Search results for "molecular sequence data"
showing 10 items of 1928 documents
Polyphasic study of wine Lactobacillus strains: taxonomic implications
2005
One hundred and seventy-eight lactobacilli isolated from wine were characterized by a polyphasic approach. Strains were phenotypically identified at genus and species level by classical tests including the analysis of cell morphology, homo/heterofermentative character, sugar fermentation patterns, growth at different temperatures and the optical nature of the isomer of lactic acid produced from glucose. Molecular techniques such as random amplification of polymorphic DNA (RAPD), amplified 16S rDNA restriction analysis (16S-ARDRA), PFGE-RFLP and ribotyping were used to characterize strains, and their potential for identification and/or typing was evaluated. The information obtained with thes…
Acidobacteria dominate the active bacterial communities of Arctic tundra with widely divergent winter-time snow accumulation and soil temperatures.
2012
The timing and extent of snow cover is a major controller of soil temperature and hence winter-time microbial activity and plant diversity in Arctic tundra ecosystems. To understand how snow dynamics shape the bacterial communities, we analyzed the bacterial community composition of windswept and snow-accumulating shrub-dominated tundra heaths of northern Finland using DNA- and RNA-based 16S rRNA gene community fingerprinting (terminal restriction fragment polymorphism) and clone library analysis. Members of the Acidobacteria and Proteobacteria dominated the bacterial communities of both windswept and snow-accumulating habitats with the most abundant phylotypes corresponding to subdivision …
Rapid molecular dissection of viral and bacterial immunomes
2006
The development of preventive or therapeutic recombinant vaccines and the generation of serodiagnostic assays for infectious diseases depend essentially on the availability of molecularly defined antigens. A major bottleneck for the identification of suitable target antigens for many pathogens is the isolation of sufficient amounts of material for subsequent genomic or proteomic screening. Applying a highly efficient expression cloning strategy to the human pathogens vaccinia virus (VV) and Chlamydia pneumoniae (CP), we demonstrate that sub-nanogram amounts of isolated nucleic acids can be utilized to determine comprehensive sets of immunodominant antigens. Remarkably, the approach not only…
Bronchial microbiome of severe COPD patients colonised by Pseudomonas aeruginosa
2014
The bronchial microbiome in severe COPD during stability and exacerbation in patients chronically colonised by Pseudomonas aeruginosa (PA), has not been defined. Our objective was to determine the characteristics of the bronchial microbiome of severe COPD patients colonised and not colonised by P. aeruginosa and its changes during exacerbation. COPD patients with severe disease and frequent exacerbations were categorised according to chronic colonisation by P. aeruginosa. Sputum samples were obtained in stability and exacerbation, cultured, and analysed by 16S rRNA gene amplification and pyrosequencing. Sixteen patients were included, 5 of them showing chronic colonisation by P. aeruginosa.…
Characterization of a Catalase-Negative Methicillin-Resistant Staphylococcus aureus Strain
2007
ABSTRACT We describe an unusual clinical strain of catalase-negative methicillin-resistant Staphylococcus aureus sensu stricto. Sequence analysis of its catalase gene showed 99.60% identities to the catalase genes of the reference strains. A 5-base deletion, however, led to a shift of the nucleotide reading frame and a loss of the enzymatic activity.
Borrelia miyamotoi is widespread in Ixodes ricinus ticks in southern Norway.
2015
From April to October 2007, host-seeking Ixodes ricinus ticks were collected from four locations in southern Norway; Farsund, Mandal, Sogne and Tromoy, respectively. Larvae (n=210), nymphs (n=1130) and adults (n=449) were investigated for infection with Borrelia miyamotoi by real-time polymerase chain reaction (PCR) amplification of part of the 16S rRNA gene. Results were verified by direct sequencing of the PCR amplicon generated from the rrs (16S)-rrl (23S) intergenetic spacer. B. miyamotoi was detected at all sites and throughout the period of questing activity, with infection prevalence (≤1.26%) similar to what has been seen in other European countries. Detection of the relapsing fever …
PCR testing for Treponema pallidum in paraffin-embedded skin biopsy specimens: test design and impact on the diagnosis of syphilis
2007
Background: Syphilis, a chronic infection caused by Treponema pallidum (T. pallidum), is a disease which is increasing in incidence, and thus more and more becoming a differential diagnosis in routine pathology. Aim: Since histological changes are not specific, we sought to develop a polymerase chain reaction (PCR)-based molecular assay for the detection of T. pallidum in formalin-fixed, paraffin-embedded tissues, and evaluate its diagnostic power, especially in comparison with other ancillary methods, i.e. immunohistochemistry and Dieterle staining. Methods: 36 skin biopsies with the clinical and /or serological diagnosis of syphilis were evaluated by morphology, immunohistochemistry and s…
pilF polymorphism-based PCR to distinguish Vibrio vulnificus strains potentially dangerous to public health
2010
ABSTRACT Vibrio vulnificus is a heterogeneous species that comprises strains virulent and avirulent for humans and fish, and it is grouped into three biotypes. In this report, we describe a PCR-based methodology that allows both the species identification and discrimination of those isolates that could be considered dangerous to public health. Discrimination is based on the amplification of a variable region located within the gene pilF , which seems to be associated with potential human pathogenicity, regardless of the biotype of the strain.
Cloning and characterization of the genes encoding the malolactic enzyme and the malate permease of Leuconostoc oenos
1996
Using degenerated primers from conserved regions of the protein sequences of malic enzymes, we amplified a 324-bp DNA fragment by PCR from Leuconostoc oenos and used this fragment as a probe for screening a Leuconostoc oenos genomic bank. Of the 2,990 clones in the genomic bank examined, 7 with overlapping fragments were isolated by performing colony hybridization experiments. Sequencing 3,453 bp from overlapping fragments revealed two open reading frames that were 1,623 and 942 nucleotides long and were followed by a putative terminator structure. The first deduced protein (molecular weight, 59,118) is very similar (level of similarity, 66%) to the malolactic enzyme of Lactococcus lactis; …
Marinomonas aquamarina sp. nov., isolated from oysters and seawater.
2005
Abstract The characterization of three bacterial strains isolated from cultured oysters and seawater at the Spanish Mediterranean coast has been performed. Strains were phenotypically and genetically characterized and the results led us to identify them as members of the genus Marinomonas . A phylogenetic analysis based on the almost complete 16S rDNA sequences clustered all three strains together (with sequence similarities around 99.8%) in the vicinity of M. communis and M. vaga sequences and distantly related to the other four species of the genus. The most closely related species was M. communis that shared 97.4–97.6% with the Mediterranean strains. DNA–DNA hybridizations were performed…