No abstract

Emerging next-generation sequencing technologies have revolutionized the collection of genomic data for applications in bioforensics, biosurveillance, and for use in clinical settings. However, to make the most of these new data, new methodology needs to be developed that can accommodate large volumes of genetic data in a computationally efficient manner. We present a statistical framework to analyze raw next-generation sequence reads from purified or mixed environmental or targeted infected tissue samples for rapid species identification and strain attribution against a robust database of known biological agents. Our method, Pathoscope, capitalizes on a Bayesian statistical framework that accommodates information on sequence quality, mapping quality, and provides posterior probabilities of matches to a known database of target genomes. Importantly, our approach also incorporates the possibility that multiple species can be present in the sample and considers cases when the sample species/strain is not in the reference database. Furthermore, our approach can accurately discriminate between very closely related strains of the same species with very little coverage of the genome and without the need for multiple alignment steps, extensive homology searches, or genome assembly-which are time-consuming and labor-intensive steps. We demonstrate the utility of our approach on genomic data from purified and in silico ''environmental'' samples from known bacterial agents impacting human health for accuracy assessment and comparison with other approaches.

SummaryMedical implants are sometimes colonized by biofilm-forming bacteria that are very difficult to treat effectively. The combination of gentamicin and ultrasonic exposure for 24 h was previously shown to reduce the viability of E. coli biofilms in vivo. This article shows that such treatment for 48 h reduced viable E. coli bacteria to nearly undetectable levels. However, when P. aeruginosa biofilms were implanted and treated for 24 and 48 h, no significant ultrasonic-enhanced reduction of viable bacteria was observed. The difference in response of these two organisms is attributed to greater impermeability and stability of the outer membrane of P. aeruginosa.

Escherichia coli biofilms on two polyethylene disks were implanted subcutaneously into rabbits receiving systemic gentamicin. Ultrasound was applied for 24 h to one disk. Both disks were removed, and viable bacteria were counted. Pulsed ultrasound significantly reduced bacterial viability below that of nontreated biofilms without damage to the skin.

This study investigated Type I error rates for tests of fixed effects in mixed linear models using Wald F-statistics with the Kenward-Roger adjustment. Data were generated using 15 covariance structures. Correct covariance structures as well as those selected using the Akaike's Information Criterion (AIC) and Schwarz's Bayesian Information Criterion (BIC) criteria were examined. Performance of the AIC and BIC criteria in selecting the true covariance structure was also studied. Type I error rates for the correct models were often adequate depending on the sample size and complexity of covariance structure. Type I error rates for the best AIC and BIC models were always higher than target values, but those obtained using BIC were closer to the target value than those obtained using AIC. For unbalanced data, Type I error rates for the between-subjects effect were closer to target values for positive pairing while those for the within-subject effect were closer for negative pairing. Success of AIC and BIC in selecting the correct covariance structure was low.

Excess postexercise oxygen consumption (EPOC) may describe the impact of previous exercise on energy metabolism. Ten males completed Resistance Only, Run Only, Resistance-Run, and Run-Resistance experimental conditions. Resistance exercise consisted of 7 lifts. Running consisted of 25 minutes of treadmill exercise. Vo(2) was determined during treadmill exercise and after each exercise treatment. Our findings indicated that treadmill exercise Vo(2) was significantly higher for Resistance-Run compared with Run-Resistance and Resistance Only at all time intervals. At 10 minutes postexercise, Vo(2) was greater for Resistance Only and Run-Resistance than for Resistance-Run. At 20 and 30 minutes, Vo(2) following Resistance Only was significantly greater than following Run Only. In conclusion, EPOC is greatest following Run-Resistance; however, treadmill exercise is more physiologically difficult following resistance exercise. Furthermore, the sequence of resistance and treadmill exercise influences EPOC, primarily because of the effects of resistance exercise rather than the exercise combination. We recommend performing aerobic exercise before resistance exercise when combining them into 1 exercise session.

The hypothesis that ultrasound increases antibiotic transport through biofilms of Escherichia coli and Pseudomonas aeruginosa was investigated using colony biofilms. Biofilms grown on membrane filters were transferred to nutrient agar containing 50 μg/mL gentamicin. A smaller filter was placed on top of the biofilm and a blank concentration disk was situated atop the filter. Diffusion of antibiotic through the biofilms was allowed for 15, 30, or 45 min at 37°C. Some of these biofilms were exposed to 70 kHz ultrasound and others were not. Each concentration disk was then placed on a nutrient agar plate spread with a lawn of E. coli. The resulting zone of inhibition was used to calculate the amount of gentamicin that was transported through the biofilm into the disk. The E. coli and P. aeruginosa biofilms grown for 13 and 24 h were exposed to two different ultrasonic power densities. Ultrasonication significantly increased the transport of gentamicin through the biofilm. Insonation of biofilms of E. coli for 45 minutes more than doubled the amount of gentamicin compared to their non-insonated counterparts. For P. aeruginosa biofilms, no detectable gentamicin penetrated the biofilm within 45 min without ultrasound; however, when insonated (1.5 W/cm 2 ) for 45 min, the disks collected more than 0.45 μg of antibiotic. Ultrasonication significantly increased transport of gentamicin across biofilms that normally blocked or slowed gentamicin transport when not exposed to ultrasound. This enhanced transport may be partially responsible for the increased killing of biofilm bacteria exposed to combinations of antibiotic and ultrasound.

cootiouous stockiog usu8Ily leads to the fonlutioo of grued patclkea. However, the effect of p&bee 00 the grazelMd c0mmunity is related to their stability. Therefore, we ztudied the spatial stability of grazed pat&e oo Rough Fezcue Gramlande by map ping forage remov8l clmuee 00 10 site8 over 8 Cyeu period, tezting stability uzing the Kappa index (H), and characterizing the soila and vegetatioo of overgrazed and undergrazed patches. Spotlal stability of grazed patches between comecutivc yeam wm good (lEO.26) oo &en experieming low grazing prwsure. However, oo dtea having high grazing preezure, spatial stability waz Iese comizteot between comecutive yeuz (DKSO.45) ud low over 8 Cyeu period (K10.10). Overgrazed patches were dominated by graziogresistant zeral speck, but undergrazed patcher were dominated by climu species. Rough feecue (%cstuco SC&&~ 8nd P8rry oat grazs @u&to& porryi) plantz were 50% shorter, and forage production waz about 35% lees, on overgrazed than on undergrazed patches. Soil organic matter, carbohydratea, and depth of Ah horizon were zignificantly greater oo undergrazed patches but ureaze activity, NO& NH,, and available phosphorus were greater oo overgrazed patchez. Overgrazed and undagrazed patches were stable in the long term, although patch bouodariez fluctu8ted.