ABSTRACT
The detection limit of 2,4,6-trinitrotoluene (TNT) and ammonium nitrate (AN) in mixtures of Ottawa sand (OS) was studied using a Raman microscope applying conventional calibration curves, Pearson correlation coefficients, and two-sample t-tests. By constructing calibration curves, the conventionally defined detection limits were estimated to be 1.9 ± 0.4% by mass in OS and 1.9 ± 0.3% by mass in OS for TNT and AN. Both TNT and AN were detectable in concentrations as low as 1% by mass when Pearson correlation coefficients were used to compare averaged spectra to a library containing spectra from a range of soil types. AN was detectable in concentrations as low as 1% by mass when a test sample of spectra was compared to the same library using two-sample t-tests. TNT was not detectable at a concentration of 1% by mass when using two-sample t-tests.
ABSTRACT
BACKGROUND: The MinION™ nanopore sequencer was recently released to a community of alpha-testers for evaluation using a variety of sequencing applications. Recent reports have tested the ability of the MinION™ to act as a whole genome sequencer and have demonstrated that nanopore sequencing has tremendous potential utility. However, the current nanopore technology still has limitations with respect to error-rate, and this is problematic when attempting to assemble whole genomes without secondary rounds of sequencing to correct errors. In this study, we tested the ability of the MinION™ nanopore sequencer to accurately identify and differentiate bacterial and viral samples via directed sequencing of characteristic genes shared broadly across a target clade. RESULTS: Using a 6 hour sequencing run time, sufficient data were generated to identify an E. coli sample down to the species level from 16S rDNA amplicons. Three poxviruses (cowpox, vaccinia-MVA, and vaccinia-Lister) were identified and differentiated down to the strain level, despite over 98% identity between the vaccinia strains. The ability to differentiate strains by amplicon sequencing on the MinION™ was accomplished despite an observed per-base error rate of approximately 30%. CONCLUSIONS: While nanopore sequencing, using the MinION™ platform from Oxford Nanopore in particular, continues to mature into a commercially available technology, practical uses are sought for the current versions of the technology. This study offers evidence of the utility of amplicon sequencing by demonstrating that the current versions of MinION™ technology can accurately identify and differentiate both viral and bacterial species present within biological samples via amplicon sequencing.
