Evaluation of interference to conventional and real-time PCR for detection and quantification of fungi in dust

Advances in polymerase chain reaction (PCR) have permitted accurate, rapid and quantitative identification of microorganisms in pure cultures regardless of viability or culturability. In this study, a simple sample processing method was investigated for rapid identification and quantification of fungal spores from dust samples using both conventional and real-time PCR. The proposed method was evaluated for susceptibility to interference from environmental dust samples. Stachybotrys chartarum and Aspergillus fumigatus were used as test organisms. The sensitivity of detection in pure culture was 0.1 spore DNA equivalents per PCR reaction corresponding to 20 spores ml(-1) in the sample. However, 1 spore DNA equivalent per PCR reaction corresponding to 200 spores ml(-1) in the sample was the lowest amount of spores tested without interference in dust samples spiked with spores of either fungal species. The extent of inhibition was calculated using conventional and real-time PCR reactions containing fungal spores, specific primers, specific probes (for real-time PCR) and various amounts of dust. The results indicate that the extent of inhibition by dust on PCR varies with the type and amount of dust, and number of spores. No interference in the analysis of spiked samples was detected from 0.2 mg ml(-1) of four real-life dust samples at p-value >0.05 using 2 x 10(4) spores for conventional PCR and 2 x 10(5) spores for real-time PCR. However, samples containing >0.2 mg ml(-1) real-life dust compromised the PCR assay. These results suggest the potential usefulness of a simple sample processing method in conjunction with PCR for monitoring the fungal content of aerosols collected from indoor environments.     

Food justice youth development: using Photovoice to study urban school food systems*

How do youth learn through participation in efforts to study and change the school food system? Through our participatory youth action research (YPAR) project, we move beyond the “youth as consumer” frame to a food justice youth development (FJYD) approach. We track how a group of youth learned about food and the public policy process through their efforts to transform their own school food systems by conducting a participatory evaluation of farm-to-school efforts in collaboration with university and community partners. We used the Photovoice research method, placing cameras in the hands of young people so that they themselves could document and discuss their concerns and perspectives. The research was designed to gain insight about youths’ knowledge of food, health, and community food systems. Drawing upon the youth group’s insights, we build a framework for building critical consciousness through FJYD.     

SAOZ measurements of NO2 at Aberystwyth

We present in this paper fifteen years' measurements, from March 1991 to September 2005, of stratospheric NO2 vertical columns measured by a SAOZ zenith-sky visible spectrometer. The instrument spent most of its time at Aberystwyth, Wales, with occasional excursions to other locations. The data have been analysed with the WinDOAS analysis program with low-temperature high-resolution NO2 cross-sections and fitting a slit function to each spectrum. Because of a change in detector in May 1998 there is some uncertainty about the relative changes before and after this date, which are partially constrained by the results of an intercomparison exercise. However, the effect of the Mt Pinatubo aerosol cloud is very evident in the data from 1991-94, with a decrease of 10% in NO2 in the summer of 1992 (the SAOZ was located in Lerwick, Scotland during the winter of 1991-92 and observed very low NO2 values but these cannot be directly compared to the Aberystwyth data). To focus more on interannual and long-term variations in NO2, a seasonal variation comprising an annual and semi-annual component was fitted to the morning and evening twilight separately from 1995 to the present. This fit yielded average NO2 columns of 4.08 x 10(15) cm(-2) and 2.68 x 10(15) cm(-2) for the evening and morning twilight, respectively, with a corresponding annual amplitude of +/-2.08 x 10(15) cm(-2) and +/-1.50 x 10(15) cm(-2). Departures from the fitted curve show a trend of 6% per decade, consistent with that reported elsewhere, for the period 1998-2003, but in the past two years a distinct interannual variation of amplitude of approximately 8% has emerged.     

A two-stage cyclone using microcentrifuge tubes for personal bioaerosol sampling

Personal aerosol samplers are widely used to monitor human exposure to airborne materials. For bioaerosols, interest is growing in analyzing samples using molecular and immunological techniques. This paper presents a personal sampler that uses a two-stage cyclone to collect bioaerosols into disposable 1.5 ml Eppendorf-type microcentrifuge tubes. Samples can be processed in the tubes for polymerase chain reaction (PCR) or immunoassays, and the use of multiple stages fractionates aerosol particles by aerodynamic diameter. The sampler was tested using fluorescent microspheres and aerosolized fungal spores. The sampler had first and second stage cut-off diameters of 2.6 microm and 1.6 microm at 2 l min(-1)(geometric standard deviation, GSD = 1.45 and 1.75), and 1.8 microm and 1 microm at 3.5 l min(-1)(GSD = 1.42 and 1.55). The sampler aspiration efficiency was >or=98% at both flow rates for particles with aerodynamic diameters of 3.1 microm or less. For 6.2 microm particles, the aspiration efficiency was 89% at 2 l min(-1) and 96% at 3.5 l min(-1). At 3.5 l min(-1), the sampler collected 92% of aerosolized Aspergillus versicolor and Penicillium chrysogenum spores inside the two microcentrifuge tubes, with less than 0.4% of the spores collecting on the back-up filter. The design and techniques given here are suitable for personal bioaerosol sampling, and could also be adapted to design larger aerosol samplers for longer-term atmospheric and indoor air quality sampling.     

Transport of fecal bacteria by boots and vehicle tires in a rural Alaskan community

People living without piped water and sewer can be at increased risk for diseases transmitted via the fecal-oral route. One rural Alaskan community that relies on hauling water into homes and sewage from homes was studied to determine the pathways of fecal contamination of drinking water and the human environment so that barriers can be established to protect health. Samples were tested for the fecal indicator, Escherichia coli, and the less specific indicator group, total coliforms. Shoes transported fecal contamination from outside to floor material inside buildings. Contamination in puddles on the road, in conjunction with contamination found on all-terrain vehicle (ATV) tires, supports vehicle traffic as a mechanism for transporting contamination from the dumpsite or other source areas to the rest of the community. The abundance of fecal bacteria transported around the community on shoes and ATV tires suggests that centralized measures for waste disposal as well as shoe removal in buildings could improve sanitation and health in the community.     

Seasonal ozone behavior along an elevation gradient in the Colorado Front Range Mountains

Ambient surface ozone was monitored for one year at a series of seven sites along an elevation gradient from 1600 m to 3500 m above sea level (ASL) in Boulder County, Colorado. Spatial variability of ozone, quantified as the root mean squared deviation of hourly ozone per kilometer horizontal separation, decreased with elevation and distance from local sources, validating the assumption that (except at the City of Boulder (BO) site) the results of the study are representative of the Colorado Front Range. The northern hemisphere (NH) tropospheric spring ozone peak was clearly apparent in late April and early May and affected ozone at all elevations. Ozone consistently increased with elevation during winter, with a mean monthly rate of 1.5 ppbv per 100 m elevation. In summer, this monotonic increase in ozone with elevation was not observed; instead mean monthly ozone increased in two steps, by ～15 ppbv between 1610 m and 1940 m ASL and by ～10 ppbv between 3350 m and 3530 m ASL to a maximum of 60 ppbv. The amplitude of the diurnal ozone cycle decreased with increasing elevation. Average summertime diurnal swings in ozone concentration had a magnitude of 29 ppbv at 1610 m ASL, and 7–16 ppbv at the mid-elevation sites. In winter a diurnal cycle was observed only at the BO site, ozone concentrations at the remaining six locations changed on a multi-day timescale, indicating regional background behavior as the primary factor for wintertime ozone. Even the highest elevation site was influenced by transported urban air pollution in summer, indicated by the average 5 ppbv diurnal increase in ozone. Ozone exposure at the mid- to high-elevation sites in many instances approached and exceeded the 8-h National Ambient Air Quality Standard of 75 ppbv. The elevated ozone levels along this transect were interpreted to be caused by the confounding effects of the high elevation of these sites, increased ozone in long-range transported air, and anthropogenic ozone production in air transported from the nearby urban and suburban areas east of the Colorado Front Range Mountains.     

Hybrid poplar and forest soil response to municipal and industrial by-products: a greenhouse study

Little research has been conducted in the Lake States (Minnesota, Wisconsin, and Michigan) to evaluate the effects of municipal and industrial by-product applications on the early growth of short rotation woody crops such as hybrid poplar. Anticipated shortages of harvestable-age aspen in the next decade can be alleviated and rural development can be enhanced through the application of by-products to forest soils. This study was conducted to evaluate the effects of inorganic fertilizer, boiler ash, biosolids, and the co-application of ash and biosolids application on tree growth and soil properties by measuring hybrid poplar clone NM-6 (Populus nigra L. x P. maximowiczii A. Henry) yield, nutrient uptake, and select post-harvest soil properties after 15 wk of greenhouse growth. Treatments included a control of no amendment; agricultural lime; inorganic N, P, and K; three types of boiler ash; biosolids application rates equivalent to 70, 140, 210, and 280 kg available N ha(-1); and boiler ash co-applied with biosolids. All of the by-products treatments showed biomass production that was equal to or greater than inorganic fertilizer and lime treatments. A trend of increased biomass with increasing rates of biosolids was observed. Soil P concentration increased with increasing rates of biosolids application. None of the by-products treatments resulted in plant tissue metal concentrations greater than metal concentrations of plant tissue amended with inorganic amendments. Biosolids, boiler ash, and the co-application of biosolids and boiler ash together on forest soils were as beneficial to plant growth as inorganic fertilizers.     

Ethical issues associated with prenatal screening using non-invasive prenatal testing for sex chromosome aneuploidy

Prenatal screening for sex chromosome aneuploidies (SCAs) is increasingly available through expanded non-invasive prenatal testing (NIPT). NIPT for SCAs raises complex ethical issues for clinical providers, prospective parents and future children. This paper discusses the ethical issues that arise around NIPT for SCAs and current guidelines and protocols for management. The first section outlines current practice and the limitations of NIPT for SCAs. It then outlines key guidelines before discussing the ethical issues raised by this use of NIPT. We conclude that while screening for SCAs should be made available for people seeking to use NIPT, its implementation requires careful consideration of what, when and how information is provided to users.