Sulfitobacter mediterraneus sp. nov., a new sulfite-oxidizing member of the alpha-Proteobacteria.
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Analysis of PCR products of 16S rDNA of 680 isolates from Mediterranean Sea mesocosm experiments with taxon-specific 16S rDNA oligonucleotides revealed that 262 isolates belonged to the alpha subclass of the class Proteobacteria. Partial 16S rDNA sequence analysis of selected isolates and oligonucleotide probing with a Sulfitobacter-specific 16S rDNA probe affiliated 33 strains to the genus Sulfitobacter. Analysis of the HaeIII digest pattern of 16S rDNA revealed the presence of two groups; while 30 strains showed a pattern identical with that obtained for Sulfitobacter pontiacus DSM 10014T, a second group of three strains had a unique pattern that was different from that of the type strain. Five isolates of group 1 and one isolates of group 2, strain CH-B427T, were selected for detailed taxonomic analysis. All six isolates closely resembled the type strain Sulfitobacter pontiacus DSM 10014T in physiological reactions. However, strain CH-B427T differed quantitatively in the composition of fatty acids from Sulfitobacter pontiacus DSM 10014T and showed only 98.2% 16S rDNA sequence similarity with strain DSM 10014T. DNA-DNA reassociation value obtained for strains DSM 10014T and CH-B427T revealed 46% similarity. Based on the results of DNA-DNA reassociation and discrete differences in the nucleotide composition of 16S rDNA, a new species of the genus Sulfitobacter is proposed, designated Sulfitobacter mediterraneus sp. nov., the type strain being strain CH-B427T (= DSM 12244T). (+info)
Identification of antigenic escape variants in an immunodominant epitope of hepatitis C virus.
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Numerous investigators have postulated that one mechanism by which hepatitis C virus (HCV) may evade the immune system is through the formation of escape mutants. This hypothesis is based largely on the observed mutability of the viral genome resulting in evolution of diverse quasispecies over the course of infection. That such diversification is a product of viral RNA polymerase infidelity, immune-driven selection or a combination of the two processes has not been addressed. We have examined sequence variability in a specific segment of HCV RNA encoding a known immunodominant region of the viral helicase, amino acids 358-375 of the non-structural 3 protein. Using sequence-specific oligonucleotide probe hybridization and automated DNA sequencing, we report a high frequency of mutations, essentially all of which result in amino acid replacements. To assess the biological impact of such mutations, corresponding chemically synthesized peptides were compared to wild-type peptide in T cell proliferation assays. We observed that a sizeable fraction of such peptides stimulated attenuated or negligible levels of proliferation by peripheral T cells from a chronically infected patient. This observation is consistent with expectations for immune-mediated selection of escape variants at the epitope level. We postulate that such a mechanism may be important in the immunopathogenesis of HCV infections. (+info)
Evidence of high-frequency genomic reassortment of group A rotavirus strains in Bangladesh: emergence of type G9 in 1995.
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We characterized 1,534 rotavirus (RV) strains collected in Bangladesh from 1992 to 1997 to assess temporal changes in G type and to study the most common G and P types using reverse transcription-PCR, oligonucleotide probe hybridization, and monoclonal antibody-based enzyme immunoassay. Results from this study combined with our previous findings from 1987 to 1991 (F. Bingnan et al., J. Clin. Microbiol. 29:862-868, 1991, and L. E. Unicomb et al., Arch. Virol. 132:201-208, 1993) (n = 2,515 fecal specimens) demonstrated that the distribution of the four major G types varied from year to year, types G1 to G4 constituted 51% of all strains tested (n = 1,364), and type G4 was the most prevalent type (22%), followed by type G2 (17%). Of 351 strains tested for both G and P types, three globally common types, type P[8], G1, type P[4], G2, and type P[8], G4, comprised 45% (n = 159) of the strains, although eight other strains were circulating during the study period. Mixed G and/or P types were found in 23% (n = 79) of the samples tested. Type G9 RVs that were genotype P[6] and P[8] with both long and short electrophoretic patterns emerged in 1995. The finding of five different genotypes among G9 strains, of which three were frequently detected, suggests that they may have an unusual propensity for reassortment that exceeds that found among the common G types. We also detected antigenic changes in serotypes G2 and G4 over time, as indicated by the loss of reactivity with standard typing monoclonal antibodies. Our data suggest that a vaccine must provide protection against type G9 RVs as well as against the four major G types because G9 strains constituted 16% (n = 56) of the typeable RV strains and have predominated since 1996. (+info)
Quantitative analysis of hepatitis B virus precore mutant in hepatitis type B.
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Active liver disease has been detected in chronic hepatitis B after seroconversion from positive HBe antigen to positive anti-HBe antibody. Active replication of HB virus (HBV) containing a precore stop-codon mutation has been implicated in this condition. The usual methods, such as direct sequencing, to characterize the responsible mutant of HBV are not suitable for routine clinical use. Here we employed the competitive mutation site specific assay (CMSSA) to detect precore mutant HBV-DNA in patients with positive HB surface antigen. In patients with HBe antigen, precore mutant HBV-DNA was significantly higher than in patients with HBe antibody. The level of precore mutant HBV-DNA in patients with elevated serum ALT was significantly higher than in patients with normal serum ALT. Sex, age and the level of serum HBV-associated DNA polymerase levels were not correlated with levels of precore mutant HBV-DNA. Ten of 11 negative patients for the precore mutant by polymerase chain reaction followed by restriction fragment length polymorphism assay (PCRRFLP) were positive for the precore mutant by CMSSA. These results suggest that the precore mutant has already emerged in the HBeAg-positive phase as determined by CMSSA, which is more sensitive than PCR-RFLP and is useful for evaluating the clinical course of patients with chronic hepatitis B. (+info)
Identification of Id2 as a globin regulatory protein by representational difference analysis of K562 cells induced to express gamma-globin with a fungal compound.
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A fungus-derived compound (OSI-2040) which induces fetal globin expression in the absence of erythroid cell differentiation was identified in a high-throughput drug discovery program. We utilized this compound to isolate gamma-globin regulatory genes that are differentially expressed in OSI-2040-induced and uninduced cells in the human erythroleukemia cell line K562. Representational difference analysis (RDA) of cDNA revealed several genes that were significantly up- or down-regulated in OSI-2040-induced cells. One gene whose expression was markedly enhanced was the gene for the helix-loop-helix (HLH) transcription factor Id2. Southern analysis of RDA amplicons demonstrated progressive enrichment of Id2 with each successive subtraction of uninduced cDNA from induced cDNA. Northern analysis of OSI-2040-induced K562 cells confirmed that Id2 expression was directly up-regulated coordinately with gamma-globin. Analysis of other inducers of fetal globin demonstrated up-regulation of Id2 with sodium butyrate but not with hemin. Retrovirus-mediated overexpression of Id2 in K562 cells reproduced the enhancement of endogenous globin expression observed with OSI-2040 induction. Functional assays demonstrated that an E-box element in hypersensitivity site 2 is required for Id2-dependent enhancement of gamma-promoter activity. Protein binding studies suggest that alterations in E-box site occupancy by basic HLH proteins may influence this activity, thus expanding the potential role of these factors in globin gene regulation. (+info)
Expression of the Huntington's disease gene is regulated in astrocytes in the arcuate nucleus of the hypothalamus of postpartum rats.
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Huntington's disease (HD) is one of a number of neurodegenerative disorders caused by expansion of polyglutamine-encoding CAG repeats within specific genes. Huntingtin, the protein product of the HD gene, is widely expressed in neural and nonneural human and rodent tissue. The function of the wild-type or mutated form of huntingtin is currently unknown. We have observed that relative to naive and male animals, huntingtin protein was significantly increased in the arcuate nucleus of postpartum rats. Using an oligonucleotide probe, in situ and Northern blot hybridization confirmed the expression of huntingtin mRNA. Quantification of the in situ hybridization signal in the arcuate nucleus revealed an approximate sevenfold increase in the expression of huntingtin mRNA in postpartum, lactating animals compared with naive female or male animals. Emulsion autoradiography and immunohistochemistry revealed that the cells with elevated huntingtin expression had a stellate conformation that morphologically resembled astrocytes. Dual label immunofluorescence immunohistochemistry demonstrated the colocalization of huntingtin and glial fibrillary acidic protein in these cells, confirming that they were astrocytes. Astrocytes expressing huntingtin were consistently found in close apposition to neuronal soma, suggesting interactions between these cell types. During the perinatal and postnatal period, the hypothalamus undergoes alterations in metabolic function. Our results support the idea of glia-induced metabolic changes in the hypothalamus. These results provide the first demonstration of naturally occurring changes in the expression of the Huntington's disease gene in the brain and suggest that huntingtin may play an important role in the processes that regulate neuroendocrine function. (+info)
Niche-partitioning of Prochlorococcus populations in a stratified water column in the eastern North Atlantic Ocean.
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The in situ community structure of Prochlorococcus populations in the eastern North Atlantic Ocean was examined by analysis of Prochlorococcus 16S rDNA sequences with three independent approaches: cloning and sequencing, hybridization to specific oligonucleotide probes, and denaturing gradient gel electrophoresis (DGGE). The hybridization of high-light (HL) and low-light (LL) Prochlorococcus genotype-specific probes to two depth profiles of PCR-amplified 16S rDNA sequences revealed that in these two stratified water columns, an obvious niche-partitioning of Prochlorococcus genotypes occurred. In each water column a shift from the HL to the LL genotype was observed, a transition correlating with the depth of the surface mixed layer (SML). Only the HL genotype was found in the SML in each water column, whereas the LL genotype was distributed below the SML. The range of in situ irradiance to which each genotype was subjected within these distinct niches was consistent with growth irradiance studies of cultured HL- and LL-adapted Prochlorococcus strains. DGGE analysis and the sequencing of Prochlorococcus 16S rDNA clones were in full agreement with the genotype-specific oligonucleotide probe hybridization data. These observations of a partitioning of Prochlorococcus genotypes in a stratified water column provide a genetic basis for the dim and bright Prochlorococcus populations observed in flow cytometric signatures in several oceanic provinces. (+info)
Analysis of mtDNA HVRII in several human populations using an immobilised SSO probe hybridisation assay.
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Several populations were typed for the hypervariable region II (HVRII) of the mitochondrial DNA (mtDNA) control region using immobilised sequence-specific oligonucleotide (SSO) probes. A total of 16 SSO probes was used to type 1081 individuals from eight different ethnic groups (African Americans, Somali, US Europeans, US Hispanics, Bosnians, Finns, Saami and Japanese). Data was compared with already published sequence data by analysis of principal components, genetic distances and analysis of the molecular variance (AMOVA). The analyses performed group the samples in several clusters according to their geographical origins. Most of the variability detected is assigned to differences between individuals and only 7% is assigned to differences among groups of populations within and between geographical regions. Several features are patent in the samples studied: Somali, as a representative East African population, seem to have experienced a detectable amount of Caucasoid maternal influence; different degrees of admixture in the US samples studied are detected; Finns and Saami belong to the European genetic landscape, although Saami present an outlier position attributable to a strong maternal founder effect. The technique used is a rapid and simple method to detect human variation in the mtDNA HVRII in a large number of samples, which might be useful in forensic and population genetic studies. (+info)