受賞（コース全体）

1. 3月19日, 岡橋 伸幸（博士後期課程1年）, 化学工学会第80年会本部大会学生賞特別賞受賞
   受賞演題「動物培養細胞の代謝流束解析」
2. 5月1日, 高田 英昭 助教, The 5th Asian Chromosome Colloquium Best poster aword 受賞
   受賞演題「Chromatin compaction protects genome DNA from radiation damage」
3. 6月19日, 水内 良（博士後期課程1年）, The Astrobiology Science Conference 2015,
   The NASA Astrobiology Program award受賞
   受賞演題「Adaptive Evolution and Diversity of an Artificial RNA Self-Replication System」
   詳細リンク：http://nai.nasa.gov/articles/2015/6/19/results-of-the-abscicon-2015-student-poster-competition/
4. 6月19日, 岡橋 伸幸（博士後期課程2年）, 第63回質量分析総合討論会
   ベストプレゼンテーション賞ポスター発表部門・優秀賞受賞
   受賞演題「動物培養細胞中枢代謝経路における13C代謝フラックス解析法の構築」
5. 7月14日, 福井 希一 教授, 大阪大学総長顕彰（教育部門）受賞
6. 7月14日, 木谷 茂 准教授, 大阪大学総長奨励賞 受賞
   受賞演題「微生物ゲノムに潜む休眠生理活性物質を生産覚醒する技術の研究」
7. 10月26日, 福崎 英一郎 教授, 日本生物工学会 第9回生物工学功績賞 受賞
   受賞演題「メタボロミクスの技術開発と精密表現型解析への応用」
8. 10月26日, 金 美海 助教, 日本生物工学会 第38回 生物工学奨励賞（照井賞）受賞
   受賞演題「幹細胞の足場タンパク発現制御に基づく分化誘導プロセスの開発」
9. 10月26日, 大政 健史 教授, 日本生物工学会 第23回 英文誌論文賞 受賞
   受賞演題「Trehalose suppresses antibody aggregation during the culture of Chinese hamster ovary cells」
   J. Biosci. Bioeng. 117, 632-638.
10. 10月26日, 本田 孝祐 准教授・岡野 憲司 助教, 日本生物工学会 第23回 英文誌論文賞 受賞
    受賞演題「Directed evolution of thermotolerant malic enzyme for improved malate production」
    J. Biosci. Bioeng. 117, 147-152.
11. 10月26日, 徳山 健斗（博士後期課程1年）, 日本生物工学会 第4回生物工学学生優秀賞（飛翔賞）受賞
    受賞演題「代謝シミュレーションと実験室進化実験の統合による有用発酵微生物育種の実践」
12. 12月8日, 高内 大貴（博士前期課程2年）, The 19th SANKEN International Symposium ポスター賞受賞
    受賞演題「A spontaneous switching-on fluorescent protein for high-speed single molecule localization-based super-resolution imaging」
13. 12月9日, 岡村 昂典（博士前期課程2年）, 第38回日本分子生物学会年会、第88回日本生化学会大会 合同大会
    若手優秀発表賞 受賞
    受賞演題「無細胞翻訳系を用いたジャイアントリポソーム内ヒト由来トランスポーターLetm1の合成およびその脂質依存性」

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生物資源工学領域（福崎研）

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.

Reviews

1. 津川裕司, 福崎英一郎
   (2015) 生命科学発展のためのメタボロミクス技術基盤の構築
   遺伝 69, 52-57.
2. 福崎英一郎
   (2015) メタボロミクスの食品機能解析への応用
   Bio Industry 32, 46-53.
3. 福崎英一郎
   (2015) メタボロミクスの高解像度表現型解析への応用
   臨床病理 63, 736-745.
4. 新間秀一
   (2015) 臨床薬理学におけるイメージング質量分析の活用
   ぶんせき 491, 486-490.

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ゲノム機能工学領域

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.

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生命環境システム工学領域（渡邉研）

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.

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細胞動態学領域（福井研）

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.

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細胞工学領域（村中研）

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.
2. 安本周平, 關 光, 刑部祐里子, 刑部敬史, 村中俊哉
   (2015) 植物でのゲノム編集, 論文だけではわからないゲノム編集成功の秘訣 Q&A, 実験医学別冊 羊土社（東京）228-243.
3. 安本周平, 關 光, 村中俊哉
   (2015) 人工ヌクレアーゼを用いた植物代謝工学, 進化するゲノム編集技術, エヌ・ティー・エス（東京）235-241.

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生物化学工学領域

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.
2. 岡野憲司, 本田孝祐
   (2015) In vitro代謝工学による1-ブタノール生産
   バイオサイエンスとインダストリー, 73, 481-482.

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生物プロセスシステム工学領域（紀ノ岡研）

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.

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生物工学国際交流センター（仁平研）

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.
2. 木下浩
   (2015) 昆虫病原性糸状菌が生産する生理活性物質の単離・同定

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生物工学国際交流センター（藤山研）

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.
2. 藤山和仁
   (2015) 第4編 第3章 糖鎖の合成－生物系 第3節 植物を利用した糖タンパク質合成
   糖鎖の新機能開発・応用ハンドブック、株式会社エヌ・ティー・エス、387-389.

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産業科学研究所生体分子機能科学講座（永井研）

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. 中野雅裕、永井健治
   (2015) 肉眼でも観察できる！　３色（水色, 黄緑色, 橙色）の高光度発光タンパク質
   OplusE 428, 505-506.
3. 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.
4. Saito, K. and Nagai, T.
   (2015) Recent progress in luminescent proteins development.
   Curr. Opini. Chemi. Biol. 27, 46-51.

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物質生命工学コース極限生命工学領域（大政研）

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

Reviews

1. 大政健史
   (2015) 次世代バイオ医薬品製造技術開発~高生産用CHO細胞株の開発を中心にして
   バイオサイエンスとインダストリー　73,1, 8-13.
2. 大政健史
   (2015) 次世代バイオ医薬品製造技術研究組合の取り組みについて
   ファルマシア51,5,439-441.
3. 大政健史
   (2015) 世界の成長エンジンを目指して~次世代バイオ医薬品製造技術研究組合の取り組みについて~　都市政策160, 27-30.

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情報科学研究科バイオ情報工学専攻代謝情報工学講座（清水研）

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.

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情報科学研究科バイオ情報工学専攻共生ネットワークデザイン学講座

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.

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