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  • 1
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    Sphingomonas yabuuchiae sp. nov. and Brevundimonas nasdae sp. nov., isolated from the Russian space laboratory Mir
    Microbiology Society ; 2004
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 54, No. 3 ( 2004-05-01), p. 819-825
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 54, No. 3 ( 2004-05-01), p. 819-825
    Abstract: On the basis of phenotypic and genotypic characteristics and 16S rRNA gene sequence analysis, novel species belonging to the genera Sphingomonas and Brevundimonas were identified from samples taken from the Russian space laboratory Mir. Strain A1-18 T was isolated from the air. 16S rDNA sequence analysis showed that strain A1-18 T formed a coherent cluster with Sphingomonas sanguinis , Sphingomonas parapaucimobilis , Sphingomonas paucimobilis and Sphingomonas roseiflava with sequence similarity of 97·5–98·6 %. Similar to other Sphingomonas species, the G+C content was 66·1 mol%, but DNA–DNA hybridization rates at optimal temperatures among these related species were only 24·7–51·7 %. Strain A1-18 T can be differentiated biochemically from related species. Strain W1-2B T was isolated from condensation water. It forms a distinct lineage within the genus Brevundimonas , forming a coherent cluster with Brevundimonas vesicularis , Brevundimonas aurantiaca and Brevundimonas intermedia . 16S rDNA sequence similarities were 98·6–99·5 % and the G+C content was 66·5 mol%, similar to other Brevundimonas species, but DNA–DNA relatedness was only 50·2–54·8 %. Strain W1-2B T also showed some differential biochemical properties from its related species. A series of polyphasic taxonomic studies led to the proposal of two novel species, Sphingomonas yabuuchiae sp. nov. (type strain A1-18 T =GTC 868 T =JCM 11416 T =DSM 14562 T ) and Brevundimonas nasdae sp. nov. (type strain W1-2B T =GTC 1043 T =JCM 11415 T =DSM 14572 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijs.0.02829-0
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2004
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
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  • 2
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    Sphingomonas melonis sp. nov., a novel pathogen that causes brown spots on yellow Spanish melon fruits.
    Microbiology Society ; 2002
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 52, No. 6 ( 2002-11-01), p. 2081-2087
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 52, No. 6 ( 2002-11-01), p. 2081-2087
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/00207713-52-6-2081
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2002
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
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  • 3
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    Identification of Rhodococcus equi lipids recognized by host cytotoxic T lymphocytes
    Microbiology Society ; 2010
    In:  Microbiology Vol. 156, No. 6 ( 2010-06-01), p. 1836-1847
    Details
    In: Microbiology, Microbiology Society, Vol. 156, No. 6 ( 2010-06-01), p. 1836-1847
    Abstract: Immune adult horses have CD8 + cytotoxic T lymphocytes (CTLs) that recognize and lyse Rhodococcus equi -infected cells in an equine lymphocyte alloantigen (ELA)-A [classical major histocompatibility complex (MHC) class I]-unrestricted fashion. As protein antigens are MHC class I-restricted, the lack of restriction suggests that the bacterial antigens being recognized by the host are not proteins. The goals of this study were to test the hypothesis that these CTLs recognize unique R. equi cell-wall lipids related to mycobacterial lipids. Initial experiments showed that treatment of soluble R. equi antigen with broadly reactive proteases did not significantly diminish the ability of the antigen to stimulate R. equi -specific CTLs. R. equi -specific CTLs were also shown to lyse target cells (equine macrophages) pulsed with an R. equi lipid extract. Analysis of the R. equi lipid by TLC and MS (MALDI-TOF and ES) indicated that the extracted antigen consisted of three primary fractions: trehalose monomycolate (TMM), trehalose dimycolate (TDM) and cardiolipin (CL). ELA-A-mismatched cells pulsed with purified TMM and CL, but not the TDM fraction, were recognized and lysed by R. equi -specific CTLs. Because of their role in immune clearance and pathogenesis, transcription of the cytokines gamma interferon (IFN- γ ) and interleukin-4 (IL-4) was also measured in response to R. equi lipids by using real-time PCR; elevated IFN- γ , but not IL-4, was associated with host clearance of the bacteria. The whole-cell R. equi lipid and all three R. equi lipid fractions resulted in marked increases in IFN- γ transcription, but no increase in IL-4 transcription. Together, these data support the hypothesis that immune recognition of unique lipids in the bacterial cell wall is an important component of the protective immune response to R. equi . The results also identify potential lipid antigens not previously shown to be recognized by CTLs in an important, naturally occurring actinomycete bacterial pathogen.
    Type of Medium: Online Resource
    ISSN: 1350-0872 , 1465-2080
    URL: Article
    DOI: 10.1099/mic.0.035915-0
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2010
    detail.hit.zdb_id: 2008736-6
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  • 4
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    Intact molecular characterization of cord factor (trehalose 6,6′-dimycolate) from nine species of mycobacteria by MALDI-TOF mass spectrometry
    Microbiology Society ; 2005
    In:  Microbiology Vol. 151, No. 10 ( 2005-10-01), p. 3403-3416
    Details
    In: Microbiology, Microbiology Society, Vol. 151, No. 10 ( 2005-10-01), p. 3403-3416
    Abstract: Cord factor (trehalose 6,6′-dimycolate, TDM) is an unique glycolipid with a trehalose and two molecules of mycolic acids in the mycobacterial cell envelope. Since TDM consists of two molecules of very long branched-chain 3-hydroxy fatty acids, the molecular mass ranges widely and in a complex manner. To characterize the molecular structure of TDM precisely and simply, an attempt was made to determine the mycolic acid subclasses of TDM and the molecular species composition of intact TDM by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry for the first time. The results showed that less than 1 μg mycolic acid methyl ester of TDM from nine representative species of mycobacteria and TDM from the same species was sufficient to obtain well-resolved mass spectra composed of pseudomolecular ions [ M +Na] + . Although the mass ion distribution was extremely diverse, the molecular species of each TDM was identified clearly by constructing a molecular ion matrix consisting of the combination of two molecules of mycolic acids. The results showed a marked difference in the molecular structure of TDM among mycobacterial species and subspecies. TDM from Mycobacterium tuberculosis (H 37 Rv and Aoyama B) showed a distinctive mass pattern and consisted of over 60 molecular ions with α -, methoxy- and ketomycolate. TDM from Mycobacterium bovis BCG Tokyo 172 similarly showed over 35 molecular ions, but that from M. bovis BCG Connaught showed simpler molecular ion clusters consisting of less than 35 molecular species due to a complete lack of methoxymycolate. Mass ions due to TDM from M. bovis BCG Connaught and Mycobacterium kansasii showed a biphasic distribution, but the two major peaks of TDM from M. kansasii were shifted up two or three carbon units higher compared with M. bovis BCG Connaught. Within the rapid grower group, in TDM consisting of α -, keto- and wax ester mycolate from Mycobacterium phlei and Mycobacterium flavescens , the mass ion distribution due to polar mycolates was shifted lower than that from the Mycobacterium avium–intracellulare group. Since the physico-chemical properties and antigenic structure of mycolic acid of TDM affect the host immune responses profoundly, the molecular characterization of TDM by MALDI-TOF mass analysis may give very useful information on the relationship of glycolipid structure to its biological activity.
    Type of Medium: Online Resource
    ISSN: 1350-0872 , 1465-2080
    URL: Article
    DOI: 10.1099/mic.0.28158-0
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2005
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  • 5
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    Emendation of the genus Sphingomonas Yabuuchi et al. 1990 and junior objective synonymy of the species of three genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjunction with Blastomonas ursincola.
    Microbiology Society ; 2002
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 52, No. 5 ( 2002-09-01), p. 1485-1496
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 52, No. 5 ( 2002-09-01), p. 1485-1496
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/00207713-52-5-1485
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2002
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
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  • 6
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    Rothia aeria sp. nov., Rhodococcus baikonurensis sp. nov. and Arthrobacter russicus sp. nov., isolated from air in the Russian space laboratory Mir
    Microbiology Society ; 2004
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 54, No. 3 ( 2004-05-01), p. 827-835
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 54, No. 3 ( 2004-05-01), p. 827-835
    Abstract: Four Gram-positive bacteria, strains A1-17B T , A1-22 T , A1-3 T and A1-8, isolated from the air in the Russian space laboratory Mir, were subjected to a polyphasic taxonomic study. Phylogenetic analysis of the bacteria based on their 16S rDNA sequence showed that they belong to the genera Rothia (A1-17B T ), Rhodococcus (A1-22 T ) and Arthrobacter (A1-3 T and A1-8). Morphological, physiological, chemotaxonomic and genomic characteristics supported the assignments of these strains to these genera, but they could not be classified as any existing species within each respective genus. 16S rDNA similarity values between strain A1-17B T and its neighbours, Rothia dentocariosa genomovar II, Rothia dentocariosa , Rothia mucilaginosa and Rothia nasimurium , were respectively 99·8, 98·0, 96·4 and 95·4 %. Polyphasic taxonomic evidence indicated that strain A1-17B T should be categorized together with the unofficially named Rothia dentocariosa genomovar II, but clearly differentiated them from the established species of the genus Rothia . Strain A1-22 T formed a coherent cluster with Rhodococcus erythropolis , Rhodococcus globerulus , Rhodococcus marinonascens and Rhodococcus percolatus in 16S rDNA sequence analysis, but DNA–DNA relatedness values were only 45·5, 35·3, 18·9 and 21·9 %. Strains A1-3 T and A1-8 shared 99·9 % 16S rDNA sequence similarity, and strain A1-3 T showed the highest level of 16S rDNA similarity, 96·6 %, to Arthrobacter polychromogenes . Contrasting biochemical characteristics were also identified. Finally, as a result of the polyphasic taxonomic study, three of the strains are proposed as type strains of novel species: Rothia aeria sp. nov. (A1-17B T =GTC 867 T =JCM 11412 T =DSM 14556 T ), Rhodococcus baikonurensis sp. nov. (A1-22 T =GTC 1041 T =JCM 11411 T =DSM 44587 T ) and Arthrobacter russicus sp. nov. (A1-3 T =GTC 863 T =JCM 11414 T =DSM 14555 T ).
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijs.0.02828-0
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2004
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
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  • 7
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    Genetic variation and dynamics of hepatitis C virus replicons in long-term cell culture
    Microbiology Society ; 2005
    In:  Journal of General Virology Vol. 86, No. 3 ( 2005-03-01), p. 645-656
    Details
    In: Journal of General Virology, Microbiology Society, Vol. 86, No. 3 ( 2005-03-01), p. 645-656
    Abstract: Hepatitis C virus (HCV) genomic sequences are known to vary widely among HCV strains, but to date there have been few reports on the genetic variations and dynamics of HCV in an experimental system of HCV replication. In this study, a genetic analysis of HCV replicons obtained in long-term culture of two HCV replicon cells (50-1 and 1B-2R1), which were established from two HCV strains, 1B-1 and 1B-2, respectively, was performed. One person cultured 50-1 cells for 18 months, and two people independently cultured 50-1 cells for 12 months. 1B-2R1 cells were also cultured for 12 months. The whole nucleotide sequences of the three independent replicon RNA clones obtained at several time points were determined. It was observed that genetic mutations in both replicons accumulated in a time-dependent manner, and that the mutation rates of both replicons were approximately 3·0×10 −3 base substitutions/site/year. The genetic diversity of both replicons was also enlarged in a time-dependent manner. The colony formation assay by transfection of total RNAs isolated from both replicon cells at different time points into naïve HuH-7 cells revealed that the genetic mutations accumulating with time in both replicons apparently improved colony formation efficiency. Taken together, these results suggest that the HCV replicon system is useful for the analysis of evolutionary dynamics and variations of HCV. Using this replicon cell culture system, it was demonstrated further that neither ribavirin nor its derivative mizoribine accelerated the mutation rate or the increase in the genetic diversity of HCV replicon.
    Type of Medium: Online Resource
    ISSN: 0022-1317 , 1465-2099
    URL: Article
    DOI: 10.1099/vir.0.80479-0
    RVK:
    XA 53770
    RVK:
    WA 15000
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2005
    detail.hit.zdb_id: 2007065-2
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  • 8
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    Bacterial ceramides and sphingophospholipids induce apoptosis of human leukaemic cells
    Microbiology Society ; 2003
    In:  Microbiology Vol. 149, No. 8 ( 2003-08-01), p. 2071-2081
    Details
    In: Microbiology, Microbiology Society, Vol. 149, No. 8 ( 2003-08-01), p. 2071-2081
    Abstract: The genus Sphingobacterium , whose members are Gram-negative non-fermentative rods, possesses ceramides and related sphingophospholipids (SPLs) with isoheptadecasphinganine and 2-hydroxy or non-hydroxy isopentadecanoic acid. This paper reports evidence that ceramides isolated from Sphingobacterium spiritivorum ATCC 33861 induce endonucleolytic DNA cleavage in human myeloid leukaemia HL-60 cells in vitro , which is the primary characteristic biochemical marker for apoptosis or programmed cell death. Ceramides and SPLs also induced DNA fragmentation and caspase-3 activation, followed by changes in morphology, such as alterations in the size of nuclei and cells, and cell cycle shortening. Apoptotic activity correlated with the ceramide structure. Ceramide with a 2-hydroxy fatty acid showed stronger apoptotic activity than ceramide with a non-hydroxy fatty acid. Furthermore, the major five SPLs (ceramide phosphorylethanolamine-1 and -2, ceramide phosphorylinositol-1 and -2, and ceramide phosphorylmannose-1) showed apoptosis-inducing activity in HL-60 cells, indicating that the ceramide moiety of the SPLs plays a crucial role as the intracellular second messenger but that their hydrophilicity is less important in this regard. The hydrophilic part of SPLs may play a role in other cellular response systems. The involvement of Fas antigen was implicated in the apoptotic event since Fas antigen expression was observed after 3 or 4 h stimulation of HL-60 cells with bacterial ceramides. However, a time-course study for caspase-3 activation indicated maximal activity at 1 h after stimulation with bacterial ceramides, suggesting that two (or possibly more) mechanisms of signal transduction, Fas-dependent and Fas-independent, may be involved. Fas antigen expression and caspase-3 activation by five kinds of SPLs were observed after 3 or 4 h. These results indicate that there is a difference in the response of HL-60 cells to bacterial ceramides and SPLs.
    Type of Medium: Online Resource
    ISSN: 1350-0872 , 1465-2080
    URL: Article
    DOI: 10.1099/mic.0.25922-0
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2003
    detail.hit.zdb_id: 2008736-6
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  • 9
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    Direct molecular mass determination of trehalose monomycolate from 11 species of mycobacteria by MALDI-TOF mass spectrometry
    Microbiology Society ; 2005
    In:  Microbiology Vol. 151, No. 5 ( 2005-05-01), p. 1443-1452
    Details
    In: Microbiology, Microbiology Society, Vol. 151, No. 5 ( 2005-05-01), p. 1443-1452
    Abstract: Direct estimation of the molecular mass of single molecular species of trehalose 6-monomycolate (TMM), a ubiquitous cell-wall component of mycobacteria, was performed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. When less than 1 μg TMM was analysed by MALDI-TOF mass spectrometry, quasimolecular ions [M+Na] + of each molecular species were demonstrated and the numbers of carbons and double bonds (or cyclopropane rings) were determined. Since the introduction of oxygen atoms such as carbonyl, methoxy and ester groups yielded the appropriate shift of mass ions, the major subclasses of mycolic acid ( α , methoxy, keto and wax ester) were identified without resorting to hydrolytic procedures. The results showed a marked difference in the molecular species composition of TMM among mycobacterial species. Unexpectedly, differing from other mycoloyl glycolipids, TMM from Mycobacterium tuberculosis showed a distinctive mass pattern, with abundant odd-carbon-numbered monocyclopropanoic (or monoenoic) α -mycolates besides dicyclopropanoic mycolate, ranging from C 75 to C 85 , odd- and even-carbon-numbered methoxymycolates ranging from C 83 to C 94 and even- and odd-carbon-numbered ketomycolates ranging from C 83 to C 90 . In contrast, TMM from Mycobacterium bovis (wild strain and BCG substrains) possessed even-carbon-numbered dicyclopropanoic α -mycolates. BCG Connaught strain lacked methoxymycolates almost completely. These results were confirmed by MALDI-TOF mass analysis of mycolic acid methyl esters liberated by alkaline hydrolysis and methylation of the original TMM. Wax ester-mycoloyl TMM molecular species were demonstrated for the first time as an intact form in the Mycobacterium avium – intracellulare group, M. phlei and M. flavescens . The M. avium – intracellulare group possessed predominantly C 85 and C 87 wax ester-mycoloyl TMM, while M. phlei and the rapid growers tested contained C 80 , C 81 , C 82 and C 83 wax ester-mycoloyl TMM. This technique has marked advantages in the rapid analysis of not only intact glycolipid TMM, but also the mycolic acid composition of each mycobacterial species, since it does not require any degradation process.
    Type of Medium: Online Resource
    ISSN: 1350-0872 , 1465-2080
    URL: Article
    DOI: 10.1099/mic.0.27791-0
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2005
    detail.hit.zdb_id: 2008736-6
    SSG: 12
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