生物資源工学領域（福崎研）

Original Papers

1. Ishibashi, M., Ando, T., Sakai, M., Matsubara, A., Uchikata, T., Fukusaki, E. and Bamba, T.
   (2012) High-throughput simultaneous analysis of pesticides by supercritical fluid chromatography/tandem mass spectrometry.
   J. Chromatogr. A. 1266, 143-8.
2. Ochi, H., Bamba, T., Naito, H., Iwatsuki, K. and Fukusaki, E.
   (2012) Metabolic fingerprinting of hard and semi-hard natural cheeses using gas chromatography with flame ionization detector for practical sensory prediction modeling.
   J. Biosci. Bioeng. 114, 506-511.
3. Suzuki, N., Uefuji, H., Nishikawa, T., Mukai, Y., Yamashita, A., Hattori, M., Ogasawara, N., Bamba, T., Fukusaki, E., Kobayashi, A., Ogata, Y., Sakurai, N., Suzuki, H., Shibata, D. and Nakazawa, Y.
   (2012) Construction and analysis of EST libraries of the trans-polyisoprene producing plant, Eucommia ulmoides Oliver.
   Planta, 236, 1405-1417.
4. Lai, P., Okazawa, A., Izumi, Y., Bamba, T., Fukusaki, E., Yoshikawa, M. and Kobayashi, A.
   (2012) Gallic acid oxidizes Met residues in peptides released from bovine β-lactoglobulin by in vitro digestion.
   J. Biosci. Bioeng. 114, 297-305.
5. Fujieda, Y., Ueno, S., Ogino, R., Kuroda, M., Jönsson, T.J., Guo, L., Bamba, T. and Fukusaki, E.
   (2012) Metabolite profiles correlate closely with neurobehavioral function in experimental spinal cord injury in rats.
   PLoS One. 7, e43152.
6. Hori, K., Matsubara, A., Uchikata, T., Tsumura, K., Fukusaki, E. and Bamba, T.
   (2012) High-throughput and sensitive analysis of 3-monochloropropane-1,2-diol fatty acid esters in edible oils by supercritical fluid chromatography/tandem mass spectrometry.　
   J. Chromatogr. A. 1250, 99-104.
7. Uchikata. T., Matsubara, A., Fukusaki, E. and Bamba, T.
   (2012) High-throughput phospholipid profiling system based on supercritical fluid extraction-supercritical fluid chromatography/mass spectrometry for dried plasma spot analysis.　
   J. Chromatogr. A. 1250, 69-75.
8. Uchikata, T., Matsubara, A., Nishiumi, S., Yoshida, M., Fukusaki, E. and Bamba, T.
   (2012) Development of oxidized phosphatidylcholine isomer profiling method using supercritical fluid chromatography/tandem mass spectrometry.　
   J. Chromatogr. A. 1250, 205-211.
9. Bamba, T., Lee, JW., Matsubara, A. and Fukusaki, E.
   (2012) Metabolic profiling of lipids by supercritical fluid chromatography/mass spectrometry.
   J. Chromatogr. A. 1250, 212-219.
10. Matsubara, A., Harada, K., Hirata, K., Fukusaki, E. and Bamba, T.　
    (2012) High-accuracy analysis system for the redox status of coenzyme Q(10) by online supercritical fluid extraction-supercritical fluid chromatography/mass spectrometry.　
    J. Chromatogr. A. 1250, 76-79.
11. Hasokawa, M., Shinohara, M., Tsugawa, H., Bamba, T., Fukusaki, E., Nishiumi, S., Nishimura, K., Yoshida, M., Ishida, T. and Hirata, K.
    (2012) Identification of biomarkers of stent restenosis with serum metabolomic profiling using gas chromatography/mass spectrometry.　
    Circ. J. 76, 1864-1873.
12. Yamamoto, S., Bamba, T., Sano, A., Kodama, Y., Imamura, M., Obata, A. and Fukusaki, E.　
    （2012） Metabolite profiling of soy sauce using gas chromatography with time-of-flight mass spectrometry and analysis of correlation with quantitative descriptive analysis.
    J. Biosci. Bioeng.114, 170-175.
13. Kobayashi, S., Putri, S.P., Yamamoto, Y., Donghyo, K., Bamba, T. and Fukusaki, E.　
    (2012) Gas chromatography-mass spectrometry based metabolic profiling for the identification of discrimination markers of Angelicae Radix and its application to gas chromatography-flame ionization detector system.
    J. Biosci. Bioeng. 114, 232-236.
14. Kobayashi, S., Nagasawa, S., Yamamoto, Y., Donghyo, K., Bamba, T. and Fukusaki, E.　
    (2012) Metabolic profiling and identification of the genetic varieties and agricultural origin of Cnidium officinale and Ligusticum chuanxiong.　
    J. Biosci. Bioeng. 214, 86-91.　
15. Nomura, H., Komori, T., Uemura, S., Kanda, Y., Shimotani, K., Nakai, K., Furuichi, T., Takebayashi, K., Sugimoto, T., Sano, S., Suwastika, I.N., Fukusaki, E., Yoshioka, H., Nakahira, Y. and Shiina, T.　
    (2012) Chloroplast-mediated activation of plant immune signalling in Arabidopsis.　
    Nat. Commun. 3, 926.　
16. Ochi, H., Naito, H., Iwatsuki, K., Bamba, T. and Fukusaki E.　
    (2012) Metabolomics-based component profiling of hard and semi-hard natural cheeses with gas chromatography/time-of-flight-mass spectrometry, and its application to sensory predictive modeling.　
    J. Biosci. Bioeng. 113, 751-758.
17. Matsubara, A., Uchikata, T., Shinohara, M., Nishiumi, S., Yoshida, M., Fukusaki, E. and Bamba, T.　
    (2012) Highly sensitive and rapid profiling method for carotenoids and their epoxidized products using supercritical fluid chromatography coupled with electrospray ionization-triple quadrupole mass spectrometry.　
    J. Biosci. Bioeng. 113, 782-787.
18. Ikeda, A., Nishiumi, S., Shinohara, M., Yoshie, T., Hatano, N., Okuno, T., Bamba, T., Fukusak,i E., Takenawa, T., Azuma, T. and Yoshida, M.　
    (2012) Serum metabolomics as a novel diagnostic approach for gastrointestinal cancer.　
    Biomed. Chromatogr. 26, 548-558.
19. Izumi, Y., Takimura, S., Yamaguchi, S., Iida, J., Bamba, T. and Fukusaki, E.　
    (2012) Application of electrospray ionization ion trap/time-of-flight mass spectrometry for chemically-synthesized small RNAs.　
    J. Biosci. Bioeng. 113, 412-419.

Reviews

1. Lee, JW, Fukusaki, E. and Bamba, T.
   (2012) Application of supercritical fluid carbon dioxide to the extraction and analysis of lipids.
   Bioanalysis. 4, 2413-2422.
2. 山本慎也，福崎英一郎
   (2012) part3, Q42. オミクス研究って何ですか？
   ひらく，ひらく「バイオの世界」14歳からの生物工学入門, 日本生物工学会編, 化学同人出版(京都), pp.88-89.
3. 山本慎也，津川裕司，中山泰宗，福崎英一郎
   (2012) 第2章-第4項, メタボロミクス,
   極限環境生物の産業展開, 今中忠行監修, CMC出版(東京), pp.59-64.
4. 光永均，馬場健史，Danang Waluyo，畠中治代，福崎英一郎
   (2012) 第3章-第1項,　メタボローム解析を用いたキシロース資化性酵母の育種
   合成生物学の隆起（有用物質の新たな生産法構築をめざして）, 植田充美監修, CMC出版(東京), pp.47 -56.

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ゲノム機能工学領域

Original Papers

1. Sasano, Y., Haitani, Y., Ohtsu, I., Shima, J. and Takagi H.
   (2012) Proline accumulation in baker’s yeast enhances high-sucrose stress tolerance and fermentation
   ability in sweet dough.
   Int. J. Food Microbiol. 152, 40-43.
2. Benjaphokee, S., Hasegawa, D., Yokota, D., Asvarak, T., Auesukaree, C., Sugiyama, M., Kaneko, Y.,
   Boonchird, C. and Harasima, S.
   (2012) Highly efficient bioethanol production by a Saccharomyces cerevisiae strain with multiple stress tolerance to high temperature, acid and ethanol.
   N. Biotechnol. 29, 379-386.
3. Park, A. H., Sugiyama, M., Harashima, S. and Kim, Y. H.
   (2012) Creation of an ethanol-tolerant yeast strain by genome reconstruction based on chromosome
   splitting technology.
   J. Microbiol. Biotechnol. 22, 184-189.
4. Sasano, Y., Haitani, Y., Hashida, K., Ohtsu, I., Shima, J. and Takagi, H.
   (2012) Overexpression of the transcription activator Msn2 enhances fermentation ability of industrial baker’s yeast in frozen dough.
   Biosci. Biotech. Biochem. 76, 624-627.
5. Benjaphokee, S., Koedrith, P., Auesukaree C., Asvarak, T., Sugiyama, M., Kaneko, Y., Boonchird, C. and Harashima, S.
   (2012) CDC19 encoding pyruvate kinase is important for high-temperature tolerance in Saccharomyces cerevisiae.　
   N. Biotechnol. 29, 166-176.
6. Suzuki, T., Sugiyama, M., Wakazono, K., Kaneko, Y. and Harashima, S.
   (2012) Lactic-acid stress causes vacuolar fragmentation and impairs intracellular amino-acid homeostasis in Saccharomyces cerevisiae.
   J. Biosci. Bioeng. 113, 421-430.
7. Sasano, Y., Watanabe, D., Ukibe, K., Inai, T., Ohtsu, I. Shimoi, H. and Takagi, H.
   (2012) Overexpression of the yeast transcription activator Msn2 confers furfural resistance and increases the initial fermentation rate in ethanol production.
   J. Biosci. Bioeng. 113, 451-455.　
8. Sasano, Y., Haitani, Y., Hashida, K., Ohtsu, I. Shima, J. and Takagi, H.
   (2012) Enhancement of the proline and nitric oxide synthetic pathway improves fermentation ability under multiple baking-associated stress conditions in industrial baker’s yeast.
   Microb. Cell Fact. 11, 40.
9. Sasano, Y., Haitani, Y., Hashida, K., Ohtsu, I. Shima, J. and Takagi, H.
   (2012) Simultaneous accumulation of proline and trehalose in industrial baker’s yeast enhances fermentation ability in frozen dough.
   J. Biosci. Bioeng. 113, 592-595.
10. Ueda, Y., Ikushima, S., Sugiyama, M., Matoba, R., Kaneko, Y., Matsubara, K. and Harashima, S.
    (2012) Large-scale genome reorganization in Saccharomyces cerevisiae through combinatorial loss of mini-chromosomes.
    J. Biosci. Bioeng. 113, 675-682.
11. Dwiarti, L., Boonchird, C., Harashima, S. and Park, Y. E.
    (2012) Simultaneous saccharification and fermentation of paper sludge without pretreatment using
    cellulase from Acremonium cellulolyticus and thermotolerant Saccharomyces cerevisiae.　
    Biomass Bioenerg. 42, 114-122.
12. Chuwattanakul, V., Sugiyama, M., Khatun, F., Kurata, K., Tomita, I., Kaneko, Y. and Harashima, S.
    (2012) Increased transcription of NOP15, involved in ribosome biogenesis in Saccharomyces
    cerevisiae, enhances the production yield of RNA as a source of nucleotide seasoning.
    J. Biosci. Bioeng. 114, 17-22.
13. Auesukaree, C., Koedrith, P., Saenpayavai, P., Asvarak, T., Benjaphokee, S., Sugiyama, M., Kaneko, Y., Harashima, S. and Boonchird, C.
    (2012) Characterization and gene expression profiles of thermotolerant Saccharomyces cerevisiae
    isolates from Thai fruits.
    J. Biosci. Bioeng. 114, 144-149.
14. Bach, T. M., Hibi, T., Nasuno, R., Matsuo, G., Sasano, Y. and Takagi, H.
    (2012) Production of N-acetyl cis-4-hydroxy-L-proline by the yeast N-acetyltransferase Mpr1.
    J. Biosci. Bioeng. 114, 160-165.
15. Shahsavarani, H., Sugiyama, M., Kaneko, Y., Chuenchit, B. and Harashima, S.
    (2012) Superior thermotolerance of Saccharomyces cerevisiae for efficient bioethanol fermentation
    can be achieved by overexpression of RSP5 ubiquitin ligase.
    Biotechnol. Adv. 30, 1289-1300.

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生命環境システム工学領域（渡邉研）

Original Papers

1. Nishikawa, T., Sunami, T., Matsuura, T., Ichihashi, N. and Yomo, T.
   (2012) Construction of a Gene Screening System Using Giant Unilamellar Liposomes and a Fluorescence-Activated Cell Sorter.
   Anal. Chem. 84, 5017-5024.
2. Terasawa, H., Nishimura, K., Suzuki, H., Matsuura, T. and Yomo, T.
   (2012) Coupling of the fusion and budding of giant phospholipid vesicles containing macromolecules.
   P. Natl. Acad. Sci. USA 109, 5942-5947.
3. Okano, T., Matsuura, T., Kazuta, Y., Suzuki, H. and Yomo, T.
   (2012) Cell-free protein synthesis from a single copy of DNA in a glass microchamber.
   Lab Chip 12, 2704-2711.
4. Nishimura, K., Matsuura, T., Nishimura, K., Sunami, T., Suzuki, H. and Yomo, T.
   (2012) Cell-Free Protein Synthesis inside Giant Unilamellar Vesicles Analyzed by Flow Cytometry.
   Langmuir 28, 8426-8432.
5. Matsuura, T., Hosoda, K., Kazuta, Y., Ichihashi, N., Suzuki, H. and Yomo, T.
   (2012) Effects of Compartment Size on the Kinetics of Intracompartmental Multimeric Protein Synthesis.
   Acs. Synth. Biol. 1, 431-437.
6. Kobori, S., Ichihashi, N., Kazuta, Y., Matsuura, T. and Yomo, T.
   (2012) Kinetic analysis of aptazyme-regulated gene expression in a cell-free translation system: Modeling of ligand-dependent and -independent expression.
   RNA 18, 1458-1465.
7. Hirata, K., Ichii, T., Suzuki, H., Matsuura, T., Hosoda, K. and Yomo, T.
   (2012) Fractal-shaped microchannel design for a kinetic analysis of biochemical reaction in a delay line.
   Microfluid Nanofluid 13, 273-278.
8. Bansho, Y., Ichihashi, N., Kazuta, Y., Matsuura, T., Suzuki, H. and Yomo, T.
   (2012) Importance of parasite RNA species repression for prolonged translation-coupled RNA self-replication.
   Chemistry & biology 19, 478-487.
9. Kato, Y., Matsuura, T. and Watanabe, H.
   (2012) Genomic Integration and Germline Transmission of Plasmid Injected into Crustacean Daphnia magna Eggs.
   Plos One 7, DOI 10.1371/journal.pone.0045318

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細胞動態学領域（福井研）

Original Papers

1. Fujita, D., Suzuki, K., Sato, S., Yagi-Utsumi, M., Yamaguchi, Y., Mizuno, N., Kumasaka, T., Takata, M., Noda, M., Uchiyama, S., Kato, K. and Fujita, M.
   (2012) Protein encapsulation within synthetic molecular hosts.
   Nat. Commun. 3, 1093.
2. Hatoh, T., Maeda, T., Takeuchi, K., Ogikubo, O., Uchiyama, S., Otsuka, T., Ohkubo, I. and Ogita, H.
   (2012) Domain 5 of high molecular weight kininogen inhibits collagen-mediated cancer cell adhesion and invasion in association with α-actinin-4.
   Biochem. Biophys. Res. Commun. 427, 497-502.
3. Nose, K., Ozeki, Y., Kishi, T., Sumimura, K., Nishizawa, N., Fukui, K., Kanematsu, Y. and Itoh, K.
   (2012) Sensitivity enhancement of fiber-laser-based stimulated Raman scattering microscopy by collinear balanced detection technique.
   Opt. Express 20, 13958-13965.
4. Ozeki, Y., Umemura, W., Sumimura, K., Nishizawa, N., Fukui, K. and Itoh, K.
   (2012) Stimulated Raman hyperspectral imaging based on spectral filtering of broadband fiber laser pulses.
   Opt. Lett. 37, 431-433.
5. Shiga, D., Funahashi, Y., Masuda, H., Kikuchi, A., Noda, M., Uchiyama, S., Fukui, K., Kanaori, K., Tajima, K., Takano, Y., Nakamura, H., Kamei, M. and Tanaka, T.
   (2012) Creation of a binuclear purple copper site within a de novo coiled-coil protein.
   Biochemistry 51, 901-907.
6. Krayukhina, E., Uchiyama, S. and Fukui, K.
   (2012) Effects of rotational speed on the hydrodynamic properties of pharmaceutical antibodies measured by analytical ultracentrifugation sedimentation velocity.
   Eur. J. Pharm. Sci. 47, 367-374.
7. Dwiranti, A., Lin, L., Mochizuki, E., Kuwabata, S., Takaoka, A., Uchiyama, S. and Fukui, K.
   (2012) Chromosome observation by scanning electron microscopy using ionic liquid.
   Microsc. Res. Tech. 75, 1113-1118.
8. Kawahara, K., Nemoto, N., Motooka, D., Nishi, Y., Doi, M., Uchiyama, S., Nakazawa, T., Nishiuchi, Y., Yoshida, T., Ohkubo, T. and Kobayashi, Y.
   (2012) Polymorphism of collagen triple helix revealed by 19F NMR of model peptide [Pro-4(R)-Hydroxyprolyl-Gly]3-[Pro-4(R)-Fluoroprolyl-Gly]- [Pro-4(R)-Hydroxyprolyl-Gly]3
   J. Phys. Chem. 116, 6908-6915.
9. Nomura, N., Honda, T., Baba, K., Naganuma, T., Tanzawa, T., Arisaka, F., Noda, M., Uchiyama, S., Tanaka, I., Yao, M. and Uchiumi, T.
   (2012) The archaeal ribosomal stalk protein interacts with translation factors in a nucleotide-independent manner via its conserved C-terminus.
   Proc. Natl. Acad. Sci. USA 109, 3748-3753.
10. Yagi, H., Ishimoto, K., Hiromoto, T., Fujita, H., Mizushima, T., Uekusa, Y., Yagi-Utsumi, M., Kurimoto, E., Noda, M., Uchiyama, S., Tokunaga, F., Iwai, K. and Kato, K.
    (2012) Non-canonical UBA-UBL interaction mediates formation of linear ubiquitin chain assembly complex.
    EMBO rep. 13, 462-468.
11. Matsunaga, S., Takata, H., Morimoto, A., Hayashihara, K., Higashi, T., Akatsuchi, K., Mizusawa, E., Yamakawa, M., Ashida, M., Matsunaga, T., Azuma, T., Uchiyama, S. and Fukui, K.
    (2012) RBMX: a regulator for maintenance and centromeric protection of sister chromatid cohesion.
    Cell Rep. 19, 299-308.
12. Saito, S., Hasegawa, J., Kobayashi, N., Kishi, N., Uchiyama, S. and Fukui, K.
    (2012) Behavior of monoclonal antibodies: Relation between the second virial coefficient (B₂) at low concentrations and aggregation propensity and viscosity at high concentrations.
    Pharm. Res. 29, 397-410.
13. Fukuhara, A., Nakajima, H., Miyamoto, Y., Inoue, K., Kume, S., Noda, M., Uchiyama, S., Shimamoto, S., Nishimura, S., Ohkubo, T., Goto, Y., Takeuchi, T. and Inui, T.
    (2012) Drug delivery system for poorly water-soluble compounds using lipocalin-type prostaglandin D synthase.
    Journal of Controlled Release 159, 143-150.
14. Motooka, D., Kawahara, K., Nakamura, S., Doi, M., Nishi, N., Nishiuchi, Y., Kang, Y.K., Nakazawa, T., Uchiyama, S., Yoshida, T., Ohkubo, T. and Kobayashi, Y.
    (2012) The triple helical structure and stability of collagen model peptide with 4(S)-Hydroxyprolyl-Pro-Gly Units.
    Biopolymers; Peptide Science 98, 111-121.
15. Umemura, W., Fujita, K., Ozeki, Y., Goto, K., Sumimura, K., Nishizawa, N., Fukui, K. and Itoh, K.
    (2012) Subharmonic synchronization of picosecond Yb fiber laser to picosecond Ti:sapphire laser for stimulated Raman scattering microscopy.
    Jpn. J. Appl. Phys. 51, 022702.
16. Tsuchimoto, S., Cartagena, J., NKhemkladngoen, N., Singkaravanit, S., Kohinata, T., Wada, N., Sakai, H., Morishita, Y., Suzuki, H., Shibata, D. and Fukui, K.
    (2012) Development of transgenic plants of jatropha with drought resistance.
    Plant Biotechnology 29, 137-143.
17. Hirakawa, H., Tsuchimoto, S., Sakai, H., Nakayama, S., Fujishiro, T., Kishida, Y., Kohara, M., Watanabe, A., Yamada, M., Aizu, T., Toyoda, A., Fujiyama, A., Tabata, S., Fukui, K. and Sato, S.
    (2012) Upgraded genomic information of Jatropha curcas L.
    Plant Biotechnology 29, 123–130.

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細胞工学領域（村中研）

Original Papers

1. Heintz, D., Gallien, S., Compagnon, V., Berna, A., Suzuki, M., Yoshida, S., Muranaka, T., Dorsselaer, A.V., Schaeffer, C., Bach, T.J. and Schaller, H.
   (2012) Phosphoproteome exploration reveals a reformatting of cellular processes in response to low sterol biosynthetic capacity in Arabidopsis.
   J. Proteome Res. 11, 1228-1239.
2. Kunii, M., Kitahama, Y., Fukushima, E.O., Seki, H., Muranaka, T., Yoshida, Y. and Aoyama, Y.
   (2012) β-Amyrin oxidation by oat CYP51H10 expressed heterologously in yeast cells: The first example of CYP51-dependent metabolism other than the 14-demethylation of sterol precursors.
   Biol. Pharm. Bull. 35, 801-804.
3. Hirao, T., Okazawa, A., Harada, K., Kobayashi, A., Muranaka, T. and Hirata, K.
   (2012) Green leaf volatiles enhance methyl jasmonate response in Arabidopsis.
   J. Biosci. Bioeng. 114, 540-545.
4. Go, Y.S., Lee, S.B., Kim, H.J., Kim, J., Park, H.Y., Kim, J.K., Shibata, K., Yokota, T., Ohyama, K., Muranaka, T., Arseniyadis, S. and Suh, M.C.
   (2012) Identification of marneral synthase, which is critical for Arabidopsis growth and development.
   Plant J. 72, 791-804.

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生物化学工学領域

Original Papers

1. Honda, K., Imura, M., Okano, K., Omasa, T., Kato, J. and Ohtake, H.
   (2012) Identification of the replicon of 111-kb circular plasmid from Rhodococcus opacus B-4.
   Biosci. Biotechnol. Biochem., 76, 1758-1764.
2. Ye, X., Honda, K., Sakai, T., Okano, K., Omasa, T., Hirota, R., Kuroda, A. and Ohtake, H.
   (2012) Synthetic metabolic engineering-a novel technology for designing a chimeric metabolic pathway.
   Microbial Cell Fact. 11, 120.
3. Siriphongphaew, A., Pisnupong, P., Wongkongkatep, J., Inprakhon, P., Vangnai, A.S., Honda, K., Ohtake, H., Kato, J., Ogawa, J., Shimizu, S., Urlacher, V.B., Schmid, R.D. and Pongtharangkul, T.
   (2012) Development of a whole-cell biocatalyst co-expressing P450 monooxygenase and glucose dehydrogenase for synthesis of epoxyhexane.
   Appl. Microbiol. Biotechnol. 95, 357-367.
4. Wongkongkatep, P., Manopwisedjaroen, K., Tiposoth, P., Archakunakorn, S., Pongtharangkul,T., Suphantharika, M., Honda, K., Hamachi, I. and Wongkongkatep, J.
   (2012) Bacteria interface pickering emulsions stabilized by self-assembled bacteria-chitosan network. Langmuir 28, 5729−5736.
5. Mizuguchi, S., Sasaki, T. and Honda, K.
   (2012) Growth inhibitory effects of anthranilic acid and its derivatives against Legionella pneumophila.
   J. Biosci. Bioeng. 113, 726-729.
6. Onitsuka M, Kim WD, Ozaki H, Kawaguchi A, Honda K, Kajiura H, Fujiyama K, Asano R, Kumagai I, Ohtake H and Omasa T.
   (2011) Enhancement of sialylation on humanized IgG-like bispecific antibody by overexpression of α2,6-sialyltransferase derived from Chinese hamster ovary cells.
   Appl. Microbiol. Biotechnol. 94, 69–80.
7. Restiawaty, E., Honda, K., Okano, K., Hirota, R., Omasa, T., Kuroda, A. and Ohtake, H. (2012) Construction of membrane-anchoring fusion protein of Thermococcus kodakaraensis glycerol kinase and its application to repetitive batchwise reactions.
   J. Biosci. Bioeng. 113, 521–525.
8. Cao, Y., Kimura, S., Itoi, T., Honda, K., Ohtake, H. and Omasa, T.
   (2012) Fluorescence in situ hybridization using bacterial artificial chromosome (BAC) clones for the analysis of chromosome rearrangement in Chinese hamster ovary cells.
   Methods 56, 418–423.
9. Cao, Y., Kimura, S., Itoi, T., Honda, K., Ohtake, H. and Omasa, T.
   (2012) Construction of BAC-based physical map and analysis of chromosome rearrangement in Chinese hamster ovary cell lines.
   Biotechnol. Bioeng. 109, 1357-1367.
10. Wangrangsimagul, N., Klinsakul, K., Vangnai, A.S., Wongkongkatep, J., Inprakhon, P., Honda, K., Ohtake, H., Kato, J. and Pongtharangkul, T.
    (2012) Bioproduction of vanillin using an organic solvent-tolerant Brevibacillus agri 13.
    Appl. Microbiol. Biotechnol. 93, 555-563.

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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. Kino-oka, M., Ngo, T.X., Nagamori, E., Takezawa, Y., Miyake, Y., Sawa, Y., Saito, A., Shimizu, T., Okano, T. and Taya, M.
   (2012) Evaluation of vertical cell fluidity in a multilayered sheet of skeletal myoblasts.
   J. Biosci. Bioeng. 113, 128-131.
2. Kim, M-H., Sonoi, R., Yamada, K., Inamori, M. and Kino-oka, M.
   (2012) Analysis of locality of early-stage maturation in confluent state of human retinal pigment epithelial cells.
   J. Biosci. Bioeng. 113, 778-781.
3. Nadzir, M.M., Kino-oka, M., Sugawara, K. and Taya, M.
   (2012) Effect of preservation conditions of collagen substrate on its fibril formation and rabbit chondrocyte morphology.
   J. Biosci. Bioeng. 114, 360-363.

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生物工学国際交流センター（仁平研）

Original Papers

1. Siriwach, R., Kinoshita, H., Kitani, S., Igarashi, Y., Pansuksan, K., Panbangred, W. and Nihira T.
   (2012) Mycoleptione, a new chromone derivative isolated from the endophytic fungus Mycoleptodiscus sp. MU41.
   J. Antibiot. (Tokyo) 65, 627-629.
2. Aroonsri, A., Kitani, S., Hashimoto, J., Kosone, I., Izumikawa, M., Komatsu, M., Fujita, N., Takahashi, Y., Shin-ya, K., Ikeda, H. and Nihira T.
   (2012) Pleiotropic control of secondary metabolism and morphological development by KsbC, a butyrolactone-autoregulator receptor homologue in Kitasatospora setae.
   Appl. Environ. Microbiol. 78, 8015-8024.
3. Igarashi, Y., Yu, L., Ikeda, M., Oikawa, T., Kitani, S., Nihira, T., Bayanmunkh, B. and Panbangred, W.
   (2012) Jomthonic acid A, a modified amino acid from a soil-derived Streptomyces.
   J. Nat. Prod. 75, 986-990.
4. Aroonsri, A., Kitani, S., Ikeda, H. and Nihira, T.
   Kitasetaline, a novel β-carboline alkaloid from Kitasatospora setae NBRC 14216T.
   (2012) J. Biosci. Bioeng. 114, 56-58.
5. Igarashi, Y., Tanaka, Y., Ikeda, M., Oikawa, T., Kitani, S., Nihira, T., Mongkol, P., Janhom, M. and Panbangred, W.
   (2012) Prajinamide, a new modified peptide from a soil-derived Streptomyces.
   J. Antibiot. (Tokyo) 65, 157-159.
6. Baba, S., Kinoshita, H. and Nihira, T.
   (2012) Identification and characterization of Penicillium citrinum VeA and LaeA as global regulators for ML-236B production.
   Curr. Genet. 58, 1-11.
7. Sakai, K., Kinoshita, H. and Nihira, T.
   (2012) Heterologous expression system in Aspergillus oryzae for fungal biosynthetic gene clusters of secondary metabolites.
   Appl. Microbiol. Biotechnol. 93, 2011-2022.

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生物工学国際交流センター（藤山研）

Original Papers

1. Kajiura, H., Okamoto, T., Misaki, R., Matsuura, Y. and Fujiyama, K.
   (2012) Arabidopsis 1,2-xylosyltransferase: substrate specificity and participation in the plant-specific N-glycosylation pathway.
   J. Biosci. Bioeng. 113, 48-54.
2. Onitsuka, M., Kim, W.D., Ozaki, H., Kawaguchi, A., Honda, K., Kajiura, H., Fujiyama, K., Asano, R., Kumagai, I., Ohtake, H. and Omasa, T.
   (2012) Enhancement of sialylation on humanized IgG-like bispecific antibody by overexpression of 2,6-sialyltransferase derived from Chinese hamster ovary cells.
   Appl. Microbiol. Biotechnol. 94, 69-80.
3. Lombardi, R., Donini, M., Villani, M.E., Brunetti, P., Fujiyama, K., Kajiura, H., Paul, M., Ma, J.K. and Benvenuto, E.
   (2012) Production of different glycosylation variants of the tumour-targeting mAb H10 in Nicotiana benthamiana: influence on expression yield and antibody degradation.
   Transgenic. Res. 21, 1005-21.
4. Hong, Z., Kajiura, H., Su, W., Jin, H., Kimura, A., Fujiyama, K. and Li, J.
   (2012) Evolutionarily conserved glycan signal to degrade aberrant brassinosteroid receptors in Arabidopsis.
   Proc. Natl. Acad. Sci. U. S. A. 109, 11437-11442.
5. Ohashi, T., Fujiyama, K. and Takegawa K.
   (2012) Identification of novel 1,3-galactosyltransferase and elimination of -galactose-containing glycans by disruption of multiple -galactosyltransferase genes in Schizosaccharomyces pombe.
   J. Biol. Chem. 287, 38866-38875.

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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. Ohtsuka, K., Sato, S., Sato, Y., Sota, K., Ohzawa, S., Matsuda, T., Takemoto, K., Takamune, N., Juskowiak, B., Nagai, T. and Takenaka, S.
   (2012) Fluorescence imaging of potassium ions in living cells using a fluorescent probe based on a thrombin binding aptamer-peptide conjugate.
   Chem Commun (Camb). 48, 4740–4742.
2. Chang, Y., Arai, Y. and Nagai, T.
   (2012) Optogenetic activation during detector "dead time" enables compatible real-time fluorescence imaging.
   Neurosci Res. 73, 341–347.
3. Kominami, K., Nakabayashi, J., Nagai, T., Tsujimura, Y., Chiba, K., Kimura, H., Miyawaki, A., Sawasaki, T., Yokota, H., Manabe, N. and Sakamaki, K.
   (2012) The molecular mechanism of apoptosis upon caspase-8 activation: quantitative experimental validation of a mathematical model.
   Biochim Biophys Acta. 1823, 1825–1840.
4. Hatsugai, N., Perez Koldenkova, V., Imamura, H., Noji, H. and Nagai, T.
   (2012) Changes in Cytosolic ATP Levels and Intracellular Morphology during Bacteria-Induced Hypersensitive Cell Death as Revealed by Real-Time Fluorescence Microscopy Imaging.
   Plant Cell Physiol. 53, 1768-1775.
5. Iwano, M., Ngo, QA., Entani, T., Shiba, H., Nagai, T., Miyawaki, A., Isogai, A., Grossniklaus, U. and Takayama, S.
   (2012) Cytoplasmic Ca2+ changes dynamically during the interaction of the pollen tube with synergid cells.
   Development. 139, 4202-4209.
6. Kominami, K., Nagai, T., Sawasaki, T., Tsujimura, Y., Yashima, K., Sunaga, Y., Tsuchimochi, M., Nishimura, J., Chiba, K., Nakabayashi. J., Koyamada, K., Endo, Y., Yokota, H., Miyawaki, A., Manabe, N. and Sakamaki, K.
   (2012) In vivo imaging of hierarchical spatiotemporal activation of caspase-8 during apoptosis.
   PLoS ONE. 7, e50218.
7. Saito, K., Chang, Y., Horikawa, K., Hatsugai, N., Higuchi, Y., Hashida, M., Yoshida, Y., Matsuda, T., Arai, Y. and Nagai, T.
   (2012) A luminescent protein for high-speed single-cell and whole-body imaging.
   Nat Commun. 3:1262, 1-9.
8. Hihara, S., Pack, CG., Hanafusa, T., Kaizu. K., Tani, T., Takemoto, S., Yoshimi, T., Sako, Y., Yokota, H., Imamoto, N., Kinjo, M., Takahashi, K., Nagai, T. and Maeshima, K.
   (2012) Local Nucleosome Dynamics Facilitate Chromatin Accessibility in Living Mammalian Cells.
   Cell Rep. 2, 1645-1656.

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物質生命工学コース極限生命工学領域（金谷研）

Original Papers

1. Sulaiman, S., Yamato, S., Kanaya, E., Kim, J-J., Koga, Y., Takano, K. and Kanaya, S.
   (2012) Isolation of a novel cutinase with polyethylene terephthalate degrading activity from leaf-branch compost using a metagenomic approach.
   Appl. Environ. Microbiol. 78, 1556-1562.
2. Budiman, C., Tadokoro, T., Angkawidjaja, C., Koga, Y. and Kanaya, S.
   (2012) Role of polar and nonpolar residues at the active site for PPIase activity of FKBP22 from Shewanella sp. SIB1.
   FEBS J. 279, 976–986.
3. Nguyen, T-N., Angkawidjaja, C., Kanaya, E., Koga, Y., Takano, K. and Kanaya, S.
   (2012) Activity, stability, and structure of metagenome-derived LC11-RNase H1, a homolog of Sulfolobus tokodaii RNase H1.
   Protein Sci. 21, 553-561.
4. Uehara, R., Takeuchi, Y., Tanaka, S., Takano, K., Koga, Y. and Kanaya, S.
   (2012) Requirement of Ca2+ ions for the hyperthermostability of Tk-subtilisin from Thermococcus kodakarensis.
   Biochemistry, 51, 5369–5378.
5. Okada, K., Angkawidjaja, C., Koga, Y., Takano, K. and Kanaya, S.
   (2012) Characteristic features of kynurenine aminotransferase allosterically regulated by -ketoglutarate in cooperation with kynurenine.
   PLoS ONE, 7, e40307.
6. Kim, J-J., Kanaya, E., Weon, H-Y., Koga, Y., Takano, K., Dunfield, P. F., Kwon, S-W. and Kanaya, S.　
   (2012) Flavobacterium compostarboris sp. nov., isolated from leaf-and-branch compost, and emended descriptions of Flavobacterium hercynium, Flavobacterium resistens and Flavobacterium johnsoniae. Int.
   J. Syst. Evol. Microbiol. 62, 2018-2024.
7. Jongruja, N., You, D-J., Angkawidjaja, C., Kanaya, E., Koga, Y. and Kanaya, S.
   (2012) Structure and characterization of RNase H3 from Aquifex aeolicus.
   FEBS J. 279, 2737-2753.　 (selected for Virtual Issue of FEBS Journal, Structural Biology)
8. Angkawidjaja, C., Koga, Y., Takano, K. and Kanaya, S.
   (2012) Structure and stability of a thermostable carboxylesterase from the thermoacidophilic archaeon Sulfolobus tokodaii.　
   FEBS J. 279, 3071-3084.　(selected for Virtual Issue of FEBS Journal, Structural Biology)
9. Cheng, M., Angkawidjaja, C., Koga, Y. and Kanaya, S.
   (2012) Requirement of lid2 for interfacial activation of a family I.3 lipase with unique two lid structures.
   FEBS J. 279, 3727-3737.
10. Uehara, R., Tanaka, S., Takano, K., Koga, Y. and Kanaya, S.
    (2012) Requirement of insertion sequence IS1 for thermal adaptation of Pro-Tk-subtilisin from hyperthermophilic archaeon.
    Extremophiles 16, 841-851.
11. Tannous, E., Yokoyama, K., You, D-J., Koga, Y. and Kanaya, S.
    (2012) A dual role of divalent metal ions in catalysis and folding of RNase H1 from extreme halophilic archaeon Halobacterium sp. NRC-1.
    FEBS Open Bio 2, 345-352.
12. Kobayashi, H., Hirano, N., Kanaya, S. and Haruki M.
    (2012) Enhancement of the enzymatic activity of Escherichia coli acetyl esterase by a double mutation obtained from random mutagenesis.
    Biosci. Biotechnol. Biochem. 76, 2082-2088.
13. Okada, J., Koga, Y., Takano, K. and Kanaya, S.
    (2012) Slow unfolding pathway of the hyperthermophilic Tk-RNase H2 examined by pulse proteolysis using the stable protease Tk-subtilisin.
    Biochemistry 51, 9178-9191.

Reviews

1. Hirata, A., Sato, A., Koga, A., Kanaya, S. and Takano, K.
   (2012) A stable protein; CutA1.
   In Protein Structure (Faraggi, E. ed.), pp. 249-262, InTech, Rijeka (Croatia).
2. Tanaka, S., Uehara, R. and Kanaya, S.
   (2012) Maturation and stabilization mechanisms of two hyperthermostable subtilisin-like serine proteases from Thermococcus kodakarensis.
   In Serine Proteases: Mechanism, Structure and Evolution (Chiba, I, & Kamio, T., eds), pp. 1-32, Nova Science Publishers, Inc., (NY).

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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. Ida, Y., Furusawa, C., Hirasawa, T. and Shimizu, H.
   (2012) Stable disruption of ethanol production by deletion of the genes encoding alcohol dehydrogenase isozymes in Saccharomyces cerevisiae.
   J. Biosci. Bioeng.113,192-195.
2. Mahmud, S, A., Hirasawa, T., Furusawa, C., Yoshikawa, K. and Shimizu, H.
   (2012) Understanding the mechanism of heat stress tolerance caused by high trehalose accumulation in Saccharomyces cerevisiae using DNA microarray.
   J. Biosci. Bioeng.113, 526-528.
3. Usui, Y., Hirasawa, T., Furusawa, C., Shirai, T., Yamamoto, N., Mori, H. and Shimizu, H.
   (2012) Investigating the effects of perturbations to pgi and eno geneexpression on central carbon metabolism in Escherichia coli using 13C metabolic flux analysis.
   Microbial Cell Factories 11, 87.
4. Chatsurachai, S., Furusawa, C. and Shimizu, H.
   (2012) An in silico platform for the design of heterologous pathways in nonnative metabolite production.
   BMC Bioinformatics 13, 93.

Reviews

1. Furusawa, C., Horinouchi, T., Hirasawa, T. and Shimizu, H.
   (2012) Systems metabolic engineering: the creation of microbial cell factories by rational metabolic design and evolution.
   In Biochem.Eng./Biotechnol.(Zhong J. J.ed.), 1-23.
2. Hirasawa, T., Kim, J., Shirai, T., Furusawa, C. and Shimizu, H.
   (2012) Molecular mechanisms and metabolic engineering of glutamate overproduction in Corynebacterium glutamicum
   In Subcellular Biochemistry(Wang, X., Chen, J. and Quinn, P. J.,eds.), Reprogramming Microbial Metabolic Pathways. 64, 261-281.
3. Yoshikawa, K., Furusawa, C., Hirasawa, T. and Shimizu, H.
   (2012) Design of Superior Cell Factories Based on Systems Wide Omics Analysis.
   In Systems Metabolic Engineering(Wittmann, C. and Lee S. Y.,eds.), 57-82.

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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. Nishimura, K., Suzuki, K., Toyota, T. and Yomo, T.
   (2012) Size control of giant unilamellar vesicles prepared from inverted emulsion droplets.
   J. Colloid Interface Sci. 376, 119–125.
2. Hirata, K., Ichii, T., Suzuki, H., Matsuura, T., Hosoda, K. and Yomo, T.
   (2012) Fractal-shaped microchannel design for a kinetic analysis of biochemical reaction in a delay line.
   Microfluidics and Nanofluidics 13, 273-278.
3. Terasawa, H., Nishimura, K., Suzuki, H., Matsuura, T. and Yomo, T.
   (2012) Coupling of the fusion and budding of giant phospholipid vesicles containing macromolecules.
   Proc. Natl. Acad. Sci. USA 109, 5942-5947.
4. Sakakura, T., Nishimura, K., Suzuki, H. and Yomo, T.
   (2012) Statistical analysis of discrete encapsulation of nanomaterials in colloidal capsules.
   Analytical methods2012 4, 1648-1655.
5. Okano, T., Matsuura, T., Kazuta, Y., Suzuki, H. and Yomo, T.
   (2012) Cell-free protein synthesis from a single copy of DNA in a 1 glass microchamber.
   Lab on a Chip2012 12, 2704–2711.
6. Nishikawa, T., Sunami, T., Matsuura, T., Ichihashi, N. and Yomo, T.
   (2012) Construction of Gene Screening System Using Giant Unilamellar Liposomes and Fluorescence Activated Cell Sorter.
   analytical chemistry 84, 5017-5024.
7. Bansho, Y., Ichihashi, N., Kazuta, Y., Matsuura, T., Suzuki, H. and Yomo, T.
   (2012) Importance of parasite RNA species repression for prolonged translation-coupled RNA self-replication.
   CHEMISTRY BIOLOGY 19, 478-487.
8. Nishimura, K., Matsuura, T., Nishimura, K., Sunami, T., Suzuki, H. and Yomo, T.
   (2012) Cell-free protein synthesis inside giant unilamellar vesicles analyzed by flow cytometry.
   Langmuir2012 28, 8426-8432.
9. Kumano, I., Hosoda, K., Suzuki, H., Hirata, K. and Yomo, T.
   (2012) Hydrodynamic trapping of Tetrahymena thermophila for the long-term monitoring of cell behaviors.
   Lab on a Chip2012 12, 3451–3457.
10. Kobori, S., Ichihashi, N., Kazuta, Y., Matsuura, T. and Yomo, T.
    (2012) Kinetic analysis of aptazyme-regulated gene expression in a cell-free translation system: modeling of ligand-dependent and -independent expression.
    RNA 18, 1458-1465.
11. Matsuura, T., Hosoda, K., Kazuta, Y., Ichihashi, N., Suzuki, H. and Yomo, T.
    (2012) Effects of Compartment Size on the Kinetics of Intracompartmental　Multimeric Protein Synthesis.
    ACS Synth. Biol2012 1, 431−437.
12. Wu, T., Hirata, K., Suzuki, H., Xiang, R., Tang, Z. and Yomo, T.
    (2012) Shrunk to Femtolitre: Tuning High-throughput Monodisperse Water-in-oil Droplet Arrays for Ultra-small Micro-reactors.
    Applied Physics Letters 101, 074108-1-4.
13. Nishikawa, T., Sunami, T., Matsuura, T. and Yomo, T.
    (2012) Directed Evolution of Proteins through In Vitro Protein Synthesis in Liposomes.
    Journal of Nucleic Acids2012, 1-11.
14. Nishiyama, K., Ichihashi, N., Matsuura, T., Kazuta, Y. and Yomo, T.
    (2012) α-Complementation in an artificial genome replication system in liposomes.
    Chembiochem2012 13, 2701-2706.

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