6 research outputs found
Comparison of Eight Methods for the Extraction of Bacillus atrophaeus Spore DNA from Eleven Common Interferents and a Common Swab
Eight DNA extraction products or methods (Applied Biosystems PrepFiler Forensic DNA Extraction Kit; Bio-Rad Instagene Only, Bio-Rad Instagene & Spin Column Purification; EpiCentre MasterPure DNA & RNA Kit; FujiFilm QuickGene Mini80; Idaho Technologies 1-2-3 Q-Flow Kit; MoBio UltraClean Microbial DNA Isolation Kit; Sigma Extract-N-Amp Plant and Seed Kit) were adapted to facilitate extraction of DNA under BSL3 containment conditions. DNA was extracted from 12 common interferents or sample types, spiked with spores of Bacillus atropheaus. Resulting extracts were tested by real-time PCR. No one method was the best, in terms of DNA extraction, across all sample types. Statistical analysis indicated that the PrepFiler method was the best method from six dry powders (baking, biological washing, milk, plain flour, filler and talcum) and one solid (Underarm deodorant), the UltraClean method was the best from four liquids (aftershave, cola, nutrient broth, vinegar), and the MasterPure method was the best from the swab sample type. The best overall method, in terms of DNA extraction, across all sample types evaluated was the UltraClean method
Results from Bg sp PCR when tested against DNA extracts produced from a 100 µL (0.001% w/v) Bg aliquot (with an added 1 µL microbiological loopful of grated deodorant) and 100 µL (0.001% w/v) Bg aliquots removed from a cotton swab.
a<p>No. of PCR positives from <i>n</i> replicates.</p>b<p>C<sub>T</sub> value: PCR cycle number at which fluorescence first detected in a 50 cycle PCR. Mean of positive results only. Variance of mean in parenthesis.</p
Results from Bg sp PCR when tested against DNA extracts produced from liquid sample types spiked with two concentrations of <i>B. atropheaus</i> spores.
a<p>weight/volume Bg spores/liquid.</p>b<p>No. of PCR positives from <i>n</i> replicates.</p>c<p>C<sub>T</sub> value: PCR cycle number at which fluorescence first detected in a 50 cycle PCR. Mean of positive results only. Variance of mean in parenthesis.</p
Ranking of each method, as determined by statistical analysis, by individual sample type and combined sample types.
<p>Ranking of each method, as determined by statistical analysis, by individual sample type and combined sample types.</p
Results from Bg sp PCR when tested against DNA extracts produced from powder sample types spiked with two concentrations of <i>B. atropheaus.</i>
a<p>weight/weight powder/Bg spores.</p>b<p>No. of PCR positives from <i>n</i> replicates.</p>c<p>C<sub>T</sub> value: PCR cycle number at which fluorescence first detected in a 50 cycle PCR. Mean of positive results only. Variance of mean in parenthesis.</p