Linked Life Data

15658992

Source:http://linkedlifedata.com/resource/pubmed/id/15658992

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
2
pubmed:dateCreated
2005-1-20
pubmed:databankReference
pubmed:abstractText
The human-specific HF183 Bacteriodes 16S rRNA genetic marker can be used to detect human faecal pollution in water environments. However, there is currently no method to quantify the prevalence of this marker in environmental samples. We developed a real-time polymerase chain reaction (PCR) assay using SYBR Green I detection to quantify this marker in faecal and environmental samples. To decrease the amplicon length to a suitable size for real-time PCR detection, a new reverse primer was designed and validated on human and animal faecal samples. The use of the newly developed reverse primer in combination with the human-specific HF183 primer did not decrease the specificity of the real-time PCR assay but a melting curve analysis must always be included. This new assay was more sensitive than conventional PCR and highly reproducible with a coefficient of variation of less than 1% within an assay and 3% between assays. As the Bacteroides species that carries this human-specific marker has never been isolated, a bacteria real-time assay was used to determine the detection efficiency. The estimated detection efficiency in freshwater ranged from 78% to 91% of the true value with an average detection efficiency of 83+/-4% of the true value. Using a simple filtration method, the limit of quantification was 4.7+/-0.3x10(5) human-specific Bacteroides markers per litre of freshwater. The aerobic incubation of the human-specific Bacteroides marker in freshwater for up to 24 days at 4 and 12 degrees C, and up to 8 days at 28 degrees C, indicated that the marker persisted up to the end of the incubation period for all incubation temperatures.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Feb
pubmed:issn
1462-2912
pubmed:author
pubmed:issnType
Print
pubmed:volume
7
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
249-59
pubmed:dateRevised
2006-11-15
pubmed:meshHeading
pubmed-meshheading:15658992-Bacteroides, pubmed-meshheading:15658992-Colony Count, Microbial, pubmed-meshheading:15658992-DNA, Bacterial, pubmed-meshheading:15658992-DNA, Ribosomal, pubmed-meshheading:15658992-Feces, pubmed-meshheading:15658992-Fresh Water, pubmed-meshheading:15658992-Genes, rRNA, pubmed-meshheading:15658992-Genetic Markers, pubmed-meshheading:15658992-Humans, pubmed-meshheading:15658992-Molecular Sequence Data, pubmed-meshheading:15658992-Organic Chemicals, pubmed-meshheading:15658992-Polymerase Chain Reaction, pubmed-meshheading:15658992-RNA, Bacterial, pubmed-meshheading:15658992-RNA, Ribosomal, 16S, pubmed-meshheading:15658992-Reproducibility of Results, pubmed-meshheading:15658992-Sensitivity and Specificity, pubmed-meshheading:15658992-Sequence Analysis, DNA, pubmed-meshheading:15658992-Temperature, pubmed-meshheading:15658992-Time Factors, pubmed-meshheading:15658992-Water Microbiology
pubmed:year
2005
pubmed:articleTitle
Detection and quantification of the human-specific HF183 Bacteroides 16S rRNA genetic marker with real-time PCR for assessment of human faecal pollution in freshwater.
pubmed:affiliation
Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't, Evaluation Studies