scholarly journals Simultaneous detection and genotyping of three genomic groups of Borrelia burgdorferi sensu lato in Dutch Ixodes ricinus ticks by characterization of the amplified intergenic spacer region between 5S and 23S rRNA genes.

1995 ◽  
Vol 33 (12) ◽  
pp. 3091-3095 ◽  
Author(s):  
S G Rijpkema ◽  
M J Molkenboer ◽  
L M Schouls ◽  
F Jongejan ◽  
J F Schellekens
Keyword(s):  
Borrelia Burgdorferi ◽  
Simultaneous Detection ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
23S Rrna ◽  
Borrelia Burgdorferi Sensu Lato ◽  
Intergenic Spacer Region ◽  
Ixodes Ricinus Ticks ◽  
23S Rrna Genes

Limitations of the widely used GAM42a and BET42a probes targeting bacteria in the Gammaproteobacteria radiation

Microbiology ◽  
2003 ◽  
Vol 149 (5) ◽  
pp. 1239-1247 ◽  
Author(s):  
Christine Yeates ◽  
Aaron M. Saunders ◽  
Gregory R. Crocetti ◽  
Linda L. Blackall
Keyword(s):  
Intergenic Spacer ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Target Region ◽  
Intergenic Spacer Region ◽  
Probe Target ◽  
Pcr Products ◽  
23S Rrna Genes

The 23S rRNA-targeted probes GAM42a and BET42a provided equivocal results with the uncultured gammaproteobacterium ‘Candidatus Competibacter phosphatis' where some cells bound GAM42a and other cells bound BET42a in fluorescence in situ hybridization (FISH) experiments. Probes GAM42a and BET42a span positions 1027–1043 in the 23S rRNA and differ from each other by one nucleotide at position 1033. Clone libraries were prepared from PCR products spanning the 16S rRNA genes, intergenic spacer region and 23S rRNA genes from two mixed cultures enriched in ‘Candidatus C. phosphatis’. With individual clone inserts, the 16S rDNA portion was used to confirm the source organism as ‘Candidatus C. phosphatis' and the 23S rDNA portion was used to determine the sequence of the GAM42a/BET42a probe target region. Of the 19 clones sequenced, 8 had the GAM42a probe target (T at position 1033) and 11 had G at position 1033, the only mismatch with GAM42a. However, none of the clones had the BET42a probe target (A at 1033). Non-canonical base-pairing between the 23S rRNA of ‘Candidatus C. phosphatis' with G at position 1033 and GAM42a (G–A) or BET42a (G–T) is likely to explain the probing anomalies. A probe (GAM42_C1033) was optimized for use in FISH, targeting cells with G at position 1033, and was found to highlight not only some ‘Candidatus C. phosphatis' cells, but also other bacteria. This demonstrates that there are bacteria in addition to ‘Candidatus C. phosphatis' with the GAM42_C1033 probe target and not the BET42a or GAM42a probe target.

scholarly journals Sequencing of the Ribosomal Intergenic Spacer Region for Strain Identification of Porphyromonas gingivalis

1999 ◽  
Vol 37 (8) ◽  
pp. 2723-2725 ◽  
Author(s):  
Robert W. Rumpf ◽  
Ann L. Griffen ◽  
Bo-Gui Wen ◽  
Eugene J. Leys
Keyword(s):  
Porphyromonas Gingivalis ◽  
Intergenic Spacer ◽  
Variable Region ◽  
Rrna Genes ◽  
23S Rrna ◽  
Clinical Samples ◽  
Strain Identification ◽  
Intergenic Spacer Region ◽  
Ribosomal Intergenic Spacer ◽  
23S Rrna Genes

The ribosomal intergenic spacer regions (ISRs) of 19 laboratory strains and 30 clinical samples of Porphyromonas gingivaliswere amplified by PCR and sequenced to provide a strain identifier. The ISR is a variable region of DNA located between the conserved 16S and 23S rRNA genes. This makes it an ideal locus for differentiation of strains within a species: primers specific for the conserved flanking genes were used to amplify the ISR, which was then sequenced to identify the strain. We have constructed a P. gingivalisISR sequence database to facilitate strain identification. ISR sequence analysis provides a strain identifier that can be easily reproduced among laboratories and catalogued for unambiguous comparison.

Genomic fingerprinting ofFrankiamicrosymbionts fromCeanothuscopopulations using repetitive sequences and polymerase chain reactions

1999 ◽  
Vol 77 (9) ◽  
pp. 1220-1230 ◽  
Author(s):  
Soon-Chun Jeong ◽  
David D Myrold
Keyword(s):  
Dna Sequencing ◽  
Dna Analysis ◽  
Repetitive Sequences ◽  
Intergenic Spacer ◽  
Rrna Genes ◽  
23S Rrna ◽  
Genomic Fingerprinting ◽  
Chain Reactions ◽  
Intergenic Spacer Region ◽  
Polymerase Chain

Specificity between Ceanothus species and their microsymbionts, Frankia, were investigated with nodules collected from three geographically separated copopulations of Ceanothus species. Nodules were analyzed using DNA sequencing and repetitive sequence polymerase chain reaction (rep-PCR) techniques. DNA sequencing of the intergenic spacer region between 16S and 23S rRNA genes suggested that Ceanothus-microsymbiotic Frankia are closely related at the intraspecific level. Diversity of the microsymbionts was further analyzed by genomic fingerprinting using repetitive sequences and PCR. A newly designed direct repeat (DR) sequence and a BOX sequence were used as PCR primers after justification that these primers can generate Frankia-specific fingerprints from nodule DNA. Analysis of the nodules using BOX- and DR-PCR showed that Ceanothus-microsymbiotic Frankia exhibited less diversity within each copopulation than among copopulations. These data suggested that geographic separation plays a more important role for divergence of Ceanothus-microsymbiotic Frankia than host plant.Key words: Frankia, Ceanothus, rep-PCR, diversity.

scholarly journals Characterization of Agrobacterium vitis Strains Isolated from Feral Vitis riparia

Plant Disease ◽  
1999 ◽  
Vol 83 (2) ◽  
pp. 102-107 ◽  
Author(s):  
T. J. Burr ◽  
C. L. Reid ◽  
C. E. Adams ◽  
E. A. Momol
Keyword(s):  
New York ◽  
New York State ◽  
Rrna Genes ◽  
23S Rrna ◽  
Agrobacterium Vitis ◽  
Control Activity ◽  
Vitis Riparia ◽  
23S Rrna Genes ◽  
Physiological Tests

Agrobacterium vitis was isolated from roots of 41 of 66 feral Vitis riparia vines collected in three different regions of New York State. Two of the regions were more than 150 km from commercial vineyards. The strains were highly diverse as determined by DNA fingerprinting of the chromosomal region lying between the 16S and 23S rRNA genes. Of 24 strains examined, 15 different fingerprints were generated, and none was identical to fingerprints generated by previously identified groups of tumorigenic A. vitis strains. Results of physiological tests that were done to characterize strains from V. riparia conformed closely to those expected for A. vitis, except that 23 of 26 strains did not utilize tartrate. All strains were nontumorigenic, did not hybridize with a probe consisting of T-DNA genes, did not utilize octopine or nopaline, and carried zero to three plasmids. Of 26 strains, 7 inhibited A. vitis strain K306 from causing galls at wound sites on grape as well as or better than a previously studied nontumorigenic A. vitis strain, F2/5, that is known to have biological control activity.

scholarly journals First isolation and characterization of Borrelia burgdorferi sensu lato strains from Ixodes ricinus ticks in Turkey

2003 ◽  
Vol 52 (9) ◽  
pp. 807-813 ◽  
Author(s):  
Ece S. Güner ◽  
Naoya Hashimoto ◽  
Nobuhiro Takada ◽  
Kazuhide Kaneda ◽  
Yasuyuki Imai ◽  
...  
Keyword(s):  
Borrelia Burgdorferi ◽  
Ixodes Ricinus ◽  
Borrelia Burgdorferi Sensu Lato ◽  
Isolation And Characterization ◽  
Ixodes Ricinus Ticks

scholarly journals Construction and Initial Characterization of Escherichia coli Strains with Few or No Intact Chromosomal rRNA Operons

1999 ◽  
Vol 181 (12) ◽  
pp. 3803-3809 ◽  
Author(s):  
Tsuneaki Asai ◽  
Ciarán Condon ◽  
Justina Voulgaris ◽  
Dmitry Zaporojets ◽  
Binghua Shen ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Growth Rate ◽  
Rrna Operon ◽  
Rrna Genes ◽  
23S Rrna ◽  
Multicopy Plasmid ◽  
Wild Type ◽  
Protein Ratio ◽  
23S Rrna Genes

ABSTRACT The Escherichia coli genome carries seven rRNA (rrn) operons, each containing three rRNA genes. The presence of multiple operons has been an obstacle to many studies of rRNA because the effect of mutations in one operon is diluted by the six remaining wild-type copies. To create a tool useful for manipulating rRNA, we sequentially inactivated from one to all seven of these operons with deletions spanning the 16S and 23S rRNA genes. In the final strain, carrying no intact rRNA operon on the chromosome, rRNA molecules were expressed from a multicopy plasmid containing a single rRNA operon (prrn). Characterization of these rrndeletion strains revealed that deletion of two operons was required to observe a reduction in the growth rate and rRNA/protein ratio. When the number of deletions was extended from three to six, the decrease in the growth rate was slightly more than the decrease in the rRNA/protein ratio, suggesting that ribosome efficiency was reduced. This reduction was most pronounced in the Δ7 prrn strain, in which the growth rate, unlike the rRNA/protein ratio, was not completely restored to wild-type levels by a cloned rRNA operon. The decreases in growth rate and rRNA/protein ratio were surprisingly moderate in the rrndeletion strains; the presence of even a single operon on the chromosome was able to produce as much as 56% of wild-type levels of rRNA. We discuss possible applications of these strains in rRNA studies.

scholarly journals Borrelia carolinensis sp. nov., a novel species of the Borrelia burgdorferi sensu lato complex isolated from rodents and a tick from the south-eastern USA

2011 ◽  
Vol 61 (2) ◽  
pp. 381-383 ◽  
Author(s):  
Nataliia Rudenko ◽  
Maryna Golovchenko ◽  
Libor Grubhoffer ◽  
James H. Oliver
Keyword(s):  
South Carolina ◽  
Borrelia Burgdorferi ◽  
Novel Species ◽  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Borrelia Burgdorferi Sensu Lato ◽  
Rrna Gene ◽  
The Novel ◽  
Intergenic Spacer Region ◽  
Peromyscus Gossypinus

A group of 16 isolates with genotypic characteristics different from those of known species of the Borrelia burgdorferi sensu lato complex were cultured from ear biopsies of the rodents Peromyscus gossypinus and Neotoma floridana trapped at five localities in South Carolina, USA, and from the tick Ixodes minor feeding on N. floridana. Multilocus sequence analysis of members of the novel species, involving the 16S rRNA gene, the 5S–23S (rrf–rrl) intergenic spacer region and the flagellin, ospA and p66 genes, was conducted and published previously and was used to clarify the taxonomic status of the novel group of B. burgdorferi sensu lato isolates. Phylogenetic analysis based on concatenated sequences of the five analysed genomic loci showed that the 16 isolates clustered together but separately from other species in the B. burgdorferi sensu lato complex. The analysed group therefore represents a novel species, formally described here as Borrelia carolinensis sp. nov., with the type strain SCW-22T (=ATCC BAA-1773T =DSM 22119T).

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