Assessing chlorinated ethene degradation in a large scale contaminant plume by dual carbon-chlorine isotope analysis and quantitative PCR

The fate of chlorinated ethenes in a large contaminant plume originating from a tetrachloroethene (PCE) source in a sandy aquifer in Denmark was investigated using novel methods including compound-specific carbon and chlorine isotope analysis and quantitative real-time polymerase chain reaction (qPCR) methods targeting Dehaloccocoides sp. and vcrA genes. Redox conditions were characterized as well based on concentrations of dissolved redox sensitive compounds and sulfur isotopes in SO(4)(2-). In the first 400 m downgradient of the source, the plume was confined to the upper 20 m of the aquifer. Further downgradient it widened in vertical direction due to diverging groundwater flow reaching a depth of up to 50 m. As the plume dipped downward and moved away from the source, O(2) and NO(3)(-) decreased to below detection levels, while dissolved Fe(2+) and SO(4)(2-) increased above detectable concentrations, likely due to pyrite oxidation as confirmed by the depleted sulfur isotope signature of SO(4)(2-). In the same zone, PCE and trichloroethene (TCE) disappeared and cis-1,2-dichloroethene (cDCE) became the dominant chlorinated ethene. PCE and TCE were likely transformed by reductive dechlorination rather than abiotic reduction by pyrite as indicated by the formation of cDCE and stable carbon isotope data. TCE and cDCE showed carbon isotope trends typical for reductive dechlorination with an initial depletion of (13)C in the daughter products followed by an enrichment of (13)C as degradation proceeded. At 1000 m downgradient of the source, cDCE was the dominant chlorinated ethene and had reached the source δ(13)C value confirming that cDCE was not affected by abiotic or biotic degradation. Further downgradient (up to 1900 m), cDCE became enriched in (13)C by up to 8 ‰ demonstrating its further transformation while vinylchloride (VC) concentrations remained low (<1 μg/L) and ethene was not observed. The correlated shift of carbon and chlorine isotope ratios of cDCE by 8 and 3.9 ‰, respectively, the detection of Dehaloccocides sp genes, and strongly reducing conditions in this zone provide strong evidence for reductive dechlorination of cDCE. The significant enrichment of (13)C in VC indicates that VC was transformed further, although the mechanism could not be determined. The transformation of cDCE was the rate limiting step as no accumulation of VC occurred. In summary, the study demonstrates that carbon-chlorine isotope analysis and qPCR combined with traditional approaches can be used to gain detailed insight into the processes that control the fate of chlorinated ethenes in large scale plumes.     

Altered vegetative assemblage trajectories within an urban brownfield

Recognizing the growing importance of both structure (maintenance of biodiversity) and function (fostering natural cycles) of urban ecologies, we examine coarse scale (herbaceous, shrub and forest) beta guild trajectory in an urban brownfield. The distribution of the pioneer forest assemblage dominated by Betula populifolia Marsh. and Populus spp. could be correlated positively with total soil metal load (arsenic, cadmium, chromium, copper, lead, zinc, lead and vanadium),whereas herbaceous and shrub guilds were negatively correlated. Distinct assemblage development trajectories above and below a critical soil metal threshold are demonstrated. In addition, we postulate that the translocation of metals into the plant tissue of several dominant species may provide a positive feedback loop, maintaining relatively high concentrations of metals in the litter and soil. Therefore assembly theory, which allows for the development of alternate stable states, may provide a better model for the establishment of restoration objectives on degraded urban sites.     

Outdoor and indoor cadmium distributions near an abandoned smelting works and their relations to human exposure

The relationship of measured or modelled Cd concentrations in soil, house dust and available to plants with human urinary Cd concentrations were assessed in a population living around a Cd/Pb/Zn smelter in the UK. Modelled air concentrations explained 35% of soil Cd variation indicating the smelter contributed to soil Cd loads. Multi-variate analysis confirmed a significant role of biological and life-style factors in determining urinary Cd levels. Significant correlations of urinary Cd with soil, house dust and modelled plant available Cd concentrations were not, however, found. Potential reasons for the absence of clear relationships include limited environmental contact in urban populations; the role of undefined factors in determining exposure; and the limited spatial scope of the survey which did not sample from the full pollution gradient. Further, the absence of any significant relationship indicates that environmental measures provide limited advantage over atmospheric model outputs for first stage human exposure assessment.     

Polycyclic aromatic hydrocarbon concentrations,mutagenicity, and Microtox® acute toxicity testing of Peruvian crude oil and oil-contaminated water and sediment

The oil industry is a major source of contamination in Peru, and wastewater and sediments containing oil include harmful substances that may have acute and chronic effects. This study determined polycyclic aromatic hydrocarbon (PAH) concentrations by GC/MS, mutagenicity using TA98 and TA100 bacterial strains with and without metabolic activation in the Muta-ChromoPlate? test, and Microtox® 5-min EC₅₀ values of Peruvian crude oil, and water and sediment pore water from the vicinity of San José de Saramuro on the Marañón River and Villa Trompeteros on the Corrientes River in Loreto, Peru. The highest total PAH concentration in both areas was found in water (Saramuro?=?210.15 μg/ml, Trompeteros?=?204.66 μg/ml). Total PAH concentrations in water from San José de Saramuro ranged from 9.90 to 210.15 μg/ml (mean?=?66.48 μg/ml), while sediment pore water concentrations ranged from 2.19 to 70.41 μg/ml (mean?=?24.33 μg/ml). All water samples tested from Saramuro and Trompeteros sites, and one out of four sediment pore water samples from Trompeteros, were found to be mutagenic (P?<?0.001). One sediment pore water sample in Saramuro was determined to have a measurable toxicity (Microtox EC₅₀?=?335.1 mg/l), and in Trompeteros, the EC₅₀ in water and sediment pore water ranged from 25.67 to 133.86 mg/l. Peruvian crude oil was mutagenic using the TA98 strain with metabolic activation, and the EC₅₀ was 17.18 mg/l. The two areas sampled had very high PAH concentrations that were most likely associated with oil activities, but did not lead to acute toxic effects. However, since most of the samples were mutagenic, it is thought that there is a greater potential for chronic effects.     

Single-cell sequencing and mini-sequencing for preimplantation genetic diagnosis

There is increasing interest in the use of preimplantation genetic diagnosis (PGD) as an alternative to routine prenatal diagnosis. However, the costs associated with development and testing of new PGD protocols have forced some PGD centres to limit the number of diseases for which PGD is offered. One of the main factors in the design of new protocols, which affects cost and accuracy, is the choice of the mutation-detection technique. We have assessed the reliability of DNA sequencing and mini-sequencing for clinical diagnosis at the single-cell level and have found them to be rapid and accurate. Extensive optimisation for individual mutations is not usually necessary when employing these versatile techniques and consequently a smaller investment of time and resources should be required during development of new protocols. Additionally, we report single-cell protocols for the diagnoses of cystic fibrosis, sickle cell anaemia and β-thalassaemia, which utilise mini-sequencing. Unlike most mutation-detection techniques, mini-sequencing permits analysis of very small DNA fragments. Small amplicons experience low allele dropout (ADO) rates, and consequently this approach could potentially improve the reliability of PGD. Copyright © 2003 John Wiley & Sons, Ltd.     

The variation of risk estimates through pregnancy in second trimester maternal serum screening for Down syndrome

The variation of risk estimates in second trimester maternal serum screening for Down's syndrome has been shown to be considerable in quality control schemes, i.e. UKNEQAS. We studied the biological variation of risk estimates in 16 women through pregnancy. The maternal serum markers alpha-fetoprotein (AFP), human chorionic gonadotrophin (hCG), unconjugated estriol (uE3) and β-hCG were determined six times during late first to late second trimester, and the associated likelihood ratios for Down syndrome were calculated. The interpersonal variation of markers, as well as that of the likelihood ratio, was much greater than the intrapersonal variation. The average intrapersonal standard deviation (SD) of the triple test log likelihood ratio was 0.2291, corresponding to a central 95-percentile interval 0.36–2.81 of the likelihood ratio. The interpersonal SD of the log likelihood ratio was 0.5482, corresponding to a central 95-percentile interval 0.08–11.87 of the likelihood ratio. The large difference between the intra- and interpersonal variation makes it unlikely that biological variation through pregnancy is a major contributor to the variation of risk estimates obtained several times in the same pregnancy. Rather, improvements in analytical quality and laboratory management must be expected to result in reduced variation and, in consequence, better performance of screening. Copyright © 2002 John Wiley & Sons, Ltd.