Search results for "Base Sequence"
showing 10 items of 1146 documents
Quantification of a novel group of nitrate-reducing bacteria in the environment by real-time PCR
2004
Abstract Nitrate reduction is performed by phylogenetically diverse bacteria. Analysis of narG (alpha subunit of the membrane bound nitrate reductase) trees constructed using environmental sequences revealed a new cluster that is not related to narG gene from known nitrate-reducing bacteria. In this study, primers targeting this as yet uncultivated nitrate-reducing group were designed and used to develop a real-time SYBR® Green PCR assay. The assay was tested with clones from distinct nitrate-reducing groups and applied to various environmental samples. narG copy number was high ranging between 5.08×108 and 1.12×1011 copies per gram of dry weight of environmental sample. Environmental real-…
Identification of a clone of Escherichia coli O103:H2 as a potential agent of hemolytic-uremic syndrome in France
1993
In a French multicenter study, six verocytotoxin-producing Escherichia coli strains were isolated from the stools of 6 of 69 children suffering from hemolytic-uremic syndrome. All strains belonged to serotype O103:H2, a serotype commonly associated with diarrhea in weaned rabbits in France. To determine whether the strains from humans and rabbits were genetically related, they were compared by analyzing their esterase electropherotypes and the restriction fragment length polymorphisms of the ribosomal DNA regions. A common clonal origin of these pathogenic strains was suggested by their identical esterase electropherotypes and their identical ribotypes, in addition to their identical seroty…
DNA Amplification Fingerprinting for Subtyping Neisseria gonorrhoeae Strains
1995
Background and Objectives DNA amplification fingerprinting is used in most epidemiologic studies as a substitute for conventional typing methods. DNA amplification fingerprinting and conventional typing methods were compared in this epidemiologic study of Neisseria gonorrhoeae. Goal of This Study To differentiate 70 Neisseria gonorrhoeae isolates from untreated patients with urogenital gonococcal infection. Study Design Gonococcal strains were characterized by auxo-typing, serotyping, plasmid profile, antibiotic sensitivity, and DNA amplification fingerprinting. The method of unweighted pair-group average linkage was used for cluster analysis. Discriminatory power was calculated applying Si…
A novel VIM‐type metallo‐beta‐lactamase (VIM‐14) in a Pseudomonas aeruginosa clinical isolate from a neonatal intensive care unit
2011
AbstractA Pseudomonas aeruginosa highly resistant to carbapenems was isolated in a neonatal intensive care unit in Palermo, Italy. The strain was found to carry a novel VIM‐type enzyme, classified as VIM‐14. The novel enzyme differs from VIM‐4 in a G31S mutation. VIM‐14 was harboured in a class 1 integron with a new organization. The integron carried the genes aac7, blaVIM‐14, blaOXA‐20 and aac4 in that order.
Description of Alcanivorax venustensis sp. nov. and reclassification of Fundibacter jadensis DSM 12178T (Bruns and Berthe-Corti 1999) as Alcanivorax …
2003
Two strains of a novel bacterium were isolated independently of each other, from different depths in the Mediterranean Sea, within a time period of 7 months, using two different isolation approaches that were focused on different objectives. Both strains, designated ISO1 and ISO4T, were halophilic, Gram-negative, strictly aerobic, straight rods that were oxidase- and catalase-positive. Both strains produced mucoid colonies in some defined minimal media and were able to grow with organic acids and some alkanes; they were also able to accumulate intracellular poly-beta-hydroxybutyrate granules. The G + C content of the DNA of strain ISO4T was 66 mol%. Comparative analysis of 16S rRNA gene seq…
Fast protocols for the 5S rDNA and ITS-2 based identification ofOenococcus oeni
2005
To identify specific marker sequences for the rapid identification of Oenococcus oeni, we sequenced the 23S-5S internal transcribed spacer (ITS-2) region and the 5S rDNA of five different O. oeni strains and three phylogenetically related lactic acid bacteria (LAB). Comparative analysis revealed 100% identity among the ITS-2 region of the O. oeni strains and remarkable differences in length and sequence compared to related LAB. These results enabled us to develop a primer set for a rapid PCR-identification of O. oeni within three hours. Moreover, the comparison of the 5S rDNA sequences and the highly conserved secondary structure provided the template for the design of three fluorescence-la…
Conjugative plasmid pIP501 undergoes specific deletions after transfer from Lactococcus lactis to Oenococcus oeni
2003
Conjugal transfer of plasmids pIP501 and its derivative pVA797 from Lactococcus lactis to Oenococcus oeni was assayed by filter mating. Plasmid pIP501 was transferred to a number of O. oeni strains whereas a single transconjugant of O. oeni M42 was recovered when pVA797 was used. Physical analysis of the transconjugant plasmids revealed that pIP501 and pVA797 underwent extensive deletions in O. oeni that affected the tra region (conjugal transfer) and SegB region (stability). All derivatives showed segregational instability in O. oeni, but were stably maintained in L. lactis. These differences correlated with the different plasmid copy numbers and the extent of deletions within the SegB reg…
Nested PCR method for rapid and sensitive detection of Vibrio vulnificus in fish, sediments, and water
1995
A nested PCR for the detection of Vibrio vulnificus in fish farms was developed as an alternative to cultural methods by using universal primers flanking the V. vulnificus-specific sequences directed against 23S rRNA genes. This specific assay detected 10 fg of DNA or 12 to 120 cells in artificially inoculated samples without enrichment and within 24 h.
Cloning and sequencing of the dnaK region of Streptomyces coelicolor A3(2)
1993
Abstract The dnaK homologue of Streptomyces coelicolor A3(2) strain M145 has been cloned and sequenced. Nucleotide sequence analysis of a 2.5-kb region revealed an open reading frame (ORF) encoding a predicted DnaK protein of 618 amino acids (Mr = 66 274). The dnaK coding sequence displays extreme codon bias and shows a strong preference for CGY and GGY, for Arg and Gly codons, respectively. The predicted DnaK sequence has a high Lys:Arg ratio which is not typical of streptomycete proteins. The region immediately downstream from dnaK contains an ORF for a GrpE-like protein; the predicted start codon of grpE overlaps the last two codons of dnaK, indicating that the two genes are translationa…
Identification of a third secondary carrier (DcuC) for anaerobic C4-dicarboxylate transport in Escherichia coli: roles of the three Dcu carriers in u…
1996
In Escherichia coli, two carriers (DcuA and DcuB) for the transport of C4 dicarboxylates in anaerobic growth were known. Here a novel gene dcuC was identified encoding a secondary carrier (DcuC) for C4 dicarboxylates which is functional in anaerobic growth. The dcuC gene is located at min 14.1 of the E. coli map in the counterclockwise orientation. The dcuC gene combines two open reading frames found in other strains of E. coli K-12. The gene product (DcuC) is responsible for the transport of C4 dicarboxylates in DcuA-DcuB-deficient cells. The triple mutant (dcuA dcuB dcuC) is completely devoid of C4-dicarboxylate transport (exchange and uptake) during anaerobic growth, and the bacteria are…