T., Omasa, T., Takuma, S., Terashima, I., Tsukahara, M., Tsutsui, M., Yano, T., Kawasaki, N.,
  (2015) Approaches to quality risk management when using single use systems in the manufacture of biologics
  AAPS PharmSciTech 16,5,993-1001.

• 7.

  Hirata, A., Sakudo, A., Takano, K., Kanaya, S. and Koga, Y.
  (2015), Effects of surfactant and a hyperthermostable protease on infectivity of Scrapie-infected mouse brain homogenate.
  Journal of Biotechnol and Biomater, 5(3), 194

Original Papers

• 1.

  Nomura, T., Suganuma, M., Higa, Y., Kataoka, Y., Funaguma, S., Okazaki, H., Suzuki, T., Kobayashi, I., Sezutsu, H. and Fujiyama, K.
  (2015) Improvement of glycosylation structure by suppression of -N-acetylglucosaminidases in silkworm.
  J. Biosci. Bioeng. 119, 131-136.

• 2.

  Srichaisupakit, A., Ohashi, T., Misaki, R. and Fujiyama, K.
  (2015) Production of initial-stage eukaryotic N-glycan and its protein glycosylation in Escherichia coli.
  J. Biosci. Bioeng. 119, 399-405.

• 3.

  Hamorsky, K.T., Kouokam, J.C., Jurkiewicz, J.M., Nelson, B., Moore, L.J., Husk, A.S., Kajiura, H., Fujiyama, K. and Matoba, N.
  (2015) N-glycosylation of cholera toxin B subunit in Nicotiana benthamiana: impacts on host stress response, production yield and vaccine potential.
  Sci. Rep. 5, 8003.

• 4.

  Arief, I.I., Jenie, B.S.L., Astawan, M., Fujiyama, K. and Witarto, A.B.
  (2015) Identification and probiotic characteristics of lactic acid bacteria isolated from Indonesian local beef.
  Asian J. Animal Sciences. 9, 25-36.

• 5.

  Kajiura, H., Hamaguchi, Y., Mizushima, H., Misaki, R. and Fujiyama, K.
  (2015) Sialylation potentials of the silkworm, Bombyx mori; B. mori possesses an active 2,6-sialyltransferase.
  Glycobiology. 25, 1441-1453.

• 6.

  Limkul, J., Misaki, R., Kato, K. and Fujiyama, K.
  (2015) The combination of plant translational enhancers and terminator increase the expression of human glucocerebrosidase in Nicotiana benthamiana plants.
  Plant Sci. 240, 41-49.

• 7.

  Polburee, P., Yongmanitchai, W., Lertwattanasakul, N., Ohashi, T., Fujiyama, K. and Limtong, S.
  (2015) Characterization of oleaginous yeasts accumulating high levels of lipid when cultivated in glycerol and their potential for lipid production from biodiesel-derived crude glycerol.
  Fungal Biol. 119, 1194-1204.

Reviews

• 1.

  Kajiura, H. and Fujiyama, K.
  (2015) Im"plant"ing of Mammalian Glycosyltransferase Gene into Plant Suspension-Cultured Cells Using Agrobacterium-Mediated Transformation.
  Methods Mol. Biol. 1321, 225-232.

Original Papers

• 1.

  Daduang, R., Kitani, S., Hashimoto, J., Thamchaipenet, A., Igarashi, Y., Shin-ya, K., Ikeda, H. and Nihira, T.
  (2015) Characterization of the biosynthetic gene cluster for maklamicin, a spirotetronate-class antibiotic of the endophytic Micromonospora sp. NBRC 110955.
  Microbiol. Res. 180, 30-39.

• 2.

  Daduang, R., Kitani, S., Sudoh, Y., Pait, I.G.U., Thamchaipenet, A., Ikeda, H., Igarashi, Y. and Nihira, T.
  (2015) 29-Deoxymaklamicin, a new maklamicin analogue produced by a genetically engineered strain of Micromonospora sp. NBRC 110955.
  J. Biosci. Bioeng. 120, 608-613.

• 3.

  Euanorasetr, J., Intra, B., Mongkol, P., Chankhamhaengdecha, S., Tuchinda, P., Mori, M., Shiomi, K., Nihira, T. and Panbangred, W.
  (2015) Spirotetronate antibiotics with anti-Clostridium activity from Actinomadura sp. 2EPS.
  World. J. Microbiol. Biotechnol. 31, 391-398.

Reviews

• 1.

  Kitani, S.
  (2015) Deciphering regulatory mechanisms for antibiotic production by Streptomyces hormones.
  Actimomycetologica. 29, 10-17.

Original Papers

• 1.

  Ichijo, H., Hamada, M., Takahashi, S., Kobayashi, M., Nagai, T., Toyama, T. and Kawaguchi, M.
  (2015) Lateralization, maturation, and anteroposterior topography in the lateral habenula revealed by ZIF268/EGR1 immunoreactivity and labeling history of neuronal activity.
  Neurosci.Res. 95, 27-37.

• 2.

  Sugiura, K., Nagai, T., Nakano, M., Ichinose, H., Nakabayashi, T., Ohta, N. and Hisabori, T.
  (2015) Redox sensor proteins for highly sensitive direct imaging of intracellular redox state.
  Biochem. Biophys. Res. Commun. 457, 242-248.

• 3.

  Takai, A., Nakano, M., Saito, K., Haruno, R., Watanabe, TM., Ohyanagi, T., Jin, T., Okada, Y. and Nagai, T.
  (2015) Expanded palette of Nano-lantern for real-time muliti-color luminescence imaging.
  Proc. Natl. Acad. Sci. USA. 112, 4352-4356.

• 4.

  Tiwari, DK., Arai, Y., Yamanaka, M., Matsuda, T., Agetsuma, M., Nakano, M., Fujita, K. and Nagai, T.
  (2015) A fast- and positively photoswitchable fluorescent protein for ultralow-laser-power RESOLFT nanoscopy.
  Nat. Methods 12, 515-518.

• 5.

  Arai, Y., Yamamoto, T., Minamikawa, T., Takamatsu, T. and Nagai, T.
  (2015) Spectral fingerprinting of individual cells visualized by cavity-reflection-enhanced light-absorption microscopy.
  PLoS ONE 10, e0125733.

• 6.

  Nezu, A., Morita, T.,Tojyo, Y., Nagai, T. and Tanimura, A.
  (2015) Partial agonistic effects of pilocarpine on Ca2+ responses and salivary secretion in the submandibular glands of live animals.
  Exp. Physiol. 100, 640-651.

• 7.

  Yamanaka, M., Saito, K., Smith, IN., Arai, Y., Uegaki, K., Yonemaru, Y., Mochizuki, K., Kawata, S., Nagai, T. and Fujita, K.
  (2015) Visible-wavelength two-photon excitation microscopy for fluorescent protein imaging.
  J. Biomed. Opt. 20, 101202.

• 8.

  Koldenkova VP., Matsuda, T. and Nagai, T.
  (2015) MagIC, a genetically encoded fluorescent indicator for monitoring cellular Mg2+ using a non-FRET ratiometric imaging approach.
  J. Biomed. Opt. 20, 101203.

• 9.

  Kim, K., Lakhanpal, G., Lu, HE., Khan, M., Suzuki, A., Kato-Hayashi, M., Narayanan, R., Luyben, TT., Matsuda, T., Nagai, T., Blanpied, TA., Hayashi, Y. and Okamoto K.
  (2015) A Temporary Gating of Actin Remodeling during Synaptic Plasticity Consists of the Interplay between the Kinase and Structural Functions of CaMKII
  Neuron 87, 813-826.

• 10.

  Iwano, M., Ito, K., Fujii, S., Kakita, M., Asano-Shimosato, H., Igarashi, M., Kaothien-Nakayama, P., Entani, T., Kanatani, A., Takahisa, M., Tanaka, M., Komatsu, K., Shiba, H., Nagai, T., Miyawaki, A., Isogai, A. and Takayama, S.
  (2015) Calcium signalling mediates self-incompatibility response in the Brassicaceae.
  Nature Plants. 1, 15128.

• 11.

  Hanasaki, I., Uehara, S., Arai, Y., Nagai, T. and Kawano, S.
  (2015) Threshold-free evaluation of near-surface diffusion and adsorption-dominated motion from single-molecule tracking data of single-stranded DNA through total internal reflection fluorescence microscopy.
  Jpn. J. Appl. Phys. 54. 125601.

• 12.

  Wazawa, T., Morimoto,N., Nagai T. and Suzuki M.
  (2015) Rotational motion of rhodamine 6G tethered to actin through oligo(ethylene glycol) linkers studied by frequency-domain fluorescence anisotropy.
  Biophysics and Physicobiology 12. 87-102.

Reviews

• 1.

  Saito, K., Chang, Y-F., Horikawa K., Higuchi, Y., Hashida, M., Matsuda, T., Arai, Y. and Nagai, T.
  (2015) Real time imaging of biological phenomena with super-duper luminescent proteins.
  CYTOLOGIA. 80, 1-2.

• 2.

  Uno, S., Tiwari, DK., Kamiya, M., Arai, Y., Nagai, T. and Urano, Y.
  (2015) A guide to use photocontrollable fluorescent proteins and synthetic smart fluorophores for nanoscopy.
  Microscopy 64, 263-277.

• 3.

  Saito, K. and Nagai, T.
  (2015) Recent progress in luminescent proteins development.
  Curr. Opini. Chemi. Biol. 27, 46-51.

Original Papers

• 1.

  Yoshikawa, K., Hirasawa, T. and Shimizu, H.
  (2015) Effect of malic enzyme on ethanol production by Synechocystis sp. PCC 6803.
  J. Biosci. Bioeng. 119(1), 82-84.

• 2.

  Matsuda, F., Nakabayashi, R., Yang, Z., Okazaki, Y., Yonemaru, J., Ebana, K., Yano, M. and Saito, K.
  (2015) Metabolome-genome-wide association study (mGWAS) dissects genetic architecture for generating natural variation in rice secondary metabolism.
  Plant J. 81(1), 13-23.

• 3.

  Matsuda, F., Ogura, T., Okahashi, N., Tomita, A., Hirano, I. and Shimizu, H.
  (2015) NanoLC-MRM based quantitative platform for analyzing multiple enzymes associated with central metabolic pathways of Saccharomyces cerevisiae using ultra-fast mass spectrometry.
  J. Biosci. Bioeng. 119(1), 117-20.

• 4.

  Toya, Y., Shiraki, T. and Shimizu, H.
  (2015) SSDesign: Computational metabolic pathway design based on flux variability using elementary flux modes.
  Biotech. Bioeng. 112(4), 759-768.

• 5.

  Kajihata, S., Matsuda, F., Yoshimi, M., Hayakawa, K., Furusawa, C., Kanda, A. and Shimizu, H.
  (2015) 13C-based metabolic flux analysis of Saccharomyces cerevisiae with a reduced Crabtree effect.
  J. Biosci. Bioeng. 120(2), 140-144.

• 6.

  Nishino, S., Okahashi, N., Matsuda, F. and Shimizu, H.
  (2015) Absolute quantitation of glycolytic intermediates reveals thermodynamic shifts in Saccharomyces cerevisiae strains lacking PFK1 or ZWF1 genes.
  J. Biosci. Bioeng. 120(3), 280-6.

• 7.

  Horinouchi, T., Suzuki, S., Hirasawa, T., Ono, N., Yomo, T., Shimizu, H. and Furusawa, C.
  (2015) Phenotypic convergence in bacterial adaptive evolution to ethanol stress.
  BMC Evol. Biol. 15, 180.

• 8.

  Nugroho, R.H., Yoshikawa, K. and Shimizu, H.
  (2015) Metabolomic analysis of acid stress response in Saccharomyces cerevisiae.
  J. Biosci. Bioeng. 120(4), 396-404.

• 9.

  Hayakawa, K., Kajihata, S., Matsuda, F. and Shimizu, H.
  (2015) 13C-metabolic flux analysis in S-adenosyl-L-methionine production by Saccharomyces cerevisiae.
  J. Biosci. Bioeng. 120(5), in print.

• 10.

  Yoshikawa, K., Aikawa, S., Kojima, Y., Toya, Y., Furusawa, C., Kondo, A. and Shimizu, H.
  (2015) Construction of a genome-scale metabolic model of Arthrospira platensis NIES-39 and metabolic design for cyanobacterial bioproduction.
  PLoS ONE 10, 12.

• 11.

  Okahashi, N., Kohno, S., Kitajima, S., Matsuda, F., Takahashi, C. and Shimizu, H.
  (2015) Metabolic characterization of cultured mammalian cells by mass balance analysis, tracer labeling experiments and computer-aided simulations.
  J. Biosci. Bioeng. 120(6), 725-31.

• 12.

  Toya, Y., Hirasawa, T., Ishikawa, S., Chumsakul, O., Morimoto, T., Liu, S., Masuda, K., Kageyama, Y., Ozaki, K., Ogasawara, N. and Shimizu, H.
  (2015) Enhanced dipicolinic acid production during the stationary phase in Bacillus subtilis by blocking acetoin synthesis.
  Biosci. Biotech. Biochem. 79(12):2073-80.

Original Papers

• 1.

  Murakami, Y., Matsumoto, Y., Tsuru, S., Ying, BW. and Yomo, T.
  (2015) Global coordination in adaptation to gene rewiring.
  Nucleic Acids Res. 42, 1304-1316.

• 2.

  Ichihashi, N., Kobori, S. and Yomo, T.
  (2015) Simple identification of two causes of noise in an aptazyme system by monitoring cell-free transcription.
  Methods Enzymol. 550, 93-107.

• 3.

  Fujii, S., Matsuura, T. and Yomo, T.
  (2015) In vitro directed evolution of alpha-hemolysin by liposome display.
  Biophysics 11, 67-72.

• 4.

  Kaneko, K., Furusawa, C. and Yomo, T.
  (2015) Universal Relationship in Gene-Expression Changes for Cells in Steady-Growth State.
  Phys. Rev. X. 5, 011014.

• 5.

  Nishiyama, K., Ichihashi, N. and Yomo, T.
  (2015) Development of a reporter peptide that catalytically produces a fluorescent signal through α-complementation.
  Protein Sci. 24, 599-603.

• 6.

  Fujii, S., Matsuura, T. and Yomo, T.
  (2015) Membrane Curvature Affects the Formation of α-Hemolysin Nanopores.
  ACS Chem. Biol. 10, 1694-1701.

• 7.

  Sakatani, Y., Ichihashi, N., Kazuta, Y. and Yomo, T.
  (2015) A transcription and translation-coupled DNA replication system using rolling-circle replication.
  Scientific Rep. 5, 1-9.

• 8.

  Iwai, T., Kominami, D., Murata, M. and Yomo, T.
  (2015) Free-Energy-Based Design Policy for Robust Network Control against Environmental Fluctuation.
  Scientific World Journal 2015, 1-12.

• 9.

  Uyeda, A., Watanabe, T., Kato, Y., Watanabe, H., Yomo, T., Hohsaka, T. and Matsuura, T.
  (2015) Liposome-based in vitro evolution of aminoacyl-tRNA synthetase for enhanced pyrrolysine derivative incorporation.
  ChemBioChem 16, 1797-1802.

• 10.

  Tsuda, S., Sakakura, T., Fujii, S., Suzuki, H. and Yomo, T.
  (2015) Shape Transformations of Lipid Vesicles by Insertion of Bulky-Head Lipids.
  PLoS One 10, e0132963.

• 11.

  Kishimoto, T., Ying, BW., Tsuru, S., Iijima, L., Suzuki, S., Hashimoto, T., Oyake, A., Kobayashi, H., Someya, Y., Narisawa, D. and Yomo, T.
  (2015) Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process.
  PLoS Genet. 11, e1005392.

• 12.

  Usui, K., Ichihashi, N. and Yomo, T.
  (2015) A design principle for a single-stranded RNA genome that replicates with less double-strand formation.
  Nucleic Acids Res. 43, 8033-8043.

• 13.

  Aita, T. and Yomo, T.
  (2015) Evolutionary dynamics of a polymorphic self-replicator population with a finite population size and hyper mutation rate.
  J Theor Biol. 382, 298-308.

• 14.

  Awai, T., Ichihashi, N. and Yomo, T.
  (2015) Activities of 20 aminoacyl-tRNA synthetases expressed in a reconstituted translation system in Escherichia coli.
  Biochem. Biophys. Rep. 3, 140-143.

• 15.

  Ying, BW., Honda, T., Tsuru, S., Seno, S., Matsuda, H., Kazuta, Y. and Yomo, T.
  (2015) Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages.
  PLOS ONE 10, e0135639.

• 16.

  Horinouchi, T., Suzuki, S., Hirasawa, T., Ono, N., Yomo, T., Shimizu, H. and Furusawa, C.
  (2015) Phenotypic convergence in bacterial adaptive evolution to ethanol stress.
  BMC Evol. Biol. 15, 1-14.

• 17.

  Ichihashi, N., Aita, T., Motooka, D., Nakamura, S. and Yomo, T.
  (2015) Periodic pattern of genetic and fitness diversity during evolution of an artificial cell-like system.
  Mol. Biol. Evol. 32, 3205-3214.

• 18.

  Yama, K., Matsumoto, Y., Murakami, Y., Seno, S., Matsuda, H., Gotoh, K., Motooka, D., Nakamura, S., Ying, BW. and Yomo, T.
  (2015) Functional specialization in regulation and quality control in thermal adaptive evolution.
  Genes to Cells 20, 943-955.

• 19.

  Tsuru, S., Ishizawa, Y., Shibai, A., Takahashi, Y., Motooka, D., Nakamura, S. and Yomo, T.
  (2015) Genomic confirmation of nutrient-dependent mutability of mutators in Escherichia coli.
  Genes to Cells 20, 972-981.

• 20.

  Tomita, K., Ichihashi, N. and Yomo, T.
  (2015) Replication of partial double-stranded RNAs by Qβ replicase.
  Biochem. Biophys. Res. Commun. 467, 293-296.

• 21.

  Ying, BW., Matsumoto, Y., Kitahara, K., Suzuki, S., Ono, N., Furusawa, C., Kishimoto, T. and Yomo, T.
  (2015) Bacterial transcriptome reorganization in thermal adaptive evolution.
  BMC Genomics 16, 1-11.

• 22.

  Baumstark, R., Hänzelmann, S., Tsuru, S., Schaerli, Y., Francesconi, M., Mancuso, FM., Castelo, R. and Isalan, M.
  (2015) The propagation of perturbations in rewired bacterial gene networks.
  Nat. Commun. 6, 10105.