Fecal source tracking in water using a mitochondrial DNA microarray

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DOIResolve DOI: http://doi.org/10.1016/j.watres.2012.09.011
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Journal titleWater Research
Pages1630; # of pages: 15
SubjectDNA micro-array; Fecal; PCR clamping; Peptide nucleic acid; Quantitative PCR; Source tracking; DNA; Extraction; Fish; Mitochondria; Oligonucleotides; Peptides; Probes; RNA; Tissue; Water pollution; Polymerase chain reaction; mitochondrial DNA; RNA 12S; RNA 16S; transfer RNA; array; deer; discriminant analysis; domestic species; environmental monitoring; genome; identification method; mitochondrial DNA; nucleic acid; polymerase chain reaction; watershed; animal tissue; article; cat; controlled study; cow; coyote; deer; DNA extraction; DNA microarray; DNA sequence; dog; duck; emu; fecal coliform; feces; feces analysis; gene amplification; gene sequence; gene targeting; genetic identification; genetic variability; goat; horse; human; limit of detection; moose; mouse; muskrat; nonhuman; nucleotide sequence; oligonucleotide probe; ostrich; pigeon; polymerase chain reaction; poultry; priority journal; quail; quantitative analysis; rabbit; raccoon; reindeer; sheep; swine; turkey (bird); water pollution; water sampling; watershed; Animals; DNA, Mitochondrial; Enterobacteriaceae; Environmental Monitoring; Feces; Humans; Oligonucleotide Array Sequence Analysis; RNA, Ribosomal; RNA, Ribosomal, 16S; RNA, Transfer; Species Specificity; Water Pollutants; Animalia; Cervidae
AbstractA mitochondrial-based microarray (mitoArray) was developed for rapid identification of the presence of 28 animals and one family (cervidae) potentially implicated in fecal pollution in mixed activity watersheds. Oligonucleotide probes for genus or subfamily-level identification were targeted within the 12S rRNA - Val tRNA - 16S rRNA region in the mitochondrial genome. This region, called MI-50, was selected based on three criteria: 1) the ability to be amplified by universal primers 2) these universal primer sequences are present in most commercial and domestic animals of interest in source tracking, and 3) that sufficient sequence variation exists within this region to meet the minimal requirements for microarray probe discrimination. To quantify the overall level of mitochondrial DNA (mtDNA) in samples, a quantitative-PCR (Q-PCR) universal primer pair was also developed. Probe validation was performed using DNA extracted from animal tissues and, for many cases, animal-specific fecal samples. To reduce the amplification of potentially interfering fish mtDNA sequences during the MI-50 enrichment step, a clamping PCR method was designed using a fish-specific peptide nucleic acid. DNA extracted from 19 water samples were subjected to both array and independent PCR analyses. Our results confirm that the mitochondrial microarray approach method could accurately detect the dominant animals present in water samples emphasizing the potential for this methodology in the parallel scanning of a large variety of animals normally monitored in fecal source tracking. © 2012 Elsevier Ltd.
Publication date
AffiliationNational Research Council Canada (NRC-CNRC); NRC Biotechnology Research Institute (BRI-IRB)
Peer reviewedYes
NPARC number21269821
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Record identifierb76c73b1-8b05-4445-8bb5-87400332ac74
Record created2013-12-13
Record modified2016-05-09
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