Original Papers

• 1.

  Lai, P., Okazawa, A., Izumi, Y., Bamba, T., Fukusaki, E., Yoshikawa, M. and Kobayashi A.
  (2013) Effect of gallic acid on peptides released by trypsin digestion of bovine α-casein.
  J. Biosci. Bioeng. 115, 259-267.

• 2.

  Takebayashi, K., Hirose, K., Izumi, Y., Bamba, T. and Fukusaki, E.
  (2013) Application of ion mobility-mass spectrometry to microRNA analysis.
  J. Biosci. Bioeng. 115, 332-338.

• 3.

  Lee, J.W., Nishiumi, S., Yoshida, M., Fukusaki, E. and Bamba, T.
  (2013) Simultaneous profiling of polar lipids by supercritical fluid chromatography/tandem mass spectrometry with methylation.
  J. Chromatogr. A, 1279:98-107.

• 4.

  Tsugawa, H., Arita, M., Kanazawa, M., Ogiwara, A., Bamba, T. and Fukusaki, E.
  (2013) MRMPROBS: Data assessment and metabolite identification tool for large-scale MRM-based widely targeted metabolomics.
  Anal. Chem. 85, 5191-5199.

• 5.

  Kakuta, S., Bando, Y., Nishiumi, S., Yoshida, M., Fukusaki, E. and Bamba, T.
  (2013) Metabolic profiling of oxidized lipid-derived volatiles in blood by gas chromatography/mass spectrometry with in-tube extraction.
  Mass Spectrometry, 2, A0018, DOI:10.5702/massspectrometry.A0018, Epub 2013 April 26.

• 6.

  Satomura, A., Katsuyama, Y., Miura, N., Kuroda, K., Tomio, A., Bamba, T., Fukusaki, E. and Ueda M.
  (2013) Acquisition of thermotolerant yeast Saccharomyces cerevisiae by breeding via stepwise adaptation.
  Biotechnol. Prog. 29, 1116-1123.

• 7.

  Nakai, Y., Nakahira, Y., Sumida, H., Takebayashi, K., Nagasawa, Y., Yamasaki, K., Akiyama, M., Ohme-Takagi, M., Fujiwara, S., Shiina, T., Mitsuda, N., Fukusaki, E., Kubo, Y. and Sato, M.H.
  (2013) Vascular plant one-zinc finger protein 1/2 transcription factors regulate abiotic and biotic stress responses in Arabidopsis.
  Plant J. 73, 761-775.

• 8.

  Yamada, T., Uchikata, T., Sakamoto, S., Yokoi, Y., Fukusaki, E. and Bamba, T.
  （2013) Development of a lipid profiling system using reverse-phase liquid chromatography coupled to high-resolution mass spectrometry with rapid polarity switching and an automated lipid identification software.
  J. Chromatogr. A, 1292, 211-218.

• 9.

  Fujieda, Y., Manno, A., Hayashi, Y., Rhodes, N., Guo, L., Arita, M., Bamba, T. and Fukusaki, E.
  (2013) Inflammation and resolution are associated with upregulation of fatty acid -oxidation in Zymosan-induced peritonitis.
  PLoS One, 8, e66270. doi: 10.1371/journal.pone.0066270.

• 10.

  Nirala, N.K., Rahman, M., Walls, S.M., Singh, A., Zhu, L.J., Bamba, T., Fukusaki, E., Srideshikan, S.M., Harris, G.L., Ip, Y.T., Bodmer, R. and Acharya, U.R.
  (2013) Survival response to increased ceramide involves metabolic adaptation through novel regulators of glycolysis and lipolysis.
  PLoS Genet. 9, e1003556. doi: 10.1371/journal.pgen.1003556.

• 11.

  Taguchi, K., Fukusaki, E. and Bamba, T.
  (2013) Simultaneous and rapid analysis of bile acids including conjugates by supercritical fluid chromatography coupled to tandem mass spectrometry.
  J. Chromatogr. A, 1299, 103-109.

• 12.

  Ogura, T., Bamba, T. and Fukusaki, E.
  (2013) Development of a practical metabolite identification technique for non-targeted metabolomics.
  J. Chromatogr. A, 1301, 73-79.

• 13.

  Yamada. T., Uchikata, T., Sakamoto, S., Yokoi, Y., Nishiumi, S., Yoshida, M., Fukusaki, E. and Bamba, T.
  (2013) Supercritical fluid chromatography/Orbitrap mass spectrometry based lipidomics platform coupled with automated lipid identification software for accurate lipid profiling.
  J. Chromatogr. A, 1301, 237-242.

• 14.

  Jumhawan, U., Putri, S.P., Yusianto, Marwanni, E., Bamba, T. and Fukusaki, E.
  (2013) Selection of discriminant marker for authentication of Asian palm civet coffee (Kopi Luwak): a metabolomics approach.
  J. Agric. Food Chem. 61, 7994-8001.

• 15.

  Matsuda, F., Tsugawa, H. and Fukusaki, E.
  (2013) Method for assessing the statistical significance of mass spectral similarities using basic local alignment search tool statistics.
  Anal. Chem. 85, 8291-8297.

• 16.

  Wada, Y., Matsubara, A., Uchikata, T., Iwasaki, Y., Morimoto, S., Kan, K., Ookura, T., Fukusaki, E. and Bamba, T.
  (2013) Investigation of β-cryptoxanthin fatty acid ester compositions in citrus fruits cultivated in Japan.
  Food and Nutrition 4, 98-104.

• 17.

  Shinohara, M., Sakuragi, H., Morisaka, H., Miyake, H., Tamaru, Y., Fukusaki, E., Kuroda, K. and Ueda, M.
  (2013) Fixation of CO2 in Clostridium cellulovorans analyzed by 13C-isotopomer-based target metabolomics.
  AMB Express. doi: 10.1186/2191-0855-3-61.

• 18.

  Ulanova, D., Kitani, S., Fukusaki, E., and Nihira, T.
  (2013) SdrA, a new DeoR family regulator involved in Streptomyces avermitilis morphological development and antibiotic production.
  Appl. Environ. Microbiol. 79, 7916-7921.

• 19.

  Ochi, H., Sakai, Y., Koishihara, H., Abe, F., Bamba, T., and Fukusaki, E.
  (2013) Monitoring the ripening process of Cheddar cheese based on hydrophilic component profiling using gas chromatography-mass spectrometry.
  J. Dairy Sci. 96, 7427-7441.

• 20.

  Sangwallek, J., Kaneko, Y., Sugiyama, M., Ono, H., Bamba, T., Fukusaki, E. and Harashima, S.
  (2013) Ketoacyl synthase domain is a major determinant for fatty acyl chain length in Saccharomyces cerevisiae.
  Arch. Microbiol. 195, 843-852.

Reviews

• 1.

  Putri, S.P., Nakayama, Y., Matsuda, F., Uchikata, T., Kobayashi, S., Matsubara, A. and Fukusaki, E.
  (2013) Current metabolomics: Practical applications.
  J. Biosci. Bioeng. 115, 579-89.

• 2.

  Putri, S.P., Yamamoto, S., Tsugawa, H. and Fukusaki, E.
  (2013) Current metabolomics: Technological advances.
  J. Biosci. Bioeng. 116, 9-16.

Original Papers

• 1.

  Kino-oka, M., Kim, J-P., Kurisaka, K. and Kim, M-H.
  (2013) Preferential growth of skeletal myoblasts and fibroblasts in co-culture on a dendrimer-immobilized surface.
  J. Biosci. Bioeng. 115, 96-99.

• 2.

  Nagamori, E., Ngo, T.X., Takezawa, Y., Saito, A., Sawa, Y., Shimizu, T., Okano, T., Taya，T. and Kino-oka, M.
  (2013) Network formation through active migration of human vascular endothelial cells in a multilayered skeletal myoblast sheet.
  Biomaterials. 34, 662-668.

• 3.

  Nadzir, M.M., Kino-oka, M., Sugawara, K. and Taya, M.
  (2013) Modulation of chondrocyte migration and aggregation by insulin-like growth factor-1 in cultured cartilage.
  Biotechnol. lett. 35, 295-300.

• 4.

  Ngo, T.X., Nagamori, E., Kikuchi, T., Shimizu, T., Okano, T., Taya, T. and Kino-oka, M.
  (2013) Endothelial cell behavior inside myoblast sheets with different thickness.
  Biotechnol. lett. 35, 1001-1008.

Original Papers

• 1.

  Saito, S., Hasegawa, J., Kobayashi, N., Tomitsuka, T., Uchiyama, S. and Fukui, K.
  (2013) Effects of Ionic Strength and Sugars on the Aggregation Propensity of Monoclonal
  Antibodies: Influence of Colloidal and Conformational Stabilities.
  Pharm Res. 30, 1263-1280.

• 2.

  Ishii, M., Uchiyama, S., Ozeki, Y., Kajiyama, S., Itoh, K. and Fukui, K.
  (2013) Visualization of oil body distribution in Jatropha curcas L. by four－wave mixing microscopy.
  Jpn. J. Appl. Phys., 52, 062403

• 3.

  Equilibrina, I., Matsunaga, S., Morimoto, A., Hashimoto, T., Uchiyama, S. and Fukui, K.
  (2013) ASURA (PHB2) Interacts with Scc1 through Chromatin.
  Cytogenet Genome Res, 139:225-233

• 4.

  Uchiyama, S., Ohshima, A., Yoshida, T., Ohkubo, T. and Kobayashi, K.
  (2013) Thermodynamic assessment of domain-domain interactions and in vitro activities of mesophilic and thermophilic ribosome recycling factors.
  Biopolymers 100, 366-379.

• 5.

  Takemoto, K., Matsuda, T., Sakai, N., Donald Fu, Noda, M., Uchiyama, S., Kotera, I., Arai, Y., Horiuchi, M., Fukui, K., Ayabe, T., Inagaki, F., Suzuki, H. and Nagai, T.
  (2013) SuperNova, a monomeric photosensitizing fluorescent protein for chromophore-assisted light inactivation.
  Sci Rep. 3, 2629.

• 6.

  Atefeh Alipour, Tsuchimoto, S., Sakai, H., Ohmido, N. and Fukui, K.
  (2013) Structural characterization of copia-type retrotransposons leads to insights into the marker development in a biofuel crop, Jatropha curcas L.
  Biotechnology for Biofuels. 6, 129.

• 7.

  Astari Dwiranti, Hamano, T., Takata, H., Nagano, S., Hongxuan Guo, Onishi, K., Wako, T., Uchiyama, S. and Fukui, K.
  (2013) The effect of magnesium ions on chromosome structure as observed by Helium Ion Microscopy. Microsc. Microanal. 20, 184-188.

Reviews

• 1.

  Wako, T., Kato, S., Ohmido, N. and Fukui, K.
  (2013) Advances in Imaging Methods on Plant Chromosomes.
  Plant Image Analysis: Fundamentals and Applications

• 2.

  Sato, S., Hirakawa, H., Tsuchimoto, S., Sakai, H., Shibagaki, N., Matsunaga, S., Fukui, K. and Tabata, S.
  (2013) Genome Structure of Jatropha curcas L.
  Jatropha, Challenges for a New Energy Crop. 563-576.

Original Papers

• 1.

  Usui, K., Ichihashi, N., Kazuta, Y., Matsuura, T. and Yomo, T.
  (2013) Effects of ribosomes on the kinetics of Qbeta replication.
  FEBS letters 588,117-23.

• 2.

  Asada, M., Kato, Y., Matsuura, T. and Watanabe, H.
  (2013) Visualization of ecdysteroid activity using a reporter gene in the crustacean, Daphnia.
  Marine environmental research 93,118-122.

• 3.

  Toyota, K., Kato, Y., Sato, M., Sugiura, N., Miyagawa, S., Miyakawa, H., Watanabe, H., Oda, S., Ogino, Y., Hiruta, C., Mizutani, T., Tatarazako, N., Paland, S., Jackson, C., Colbourne, J. K. and Iguchi, T.
  (2013) Molecular cloning of doublesex genes of four cladocera (water flea) species.
  BMC genomics 14, 239.

• 4.

  Hotta, K., Nashimoto, A., Yasumura, E., Suzuki, M., Azuma, M., Iizumi, Y., Shima, D., Nabeshima, R., Hiramoto, M., Okada, A., Sakata-Sogawa, K., Tokunaga, M., Ito, T., Ando, H., Sakamoto, S., Kabe, Y., Aizawa, S., Imai, T., Yamaguchi, Y., Watanabe, H. and Handa, H.
  (2013) Vesnarinone suppresses TNFalpha mRNA expression by inhibiting valosin-containing
  protein.
  Molecular pharmacology 83, 930-938.

• 5.

  Toyota, K., Kato, Y., Miyakawa, H., Yatsu, R., Mizutani, T., Ogino, Y., Miyagawa, S., Watanabe, H., Nishide, H., Uchiyama, I., Tatarazako, N. and Iguchi, T.
  (2013) Molecular impact of juvenile hormone agonists on neonatal Daphnia magna.
  Journal of applied toxicology : JAT,34,537-44.

• 6.

  Usui, K., Ichihashi, N., Kazuta, Y., Matsuura, T. and Yomo, T.
  (2013) Kinetic model of double-stranded RNA formation during long RNA replication by Qbeta
  replicase.
  FEBS letters 587, 2565-2571.

• 7.

  Fujii, S., Matsuura, T., Sunami, T., Kazuta, Y. and Yomo, T.
  (2013) In vitro evolution of alpha-hemolysin using a liposome display.
  Proc Natl Acad Sci USA.110,16796-801.

• 8.

  Ichihashi, N., Usui, K., Kazuta, Y., Sunami, T., Matsuura, T. and Yomo, T.
  (2013) Darwinian evolution in a translation-coupled RNA replication system within a cell-like
  compartment.
  Nature communications 4, 2494.

Original Papers

• 1.

  Komori, A., Suzuki, M., Seki, H., Nishizawa, T., Meyer, J.J., Shimizu, H., Yokoyama, S. and Muranaka, T.
  (2013) Comparative functional analysis of CYP71AV1 natural variants reveals an important residue for the successive oxidation of amorpha-4,11-diene.
  FEBS Lett. 587, 278-284.

• 2.

  Ramilowski, J., Sawai, S., Seki, H., Mochida, K., Yoshida, T., Sakurai, T., Muranaka, T., Saito, K. and Daub, C.
  (2013) Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals.
  Plant Cell Physiol. 54, 697-710.

• 3.

  Fukushima, E.O., Seki, H., Sawai, S., Suzuki, M., Ohyama, K., Saito, K. and Muranaka, T.
  (2013) Combinatorial biosynthesis of legume natural and rare triterpenoids in engineered yeast.
  Plant Cell Physiol. 54, 740-749.

Original Papers

• 1.

  Ye, X., Honda, K., Morimoto, Y., Okano, K. and Ohtake, H.
  (2013) Direct conversion of glucose to malate by synthetic metabolic engineering.
  J. Biotechnol. 164, 34-40

• 2.

  Ninh, P. H., Honda, K. , Yokohigashi, Y. , Okano, K., Omasa, T. and Ohtake, H.
  (2013) Development of continuous bioconversion system using thermophilic whole-cell biocatalyst.
  Appl. Environ. Microbiol. 79, 1996-2001.

• 3.

  Okano, K., Uemoto, M., Kagami, J., Miura, K., Aketo, T., Toda, M., Honda, K. and Ohtake, H.
  (2013) Novel technique for recovering phosphorus from aqueous solutions using
  amorphous calcium silicate hydrates (A-CSHs).
  Water Res. 47, 2251-2259.

• 4.

  Hibino, A. and Ohtake, H.
  (2013) Utilization of hydrophobic bacterium Rhodococcus rhodochrous NBRC15564
  as whole-cell catalyst in solvent-free organic media.
  Process Biochem. 48, 838-843 .

• 5.

  Hibino, A., Petri, R., Buchs, J. and Ohtake, H.
  (2013) Production of uroporphyrinogen III from 5-aminolevulinic acid using Escherichia coli expressing thermostable enzymes.
  Appl. Microbiol. Biotechnol. 97, 7337-7344.

• 6.

  Lee, K-H., Onitsuka, M., Honda, K., Ohtake, H. and Omasa, T.
  (2013) Rapid Construction of Transgene-amplified CHO Cell Lines by Cell Cycle Checkpoint Engineering.
  Appl. Microbiol. Biotechnol. 97,5731-5141.

• 7.

  Lee, K-H., Tsutsui, T., Honda, K., Asano, R., Kumagai, I., Ohtake, H. and Omasa, T.
  (2013) Generation of High-producing Cell Lines by Overexpression of Cell Division Cycle 25 Homolog A in Chinese Hamster Ovary Cells.
  J. Biosc. Bioeng. 116, 754-760.

• 8.

  Morimoto, Y., Honda, K., Ye X., Okano, K. and Ohtake, H.
  (2013) Directed evolution of thermotolerant malic enzyme for improved malate production.
  J. Biosc. Bioeng. 117,147-152

• 9.

  Krutsakorn, B., Honda, K., Ye, X., Imagawa, T., Bei, X., Okano, K. and Ohtake, H.
  (2013) In vitro production of n-butanol from glucose.
  Metabolic Eng. 20, 84-91

• 10.

  Krutsakorn, B., Imagawa, T., Honda, K., Okano, K. and Ohtake, H.
  (2013) Construction of an in vitro bypassed pyruvate decarboxylation pathway using thermostable enzyme modules and its application to N-acetylglutamate production.
  Microb.Cell Fact. 12,91

• 11.

  Haredy, A.M., Nishizawa, A., Honda, K., Ohya, T., Ohtake, H. and Omasa, T.
  (2013) Improved antibody production in Chinese hamster ovary cells by ATF4 overexpression.
  Cytotechnology 65, 993-1002.

• 12.

  Lee, K-H., Tsutsui, T., Honda, K., Ohtake, H. and Omasa, T.
  (2013) Overexpression of Mutant Cell Division Cycle 25 Homolog B enhances the Efficiency of Gene Amplification in Chinese Hamster Ovary Cells.
  Cytotechnology, 65, 1017-1026.

Original Papers

• 1.

  Shahsavarani, H., Hasegawa, D., Yokota, D., Sugiyama, M., Kaneko, Y., Boonchird, C. and Harashima, S.
  (2013) Enhanced bio-ethanol production from cellulosic materials by semi-simultaneous saccharification and fermentation using high temperature resistant Saccharomyces cerevisiae TJ14.
  J. Biosci. Bioeng. 115, 20-23.

• 2.

  Lavina, W. A., Hermansyah, Sugiyama, M., Kaneko, Y. and Harashima, S.
  (2013) Functionally redundant protein phosphatase genes PTP2 and MSG5 co-regulate the calcium signaling pathway in Saccharomyces cerevisiae upon exposure to high extracellular calcium concentration.
  J. Biosci. Bioeng. 115, 138-146.

• 3.

  Suzuki, T., Sakamoto, T., Sugiyama, M., Ishida, N., Kambe, H., Obata, S., Kaneko, Y., Takahashi, H. and Harashima, S.
  (2013) Disruption of multiple genes whose deletion causes lactic-acid resistance improves lactic-acid resistance and productivity in Saccharomyces cerevisiae.
  J. Biosci. Bioeng. 115, 467-474.

• 4.

  Sooksai, S., Chewchanlertfa, P., Kaneko, Y., Harashima, S. and Laoteng, K.
  (2013) Alterations in growth and fatty acid profiles under stress conditions of Hansenula polymorpha defective in polyunsaturated fatty acid synthesis.
  Mol. Biol. Rep. 40, 4935-4945.

• 5.

  Sasano, Y., Haitani, Y., Hashida, K., Oshiro, S., Shima, J. and Takagi, H.
  (2013) Improvement of fermentation ability under baking-associated stress conditions by altering the POG1 gene expression in baker`s yeast.
  Int. J. Food Microbiol. 165, 241-245.

• 6.

  Khatun, F., Kurata, K., Chuwattanakul, V., Sugiyama, M., Kaneko, Y. and Harashima, S.
  (2013) Increased transcription of RPL40A and RPL40B is important for the improvement of RNA production in Saccharomyces cerevisiae.
  J. Biosci. Bioeng. 116, 423-432.

• 7.

  Khatun, F., Sasano, Y., Sugiyama, M., Kaneko, Y. and Harashima, S.
  (2013) Increase in rRNA content in a Saccharomyces cerevisiae suppressor strain from rrn10 disruptant by rDNA cluster duplication.
  Appl. Microbiol. Biotechnol. 97, 9011-9019.

• 8.

  Sangwallek, J., Kaneko, Y., Sugiyama, M., Ono, H., Bamba, T., Fukusaki, E. and Harashima, S.
  (2013) Ketoacyl synthase domain is a major determinant for fatty acyl chain length in Saccharomyces cerevisiae.
  Arch. Microbiol. 195, 843-852.

Original Papers

• 1.

  Uehara, R., Ueda, Y., You, D.-J., Koga, Y., and Kanaya, S.
  (2013) Accelerated maturation of Tk-subtilisin by a Leu→Pro mutation at the C-terminus of propeptide which reduces the binding of propeptide to Tk-subtilisin.
  FEBS J. 280, 994-1006.

• 2.

  Hirata, A., Hori, Y., Koga, Y., Sakudo, A., Ikuta, K., Kanaya, S., and Takano, K.
  (2013) Enzymatic activity of a subtilisin homolog, Tk-SP, from Thermococcus kodakarensis in detergents and its ability to degrade the abnormal prion protein.
  BMC Biotechnology 13:19.

• 3.

  Tayyab, M, Rashid, N., Angkawidjaja, C., Kanaya, S., and Akhtar, M.
  (2013) Activation studies of LIPSBS by molecular dynamics simulation: X-ray diffraction analysis of crystals of lipase from Geobacillus SBS-4S.
  Acta Crystallogr. Sect. F 69, 355-357.

• 4.

  Tadokoro, T., Kazama, H., Koga, Y., Takano, K., and Kanaya, S.
  (2013) Investigating the structural dependence of protein stabilization by amino acid substitution.
  Biochemistry 52, 2839?2847.

• 5.

  Nguyen, T.-N., You, D.-J., Kanaya, E., Koga, Y., and Kanaya, S.
  (2013) Crystal structure of metagenome-derived LC9-RNase H1 with atypical DEDN active site motif.
  FEBS Lett. 587, 1418-1423.

• 6.

  Nguyen, T.-N., You, D.-J., Matsumoto, H., Kanaya, E., Koga, Y., and Kanaya, S.
  (2013) Crystal structure of metagenome-derived LC11-RNase H1 in complex with RNA/DNA hybrid.
  J. Struct. Biol. 182, 144-154.

• 7.

  Takano, K., Aoi, A., Koga, Y., and Kanaya, S.
  (2013) Evolvability of thermophilic proteins from archaea and bacteria.
  Biochemistry 52, 4774-4780.

• 8.

  Permanasari, E.-D., Angkawidjaja, C., Koga, Y., and Kanaya, S.
  (2013) Role of N-terminal extension of Bacillus stearothermophilus RNase H2 and C-terminal extension of Thermotoga maritima RNase H2.
  FEBS J. 280, 5065-5079.

• 9.

  Yuzaki, K., Sanda, Y., You, D.-J., Uehara, R., Koga, Y., and Kanaya, S.
  (2013) Increase in activation rate of Pro-Tk-subtilisin by a single nonpolar-to-polar amino acid substitution at the hydrophobic core of the propeptide domain.
  Protein Sci. 22, 1711-1721.

• 10.

  Uehara, R., Angkawidjaja, C., Koga, Y., and Kanaya, S.
  (2013) Formation of the high-affinity calcium binding site in Pro-subtilisin E with the insertion sequence IS1 of Pro-Tk-subtilisin.
  Biochemistry 52, 9080-9088.

Original Papers

• 1.

  Yasugi M., Kubota-Koketsu R., Yamashita A., Kawashita N., Du A., Sasaki T., Nishimura M., Misaki R., Kuhara M., Boonsathorn N., Fujiyama K., Okuno Y., Nakaya T. and Ikuta K.
  (2013) Human monoclonal antibodies broadly neutralizing against influenza B virus.
  PLoS Pathog. 9, e1003150.

• 2.

  Hamorsky KT., Kouokam JC., Bennett LJ., Baldauf KJ., Kajiura H., Fujiyama K. and Matoba N.
  (2013) Rapid and scalable plant-based production of a cholera toxin B subunit variant
  to aid in mass vaccination against cholera outbreaks.
  PLoS Negl Trop Dis. 7, e2046.

• 3.

  Watanabe S., Kakudo A., Ohta M., Mita K., Fujiyama K. and Inumaru S.
  (2013) Molecular cloning and characterization of the α-glucosidase II from Bombyx mori and Spodoptera frugiperda.
  Insect Biochem Mol Biol. 43, 319-27.

• 4.

  Sasaki T., Setthapramote C., Kurosu T., Nishimura M., Asai A., Omokoko MD., Pipattanaboon C., Pitaksajjakul P., Limkittikul K., Subchareon A., Chaichana P., Okabayashi T., Hirai I., Leuangwutiwong P., Misaki R., Fujiyama K., Ono K., Okuno Y., Ramasoota P. and Ikuta K.
  (2013) Dengue virus neutralization and antibody-dependent enhancement activities of human monoclonal antibodies derived from dengue patients at acute phase of secondary infection.
  Antiviral Res. 98, 423-31.

• 5.

  Wang S., Takahashi H., Kajiura H., Kawakatsu T., Fujiyama K. and Takaiwa F.
  (2013) Transgenic rice seeds accumulating recombinant hypoallergenic birch pollen allergen Bet v 1 generate giant protein bodies.
  Plant Cell Physiol. 54, 917-33.

• 6.

  Kajiura H., Wasai M., Kasahara S., Takaiwa F. and Fujiyama K.
  (2013) N-Glycosylation and N-glycan moieties of CTB expressed in rice seeds.
  Mol Biotechnol. 54, 784-94.

• 7.

  Yasugi M., Kubota-Koketsu R., Yamashita A., Kawashita N., Du A., Misaki R., Kuhara M., Boonsathorn N., Fujiyama K., Okuno Y., Nakaya T. and Ikuta K.
  (2013) Emerging antigenic variants at the antigenic site Sb in pandemic A(H1N1)2009 influenza virus in Japan detected by a human monoclonal antibody.
  PLoS One. 8, e77892.

Original Papers

• 1.

  Kitani, S., Tomio, A., Srichaisupakit, A., Daduang, R., Intra, B., Panbangred, W., Oku, N., Igarashi, Y. and Nihira, T.
  (2013) Sarmentosamide, a novel hexadienamide from Thai soil actinomycetes.
  Nat. Prod. Res. 27, 226-231.

• 2.

  Ulanova, D., Kitani, S., Fukusaki, E. and Nihira, T.
  (2013) SdrA, a new DeoR family regulator involved in Streptomyces avermitilis morphological development and antibiotic production.
  Appl. Environ. Microbiol. 79, 7916-7921.

Original Papers

• 1.

  Hoi, H., Matsuda, T., Nagai, T. and Campbell, RE.
  (2013) Highlightable Ca2+ Indicators for Live Cell Imaging.
  J Am Chem Soc. 135, 46-49.

• 2.

  Matsuda, T., Horikawa, K., Saito, K. and Nagai, T.
  (2013) Highlighted Ca2+ imaging with a genetically encoded ‘caged’ indicator.
  Sci Rep. 3:1398, 1-4.

• 3.

  Wu, J., Liu, L., Matsuda, T., Zhao, Y., Rebane, A., Drobizhev, M., Chang, YF., Araki, S., Arai, Y., March, K., Hughes, TE., Sagou, K., Miyata, T., Nagai, T., Li, WH. and Campbell, RE.
  (2013) Improved orange and red Ca2+ indicators and photophysical considerations for optogenetic applications.
  ACS Chem Neurosci. 4, 963-972.

• 4.

  Yamada, M., Kumamoto, K., Mikuni, S., Arai, Y., Kinjo, M., Nagai, T., Tsukasaki, Y., Watanabe, TM., Fukui, M., Jin, M., Toba, S. and Hirotsune, S.
  (2013) Rab6a releases LIS1 from a dynein idling complex and activates dynein for retrograde movement.
  Nat Commun. 4:2033, 1-10.

• 5.

  Nozaki, T., Kaizu, K., Pack, CG., Tamura, S., Tani, T., Hihara, S., Nagai, T., Takahashi, K. and Maeshima, K.
  (2013) Flexible and dynamic nucleosome fiber in living mammalian cells.
  Nucleus. 4, 349-356.

• 6.

  Takemoto, K., Matsuda, T., Sakai, N., Fu, D., Noda, M., Uchiyama, S., Kotera, I., Arai, Y., Horiuchi, M., Fukui, K., Ayabe, T., Inagaki, F., Suzuki, H. and Nagai, T.
  (2013) SuperNova, a monomeric photosensitizing fluorescent protein for chromophore-assisted light inactivation.
  Sci Rep. 3:2629, 1-7.

• 7.

  Yamanaka, M., Saito, K., Smith, NI., Kawata, S., Nagai, T. and Fujita, K.
  (2013) Saturated excitation of fluorescent proteins for subdiffraction-limited imaging of living cells in three dimensions.
  Interface Focus. 3, 20130007.

Reviews

• 1.

  Tiwari, D.K. and Nagai, T.
  (2013) Smart fluorescent proteins: innovation for barrier-free superresolution imaging in living cells.
  Dev Growth Differ. 55, 491-507.

• 2.

  Arai, Y. and Nagai, T.
  (2013) Extensive use of FRET in biological imaging.
  Microscopy (Oxf). 62, 419-428.

Original Papers

• 1.

  Ohno, S., Furusawa, C. and Shimizu, H.
  (2013) In silico screening of triple reaction knockout Escherichia coli strains for overproduction of useful metabolites.
  J. Biosci. Bioeng. 115:2, 221-228.

• 2.

  Ono, N., Suzuki, S., Furusawa, C., Shimizu, H. and Yomo, T.
  (2013) Development of a physical model-based algorithm for the detection of single-nucleotide substitutions by using tiling microarray.
  PLoS One, 8:1, e54571

• 3.

  Ida, Y., Hirasawa, T., Furusawa, C. and Shimizu, H.
  (2013) Utilization of Saccharomyces cerevisiae recombinant strain incapable of both ethanol and glycerol biosynthesis for anaerobic bioproduction.
  Appl. Microbiol. Biot. 97:11, 4811-4819.

• 4.

  Matsuda, F., Shirai, T., Ishii, J. and Kondo, A.
  (2013) Regulation of central carbon metabolism in Saccharomyces cerevisiae by metabolic inhibitors.
  J. Biosci. Bioeng. 116:1, 59-61.

• 5.

  Sakurai, T., Yamada, Y., Sawada, Y., Matsuda, F., Akiyama, K., Shinozaki, K., Yokota Hirai, M. and Saito, K.
  (2013) PRIMe Update: Innovative content for plant metabolomics and integration of gene expression and metabolite accumulation.
  Plant Cell Physiol. 54:2, e5.

• 6.

  Yoshikawa, K., Hirasawa, T., Ogawa, K., Hidaka, Y., Nakajima, T., Furusawa, C. and Shimizu, H.
  (2013) Integrated transcriptomic and metabolomic analysis of the central metabolism of Synechocystis sp. PCC 6803 under different trophic conditions.
  Biotechnol. J. 8:5, 513-514.

• 7.

  Hirasawa, T., Takekuni, M., Yoshikawa, K., Ookubo, A., Furusawa, C. and Shimizu, H.
  (2013) Genome-wide identification of the targets for genetic manipulation to improve L-lactate production by Saccharomyces cerevisiae by using a single-gene deletion strain collection.
  J. Biotechnol. 168:2, 185-193.

• 8.

  Dubouzet, J., Matsuda, F., Ishihara, A., Miyagawa, H. and Wakasa, K.
  (2013) Production of indole alkaloids by metabolic engineering of the tryptophan pathway in rice.
  Plant Biotechnol. J. 11:9, 1103-11.

• 9.

  Matsuda, F., Tsugawa, H. and Fukusaki, E.
  (2013) Method for assessing the statistical significance of mass spectral similarities using BLAST statistics
  Anal. Chem. 85:17, 8291-8297.

• 10.

  Chatsurachai, S., Furusawa, C. and Shimizu, H.
  (2013) ArtPathDesign -Rational heterologous pathway design system for the production of nonnative metabolites.
  J. Biosci. Bioeng. 116:4, 524-527.

• 11.

  Nakashima, N., Ohno, S., Yoshikawa, K., Shimizu, H. and Tamura, T.
  (2013) A vector library for silencing central carbon-metabolism genes with antisense RNAs in Escherichia coli.
  Appl. Environ. Microb. 80:2, 564-73.

• 12.

  Matsuda, F., Ishii, J., Kondo, T., Ida, K., Tezuka, H. and Kondo, A.
  (2013) Improvement of isobutanol production in Saccharomyces cerevisiae by eliminating competing pathways and resolving cofactor imbalance.
  Microb. Cell Fact. 12:1, 119.

Original Papers

• 1.

  Ying, B., Seno, S., Kaneko, F., Matsuda, H. and Yomo, T.
  (2013) Multilevel comparative analysis of the contributions of genome reduction and heat shock to the Escherichia coli transcriptome.
  BMC GENOMICS213. 14, 1-13.

• 2.

  Ono, N., Suzuki, S., Furusawa, C., Shimizu, H. and Yomo, T.
  (2013) Development of a Physical Model-Based Algorithm for the Detection of Single-Nucleotide Substitutions by Using Tiling Microarrays.
  PLoS ONE. 8, 1-7.

• 3.

  Wu, T., Suzuki, H., Su, Y., Tang, Z., Zhang, L. and Yomo, T.
  (2013) Bio-inspired three-dimensional self-patterning of functional coatings for PDMS microfluidics.
  Soft Matter2013. 9, 3473?3477.

• 4.

  Kobori, S., Ichihashi, N., Kazuta, Y. and Yomo, T.
  (2013) A controllable gene expression system in liposomes that includes a positive feedback loop.
  Mol BioSyst 2013. 9, 1282-1285.

• 5.

  Kubo, I., Hosoda, K., Suzuki, S., Yamamoto, K., Kihara, K., Mori, K. and Yomo, T.
  (2013) Construction of bacteria-eukaryote synthetic mutualism.
  Biosystems. 113, 66-71.

• 6.

  Usui, K., Ichihashi, N., Kazuta, Y., Matsuura, T. and Yomo, T.
  (2013) Kinetic model of double-stranded RNA formation during long RNA replication by Qβ replicase.
  FEBS Letters2013. 587, 2565-2571.

• 7.

  Okano, T., Matsuura, T., Suzuki, H. and Yomo, T.
  (2013) Cell-free Protein Synthesis in a Microchamber Revealed the Presence of an Optimum Compartment Volume for High-order Reactions.
  ACS Synth Biol. 2013, A-F.

• 8.

  Fujii, S., Matsuura, T., Sunami, T., Kazuta, Y. and Yomo, T.
  (2013) In vitro evolution of hemolysin using a liposome display.
  PNAS. 110, 16796?16801.

• 9.

  Ichihashi, N., Usui, K., Kazuta, Y., Sunami, T., Matsuura, T. and Yomo, T.
  (2013) Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment.
  Nat. Commun. 4, 1-7.

• 10.

  Aita, T., Ichihashia, N. and Yomo, T.
  (2013) Probabilistic model based error correction in a set of various mutant sequences analyzed by next-generation sequencing.
  Computational Biology and Chemistry2013. 14, 221?230.

• 11.

  Matsumoto, Y., Murakami, Y., Tsuru, S., Ying, B. and Yomo, T.
  (2013) Growth rate-coordinated transcriptome reorganization in bacteria.
  BMC Genomics 2013. 14, 1-10.

• 12.

  Hadorn, M., Boenzli, E., Sorensen, K., Lucrezia, D., Hanczyc, M. and Yomo, T.
  (2013) Defined DNA-Mediated Assemblies of Gene-Expressing Giant Unilamellar Vesicles.
  Langmuir2013. 29, 15309-15319.

• 13.

  Ichii, T., Tanahashi, G., Suzuki, H. and Yomo, T.
  (2013) Modification of an amplification reaction in recursively dynamic compartments driven by stirring.
  Analytical Chemistry2013.85, 12002-12010.