16s-23s rdna intergenic: Topics by WorldWideScience.org

Molecular Variability of Pseudallescheria boydii, a Neurotropic Opportunist

This research validates a novel approach for source tracking based on denaturing gradient gel electrophoresis (DGGE) analysis of DNA extracted from Escherichia coli isolates. Escherichia coli from different animal sources and from river samples upstream from, at, and downstream of a combined sewer overflow were subjected to DGGE to determine sequence variations within the 16S-23S intergenic spacer region (ISR) of the rrnB ribosomal operon. The ISR was analyzed to determine if E. coli isolates from various animal sources could be differentiated from each other. DNA isolated from the E. coli animal sources was PCR amplified to isolate the rrnB operon. To prevent amplification of all 7 E. coli ribosomal operons by PCR amplification using universal primers, sequence-specific primers were utilized for the rrnB operon. Another primer set was then used to prepare samples of the ...

2007-10-01

Evolution of the nuclear ribosomal DNA intergenic spacer in four species of the Daphnia pulex complex

The sequences of the internal transcribed spacer (ITS) ribosomal DNA (rDNA) domain data obtained by restriction fragment length polymorphism analysis with 18S rDNA and fingerprinting (M13) for clinical...Full Text Available

2000-09-01

Sequence analysis of two alleles reveals that intra-and intergenic recombination played a role in the evolution of the radish fertility restorer (Rfo)

BackgroundConcerted evolution refers to the pattern in which copies of multigene families show high intraspecific sequence homogeneity but high interspecific sequence diversity....Full Text Available

Differential targeting of Tetrahymena ORC to ribosomal DNA and non-rDNA replication origins

BackgroundLand plant genomes contain multiple members of a eukaryote-specific gene family encoding proteins with pentatricopeptide repeat (PPR) motifs. Some PPR proteins were shown...Full Text Available

Nucleomorph Ribosomal DNA and Telomere Dynamics in Chlorarachniophyte Algae

The Tetrahymena thermophila origin recognition complex (ORC) contains an integral RNA subunit, 26T RNA, which confers specificity to the amplified ribosomal DNA (rDNA) origin by base...Full Text Available

2009-02-04

British Library Electronic Table of Contents (United Kingdom)

ABSTRACT. Chlorarachniophytes are enigmatic marine unicellular algae that acquired photosynthesis by secondary endosymbiosis. Chlorarachniophytes are unusual in that the nucleus of the engulfed algal cell (a green alga) persists in a miniaturized form, termed a nucleomorph. The nucleomorph genome of the model chlorarachniophyte, Bigelowiella natans CCMP621, is 373 kilobase pairs (kbp) in size, the smallest nuclear genome characterized to date. The B. natans nucleomorph genome is composed of three chromosomes, each with canonical eukaryotic telomeres and sub telomeric ribosomal DNA (rDNA) operons transcribed away from the chromosome end. Here we present the complete rDNA operon and telomeric region from the nucleomorph genome of Lotharella oceanica CCMP622, a newly characterized chlorarachn...

2010-01-01

Nucleotide sequence of a Euglena gracilis chloroplast gene coding for the 16S rRNA: homologies to E. coli and Zea mays chloroplast 16S rRNA.

Discrimination of Listeria monocytogenes from other Listeria species by ligase chain reaction.

The nucleotide sequence of 16S rDNA from Euglena gracilis chloroplasts has been determined representing the first complete sequence of an algal chloroplast rRNA gene. The structural part of the 16S...Full Text Available

1982-10-25

A Genetic Screen for Ribosomal DNA Silencing Defects Identifies Multiple DNA Replication and Chromatin-Modulating Factors

A ligase chain reaction assay based on a single-base-pair difference in the V9 region of the 16S rRNA gene (16S rDNA) was developed to distinguish between Listeria monocytogenes and other Listeria species....Full Text Available

1992-11-01

Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers

Transcriptional silencing in Saccharomyces cerevisiae occurs at several genetic loci, including the ribosomal DNA (rDNA). Silencing at telomeres (telomere position effect [TPE])...Full Text Available

1999-04-01

The nucleotide sequence and organization of nuclear 5S rRNA genes in yellow lupine

It is becoming clear that simple sequence repeats (SSRs) play a significant role in fungal genome organization, and they are a large source of genetic markers for population genetics and meiotic maps. We identified SSRs in the Laccaria bicolor genome by in silico survey and analyzed their distribution in the different genomic regions. We also compared the abundance and distribution of SSRs in L. bicolor with those of the following fungal genomes: Phanerochaete chrysosporium, Coprinopsis cinerea, Ustilago maydis, Cryptococcus neoformans, Aspergillus nidulans, Magnaporthe grisea, Neurospora crassa and Saccharomyces cerevisiae. Using the MISA computer program, we detected 277,062 SSRs in the L. bicolor genome representing 8% of the assembled genomic sequence. Among the analyzed basidiomycetes, L. bicolor exhibited the highest SSR density although no correlation between relative abundance and the genome sizes was observed. In most genomes the short motifs (mono- to trinucleotides) were ...

2011-01-01

International Nuclear Information System (INIS)

We have isolated a genomic clone containing 'Lupinus luteus' 5S ribosomal RNA genes by screening with 5S rDNA probe clones that were hybridized previously with the initiator methionine tRNA preparation (contaminated) with traces of rRNA or its degradation products). The clone isolated contains ten repeat units of 342 bp with 119 bp fragment showing 100% homology to the 5S rRNA from yellow lupine. Sequence analysis indicates only point heterogeneities among the flanking regions of the genes. (author). 6 refs, 3 figs.

1993-01-01

Zoonotic Bartonella Species in Fleas and Blood from Red Foxes in Australia.

Molecular characterization of Fasciola spp. from the endemic area of northern Iran based on nuclear ribosomal DNA sequences

Abstract Bartonella are arthropod-borne, fastidious, Gram-negative, and aerobic bacilli distributed by fleas, lice, sand flies, and, possibly, ticks. The zoonotic Bartonella species, Bartonella henselae and Bartonella clarridgeiae, which are the causes of cat scratch disease and endocarditis in humans, have been reported from cats, cat fleas, and humans in Australia. However, to date, there has been no report of B. henselae or B. clarridgeiae in Australian wild animals and their ectoparasites. B. henselae and B. clarridgeiae were detected in fleas (Ctenocephalides felis) from red foxes (Vulpes vulpes), an introduced pest animal species in Australia, and only B. clarridgeiae was detected in blood from one red fox. Phylogenetic analysis of the ribosomal intergenic spacer region revealed that the B. henselae detected in the current study were related to B. henselae strain Houston-1, a major pathogenic strain in humans in Australia, and confirmed the genetic ...

2011-09-15

British Library Electronic Table of Contents (United Kingdom)

Fasciolosis caused by Fasciola spp. (Platyhelminthes: Trematoda: Digenea) is considered as the most important helminth infection of ruminants in tropical countries, causing considerable socioeconomic problems. In the endemic regions of the North of Iran, Fasciola hepatica and Fasciola gigantica have been previously characterized on the basis of morphometric differences, but the use of molecular markers is necessary to distinguish exactly between species and intermediate forms. Samples from buffaloes and goats from different localities of northern Iran were identified morphologically and then genetically characterized by sequences of the first (ITS-1) and second (ITS-2) Internal Transcribed Spacers (ITS) of nuclear ribosomal DNA (rDNA). Comparison of the ITS of the northern Iranian samples ...

2011-01-01

Genotyping of Candida albicans on the basis of polymorphisms of ALT repeats in the repetitive sequence (RPS)

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SummaryBackgroundCandida albicans is one of the most important etiologic agents causing superficial and deep fungal infections. For prevention of candidiasis, it is important to develop a rapid system that discriminates C. albicans at the strain level.ObjectiveTo develop a system that can identify C. albicans at the strain level.MethodsGenomic DNAs were purified from 179 clinical isolates of C. albicans, and were used as templates for PCR amplification of 25S rDNA and ALT repeats in repetitive sequences (RPSs). PCR products generated from ALT repeats were digested with EcoRI and/or ClaI in order to study the relationships between restriction profiles and amplification profiles.ResultsOne hundred and seventy nine clinical isolates were grouped into genotypes A (92 isolates), B (38 isolates)...

2006-01-01

Decolorization of textile azo dyes by newly isolated halophilic and halotolerant bacteria

British Library Electronic Table of Contents (United Kingdom)

Studies were carried out on the decolorization of textile azo dyes by newly isolated halophilic and halotolerant bacteria. Among the 27 strains of halophilic and halotolerant bacteria isolated from effluents of textile industries, three showed remarkable ability in decolorizing the widely utilized azo dyes. Phenotypic characterization and phylogenetic analysis based on 16S rDNA sequence comparisons indicate that these strains belonged to the genus Halomonas. The three strains were able to decolorize azo dyes in a wide range of NaCl concentration (up to 20%w/v), temperature (25-40degreeC), and pH (5-11) after 4 days of incubation in static culture. They could decolorize the mixture of dyes as well as pure dyes. These strains also readily grew in and decolorized the high concentrations of dy...

2007-01-01

Chitinolytic enzyme production and genetic improvement of a new isolate belonging to Streptomyces anulatus

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Thirty bacterial isolates were obtained from different sources and sites at Jeddah, Saudi Arabia, on chitin agar medium; 9 of the 30 isolates were cultured in liquid medium containing chitin as sole carbon and nitrogen sources. Isolate SM21, which was isolated from shrimp shells, showed the best growth and chitinase production in liquid medium. According to its morphological, physiological and biochemical characteristics, SM21 belongs to the genus Streptomyces and was identified as Streptomyces anulatus SM21. Identification was confirmed using 16S rDNA analysis. The chitinase enzyme was precipitated with 80% NH4SO4 and purified using DEAE-cellulose ion exchange chromatography followed by Sephadex G-100 gel filtration. The molecular weight determined using sodium dodecyl sulfate polyacrylam...

2011-01-01

Microbial dynamics in upflow anaerobic sludge blanket (UASB) bioreactor granules in response to short-term changes in substrate feed

Morphological and molecular redescription of the myxozoan Unicapsula pflugfelderi from two teleost hosts in the Mediterranean. A review of the genus Unicapsula Davis 1924

The complexity and diversity of the microbial communities in biogranules from an upflow anaerobic sludge blanket (UASB) bioreactor were determined in response to short-term changes in substrate feeds. The reactor was fed simulated brewery wastewater (SBWW) (70% ethanol, 15% acetate, 15% propionate) for 1.5 months (phase 1), acetate / sulfate for 2 months (phase 2), acetate-alone for 3 months (phase 3), and then a return to SBWW for 2 months (phase 4). Performance of the reactor remained relatively stable throughout the experiment as shown by COD removal and gas production. 16S rDNA, methanogen-associated mcrA and sulfate reducer-associated dsrAB genes were PCR amplified, then cloned and sequenced. Sequence analysis of 16S clone libraries showed a relatively simple community composed mainly of the methanogenic Archaea (Methanobacterium and Methanosaeta), members of the Green Non-Sulfur (Chloroflexi) group of Bacteria, followed by fewer numbers of Syntrophobacter, ...

2010-08-01

British Library Electronic Table of Contents (United Kingdom)

Abstract Elongate plasmodia with myxosporean spores belonging to the genus Unicapsula, Davis, 1924 were found in the skeletal muscle of the striped seabream, Lithognathus mormyrus (L.), a candidate for the mediterranean aquaculture. The only species of Unicapsula described from the Mediterranean is Unicapsula pflugfelderi Schubert et al. 1975, which occurs in the picarel, Spicara smaris (L.). For morphological and molecular comparison of U. pflugfelderi from S. smaris with Unicapsula sp. from L. mormyrus measurements of plasmodia and spores, ultrastructural details and 18S and 28S rDNA sequences were analysed. Whereas plasmodia were 2-3 times larger in S. smaris than in L. mormyrus (length 2.47-0.81 mm; width 0.22-0.09 mm; P = 0.000), spore morphology showed minor differences and both 18S ...

2009-01-01

Molecular phylogenetic analysis of tropical freshwater mussels (Mollusca: Bivalvia: Unionoida) resolves the position of Coelatura and supports a monophyletic Unionidae.

Isolation and Identification of Achromobacter sp. DN-06 and Evaluation of Its Pyridine Degradation Kinetics

In previous molecular phylogenetic analyses of the freshwater mussel family Unionidae (Bivalvia: Unionoida), the Afrotropical genus Coelatura had been recovered in various positions, generally indicating a paraphyletic Unionidae. However that result was typically poorly supported and in conflict with morphology-based analyses. We set out to test the phylogenetic position of Coelatura by sampling tropical lineages omitted from previous studies. Forty-one partial 28S nuclear rDNA and partial COI mtDNA sequences (1130 total aligned nucleotides) were analyzed separately and in combination under both maximum parsimony and likelihood, as well as Bayesian inference. There was significant phylogenetic incongruence between the character sets (partition homogeneity test, p<0.01), but a novel heuristic for comparing bootstrap values among character sets analyzed separately and in combination illustrated that the observed conflict was due to homoplasy rather than separate ...

2011-07-30

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We report the isolation of a new bacterium species (named as DN-06) that degrades pyridine, a model compound containing both carbon and nitrogen, from the aerobic activated sludge in a coking wastewater treatment plant. DN-06 was identified as Achromobacter sp. using 16S rDNA sequence analysis. In batch culture, more than 95% of pyridine (500?mg/L) was degraded within 18?h by DN-06 grown at 35?C and pH?8 with agitation at 170?rpm. Degradation experiments of pyridine at different initial concentrations (50?4,300?mg/L) revealed that pyridine was an inhibitory substrate, and that neither yield coefficient Y nor endogenous decay coefficient K d was a constant. The values of Y and K d were 0.55?0.74 and 0.0032?0.0057?h?1, respectively. Five kinetic models (Haldane, Yano, Aiba, Webb, and Monod) ...

2011-01-01

Evidence of minimal methanogenic numbers and activity in sediments collected from the JAPEX/JNOC/GSC et al. Mallik 5L-38 gas hydrate production research well

Biological control of take-all in wheat by endophytic Bacillus subtilis E1R-j and potential mode of action

Gene analysis was used to determined the presence, abundance and phylogenetic affiliation of methanogens that exist in gas-hydrate-bearing sediment samples obtained from 23 drill cores from the JAPEX/JNOC/GSC et al. Mallik 5L-38 gas hydrate research well. Rates of methane production were examined using sediment-inoculated enrichments containing {sup 14}C-labeled carbon substrates, carbon dioxide and acetate. Archaeal 16S rDNA was only detected in 6 of the samples, resulting in 8 sequences with relationships to the Miscellaneous Crenarchaeotic Group (7 clones) and the Subsurface Euryarchaeotic Group (1 clone). The single Euryarchaeota sequence did not appear to be related to methanogens. Subsamples from the cores showed variable results upon DNA extraction and amplification. Methanogenic Coenzyme M (CoM) was detected in 13 of the 20 cores, but methanogenic methyl CoM reductase genes were not amplified from the samples when using a sensitive quantitative polymerase ...

2005-07-01

British Library Electronic Table of Contents (United Kingdom)

The bacterial strain E1R-j, isolated as an endophyte from wheat roots, exhibited high antifungal activity to Gaeumannomyces graminis var. tritici (Ggt). Strain E1R-j was identified as Bacillus subtilis based on morphological, physiological and biochemical methods as well as on 16S rDNA analysis. This strain inhibited mycelium growth in vitro of numerous plant pathogenic fungi, especially of Ggt, Coniothyrium diplodiella, Phomopsis sp. and Sclerotinia sclerotiorum. In greenhouse experiments, soil drenches with cell densities of 106, 109 and 1012CFU ml-1 E1R-j reduced significantly take-all disease, caused by Ggt, in wheat seedling by 62.6%, 68.6% and 70.7%, respectively, compared to the inoculated control, 4weeks after sowing. Growth parameters such as lengths and fresh weights of roots and...

2009-01-01

Microbiological Comparison of Core and Groundwater Samples Collected from a Fractured Basalt Aquifier with that of Dialysis Chamber Incubated in Situ

Local chromatin structure of heterochromatin regulates repeatedDNA stability, nucleolus structure, and genome integrity

Microorganisms associated with fractured basalt core were compared to those suspended in groundwater pumped from the same well in the eastern Snake River Plain Aquifer (Idaho, USA). Two wells influenced to different degrees by a mixed-waste plume in the fractured basalt aquifer were examined. In one well, an array of dialysis cells filled with either deionized water or crushed basalt was equilibrated to compare the microorganisms collected in this fashion with those from core and groundwater samples collected in a traditional manner from the same well. Analyses were performed to characterize these samples and to provide a basis for comparison. These included total cell counts by microscopy; total biomass by phospholipid fatty acid analysis; enumerations of viable aerobic heterotrophs, groups of putative aerobic co-metabolic TCE-degraders and aerobic H2-oxidizing bacteria; mineralization of 14C- labeled acetate; and enrichments for dissimilatory iron-reducing bacteria. The 16S ...

2004-04-01