生物資源工学領域（福崎研）

Original Papers

1. Takeno, S., Bamba, T., Nakazawa, Y., Fukusaki, E., Okazawa, A. and Kobayashi, A.
   (2010) High-Throughput and Highly Sensitive Analysis Method for Polyisoprene in Plants by Pyrolysis-Gas Chromatography/Mass Spectrometry.
   Biosci. Biotechnol. Biochem. 74, 13-17.
2. Hasunuma, T., Harada, K., Miyazawa, S., Kondo, A., Fukusaki, E. and Miyake, C.
   (2010) Metabolic turnover analysis by a combination of in vivo 13C-labelling from 13CO2 and metabolic profiling with CE-MS/MS reveals rate-limiting steps of the C3 photosynthetic pathway in Nicotiana tabacum leaves.
   J. Exp. Bot. 61,1041-1051.
3. Tianniam, S., Bamba, T. and Fukusaki, E.
   (2010) Pyrolysis GC-MS-based metabolite fingerprinting for quality evaluation of commercial Angelica acutiloba roots.
   J. Biosci. Bioeng. 109, 89-93.
4. Ishikawa, K., Yoshimura, K., Harada, K., Fukusaki, E., Ogawa, T., Tamoi, M. and Shigeoka, S.
   (2010) AtNUDX6, an ADP-ribose/NADH pyrophosphohydrolase in Arabidopsis, positively regulates NPR1-dependent salicylic acid signaling.
   Plant Physiol. 154, 2000-2012.
5. Yoshida, R., Tamura, T., Takaoka, C., Harada, K., Kobayashi, A., Mukai, Y. and Fukusaki, E.
   (2010) Metabolomics-based systematic prediction of yeast lifespan and its application for semi-rational screening of aging-related mutants.
   Aging Cell 9, 616-625.
6. Bando, K., Kawahara, R., Kunimatsu, T., Sakai, J., Kimura, J., Funabashi, H., Seki, T., Bamba, T. and Fukusaki, E.
   (2010) Influences of biofluid sample collection and handling procedures on GC-MS based metabolomic studies.
   J. Biosci. Bioeng. 110, 491-499.
7. Bamba, T., Murayoshi, M., Gyoksen, K., Nakazawa, Y., Okumoto, H., Katto, H., Fukusaki, E. and Kobayashi, A.
   (2010) Contribution of mevalonate and methylerythritol phosphate pathways to polyisoprenoid biosynthesis in the rubber-producing plant Eucommia ulmoides oliver.
   Z. Naturforsch. C. 65, 363-372.
8. Nishiumi, S., Shinohara, M., Ikeda, A., Yoshie, T., Hatano, N., Kakuyama, S., Mizuno, S., Sanuki, T., Kutsumi, H., Fukusaki, E., Azuma, T., Takenawa, T. and Yoshida, M.
   (2010) Serum metabolomics as a novel diagnostic approach for pancreatic cancer.
   Metabolomics 6, 518-528.

Reviews

1. Matsubara, A., Fukusaki, E. and Bamba, T.
   (2010) Metabolite analysis by supercritical fluid chromatography. Bioanalysis 2, 27-34.

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ゲノム機能工学領域

Original Papers

1. Hermansyah, Lavina, W.A., Sugiyama, M., Kaneko, Y. and Harashima, S.
   (2010) Identification of protein kinase disruptions as suppressors of the calcium sensitivity of S. cerevisiae ∆ptp2 ∆msg5 protein phosphatase double disruptant.
   Arch. Microbiol. 192, 157-165.
2. Hirasaki, M., Nakamura, F., Yamagishi, K., Numamoto, M., Shimada, Y., Uehashi, K., Muta, S., Sugiyama, M., Kaneko, Y., Kuhara, S. and Harashima, S.
   (2010) Deciphering cellular functions of protein phosphatases by comparison of gene expression profiles in Saccharomyces cerevisiae.
   J. Biosci. Bioeng. 109, 433-441.
3. Moukamnerd, C., Kino-oka, M., Sugiyama, M., Kaneko, Y., Boonchird, C., Harashima, S., Noda, H., Ninomiya, K., Shioya, S. and Katakuka, Y. 　
   (2010) Ethanol production from biomass by repetitive solid-sate fed-batch fermentation with continuous recovery of ethanol.
   Appl. Microbiol. Biotechnol. 88, 87-94.

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生命環境システム工学領域（渡邉研）

Original Papers

1. Kato, Y., Kobayashi, K., Watanabe, H. and Iguchi, T.
   (2010) Introduction of foreign DNA into the water flea, Daphnia magna, by electroporation.
   Ecotoxicology 19, 589-592.
2. Kato, Y., Kobayashi, K., Oda, S., Tatarazako, N., Watanabe, H. and Iguchi, T.
   (2010) Sequence divergence and expression of a transformer gene in the branchiopod crustacean, Daphnia magna.
   Genomics 95, 160-165.
3. Hikake, T., Hayashi, S., Chambon, P., Watanabe, H., Iguchi, T. and Sato, T.
   (2010) Differential involvement of insulin-like growth factor-I and estrogen on prolactin cells in the mouse anterior pituitary.
   Exp. Biol. Med. (Maywood) 235, 974-980.
4. Urabe, H., Ichihashi, N., Matsuura, T., Hosoda, K., Kazuta, Y., Kita, H. and Yomo, T.
   (2010) Compartmentalization in a water-in-oil emulsion repressed the spontaneous amplification of RNA by Qbeta replicase.
   Biochemistry 49, 1809-1813.
5. Sunami, T., Hosoda, K., Suzuki, H., Matsuura, T. and Yomo, T.
   (2010) Cellular compartment model for exploring the effect of the lipidic membrane on the kinetics of encapsulated biochemical reactions.
   Langmuir 26, 8544-8551.
6. Sunami, T., Caschera, F., Morita, Y., Toyota, T., Nishimura, K., Matsuura, T., Suzuki, H., Hanczyc, M.M., and Yomo, T.
   (2010) Detection of association and fusion of giant vesicles using a fluorescence-activated cell sorter.
   Langmuir 26, 15098-15103.
7. Ichihashi, N., Matsuura, T., Hosoda, K. and Yomo, T.
   (2010) Identification of Two Forms of Qbeta Replicase with Different Thermal Stabilities but Identical RNA Replication Activity.
   J. Biol. Chem. 285, 37210-37217.

Reviews

1. Yanagida, H., Matsuura, T., and Yomo, T.
   (2010). Ribosome display for rapid protein evolution by consecutive rounds of mutation and selection.
   Methods Mol. Biol. 634, 257-267.
2. Sunami, T., Matsuura, T., Suzuki, H., and Yomo, T.
   (2010). Synthesis of functional proteins within liposomes. Methods Mol.
   Biol. 607, 243-256.
3. Matsuura, T., Ichihashi, N., Sunami, T., Kita, H., Suzuki, H. and Yomo, T.
   (2010) Evolvability and Self-Replication of Genetic Information in Liposomes. In “The Minimal Cell The Biophysics of Cell Compartment and the Origin of Cell Functionality” edited by Luisi P.L. and Stano, P.
   Springer (Dordrecht, Netherland), p. 275-287.

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細胞動態学領域（福井研）

Original Papers

1. Uchiyama, S., Suzuki, Y., Otake, K., Yokoyama, M., Ohta, M., Aikawa, S., Komatsu, M., Sawada, T., Kagami, Y., Morishima, Y. and Fukui, K.
   (2010) Development of novel humanized anti-CD20 antibodies based on affinity constant and epitope.
   Cancer Sci. 101, 201-209.
2. Hayashihara, K., Uchiyama, S., Shimamoto, S., Kobayashi, S., Tomschik, M., Wakamatsu, H., No, D., Sugahara, H., Hori, N., Noda, M., Ohkubo, T., Zlatanova, J., Matsunaga, S. and Fukui, K.
   (2010) The middle region of an HP1-binding protein, HP1-BP74, associates with linker DNA at the entry/exit site of nucleosomal DNA.
   J Biol Chem. 285, 6498-6507.
3. Ohmido, N., Ishimaru, A., Kato, S., Sato, S., Tabata, S. and Fukui, K.
   (2010) Integration of cytogenetic and genetic linkage maps of Lotus japonicus, a model plant for legumes.
   Chromosome Res. 18, 287-99.
4. Nishio, M., Kamiya, Y., Mizushima, T., Wakatsuki, S., Sasakawa, H., Yamamoto, K., Uchiyama, S., Noda, M., McKay, AR., Fukui, K., Hauri, HP. and Kato, K.
   (2010) Structural basis for the cooperative interplay between the two causative gene products of combined factor V and factor VIII deficiency.
   Proc. Natl. Acad. Sci. USA. 107, 4034-4039.
5. Nishi, H., Miyajima, M., Nakagami, H., Noda, M., Uchiyama, S. and Fukui, K.
   (2010) Phase separation of an IgG1 antibody solution under a low ionic strength condition.
   Pharm Res. 27, 1348-1360.
6. Ozeki, Y., Kitagawa, Y., Sumimura, K., Nishizawa, N., Umemura, W., Kajiyama, S., Fukui, K. and Itoh, K.
   (2010) Stimulated Raman scattering microscope with shot noise limited sensitivity using subharmonically synchronized laser pulses.
   Opt. Express. 18, 13708-13719.
7. Izumi, K., Nakamura, S., Nakano, N., Shimura, K., Sakagami, Y., Watanabe, Y., Oishi, S., Uchiyama, S., Ohkubo, T., Kobayashi, Y., Fujii, N., Matsuoka, M. and Kodama, EN.
   (2010) Characterization of HIV-1 resistance to a fusion inhibitor, N36, derived from the　gp41 amino terminal heptad repeat.
   Antiviral Res. 87, 179-186.
8. Kawahara, K., Nakamura, S., Katsu, Y., Motooka, D., Hosokawa, Y., Kojima, Y., Matsukawa, K., Takinowaki, H., Uchiyama, S., Kobayashi, Y., Fukui, K. and Ohkubo, T.
   (2010) Cloning, expression, crystallization and preliminary X-ray crystallographic analysis of a human condensin SMC2 hinge domain with short coiled coils.
   Acta Crystallogr Sect F Struct Biol Cryst Commun. 66, 1067-1070.
9. Nogi, T., Yasui, N., Mihara, E., Matsunaga, Y., Noda, M., Yamashita, N., Toyofuku, T., Uchiyama, S., Goshima, Y., Kumanogoh, A. and Takagi, J.
   (2010) Structural basis for semaphorin signaling through the plexin receptor.
   Nature 467, 1123-1127.
10. Danjo, H., Hirata, K., Noda, M., Uchiyama, S., Fukui, K., Kawahata, M., Azumaya, I., Yamaguchi, K. and Miyazawa, T.
    (2010) Assembly modulation by adjusting countercharges of heterobimetallic supramolecular polymers composed of tris　(spiroborate) twin bowls.
    J Am Chem Soc. 132, 15556-15558.
11. Shiga, D., Nakane, D., Inomata, T., Funahashi, Y., Masuda, H., Kikuchi, A., Oda, M., Noda, M., Uchiyama, S., Fukui, K., Kanaori, K., Tajima, K., Takano, Y., Nakamura, H. and Tanaka, T.
    (2010) Creation of a type 1 blue copper site within a de novo coiled-coil protein scaffold.
    J Am Chem Soc. 132, 18191-18198.

Reviews

1. Ohmido, N., Fukui, K. and Kinoshita, T.
   (2010) Recent advances in rice genome and chromosome structure research by fluorescence in situ hybridization (FISH). Proc. Jpn. Acad. Ser. B. Phys. Biol. Sci. 86, 103-116.

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細胞工学領域（村中研）

Original Papers

1. Takeno, S., Bamba, T., Nakazawa, Y., Fukusaki, E., Okazawa, A. and Kobayashi, A.
   (2010) High-throughput and highly sensitive analysis method of polyisoprene in plant by pyrolysis-gas chromatography.
   Biosci. Biotechnol. Biochem. 74, 13-17.
2. Hata, N., Hayashi, Y., Okazawa, A., Ono, E., Satake, H. and Kobayashi, A.
   (2010) Comparison of sesamin contents and CYP81Q1 gene expressions in aboveground vegetative organs between two Japanese sesame (Sesamum indicum L.) varieties differing in seed sesamin contents.
   Plant Sci. 178, 510-516.
3. Ono, E., Kim, H.J., Murata, J., Morimoto, K., Okazawa, A., Kobayashi, A., Umezawa, T. and Satake, H.
   (2010) Molecular and functional characterization of novel furofuran-class lignan glucosyltransferases from Forsythia.
   Plant Biotechnol. 27, 317-324.
4. Kajiura, H., Koiwa, H., Nakazawa, Y., Okazawa, A., Kobayashi, A., Seki, T. and Fujiyama, K.
   (2010) Two Arabidopsis thaliana Golgi α-mannosidase I enzymes are responsible for plant N-glycan maturation.
   Glycobiology 20, 235-247.
5. Uchida, H., Yamashita, H., Anai, T., Muranaka, T. and Ohyama, K.
   (2010) Agrobacterium-mediated transformation of Euphorbia tirucalli callus.
   Biosci. Biotechnol. Biochem. 74, 851-853.
6. Kim, O.T., Kim, S.H., Ohyama, K., Muranaka, T., Choi, Y.E., Lee, H.Y., Kim, M.Y. and Hwang, B.
   (2010) Upregulation of phytosterol and triterpene biosynthesis in Centella asiatica hairy roots overexpressed ginseng farnesyl diphosphate synthase.
   Plant Cell Rep. 29, 403-411.
7. Kojoma, M., Ohyama, K., Seki, H., Hiraoka, Y., Asazu, S-N., Sawa, S., Sekizaki, H., Yoshida, S. and Muranaka, T.
   (2010) In vitro proliferation and triterpenoid characteristics of licorice (Glycyrrhiza uralensis Fischer, Leguminosae) stolons.
   Plant Biotechnol. 27, 59-66.
8. Tang, J., Kobayashi, K., Suzuki, M., Matsumoto, S. and Muranaka T.
   (2010) The mitochondrial PPR protein LOVASTATIN INSENSITIVE 1 plays regulatory roles in cytosolic and plastidial isoprenoid biosynthesis through RNA editing.
   Plant J. 61, 456-466.
9. Mano, K., Nemoto, K., Suzuki, M, Seki, H., Fujii, I. and Muranaka, T.
   (2010) The AMI1 gene family: indole-3-acetamide hydrolase functions in auxin biosynthesis in plants.
   J. Exp. Bot. 61, 25-32.
10. Ryden, A.M., Ruyter-Spira, C., Quax, W.J., Osada, H., Muranaka, T., Kayser, O. and Bouwmeester, H.
    (2010) The molecular cloning of dihydroartemisinic aldehyde reducatese and its implication in artemisinin biosynthesis in Artemisia annua.
    Planta Med. 76, 1778-1783.

Reviews

1. Muranaka, T. and Saito, K.
   (2010) Production of pharmaceuticals by plant tissue cultures. In “Comprehensive Natural Products II Chemisty and Biology” edited by Mander, L., Lui, H.-W. Elsevier (Oxford), volume 3, pp. 615-628.

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生物化学工学領域

Original Papers

1. Park, J.Y., Yamatani, M., Wadano, S., Takagi, Y., Honda, K., Omasa, T. and Ohtake, H.
   (2010) Effects of palindrome structure on Dhfr amplification in Chinese hamster ovary cells.
   Process Biochem. 45, 1845-1851.
2. Zhou, Y., Minami, T., Honda, K., Omasa, T. and Ohtake H.
   (2010) Enhancement of recombinant enzyme activity in cpxA-deficient mutant of Escherichia coli.
   J. Biosci. Bioeng. 110, 403-407.
3. Honda, K., Maya, S., Omasa, T., Hirota, R., Kuroda, A. and Ohtake, H.
   (2010) Production of 2-deoxyribose 5-phosphate from fructose to demonstrate a potential or artificial bio-synthetic pathway using thermophilic enzymes.
   J. Biotechnol. 148, 204-207.
4. Kashihara, H., Kang, B.M., Omasa, T., Honda, K., Sameshima, Y., Kuroda, A. and Ohtake, H.
   (2010) Electron microscopic analysis of heat-induced leakage of polyphosphate from a phoU mutant of Escherichia coli.
   Biosci. Biotechnol. Biochem. 74, 865-868.
5. Park, J.Y., Takagi, Y., Yamatani, M., Honda, K., Asakawa, S., Shimizu, N., Omasa, T. and Othake, H.
   (2010) Identification and analysis of specific chromosomal region adjacent to exogenous Dhfr-amplified region in Chinese hamster ovary genome.
   J. Biosci. Bioeng.109, 504-511.
6. Zhou, Y., Minami, T., Honda, K., Omasa, T. and Ohtake, H.
   (2010) Systematic screening of Escherichia coli single-gene knockout mutants for improving recombinant whole-cell biocatalysts.
   Appl. Microbiol. Biotechnol. 87, 647-655.
7. Kim, W.D., Tokunaga, M., Ozaki, H., Ishibashi, T., Honda, K., Kajiura, H., Fujiyama, K., Asano, R., Kumagai, I., Omasa, T. and Ohtake, H.
   (2010) Glycosylation pattern of hymanized IgG-like bispecific antibody produced by recombinant CHO cells.
   Appl. Microbiol. Biotechnol. 85, 535-542.
8. Tsuji, T., Suzuki, M., Takiguchi, N. and Ohtake, H.
   (2010) Biomimetic control based on a model of chemotaxis in Escherichia coli.
   Artificial Life 16, 155-177.

Reviews

1. Hirota, R., Kuroda, A., Kato, J. and Ohtake, H
   (2010) Bacterial phosphate metabolism and its application to phosphorus recovery and industrial bioprocesses. J. Biosci. Bioeng. 109, 423-432.
2. Omasa, T., Onitsuka M. and Kim, W.D.
   (2010) Cell engineering and cultivation of Chinese hamster ovary (CHO) cells. Curr. Pharm. Biotechnol. 11, 233-240.

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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. Kim, M.-H., Kino-oka, M., Saito, A., Sawa, Y. and Taya. M.
   (2010) Myogenic induction of human mesenchymal stem cells by culture on dendrimer-immobilized surface with D-glucose display.
   J. Biosci. Bioeng. 109, 55-61.
2. Kim, M.-H., Kino-oka, M. and Taya, M.
   (2010) Designing culture surfaces based on cell anchoring mechanisms to regulate cell morphologies and functions. Biotechnol.
   Adv. 28, 7-16.
3. Chowdhury, S.R., Muneyuki, Y., Takezawa, Y., Kino-oka, M., Saito, A., Sawa, Y. and Taya, M.
   (2010) Growth and differentiation potentials in confluent state of culture of human skeletal muscle myoblasts.
   J. Biosci. Bioeng. 109, 310-313.
4. Kino-oka, M., Kagita, S., Nadzir, M.M., Inoue, H., Sugawara, K. and Taya, M.
   (2010) Direct measurement of oxygen concentration inside cultured cartilage for relating to spatial growth of rabbit chondrocytes.
   J. Biosci. Bioeng. 110, 363-366.
5. Moukamnerd, C., Kino-oka, M., Sugiyama, M., Kaneko, Y., Boonchird, C., Harashima, S., Noda, H., Ninomiya, K., Shioya, S. and Katakura, Y.
   (2010) Ethanol production from bio mass by repetitive solid-sate fed-batch fermentation with continuous recovery of ethanol.
   Appl. Microbiol. Biotechnol. 88, 87-94.
6. Kim, M.-H., Kino-oka, M., Maruyama, N., Saito, A., Sawa, Y. and Taya, M.
   (2010) Cardimyogenic induction of human mesenchymal stem cells by altered Rho family GTPase expression on dendrimer-immobilized surface with D-glucose display.
   Biomaterials 31, 7666-7677.

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生物工学国際交流センター（仁平研）

Original Papers

1. Kitani, S., Yamauchi, T., Fukushima, E., Lee, C.K., Ningsih, F., Kinoshita, H. and Nihira, T.
   (2010) Characterization of varM encoding type II ABC transporter in Streptomyces virginiae, a virginiamycin M1 producer.
   Actinomycetologica 24, 51–57.
2. Euanorasetr, J., Nilvongse, A., Tantimavanich, S., Nihira, T., Igarashi, Y. and Panbangred, W.
   (2010) Identification and characterization of soil-isolated Streptomyces SJE177 producing actinomycin.
   Southeast Asian J. Trop. Med. Public Health 41, 1177-1187.
3. Ichikawa, N., Oguchi, A., Ikeda, H., Ishikawa, J., Kitani, S., Watanabe, Y., Nakamura, S., Katano, Y., Kishi, E., Sasagawa, M., Ankai, A., Fukui, S., Hashimoto, Y., Kamata, S., Otoguro, M., Tanikawa, S., Nihira, T., Horinouchi, S., Ohnishi, Y., Hayakawa, M., Kuzuyama, T., Arisawa, A., Nomoto, F., Miura, H., Takahashi, Y. and Fujita, N.
   (2010) Genome sequence of Kitasatospora setae NBRC 14216T: an evolutionary snapshot of the family Streptomycetaceae.
   DNA Res. 17, 393-406.
4. Igarashi, Y., Shimasaki, R., Miyanaga, S., Oku, N., Onaka, H., Sakurai, H., Saiki, I., Kitani, S., Nihira, T., Wimonsiravude, W. and Panbangred, W.
   (2010) Rakicidin D, an inhibitor of tumor cell invasion from marine-derived Streptomyces sp.
   J. Antibiot. (Tokyo). 63, 563-565.
5. Yoon, Y.H., Kawai, F., Sugiyama, K., Park, S.Y., Nihira, T., Choi, S.U. and Hwang, Y.I.
   (2010) Crystallization and preliminary crystallographic studies of the butyrolactone autoregulator receptor protein (BarA) from Streptomyces virginiae.
   Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66, 662-664.
6. Singkaravanit, S., Kinoshita, H., Ihara, F. and Nihira, T.
   (2010) Cloning and functional analysis of the second geranylgeranyl diphosphate synthase gene influencing helvolic acid biosynthesis in Metarhizium anisopliae.
   Appl. Microbiol. Biotechnol. 87, 1077-1088.
7. Putri, S.P., Kinoshita, H., Ihara, F., Igarashi, Y. and Nihira, T.
   (2010) Ophiosetin, a new tetramic acid derivative from the mycopathogenic fungus Elaphocordyceps ophioglossoides.
   J. Antibiot. (Tokyo). 63, 195-198.
8. Kitani, S., Doi, M., Shimizu, T., Maeda, A. and Nihira, T.
   (2010) Control of secondary metabolism by farX, which is involved in the γ-butyrolactone biosynthesis of Streptomyces lavendulae FRI-5.
   Arch. Microbiol. 192, 211-220.
9. Lee, Y.J., Kitani, S. and Nihira, T.
   (2010) Null mutation analysis of an afsA-family gene, barX, that is involved in biosynthesis of the γ-butyrolactone autoregulator in Streptomyces virginiae.
   Microbiology 156, 206-210.

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生物工学国際交流センター（藤山研）

Original Papers

1. Kim, W.-D., Tokunaga, M., Ozaki, H., Ishibashi, T., Honda, K., Kajiura, H., Fujiyama, K., Asano, R., Kumagai, I., Omasa, T. and Ohtake, H.
   (2010) Glycosylation pattern of humanized IgG-like bispecific antibody produced by recombinant CHO cells.
   Appl. Microbiol. Biotechnol. 85, 535-542.
2. Kaewwichian, R., Yongmanitchai, W., Srisuk, N., Fujiyama, K. and Limtong, S.
   (2010) Geotrichum siamensis sp. nov. and Geotrichum phurueaensis sp. nov., two asexual arthroconidial yeast species isolated in Thailand.
   FEMS Yeast Res. 10, 214-220.
3. Ohashi, T. and Takegawa, K.
   (2010) N- and O-linked oligosaccharides completely lack galactose residues in the gms1och1 mutant of Schizosaccharomyces pombe.
   Appl. Microbiol. Biotechnol. 86, 263-272.
4. Kajiura, H., Koiwa, H., Nakazawa, Y., Okazawa, A., Kobayashi, A., Seki, T. and Fujiyama, K.
   (2010) Molecular cloning, characterization and functional analysis of two Arabidopsis thaliana Golgi a-mannosidase I, responsible for plant N-glycan maturation.
   Glycobiology 20, 235-247.
5. Khalil, M.F.M., Kajiura, H., Fujiyama, K., Koike, K., Ishida, N. and Tanaka, N.
   (2010) The impact of the overexpression of human UDP-galactose transporter gene hUGT1 in tobacco plants.
   J. Biosci. Bioeng. 109, 159-169.
6. Park, J.H., Nishidate, T., Kijima, K., Ohashi, T., Takegawa, K., Fujikane, T., Hirata, K., Nakamura, Y. and Katagiri, T.
   (2010) Critical roles of mucin 1 glycosylation by transactivated polypeptide N-acetylgalactosaminyltransferase 6 in mammary carcinogenesis.
   Cancer Res. 70, 2759-2769.
7. Dohi, K., Isoyama-Tanaka, J., Tokuda, T. and Fujiyama, K.
   (2010) Recombinant expression and characterization of N-acetylglucosaminyltransferase I derived from Nicotiana tabacum.
   J. Biosci. Bioeng. 109, 388-391.
8. Kajiura, H., Seki, T. and Fujiyama, K.
   (2010) Arabidopsis thaliana ALG3 mutant synthesizes immature oligosaccharides in the ER and accumulates unique N-glycans.
   Glycobiology 20, 736-751.
9. Matsuzawa, T., Ohashi, T., Hosomi, A., Tanaka, N., Tohda, H. and Takegawa, K.
   (2010) The gld1+ gene encoding glycerol dehydrogenase is required for glycerol metabolism in Schizosaccharomyces pombe.
   Appl. Microbiol. Biotechnol. 87, 715-727.
10. Nomura, T.E, Ikeda, M., Ishiyama, S., Mita, K., Tamura, T., Okada, T., Fujiyama, K. and Usami, A.
    (2010) Cloning and characterization of a b-N-acetylglucosaminidase (BmFDL) from silkworm Bombyx mori.
    J. Biosci. Bioeng. 110, 386-391.
11. Low, P.C., Misaki, R., Schroder, K., Stanley, A.C., Sweet, M.J., Teasdale, R.D., Vanhaesebroeck, B., Meunier, F.A., Taguchi, T. and Stow, J.L.
    (2010) Phosphoinositide 3-kinase 　d regulates membrane fission of Golgi carriers for selective cytokine secretion.
    J. Cell Biol. 190, 1053-1065.
12. Ohashi, T., Nakakita, S., Sumiyoshi, W. and Takegawa, K.
    (2010) Production of heterologous glycoproteins by a glycosylation-defective alg3och1 mutant of Schizosaccharomyces pombe.
    J. Biotechnol. 150, 348-356.
13. Misaki, R., Morimatsu, M., Uemura, T., Waguri, S., Miyoshi, E., Taniguchi, N., Matsuda, M. and Taguchi, T.
    (2010) Palmitoylated Ras proteins traffic through recycling endosomes to the plasma membrane during exocytosis.
    J. Cell Biol. 191, 23-29.

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産業科学研究所生体応答科学部門生体分子エナジェティクス講座（野地研）

Original Papers

1. Kotera, I., Iwasaki, T., Imamura, H., Noji, H. and Nagai, T.
   (2010) Reversible dimerization of Aequorea victoria fluorescent proteins increases the dynamic range of FRET-based indicators.
   ACS Chemical Biology 5, 215-222.
2. Saita, E., Iino, R., Suzuki, T., Feniouk, B.A., Kinosita, K.Jr. and Yoshida, M.
   (2010) Activation and stiffness of the inhibited states of F1-ATPase probed by single-molecule manipulation.
   J. Biol. Chem. 285, 11411-11417.
3. Ide, T., Takeuchi, Y., Noji, H. and Tabata, K.V.
   (2010) Simultaneous Optical and Electrical Single Channel Recordings on a PEG Glass.
   Langmuir 26, 8540-8543.
4. Ueno, H., Nishikawa, S., Iino, R., Tabata, K.V., Sakakihara, S., Yanagida, T. and Noji, H.
   (2010) Simple Dark-Field Microscopy with Nanometer Spatial Precision and Microsecond Temporal Resolution.
   Biophys. J. 98, 2014-2023.
5. Hayashi, K., Ueno, H., Iino, R. and Noji, H.
   (2010) Fluctuation theorem applied to F1-ATPase.
   Phys. Rev. Lett. 104, 218103.
6. Okuno, D., Iino, R. and Noji, H.
   (2010) Stiffness of γ subunit of F1-ATPase.
   Eur. Biophys. 39, 1589-1596.
7. Watanabe, R., Iino, R. and Noji, H.
   (2010) Phosphate-release in F1-ATPase catalytic cycle follows ADP release.
   Nat. Chem Biol. 6, 814-820.
8. Sakakihara, S., Araki, S., Iino, R. and Noji, H.
   (2010) A single-molecule enzymatic assay in a directly accessible femtoliter droplet array.
   Lab on a Chip. 10, 3355-3362.

Reviews

1. Okuno, D., Ikeguchi, M. and Noji, H.
   (2010) Measurement of the conformational state of F1-ATPase by single-molecule rotation. Methods Enzymol. 475, 279-296

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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. Kato, T., Miyanaga, A., Kanaya, S. and Morikawa, M.
   (2010) Gene cloning and characterization of an aldehyde dehydrogenase from long-chain alkane-degrading Geobacillus thermoleovorans B23.
   Extremophiles 14, 33-39.
2. Foophow, T., Tanaka, S., Koga, Y., Takano, K. and Kanaya, S.
   (2010) Subtilisin-like serine protease from hyperthermophilic archaeon Thermococcus kodakaraensis with N- and C-terminal propeptides.
   Protein Eng. Des. Sel. 23, 347-355.
3. Murai, R., Yoshikawa, H.Y., Takahashi, Y., Maruyama, M., Sugiyama, S., Sazaki, G., Adachi, H., Takano, K., Matsumura, H., Murakami, S., Inoue, T. and Mori, Y.
   (2010) Enhancement of femtosecond laser-induced nucleation of protein in a gel solution.
   Appl. Phys. Let. 96, e043702.
4. Pace, C.N., Huyghues-Despointes, B.M.P., Fu, H., Takano, K., Scholtz, J.M. and Grimsley, G.R.
   (2010) Urea denatured state ensembles contain extensive secondary structure that is increased in hydrophobic proteins.
   Protein Sci. 19, 929-943.
5. Kanaya, E., Sakabe, T., Nguyen, N.T., Koikeda, S., Koga, Y., Takano, K. and Kanaya, S.
   (2010) Cloning of the RNase H genes from a metagenomic DNA library: identification of a new type 1 RNase H without a typical active-site motif.
   J. Appl. Microbiol. 109, 974-983.
6. Tanaka, M., Chon, H., Angkawidjaja, C., Koga, Y., Takano, K. and Kanaya, S.
   (2010) Protein core adaptability: crystal structures of the cavity-filling variants of E. coli RNase HI.
   Protein Pept. Lett. 17, 1163-1169.
7. Nagashima, K., Abe, M., Morita, S., Oyabu, N., Kobayashi, K., Yamada, H., Ohta, M., Kokawa, R., Murai, R., Matsumura, H., Adachi, H., Takano, K., Murakami, S., Inoue, T. and Mori, Y.
   (2010) Molecular resolution investigation of tetragonal lysozyme (110) face in liquid by FM-AFM.
   J. Vac. Sci. Technol. B28, C4C11-C4C14.
8. Angkawidjaja, C., Matsumura, H., Koga, Y., Takano, K. and Kanaya, S.
   (2010) X-ray crystallographic and MD simulation studies on the interfacial activation mechanism of a family I.3 lipase with two lids.
   J. Mol. Biol. 400, 82-95.
9. Kakinouchi, K., Nakamura, T., Tamada, T., Adachi, H., Sugiyama, S., Maruyama, M., Takahashi, Y., Takano, K., Murakami, S., Inoue, T., Kuroki, R., Mori Y. and Matsumura, H.
   (2010) Growth of large protein crystals by a large-scale hanging drop method.
   J. Appl. Cryst. 43, 937-939.
10. Shimizu, N., Sugiyama, S., Maruyama, M., Takahashi, Y., Adachi, M., Tamada, T., Hidaka, K., Hayashi, Y., Kimura, T., Kiso, Y., Adachi, H., Takano, K., Murakami, S., Inoue, T., Kuroki, R., Mori, Y. and Matsumura, H.
    (2010) Crystal growth procedure of HIV-1 protease-inhibitor KNI-272 complex for neutron structural analysis at 1.9A resolution.
    Cryst. Growth Des. 10, 2990-2994.
11. Foophow, T., Tanaka, S., Angkawidjaja, C., Koga, Y., Takano, K. and Kanaya, S.
    (2010) Crystal structure of a subtilisin homologue, Tk-SP, from Thermococcus kodakaraensis: requirement of a C-terminal b-jelly roll domain for hyperstability.
    J. Mol. Biol. 400, 865-877.
12. Maruyama, M., Shimizu, N., Sugiyama, S., Takahashi, Y., Adachi, H., Takano, K., Murakami, S., Inoue, T., Matsumura, H. and Mori, Y.
    (2010) Estimated effects of silicone glue on protein crystal growth.
    J. Cryst. Growth 312, 2771-2774.
13. Nomura, Y., Sugiyama, S., Sakamoto, T., Miyakawa, S., Adachi, H., Takano, K., Murakami, S., Inoue, T., Mori, Y., Nakamura, Y. and Matsumura, H.
    (2010) Conformational plasticity of RNA for target recognition as revealed by the 2.15 A crystal structure of a human IgG-aptamer complex.
    Nucleic Acids Res. 38, 7822-7829.
14. Okada, J., Okamoto, T., Mukaiyama, A., Tadokoro, T., You, D.-J., Chon, H., Koga, Y., Takano, K. and Kanaya, S.
    (2010) Evolution and thermodynamics for slow unfolding of hyperstable monomeric proteins.
    BMC Evol. Biol. 10, e207.
15. Kobayashi, R., Hirano, N., Kanaya, S., Saito, I. and Haruki, M.
    (2010) Enhancement of the enzymatic activity of Escherichia coli acetyl esterase by random mutagenesis.
    J. Molec. Catal. B: Enzymatic 67, 155-161.
16. Jongruja, N., You, D-J., Kanaya, E., Koga, Y., Takano, K. and Kanaya, S.
    (2010) The N-terminal hybrid binding domain of RNase HI from Thermotoga maritima is important for substrate binding and Mg2+-dependent activity.
    FEBS J. 277, 4474-4489.

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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. Yamada, T., Ou, J., Furusawa, C., Hirasawa, T., Yomo, T. and Shimizu, H.
   (2010) Relationship between noise characteristics in protein expressions and regulatory structures of amino acid biosynthesis pathways.
   IET Syst. Biol. 4, 82-89.
2. Mahmud, S.A., Hirasawa, T. and Shimizu, H.
   (2010) Differential importance of trehalose accumulation in Saccharomyces cerevisiae in response to various environmental stresses.
   J. Biosci. Bioeng. 109, 262-266.
3. Kim, J., Fukuda, H., Hirasawa, T., Nagahisa, K., Nagai, K., Wachi, M. and Shimizu, H.
   (2010) Requirement of de novo synthesis of the OdhI protein in penicillin-induced glutamate production by Corynebacterium glutamicum.
   Appl. Microbiol. Biotechnol. 86, 911-920.
4. Toya, Y., Ishii, N., Nakahigashi, K., Hirasawa, T., Soga, T., Tomita, M. and Shimizu K.
   (2010) 13C-Metabolic flux analysis for batch culture of Escherichia coli and its pyk and pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites.
   Biotechnol. Prog. 26, 975-992.
5. Kishimoto, T., Iijima, L., Tatsumi, M., Ono, N., Oyake, A., Hashimoto, T., Matsuo, M., Okubo, M., Suzuki, S., Mori, K., Kashiwagi, A., Furusawa, C., Ying, B-W. and Yomo, T.
   (2010) Transition from positive to neutral in mutation fixation along with continuing rising fitness in thermal adaptive evolution.
   PLoS Genet. 6, e1001164.
6. Horinouchi, T., Yoshikawa, K., Kawaide, R., Furusawa, C., Nakao, Y., Hirasawa, T. and Shimizu, H.
   (2010) Genome-wide expression analysis of Saccharomyces pastorianus orthologous genes using oligonucleotide microarrays.
   J. Biosci. Bioeng. 110, 602-607.
7. Horinouchi, T., Tamaoka, K., Furusawa, C., Ono, N., Suzuki, S., Hirasawa, T., Yomo, T. and Shimizu, H.
   (2010) Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress.
   BMC Genomics. 11, 579.

Reviews

1. Hirasawa, T., Furusawa, C. and Shimizu, H.
   (2010) Saccharomyces cerevisiae and DNA microarray analyses: what did we learn from it for a better understanding and exploitation of yeast biotechnology. Appl. Microbiol. Biotechnol. 87, 391-400.

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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. Yamada T, Ou J, Furusawa C, Hirasawa T, Yomo T, Shimizu H.
   (2010) Relationship between noise characteristics in protein expressions and regulatory structures of amino acid biosynthesis pathways.
   IET Syst. Biol. 4, 82-89.
2. Urabe H, Ichihashi N, Matsuura T, Hosoda K, Kazuta Y, Kita H, Yomo T.
   (2010) Compartmentalization in a water-in-oil emulsion repressed the spontaneous amplification of RNA by Q beta replicase.
   Biochemistry 49, 1809-1813.
3. Sunami T, Hosoda K, Suzuki H, Matsuura T, Yomo T.
   (2010) Cellular compartment model for exploring the effect of the lipidic membrane on the kinetics of encapsulated biochemical reactions.
   Langmuir. 26, 8544-8551.
4. Chen T, Vernazobres D, Yomo T, Bornberg-Bauer E, Chan HS.
   (2010) Evolvability and single-genotype fluctuation in phenotypic properties: a simple heteropolymer model.
   Biophys. J. 98, 2487-2496.
5. Sunami T, Caschera F, Morita Y, Toyota T, Nishimura K, Matsuura T, Suzuki H, Hanczyc MM, Yomo T.
   (2010) Detection of association and fusion of giant vesicles using a fluorescence-activated cell sorter.
   Langmuir. 26, 15098-15103.
6. Horinouchi T, Tamaoka K, Furusawa C, Ono N, Suzuki S, Hirasawa T, Yomo T, Shimizu H.
   (2010) Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress.
   BMC Genomics 11, e579.
7. Kishimoto T, Iijima L, Tatsumi M, Ono N, Oyake A, Hashimoto T, Matsuo M, Okubo M, Suzuki S, Mori K, Kashiwagi A, Furusawa C, Ying BW, Yomo T.
   (2010) Transition from positive to neutral in mutation fixation along with continuing rising fitness in thermal adaptive evolution.
   PLoS Genet. 6, e1001164.
8. Ying BW, Ito Y, Shimizu Y, Yomo T.
   (2010) Refined method for the genomic integration of complex synthetic circuits.
   J. Biosci. Bioeng. 110, 529-536.
9. Ichihashi N, Matsuura T, Hosoda K, Yomo T.
   (2010) Identification of two forms of Q{beta} replicase with different thermal stabilities but identical RNA replication activity.
   J. Biol. Chem. 285, 37210-37217.

Reviews

1. Ichihashi N, Matsuura T, Kita H, Sunami T, Suzuki H, Yomo T.
   (2010) Constructing partial models of cells. In “The Origins of Life” edited by David Deamer,Jack and W. Szostak, COLD SPRING HARBOR LABORATORY PRESS (New York, USA), p. 295-303.
2. Yanagida H, Matsuura T, Yomo T.
   (2010) Ribosome display for rapid protein evolution by consecutive rounds of mutation and selection. In “In Vitro Mutagenesis Protocols Third Edition” edited by Jeff Braman, Humana Press (New York, USA), p. 257-267.　
3. Matsuura T, Ichihashi N, Sunami T, Kita H, Suzuki H, Yomo T.
   (2010) Evolvability and Self-Replication of Genetic Information in Liposomes. In “The Minimal Cell The Biophysics of Cell Compartment and the Origin of Cell Functionality” edited by Pier Luigi Luisi and Pasquale Stano, Springer (Dordrecht, Koninkrijk der Nederlanden), p. 275-287.

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