Development of an automated DNA purification module using a micro-fabricated pillar chip

We present a fully automated DNA purification module comprised of a micro-fabricated chip and sequential injection analysis system that is designed for use within autonomous instruments that continuously monitor the environment for the presence of biological threat agents. The chip has an elliptical flow channel containing a bed (3.5 &times; 3.5 mm) of silica-coated pillars with height, width and center-to-center spacing of 200, 15, and 30 &micro;m, respectively, which provides a relatively large surface area (ca. 3 cm2) for DNA capture in the presence of chaotropic agents. We have characterized the effect of various fluidic parameters on extraction performance, including sample input volume, capture flow rate, and elution volume. The flow-through design made the pillar chip completely reusable; carryover was eliminated by flushing lines with sodium hypochlorite and deionized water between assays. A mass balance was conducted to determine the fate of input DNA not recovered in the eluent. The device was capable of purifying and recovering Bacillus anthracis genomic DNA (input masses from 0.32 to 320 pg) from spiked environmental aerosol samples, for subsequent analysis using polymerase chain reaction-based assays.<br /

Historical Distribution and Molecular Diversity of Bacillus anthracis, Kazakhstan

This study provides useful baseline data for guiding future disease control programs

A multivariable Mendelian randomization analysis investigating smoking and alcohol consumption in oral and oropharyngeal cancer

The independent effects of smoking and alcohol in head and neck cancer are not clear, given the strong association between these risk factors. Their apparent synergistic effect reported in previous observational studies may also underestimate independent effects. Here we report multivariable Mendelian randomization performed in a two-sample approach using summary data on 6,034 oral/oropharyngeal cases and 6,585 controls from a recent genome-wide association study. Our results demonstrate strong evidence for an independent causal effect of smoking on oral/oropharyngeal cancer (IVW OR 2.6, 95% CI = 1.7, 3.9 per standard deviation increase in lifetime smoking behaviour) and an independent causal effect of alcohol consumption when controlling for smoking (IVW OR 2.1, 95% CI = 1.1, 3.8 per standard deviation increase in drinks consumed per week). This suggests the possibility that the causal effect of alcohol may have been underestimated. However, the extent to which alcohol is modified by smoking requires further investigation

Long-term X-ray variability of Swift J1644+57

We studied the X-ray timing and spectral variability of the X-ray source Sw J1644+57, a candidate for a tidal disruption event. We have separated the long-term trend (an initial decline followed by a plateau) from the short-term dips in the Swift light-curve. Power spectra and Lomb-Scargle periodograms hint at possible periodic modulation. By using structure function analysis, we have shown that the dips were not random but occurred preferentially at time intervals ~ [2.3, 4.5, 9] x 10^5 s and their higher-order multiples. After the plateau epoch, dipping resumed at ~ [0.7, 1.4] x 10^6 s and their multiples. We have also found that the X-ray spectrum became much softer during each of the early dip, while the spectrum outside the dips became mildly harder in its long-term evolution. We propose that the jet in the system undergoes precession and nutation, which causes the collimated core of the jet briefly to go out of our line of sight. The combined effects of precession and nutation provide a natural explanation for the peculiar patterns of the dips. We interpret the slow hardening of the baseline flux as a transition from an extended, optically thin emission region to a compact, more opaque emission core at the base of the jet.Comment: 16 pages, 12 figures. Accepted by MNRAS on 2012 Feb 11; minor improvements in the introduction and discussion from the previous arXiv versio