Nobuhiko Nomula Lab

Paper

2020

  • Gayan, A., M. Kuchira, G. Kudo, S. Masuo, A. Ninomiya, K. Takahashi, A.S. Utada, D. Hagiwara, N. Nomura, N. Takaya, N. Obana, N. Takeshita, Fungal mycelia and bacterial thiamine establish a mutualistic growth mechanism. LIFE SCIENCE ALLIANCE, 2020 Sep, 3(12):e202000878. doi: 10.26508/lsa.202000878
  • Obana, N., K. Nakamura, N. Nomura, Temperature-regulated heterogeneous extracellular matrix gene expression defines biofilm morphology in Clostridium perfringens. NPJ BIOFILMS AND MICROBIOMES, 2020 July, 6(1):29, doi: 10.1038/s41522-020-00139-7
  • Nagasawa, R., T. Sato, N. Nomura, T. Nakamura, H. Senpuku, Potential risk to spread resistant genes within the extracellular DNA-dependent biofilm of Streptococcus mutans in response to cell envelope stress induced by sub-MIC of bacitracin. Applied and Environmental Microbiology, 2020 June, doi: 10.1128/AEM.00770-20
  • Nguyen, B.V.G., T. Nagakubo, M. Yoyofuku, N. Nomura, A.S. Utada, Synergy between Sophorolipid Biosurfactant and SDS increases efficiency of P. aeruginosa biofilm disruption. Langmuir, 2020 Apr, doi: 10.1021/acs.langmuir.0c00643
  • Morinaga, K., T. Nagakubo, N. Nomura, M. Toyofuku, Involvement of membrane vesicles in long‐chain‐AHL delivery in Paracoccus species. Environ Microbiol Rep, 2020 Apr, doi: 10.1111/1758-2229.12843
  • Kikuchi, Y., N. Obana, M. Toyofuku, N. Kodera, T. Soma, T. Ando, Y. Fukumori, N. Nomura, and A. Takao, Diversity of physical properties of bacterial extracellular membrane vesicles revealed through atomic force microscopy phase imaging. Nanoscale, 2020 Mar, 14;12(14):7950-7959. doi: 10.1039/C9NR10850E
  • Betsuyaku, S., The rise of evolutionary molecular plant-microbe interactions (EvoMPMI). Plant Cell Physiol, 2020 Feb, doi:10.1093/pcp/pcaa007
  • Suzuki, S., M. Yoshikawa, D. Imamura, K. Abe, P. Eichenberger, T. Sato, Compatibility of site-specific recombination units between mobile genetic elements. iScience, 2020 Jan, doi: 10.1016/j.isci.2019.100805
  • Nagakubo, T., N. Nomura, M. Toyofuku, Cracking open bacterial membrane vesicles. Frontiers in Microbiology, 2020 Jan, 10:3026 doi: 10.3389/fmicb.2019.03026
  • Ishiga, T., Y. Iida, N. Sakata, T. Ugajin, T. Hirata, S. Taniguchi, K. Hayashi, Y. Ishiga, Acibenzolar-S-methyl activates stomatal-based defense against Pseudomonas cannabina pv. alisalensis in cabbage. Journal of General Plant Pathology, 2020 Jan, 86 (1):48-54, doi: 10.1007/s10327-019-00883-5
  • Kunoh, T., K. Morinaga, S. Sugimoto, S. Miyazaki, M. Toyofuku, K. Iwasaki, N. Nomura, A. Utada, Polyfunctional nanofibril appendages mediate attachment, filamentation, and filament adaptability in Leptothrix cholodnii. ACS Nano 2020, 2019 Dec, doi: 10.1021/acsnano.9b04663
  • 2019

    • Senpuku, H., EB. Tuna, R. Nagasawa, R. Nakao, M. Ohnishi, The inhibitory effects of polypyrrole on the biofilm formation of Streptococcus mutans. PLoS One, 2019 Oct, 14(11): e0225584, doi: 10.1371/journal.pone.0225584
    • Shuster, B., M. Khemmani, Y. Nakaya, G. Holland, K. Iwamoto, K. Abe, D. Imamura, N. Maryn, A. Driks, T. Sato, P. Eichenberger, Expansion of the spore surface polysaccharide layer in Bacillus subtilis by deletion of genes encoding glycosyltransferases and glucose modification enzymes. J Bacteriol, 2019 Oct, 201:19,e00321-19 doi: 10.1128/JB.00321-19
    • Yawata, Y., T. Kiyokawa, Y. Kawamura, T. Hirayama, K. Takabe, N. Nomura, Intra- and interspecies variability of single-cell innate fluorescence signature of microbial cell. Applied and Environmental Microbiology.18, 2019 Sep, doi: 10.1128/AEM.00608-19
    • Ogura, M., T. Sato, K. Abe, Bacillus subtilis YlxR, which is involved in glucose-responsive metabolic changes, regulates expression of tsaD for protein quality control of pyruvate dehydrogenase. Front Microbiol, 2019 May, doi: 10.3389/fmicb.2019.00923
    • Shimada, T., S. Betsuyaku, N. Inada, K. Ebine, M. Fujimoto, T. Uemura, Y. Takano, H. Fukuda, A. Nakano, T. Ueda. Enrichment of phosphatidylinositol 4,5-bisphosphate in the extra-invasive hyphal membrane promotes Colletotrichum infection of Arabidopsis thaliana. Plant Cell Physiol, 2019 July; 60(7): 1514-1524 doi.org/10.1093/pcp/pcz058.
    • Tokunou, Y., A. Okamoto. Geometrical Changes in the hemes of bacterial surface c-type cytochromes reveal flexibility in their binding affinity with minerals. Langmuir, 2019 June 11; 35(23): 7529-7537 doi:10.1021/acs.langmuir, 8b02977.
    • Mizokami, Y., D. Sugiura, CKA. Watanabe, E. Betsuyaku, N. Inada, I. Terashima. Elevated CO2-induced changes in mesophyll conductance and anatomical traits in wild type and carbohydrate metabolism mutants of Arabidopsis thaliana. J Exp Bot, 2019 May 6, pii: erz208. doi: 10.1093/jxb/erz208. [Epub ahead of print]
    • Sugiura, D., E. Betsuyaku, I. Terashima. Interspecific differences in how sink-source imbalance causes photosynthetic downregulation among three legume species. ANNALS OF BOTANY, 2019 Mar, 14;123(4):715-726. doi: 10.1093/aob/mcy204.
    • Kinoshita, N., A. Sugita, B. Lustig, S. Betsuyaku, T. Fujikawa, T. Morishita. Automating measurements of fluorescent signals in freely moving plant leaf specimens Plant Biotechnology, 2019 Mar 16,36(1):7-11 doi: 10.5511/plantbiotechnology.18.1002a.
    • Betsuyaku, S., N. Nomura, H. Fukuda. A Versatile Method for Mounting Arabidopsis Leaves for Intravital Time-lapse Imaging. Journal of Visualized Experiments 144, e59147, 2019 Feb,
      doi: 110.3791/59147.
    • Prasad, M., N. Obana, K. Sakai, T. Nagakubo, S. Miyazaki, M. Toyofuku, J. Fattaccioli, N. Nomura, A. Utada. Point Mutations Lead to Increased Levels of c-di-GMP and Phenotypic Changes to the Colony Biofilm Morphology in Alcanivorax borkumensis SK2. Microbes and Environments, 2019 Feb,
      doi: 10.1264/jsme2.ME18151.
    • Nagakubo, T., T. Kumano, T. Ohta, Y. Hashimoto, M. Kobayashi. Copper amine oxidases catalyze the oxidative deamination and hydrolysis of cyclic imines. Nature Communications 10, 2019 Jan, Article number:413. doi: 10.1038/s41467-018-08280-w.

    2018

    • Nakanishi, Y., T. Yamamoto, N. Obana, M. Toyofuku, N. Nomura, A. Kaneko. Spatial Distribution and Chemical Tolerance of Streptococcus mutans within Dual-Species Cariogenic Biofilms. Microbes and Environments, Volume 33, Issue 4, 2018 Dec, page 455-458 doi: 10.1264/jsme2.ME18113.
    • Kinoshita, N., and Betsuyaku, S., The effects of Lepidopteran oral secretion on plant wounds: A case study on the interaction between Spodoptera litura and Arabidopsis thaliana. Plant Biotechnology, 2018 Aug 22 35(3):237-242, doi:10.5511/plantbiotechnology.18.0528a.
    • Kurusu, T., D. Mitsuka, C. Yagi, N. Kitahata, T. Tsutsui, T. Ueda, Y. Yamamoto, J. Negi, K. Iba, S. Betsuyaku,K. Kuchitsu. Involvement of S-type anion channels in disease resistance against an oomycete pathogen in Arabidopsis seedlings. Communicative & Integrative Biology,2018 Aug 10;11(3):1-6 doi: 10.1080/19420889.2018.1495007.
    • Morinaga, K., T. Yamamoto, N. Nomura, M. Toyofuku. Paracoccus denitrificans can utilize various long-chain N-acyl homoserine lactones and sequester them in membrane vesicles. Environmental Microbiology Reports, 2018 July,doi: 10.1111/1758-2229.12674.
    • Ishiga, T., Y. Ishiga, S. Betsuyaku, N. Nomura. AlgU contributes to the virulence of Pseudomonas syringae pv. tomato DC3000 by regulating production of the phytotoxin coronatine. Journal of General Plant Pathology, Volume 84, Issue 3, 2018 May, pp 189–201. doi: 10.1007/s1032 7-018-0775-6.
    • Takahashi, F., T. Suzuki, Y. Osakabe, S. Betsuyaku, Y. Kondo, N. Dohmae, H. Fukuda, K. Yamaguchi-Shinozaki & K. Shinozaki. A small peptide modulates stomatal control via abscisic acid in long-distance signalling. Nature, Volume 556, Published online 2018 April, pages 235–238. doi:10.1038/s41586-018-0009-2.
    • Nishida, H., S. Tanaka, Y. Handa, M. Ito, Y. Sakamoto, S. Matsunaga, S. Betsuyaku, K. Miura, T. Soyano, M. Kawaguchi, T. Suzaki. A NIN-LIKE PROTEIN mediates nitrate-induced control of root nodule symbiosis in Lotus japonicus. Nature Communications. 2018 Feb 5;9(1):499. doi: 10.1038/s41467-018-02831-x.
    • Betsuyaku, S., S. Katou, Y. Takebayashi, H. Sakakibara, N. Nomura, H. Fukuda. Salicylic Acid and Jasmonic Acid Pathways are Activated in Spatially Different Domains Around the Infection Site During Effector-Triggered Immunity in Arabidopsis thaliana.  Plant & Cell Physiology, Volume 59, Issue 1, 2018 Jan, Pages 8–16. doi: /10.1093/pcp/pcx181.

    2017

    • Sugiura, D., C. Watanabe, E. Betsuyaku, I. Terashima.  Sink–Source Balance and Down-Regulation of Photosynthesis in Raphanus sativus: Effects of Grafting, N and CO2. Plant and Cell Physiology, Volume 58, Issue 12, 2017 Dec, Pages 2043–2056.doi:10.1093/pcp/pcx132
    • Toyofuku, M., G. Cárcamo-Oyarce, T. Yamamoto, F. Eisenstein, C. Hsiao, M. Kurosawa, K. Gademann, M. Pilhofer, N. Nomura, L. Eberl. Prophage-triggered membrane vesicle formation through peptidoglycan damage in Bacillus subtilis Nature Communications 8, Article number: 481 (2017) doi: 10.1038/s41467-017-00492-w.
    • Kiyokawa, T., Usuba R, Obana N, Yokokawa M, Toyofuku M, Suzuki H, Nomura N. A Versatile and Rapidly Deployable Device to Enable Spatiotemporal Observations of the Sessile Microbes and Environmental Surfaces. Microbes Environ., 2017 Mar 31;32(1):88-91. doi: 10.1264/jsme2.ME16161.
    • Toyofuku, M., K. Morinaga, Y. Hashimoto, J. Uhl, H. Shimamura, H. Inaba, P. Schmitt-Kopplin, L. Eberl, N. Nomura. Membrane vesicle-mediated bacterial communication. The ISME Journal11, online publication 10 March 2017. doi:10.1038/ismej.2017.13 | [Press Release info in Japan]
    • Obana N, Nakao R, Nagayama K, Nakamura K, Senpuku H, Nomura N. Immunoactive clostridial membrane vesicle production is regulated by a sporulation factor. Infect Immun., 2017 Feb 21. pii: IAI.00096-17. doi: 10.1128/IAI.00096-17.
    • Yoshida K, Toyofuku M, Obana N, Nomura N. Biofilm formation by Paracoccus denitrificans requires a type I secretion system dependent adhesin BapA. FEMS Microbiol Lett., 2017 Feb 2. doi: 10.1093/femsle/fnx029.
    • Yang J, Toyofuku M, Sakai R, Nomura N. Influence of the alginate production on cell-to-cell communication in Pseudomonas aeruginosa PAO1 Environ Microbiol Rep., 2017 Jan 25. doi: 10.1111/1758-2229.12521."
    • Obana N, Nakamura K, Nomura N. Role of RNase Y in Clostridium perfringens mRNA Decay and Processing. J Bacteriol., 2017 Jan;199(2). pii: e00703-16. doi: 10.1128/JB.00703-16.

    2016

    • Turnbull, L., M. Toyofuku, AL. Hynen, M. Kurosawa, G. Pessi, NK. Petty, SR. Osvath, G. Cárcamo-Oyarce, ES. Gloag, R. Shimoni, U. Omasits, S. Ito, X. Yap, LG. Monahan, R. Cavaliere, CH. Ahrens, IG. Charles, N. Nomura, L. Eber and CB. Whitchurch. Explosive cell lysis as a mechanism for the biogenesis of bacterial membrane vesicles and biofilms. Nat. Commun., 2016. 7:11220. doi:10.1038/ncomms11220
    • Inada N, Betsuyaku S, Shimada TL, Ebine K, Ito E, Kutsuna N, Hasezawa S, Takano Y, Fukuda H, Nakano A, Ueda T. Modulation of Plant RAB GTPase-Mediated Membrane Trafficking Pathway at the Interface Between Plants and Obligate Biotrophic Pathogens. Plant Cell Physiol, 2016. 57(9) doi:10.1093/pcp/pcw107

    2015

    • Oura, H., Y. Tashiro, M. Toyofuku, K. Ueda, T. Kiyokawa, S. Ito, Y. Takahashi, S. Lee, H. Nojiri, T. Nakajima-Kambe, H. Uchiyama, H. Futamata and N. Nomura. Inhibition of Pseudomonas aeruginosa Swarming Motility by 1-Naphthol and Other Bicyclic Compounds Bearing Hydroxyl Groups. Appl Environ Microbiol., 2015. 81(8):2808-18.
    • Toyofuku, M., Y. Tashiro, Y. Hasegawa, M. Kurosawa and N. Nomura. Bacterial membrane vesicles, an overlooked environmental colloid: Biology, environmental perspectives and applications. Adv. Colloid. Interface. Sci., 2015. 226, 65–77.
    • Inaba, T., H. Oura, K. Morinaga, M. Toyofuku, and N. Nomura. The Pseudomonas quinolone signal inhibits biofilm development of Streptcoccus mutans. Microbes Environ., 2015. 30(2):189-191.

    2014

    • Huhe, S, Borjigin, Yunxiang Cheng, N. Nomura, T. Nakajima, T. Nakamura and H. Uchiyama, Effect of Abandonment on Diversity and Abundance of Free-Living Nitrogen-Fixing Bacteria and Total Bacteria in the Cropland Soils of Hulun Buir, Inner Mongolia. PLoS One, 2014. 9(9), e106714.
    • Gi M., J. Jeong, K. Lee, K.M. Lee, M Toyofuku, D.E. Yong, S.S. Yoon, and J.Y. Choi. A Drug Repositioning Screening Identified Pentetic Acid as a Potential Therapeutic Agent for Suppressing the Elastase-mediated Virulence of Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 2014. 58(12), 7205-7214.
    • Line, L., M. Alhede, M. Kolpen, M. Kühl, O. Ciofu, T. Bjarnsholt, C. Moser, M. Toyofuku, N. Nomura, N. Høiby, and P. Ø. Jensen, Physiological levels of nitrate support anoxic growth by denitrification of Pseudomonas aeruginosa at growth rates reported in cystic fibrosis lungs and sputum. Front. Microbiol., 2014. 00554.
    • Hamada, M., M. Toyofuku, T. Miyano, and N. Nomura, Cbb3-type Cytochrome c  Oxidases, Aerobic Respiratory Enzymes, Impact the Anaerobic Life of Pseudomonas aeruginosa PAO1. J. Bacteriol., 2014. 196(21), 09784-14.
    • Wang, A., M. Toyofuku, N. Nomura, and H. Goto. Quorum Sensing Materials as New Ligand for Palladium Catalyzed Migita-Kosugi-Stille Polycondensation. International Letters of Chemistry, Physics and Astronomy, 2014. 13(1): p. 62-70.
    • Yamamoto, T., N. Obana, L.M. Yee, K. Asai, N. Nomura, and K. Nakamura. SP10 Infectivity Is Aborted after Bacteriophage SP10 Infection Induces nonA Transcription on the Prophage SPbeta Region of the Bacillus subtilis Genome. J. Bacteriol., 2014. 196(3): p. 693-706.
    • Obana, N., K. Nakamura, and N. Nomura. A sporulation factor is involved in morphological change of Clostridium perfringens biofilm in response to temperature. J. Bacteriol., 2014. 196(8): p. 1540-50.
    • Ono, K., R. Oka, M. Toyofuku, A. Sakaguchi, M. Hamada, S. Yoshida, and N. Nomura. cAMP signaling affect the irreversible attachment in biofilm formation of Pseudomonas aeruginosa PAO1. Microbes Environ., 29(1): p. 104–106.
    • Tashiro, Y., A. Inagaki, K. Ono, T. Inaba, Y. Yawata, H. Uchiyama, and N. Nomura. Low concentrations of ethanol stimulate biofilm and pellicle formation in Pseudomonas aeruginosa. Biosci. Biotechnol. and Biochem., 2014. 78(1): p. 178-181.
    • Taguchi, R., S. Tanaka, GH. Joe, H. Mased, N. Nomura, J. Ohnishi, S. Ishizuka, H. Shimizu, and H. Miyazaki. Mucin 3 is involved in intestinal epithelialcell apoptosis via N-(3-oxododecanoyl)-l-homoserine lactone-induced suppression of Akt phosphorylation. Am. J. Physiol., Cell Physiol., 2014. 307(2): p. 162-8.
    • Nakao, R., K. Kikushima, H. Higuchi, N. Obana, N. Nomura, D. Bai, M. Ohnishi, and H. Senpuku. A novel approach for purification and selective capture of membrane vesicles of the periodontopathic bacterium, Porphyromonas gingivalis: membrane vesicles bind to magnetic beads coated with epoxygroups in a noncovalent, species-specific manner. PLoS One, 2014. 9(5), e95137.

    2013

    • Zheng, Y.T., M. Toyofuku, N. Nomura, and S. Shigeto, Correlation of Carotenoid Accumulation with Aggregation and Biofilm Development in Rhodococcus sp SD-74. Analytical Chemistry, 2013. 85(15): p. 7295-7301.
    • Zhang, W., Huhe, Y. Pan, M. Toyofuku, N. Nomura, T. Nakajima, and H. Uchiyama, Dechlorination of chloral hydrate is influenced by the biofilm adhesin protein LapA in Pseudomonas putida LF54. Appl Environ Microbiol, 2013. 79(13): p. 4166-9.
    • Toyofuku, M., S. Zhou, I. Sawada, N. Takaya, H. Uchiyama, and N. Nomura, Membrane vesicle formation is associated with pyocin production under denitrifying conditions in Pseudomonas aeruginosa PAO1. Environ Microbiol, 2013.
    • Takagi, R., J. Fukuda, K. Nagata, Y. Yawata, N. Nomura, and H. Suzuki, A microfluidic microbial culture device for rapid determination of the minimum inhibitory concentration of antibiotics. Analyst, 2013. 138(4): p. 1000-3.
    • Obana, N., N. Nomura, and K. Nakamura, Structural requirement in Clostridium perfringens collagenase mRNA 5' leader sequence for translational induction through small RNA-mRNA base pairing. J Bacteriol, 2013. 195(12): p. 2937-46.
    • Tashiro Y, Yawata Y, Toyofuku M, Uchiyama H, Nomura N. Interspecies interaction between Pseudomonas aeruginosa and other microorganisms. Microbes Environ. 2013;28(1):13-24.
    • Inaba, T., Y. Tokumoto, Y. Miyazaki, N. Inoue, H. Maseda, T. Nakajima-Kambe, H. Uchiyama, and N. Nomura, Analysis of genes for succinoyl trehalose lipid production and increasing production in Rhodococcus sp. strain SD-74. Appl Environ Microbiol, 2013. 79(22): p. 7082-90.
    • Inaba, T., T. Ichihara, Y. Yawata, M. Toyofuku, H. Uchiyama, and N. Nomura, Three-dimensional visualization of mixed species biofilm formation together with its substratum. Microbiol Immunol, 2013. 57(8): p. 589-93.
    • Fang, H., M. Toyofuku, T. Kiyokawa, A. Ichihashi, K. Tateda, and N. Nomura, The impact of anaerobiosis on strain-dependent phenotypic variations in Pseudomonas aeruginosa. Biosci Biotechnol Biochem, 2013. 77(8): p. 1747-52.

    2012

    • Yamasaki, S., N. Nomura, T. Nakajima, and H. Uchiyama, Cultivation-independent identification of candidate dehalorespiring bacteria in tetrachloroethylene degradation. Environ Sci Technol, 2012. 46(14): p. 7709-16.
    • Wang, S., N. Nomura, T. Nakajima, and H. Uchiyama, Case study of the relationship between fungi and bacteria associated with high-molecular-weight polycyclic aromatic hydrocarbon degradation. J Biosci Bioeng, 2012. 113(5): p. 624-30.
    • Toyofuku, M., H. Uchiyama, and N. Nomura, Social Behaviours under Anaerobic Conditions in Pseudomonas aeruginosa. Int J Microbiol, 2012. 2012: p. 405191.
    • Tashiro, Y., H. Uchiyama, and N. Nomura, Multifunctional membrane vesicles in Pseudomonas aeruginosa. Environ Microbiol, 2012. 14(6): p. 1349-62.
    • Taniyama, K., H. Itoh, A. Takuwa, Y. Sasaki, S. Yajima, M. Toyofuku, N. Nomura, and N. Takaya, Group X aldehyde dehydrogenases of Pseudomonas aeruginosa PAO1 degrade hydrazones. J Bacteriol, 2012. 194(6): p. 1447-56.

    2011

    • Venkata, H.N.N., N. Nomura, and S. Shigeto, Leucine pools in Escherichia coli biofilm discovered by Raman imaging. Journal of Raman Spectroscopy, 2011. 42(11): p. 1913-1915.
    • Toda, K., Y. Yawata, E. Setoyama, J. Fukuda, N. Nomura, and H. Suzuki, Continuous monitoring of ammonia removal activity and observation of morphology of microbial complexes in a microdevice. Appl Environ Microbiol, 2011. 77(12): p. 4253-5.
    • Tashiro, Y., A. Inagaki, M. Shimizu, S. Ichikawa, N. Takaya, T. Nakajima-Kambe, H. Uchiyama, and N. Nomura, Characterization of phospholipids in membrane vesicles derived from Pseudomonas aeruginosa. Biosci Biotechnol Biochem, 2011. 75(3): p. 605-7.
    • Huhe, N. Nomura, T. Nakajima, and H. Uchiyama, Assimilative and co-metabolic degradation of chloral hydrate by bacteria and their bioremediation potential. J Biosci Bioeng, 2011. 111(4): p. 448-53.

    2010

    • Goto, H., Jeong, Y-S., Kawabata, K., Takada, M., Kotanagi, T., Shigemori, H., Nomura, N.: Electrochemical preparation of an electroactive polymer poly(dodecyloxy dibenzothiophene) (polyDDBTh) from hydroxyl dibenzothiophene (HDBTh) as a bioconverted monomer. Journal of Applied Electrochemistry, 40, 191-195 (2010)
    • Goto, H., Sawada, I., Nomura, N.: Circular dichroism and circular polarized luminescence from a green fluorescent protein - initial research for chiroptical emission of biological materials. International Journal of Polymeric Materials, 59, 786–792 (2010)
    • Yawata, Y., H. Uchiyama, and N. Nomura, Visualizing the effects of biofilm structures on the influx of fluorescent material using combined confocal reflection and fluorescent microscopy. Microbes Environ, 2010. 25(1): p. 49-52.
    • Yawata, Y., K. Toda, E. Setoyama, J. Fukuda, H. Suzuki, H. Uchiyama, and N. Nomura, Monitoring biofilm development in a microfluidic device using modified confocal reflection microscopy. J Biosci Bioeng, 2010. 110(3): p. 377-80.
    • Yawata, Y., K. Toda, E. Setoyama, J. Fukuda, H. Suzuki, H. Uchiyama, and N. Nomura, Bacterial growth monitoring in a microfluidic device by confocal reflection microscopy. J Biosci Bioeng, 2010. 110(1): p. 130-3.
    • Toyofuku, M., T. Nakajima-Kambe, H. Uchiyama, and N. Nomura, The effect of a cell-to-cell communication molecule, Pseudomonas quinolone signal (PQS), produced by P. aeruginosa on other bacterial species. Microbes Environ, 2010. 25(1): p. 1-7.
    • Tashiro, Y., M. Toyofuku, T. Nakajima-Kambe, H. Uchiyama, and N. Nomura, Bicyclic compounds repress membrane vesicle production and Pseudomonas quinolone signal synthesis in Pseudomonas aeruginosa. FEMS Microbiol Lett, 2010. 304(2): p. 123-30.
    • Tashiro, Y., S. Ichikawa, M. Shimizu, M. Toyofuku, N. Takaya, T. Nakajima-Kambe, H. Uchiyama, and N. Nomura, Variation of physiochemical properties and cell association activity of membrane vesicles with growth phase in Pseudomonas aeruginosa. Appl Environ Microbiol, 2010. 76(11): p. 3732-9.
    • Tashiro, Y., S. Ichikawa, T. Nakajima-Kambe, H. Uchiyama, and N. Nomura, Pseudomonas quinolone signal affects membrane vesicle production in not only gram-negative but also gram-positive bacteria. Microbes Environ, 2010. 25(2): p. 120-5.
    • Mayumi, D., T. Yoshimoto, H. Uchiyama, N. Nomura, and T. Nakajima-Kambe, Seasonal change in methanotrophic diversity and populations in a rice field soil assessed by DNA-stable isotope probing and quantitative real-time PCR. Microbes Environ, 2010. 25(3): p. 156-63.
    • Yawata, Y., H. Maseda, S. Okabe, A. Ito, I. Sawada, H. Kurashima, H. Uchiyama, and N. Nomura, The Response of Pseudomonas aeruginosa PAO1 Efflux Pump-Defective Mutants to N-Octanoyl-L-Homoserine Lactone. Microbes Environ, 2009. 24(4): p. 338-42.
    • Tokumoto, Y., N. Nomura, H. Uchiyama, T. Imura, T. Morita, T. Fukuoka, and D. Kitamoto, Structural characterization and surface-active properties of a succinoyl trehalose lipid produced by Rhodococcus sp. SD-74. J Oleo Sci, 2009. 58(2): p. 97-102.
    • Tashiro, Y., R. Sakai, M. Toyofuku, I. Sawada, T. Nakajima-Kambe, H. Uchiyama, and N. Nomura, Outer membrane machinery and alginate synthesis regulators control membrane vesicle production in Pseudomonas aeruginosa. J Bacteriol, 2009. 191(24): p. 7509-19.
    • Nakajima-Kambe, T., K. Toyoshima, C. Saito, H. Takaguchi, Y. Akutsu-Shigeno, M. Sato, K. Miyama, N. Nomura, and H. Uchiyama, Rapid monomerization of poly(butylene succinate)-co-(butylene adipate) by Leptothrix sp. J Biosci Bioeng, 2009. 108(6): p. 513-6.
    • Yawata, Y., N. Nomura, and H. Uchiyama, Development of a novel biofilm continuous culture method for simultaneous assessment of architecture and gaseous metabolite production. Appl Environ Microbiol, 2008. 74(17): p. 5429-35.
    • Yamane, K., H. Maki, T. Nakayama, T. Nakajima, N. Nomura, H. Uchiyama, and M. Kitaoka, Diversity and similarity of microbial communities in petroleum crude oils produced in Asia. Biosci Biotechnol Biochem, 2008. 72(11): p. 2831-9.
    • Toyofuku, M., N. Nomura, E. Kuno, Y. Tashiro, T. Nakajima, and H. Uchiyama, Influence of the Pseudomonas quinolone signal on denitrification in Pseudomonas aeruginosa. J Bacteriol, 2008. 190(24): p. 7947-56.
    • Tashiro, Y., N. Nomura, R. Nakao, H. Senpuku, R. Kariyama, H. Kumon, S. Kosono, H. Watanabe, T. Nakajima, and H. Uchiyama, Opr86 is essential for viability and is a potential candidate for a protective antigen against biofilm formation by Pseudomonas aeruginosa. J Bacteriol, 2008. 190(11): p. 3969-78.
    • Mayumi, D., Y. Akutsu-Shigeno, H. Uchiyama, N. Nomura, and T. Nakajima-Kambe, Identification and characterization of novel poly(DL-lactic acid) depolymerases from metagenome. Appl Microbiol Biotechnol, 2008. 79(5): p. 743-50.
    • Toyofuku, M., N. Nomura, T. Fujii, N. Takaya, H. Maseda, I. Sawada, T. Nakajima, and H. Uchiyama, Quorum sensing regulates denitrification in Pseudomonas aeruginosa PAO1. J Bacteriol, 2007. 189(13): p. 4969-72.
    • Nakayama, T., E. Ito, N. Nomura, N. Nomura, and M. Matsumura, Comparison of Vibrio harveyi strains isolated from shrimp farms and from culture collection in terms of toxicity and antibiotic resistance. FEMS Microbiol Lett, 2006. 258(2): p. 194-9.
    • Takada, M., N. Nomura, H. Okada, T. Nakajima-Kambe, T. Nakahara, and H. Uchiyama, De-repression and comparison of oil-water separation activity of the dibenzothiophene desulfurizing bacterium, Mycobacterium sp. G3. Biotechnol Lett, 2005. 27(12): p. 871-4.
    • Nomura, N., M. Takada, H. Okada, Y. Shinohara, T. Nakajima-Kambe, T. Nakahara, and H. Uchiyama, Identification and functional analysis of genes required for desulfurization of alkyl dibenzothiophenes of Mycobacterium sp. G3. J Biosci Bioeng, 2005. 100(4): p. 398-402.
    • Shinozaki-Tajiri, Y., Y. Akutsu-Shigeno, T. Nakajima-Kambe, S. Inomata, N. Nomura, and H. Uchiyama, Matrix metalloproteinase-2 inhibition and Zn2+-chelating activities of pyoverdine-type siderophores. J Biosci Bioeng, 2004. 97(4): p. 281-3.
    • Shinozaki, Y., Y. Akutsu-Shigeno, T. Nakajima-Kambe, S. Inomata, N. Nomura, T. Nakahara, and H. Uchiyama, Inhibition of matrix metalloproteinase-2 activity by siderophores of Pseudomonas species. Appl Microbiol Biotechnol, 2004. 64(6): p. 840-7.
    • Sawada, I., H. Maseda, T. Nakae, H. Uchiyama, and N. Nomura, A quorum-sensing autoinducer enhances the mexAB-oprM efflux-pump expression without the MexR-mediated regulation in Pseudomonas aeruginosa. Microbiol Immunol, 2004. 48(5): p. 435-9.
    • Maseda, H., I. Sawada, K. Saito, H. Uchiyama, T. Nakae, and N. Nomura, Enhancement of the mexAB-oprM efflux pump expression by a quorum-sensing autoinducer and its cancellation by a regulator, MexT, of the mexEF-oprN efflux pump operon in Pseudomonas aeruginosa. Antimicrob Agents Chemother, 2004. 48(4): p. 1320-8.
    • Teeraphatpornchai, T., T. Nakajima-Kambe, Y. Shigeno-Akutsu, M. Nakayama, N. Nomura, T. Nakahara, and H. Uchiyama, Isolation and characterization of a bacterium that degrades various polyester-based biodegradable plastics. Biotechnol Lett, 2003. 25(1): p. 23-8.
    • Matsuzaka, E., N. Nomura, T. Nakajima-Kambe, N. Okada, and T. Nakahara, A simple screening procedure for heterotrophic nitrifying bacteria with oxygen-tolerant denitrification activity. J Biosci Bioeng, 2003. 95(4): p. 409-11.
    • Akutsu-Shigeno, Y., T. Teeraphatpornchai, K. Teamtisong, N. Nomura, H. Uchiyama, T. Nakahara, and T. Nakajima-Kambe, Cloning and sequencing of a poly(DL-lactic acid) depolymerase gene from Paenibacillus amylolyticus strain TB-13 and its functional expression in Escherichia coli. Appl Environ Microbiol, 2003. 69(5): p. 2498-504.
    • Uchida, H., Y. Shigeno-Akutsu, N. Nomura, T. Nakahara, and T. Nakajima-Kambe, Cloning and sequence analysis of poly(tetramethylene succinate) depolymerase from Acidovorax delafieldii strain BS-3. J Biosci Bioeng, 2002. 93(2): p. 245-7.
    • Zhao, X., T. Murata, S. Ohno, N. Day, J. Song, N. Nomura, T. Nakahara, and K.K. Yokoyama, Protein kinase Calpha plays a critical role in mannosylerythritol lipid-induced differentiation of melanoma B16 cells. J Biol Chem, 2001. 276(43): p. 39903-10.
    • Wakamatsu, Y., X. Zhao, C. Jin, N. Day, M. Shibahara, N. Nomura, T. Nakahara, T. Murata, and K.K. Yokoyama, Mannosylerythritol lipid induces characteristics of neuronal differentiation in PC12 cells through an ERK-related signal cascade. Eur J Biochem, 2001. 268(2): p. 374-83.
    • Nomura, N., T. Deguchi, Y. Shigeno-Akutsu, T. Nakajima-Kambe, and T. Nakahara, Gene structures and catalytic mechanisms of microbial enzymes able to biodegrade the synthetic solid polymers nylon and polyester polyurethane. Biotechnol Genet Eng Rev, 2001. 18: p. 125-47.
    • Zhao, X., C. Geltinger, S. Kishikawa, K. Ohshima, T. Murata, N. Nomura, T. Nakahara, and K.K. Yokoyama, Treatment of mouse melanoma cells with phorbol 12-myristate 13-acetate counteracts mannosylerythritol lipid-induced growth arrest and apoptosis. Cytotechnology, 2000. 33(1-3): p. 123-30.
    • Uchida, H., T. Nakajima-Kambe, Y. Shigeno-Akutsu, N. Nomura, Y. Tokiwa, and T. Nakahara, Properties of a bacterium which degrades solid poly(tetramethylene succinate)-co-adipate, a biodegradable plastic. FEMS Microbiol Lett, 2000. 189(1): p. 25-9.
    • Sudo, T., X. Zhao, Y. Wakamatsu, M. Shibahara, N. Nomura, T. Nakahara, A. Suzuki, Y. Kobayashi, C. Jin, T. Murata, and K.K. Yokoyama, Induction of the differentiation of human HL-60 promyelocytic leukemia cell line by succinoyl trehalose lipids. Cytotechnology, 2000. 33(1-3): p. 259-64.
    • Shibahara, M., X. Zhao, Y. Wakamatsu, N. Nomura, T. Nakahara, C. Jin, H. Nagaso, T. Murata, and K.K. Yokoyama, Mannosylerythritol lipid increases levels of galactoceramide in and neurite outgrowth from PC12 pheochromocytoma cells. Cytotechnology, 2000. 33(1-3): p. 247-51.
    • Lu, J., N. Nomura, T. Nakajima-Kambe, and T. Nakahara, Cloning and expression of genes encoding meta-cleavage enzymes from 4,6-dimethyldibenzothiophene-degrading Sphingomonas strain TZS-7. Biochim Biophys Acta, 2000. 1492(2-3): p. 493-8.
    • Zhao, X., Y. Wakamatsu, M. Shibahara, N. Nomura, C. Geltinger, T. Nakahara, T. Murata, and K.K. Yokoyama, Mannosylerythritol lipid is a potent inducer of apoptosis and differentiation of mouse melanoma cells in culture. Cancer Res, 1999. 59(2): p. 482-6.
    • Shigeno-Akutsu, Y., T. Nakajima-Kambe, N. Nomura, and T. Nakahara, Purification and properties of culture-broth-secreted esterase from the polyurethane degrader Comamonas acidovorans TB-35. J Biosci Bioeng, 1999. 88(5): p. 484-7.
    • Nakajima-Kambe, T., M. Shimomura, N. Nomura, T. Chanpornpong, and T. Nakahara, Decolorization of molasses wastewater by Bacillus sp. under thermophilic and anaerobic conditions. J Biosci Bioeng, 1999. 87(1): p. 119-21.
    • Nakajima-Kambe, T., Y. Shigeno-Akutsu, N. Nomura, F. Onuma, and T. Nakahara, Microbial degradation of polyurethane, polyester polyurethanes and polyether polyurethanes. Appl Microbiol Biotechnol, 1999. 51(2): p. 134-40.
    • Lu, J., T. Nakajima-Kambe, T. Shigeno, A. Ohbo, N. Nomura, and T. Nakahara, Biodegradation of dibenzothiophene and 4,6-dimethyldibenzothiophene by Sphingomonas paucimobilis strain TZS-7. J Biosci Bioeng, 1999. 88(3): p. 293-9.
    • Akutsu, Y., T. Nakajima-Kambe, N. Nomura, and T. Nakahara, Purification and Properties of a Polyester Polyurethane-Degrading Enzyme from Comamonas acidovorans TB-35. Appl Environ Microbiol, 1998. 64(1): p. 62-7.
    • Nomura, N., M. Yamashita, and Y. Murooka, Genetic organization of a DNA-processing region required for mobilization of a non-self-transmissible plasmid, pEC3, isolated from Erwinia carotovora subsp. carotovora. Gene, 1996. 170(1): p. 57-62.

    Book

    • Toyofuku, M., Y. Tashiro, N. Nomura, L. Eberl."Function of MVs in inter-bacterial communication", Springer, 2019(in press)
    • Masanori Toyofuku, Youske Tashiro, Inaba Tomohiro, Nobuhiko Nomura. " Bacterial interactions" In: Encyclopedia of Biocolloid and Biointerface Sciences (Hiroyuki Ohshima Ed.) Wiley, 5, 2016.
    • Masanori Toyofuku, George A. O’Toole, Nobuhiko Nomura. “Anaerobic life of Pseudomonas aeruginosa” In: Pseudomonas (Juan-Luis Ramos Ed.), Springer, 5, pp99-117, 2014
    • Masanori Toyofuku, Nobuhiko Nomura. "Biofilm as a multicellular bacterial system" In: Biodegradative Bacteira (H. Nojiri, M. Tsuda, M. Fukuda, Y. Kamagata, Ed.), Springer Japan, pp335-352, 2014 (2013.11.18)

    Review

    • Toyofuku, M., N. Nomura, L. Eberl Types and origins of bacterial membrane vesicles Nature Reviews Microbiology (2018), 5 November 2018. doi: 10.1038/s41579-018-0112-2
    • Toyofuku M., T. Inaba, T. Kiyokawa, N. Obana, Y. Yawata and N. Nomura. Environmental factors that shape biofilm formation. Biosci. Biotechnol. Biochem., 80(1), 7–12 (2015).
    • Yosuke Tashiro, Yutaka Yawata, Masanori Toyofuku (Y.T., Y.Y. and M.T.
       equally contributed), Hiroo Uchiyama, Nobuhiko Nomura. Interspecies interaction between Pseudomonas aeruginosa and other microorganisms.
      Microbes & Environments, 28:13-24, (2013).
    • Masanori Toyofuku, Hiroo Uchiyama, and Nobuhiko Nomura. Social behaviours under anaerobic conditions in Pseudomonas aeruginosa. International Journal of Microbiology. 2012: Article ID 405191, (2012).
    • Satoshi Okabe, Mamoru Oshiki, Yoichi Kamagata, Nobuyasu Yamaguchi, Masanori Toyofuku, Yutaka Yawata, Yosuke Tashiro, Nobuhiko Nomura, Hiroyuki Ohta, Moriya Ohkuma, Akira Hiraishi and Kiwamu Minamisawa. A great leap forward in microbial ecology. Microbes Environ. 25: 230-240, (2010)

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