A comparison of different lysis buffers to assess allele dropout from single cells for preimplantation genetic diagnosis

Single cell polymerase chain reaction (PCR) for preimplantation genetic diagnosis (PGD) requires high efficiency and accuracy. Allele dropout (ADO), the random amplification failure of one of the two parental alleles, remains the most significant problem in PCR-based PGD testing since it can result in serious misdiagnosis for compound heterozygous or autosomal dominant conditions. A number of different strategies (including the use of lysis buffers to break down the cell and make the DNA accessible) have been employed to combat ADO with varying degrees of success, yet there is still no consensus among PGD centres over which lysis buffer should be used (ESHRE PGD Consortium, 1999 ). To address this issue, PCR amplification of three genes (CFTR, LAMA3 and PKP1) at different chromosomal loci was investigated. Single lymphocytes from individuals heterozygous for mutations within each of the three genes were collected and lysed in either alkaline lysis buffer (ALB) or proteinase K/SDS lysis buffer (PK). PCR amplification efficiencies were comparable between alkaline lysis and proteinase K lysis for PCR products spanning each of the three mutated loci (ΔF508 in CFTR 90% vs 88%; R650X in LAMA3 82% vs 78%; and Y71X in PKP1 91% vs 87%). While there was no appreciable difference between ADO rates between the two lysis buffers for the LAMA3 PCR product (25% vs 26%), there were significant differences in ADO rates between ALB and PK for the CFTR PCR product (0% vs 23%) and the PKP1 PCR product (8% vs 56%). Based on these results, we are currently using ALB in preference to PK/SDS buffer for the lysis of cells in clinical PGD. Copyright © 2001 John Wiley & Sons, Ltd.     

Data needs for occupational epidemiologic studies

Data needs in an epidemiologic study can appear to be substantial in light of the other responsibilities of an industrial hygienist. Many of the data needed for this type of investigation, however, are already collected for other exposure assessment purposes. To increase understanding of this concept, the data needs for the major purposes for conducting an exposure assessment are identified. The purposes include determining compliance; implementing industrial hygiene programs, such as personal protective and respiratory equipment, hazard communication training, and medical surveillance; investigating health complaints and worker concerns; investigating tasks or engineering control effectiveness; investigating toxic tort or worker compensation claims; and conducting epidemiologic studies. A comprehensive exposure assessment system is then described that incorporates the data needs for all these purposes, including epidemiologic studies. The data needs of epidemiologic studies and how the data are used are then described and illustrated with examples taken from published epidemiologic studies.     

Downscaling and visioning of mountain snow packs and other climate change implications in North Vancouver, British Columbia

This paper provides an overview of a collaborative study on visualizing climate change at the local scale. A conceptual framework has been developed, in which local scenarios and visualizations of climate change impacts and response were created to facilitate local dialogue on incorporating climate change into long-term planning and implementation of community development decisions. As part of a larger effort to generate a new integrated participatory visioning process, this paper describes a case study of the District of North Vancouver which created visualizations of changing mountain snow and landscape conditions, and provides new insights on issues and dilemmas in using realistic landscape visualizations to depict scientific modelling projections, local responses to climate change, and uncertainty. Results from this study suggest that the visualizations, and subsequent dialogue sessions, did influence emotional response to climate change as well as self-assessed understanding of adaptation and mitigation response options. However, there is a need to test this visioning process with larger heterogeneous groups of participants in order to better assess its effectiveness in enabling dialogue on local responses to climate change.     

Use of CALPUFF for exposure assessment in a near-field,complex terrain setting

CALPUFF is an atmospheric source-receptor model recommended by the U.S. Environmental Protection Agency for use on a case-by-case basis in complex terrain and wind conditions. The ability of the model to provide useful information for exposure assessments in areas with those topographical and meteorological conditions has received little attention. This is an important knowledge gap for use of CALPUFF outside of regulatory applications, such as exposure analyses conducted in support of risk assessments and health studies. We compared deposition of cadmium (Cd), lead (Pb), and zinc (Zn) calculated with CALPUFF as a result of emissions from a zinc smelter with corresponding concentrations of the metals measured in attic dust and soil samples obtained from the surrounding area. On a point-by-point analysis, predictions from CALPUFF explained 11% (lead) to 53% (zinc) of the variability in concentrations measured in attic dust. Levels of heavy metals in soil interpolated to 100 residential addresses from the distribution of concentrations measured in soil samples also agreed well with deposition predicted with CALPUFF: R² of 0.46, 0.76, and 079 for Pb, Cd, and Zn, respectively. Community-average concentrations of Cd, Pb, and Zn measured in soil were significantly (p < 0.0001) and strongly correlated (R² ranged from 0.77 to 0.98) with predicted deposition rates. These findings demonstrate that CALPUFF can provide reasonably accurate predictions of the patterns of long-term air pollutant deposition in the near-field associated with emissions from a discrete source in complex terrain. Because deposition estimates are calculated as a linear function of air concentrations, CALPUFF is expected to be reliable model for prediction of long-term average, near-field ambient air concentrations in complex terrain as well.     

Bioavailability of residual polycyclic aromatic hydrocarbons following enhanced natural attenuation of creosote-contaminated soil

The impact of residual PAHs (2250 ± 71 μg total PAHs g⁻¹) following enhanced natural attenuation (ENA) of creosote-contaminated soil (7767 ± 1286 μg total PAHs g⁻¹) was assessed using a variety of ecological assays. Microtox™ results for aqueous soil extracts indicated that there was no significant difference in EC₅₀ values for uncontaminated, pre- and post-remediated soil. However, in studies conducted with Eisenia fetida, PAH bioaccumulation was reduced by up to 6.5-fold as a result of ENA. Similarly, Beta vulgaris L. biomass yields were increased 2.1-fold following ENA of creosote-contaminated soil. While earthworm and plant assays indicated that PAH bioavailability was reduced following ENA, the residual PAH fraction still exerted toxicological impacts on both receptors. Results from this study highlight that residual PAHs following ENA (presumably non-bioavailable to bioremediation) may still be bioavailable to important receptor organisms such as earthworms and plants.     

Development and Use of a Sedimentation Risk Index for Unpaved Road‐Stream Crossings in the Choctawhatchee Watershed1

Abstract: Unpaved road‐stream crossings increase sediment yields in streams and alter channel morphology and stability. Before restoration and sedimentation reduction strategies can be implemented, a priority listing of unpaved road‐stream crossings must be created. The objectives of this study were to develop a sedimentation risk index (SRI) for unpaved road‐stream crossings and to prioritize 125 sites in the Choctawhatchee watershed (southeastern Alabama) using this model. Field surveys involved qualitative and quantitative observations of 73 metrics related to waterway conditions, crossing structures, road approaches, and roadside soil erosion. The road‐stream crossing risk analyses involved elimination of candidate metrics based on redundancy, skewness, lack of data, professional judgment, lack of nonzero values, unbalanced box plots, and limited ranges of values. A final selection of 12 metrics formed the SRI and weighed factors involving soil erodibility, road sedimentation abatement features, and stream morphology alteration. The SRI was organized into narrative categories (excellent, good, fair, poor, and very poor) based on the distribution of scores. No excellent sites (scores ≥55) were found in this study, 17 (20.7%) were good (low sedimentation risk), 37 (45.1%) were fair (moderate sedimentation risk), 26 (31.7%) were poor (high sedimentation risk), and two (2.5%) were very poor (high sedimentation risk). There was no significant difference in SRI scores among crossing structure type (round culverts, box culverts, and bridges) (H = 4.31, df = 2, p = 0.058). A future study of the Choctawhatchee watershed involving the same study sites could assess the success of restoration plans and activities based on site score improvement or decline.     

Interaction webs in arctic ecosystems: Determinants of arctic change?

How species interact modulate their dynamics, their response to environmental change, and ultimately the functioning and stability of entire communities. Work conducted at Zackenberg, Northeast Greenland, has changed our view on how networks of arctic biotic interactions are structured, how they vary in time, and how they are changing with current environmental change: firstly, the high arctic interaction webs are much more complex than previously envisaged, and with a structure mainly dictated by its arthropod component. Secondly, the dynamics of species within these webs reflect changes in environmental conditions. Thirdly, biotic interactions within a trophic level may affect other trophic levels, in some cases ultimately affecting land–atmosphere feedbacks. Finally, differential responses to environmental change may decouple interacting species. These insights form Zackenberg emphasize that the combination of long-term, ecosystem-based monitoring, and targeted research projects offers the most fruitful basis for understanding and predicting the future of arctic ecosystems.     

Strontium isotope study of coal utilization by-products interacting with environmental waters

Sequential leaching experiments on coal utilization by-products (CUB) were coupled with chemical and strontium (Sr) isotopic analyses to better understand the influence of coal type and combustion processes on CUB properties and the release of elements during interaction with environmental waters during disposal. Class C fly ash tended to release the highest quantity of minor and trace elements-including alkaline earth elements, sodium, chromium, copper, manganese, lead, titanium, and zinc-during sequential extraction, with bottom ash yielding the lowest. Strontium isotope ratios ((87)Sr/(86)Sr) in bulk-CUB samples (total dissolution of CUB) are generally higher in class F ash than in class C ash. Bulk-CUB ratios appear to be controlled by the geologic source of the mineral matter in the feed coal, and by Sr added during desulfurization treatments. Leachates of the CUB generally have Sr isotope ratios that are different than the bulk value, demonstrating that Sr was not isotopically homogenized during combustion. Variations in the Sr isotopic composition of CUB leachates were correlated with mobility of several major and trace elements; the data suggest that arsenic and lead are held in phases that contain the more radiogenic (high-(87)Sr/(86)Sr) component. A changing Sr isotope ratio of CUB-interacting waters in a disposal environment could forecast the release of certain strongly bound elements of environmental concern. This study lays the groundwork for the application of Sr isotopes as an environmental tracer for CUB-water interaction.     

Analyzing the Impacts of Dams on Riparian Ecosystems: A Review of Research Strategies and Their Relevance to the Snake River Through Hells Canyon

River damming provides a dominant human impact on river environments worldwide, and while local impacts of reservoir flooding are immediate, subsequent ecological impacts downstream can be extensive. In this article, we assess seven research strategies for analyzing the impacts of dams and river flow regulation on riparian ecosystems. These include spatial comparisons of (1) upstream versus downstream reaches, (2) progressive downstream patterns, or (3) the dammed river versus an adjacent free-flowing or differently regulated river(s). Temporal comparisons consider (4) pre- versus post-dam, or (5) sequential post-dam conditions. However, spatial comparisons are complicated by the fact that dams are not randomly located, and temporal comparisons are commonly limited by sparse historic information. As a result, comparative approaches are often correlative and vulnerable to confounding factors. To complement these analyses, (6) flow or sediment modifications can be implemented to test causal associations. Finally, (7) process-based modeling represents a predictive approach incorporating hydrogeomorphic processes and their biological consequences. In a case study of Hells Canyon, the upstream versus downstream comparison is confounded by a dramatic geomorphic transition. Comparison of the multiple reaches below the dams should be useful, and the comparison of Snake River with the adjacent free-flowing Salmon River may provide the strongest spatial comparison. A pre- versus post-dam comparison would provide the most direct study approach, but pre-dam information is limited to historic reports and archival photographs. We conclude that multiple study approaches are essential to provide confident interpretations of ecological impacts downstream from dams, and propose a comprehensive study for Hells Canyon that integrates multiple research strategies.