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.     

Predicting molybdenum toxicity to higher plants: Estimation of toxicity threshold values

Four plant species (oilseed rape, Brassica napus L.; red clover, Trifolium pratense L.; ryegrass, Lolium perenne L.; and tomato, Lycopersicon esculentum L.) were tested on ten soils varying widely in soil properties to assess molybdenum (Mo) toxicity. A larger range (66-fold-609-fold) of added Mo concentrations resulting in 50% inhibition of yield (ED₅₀) was found among soils than among plant species (2-fold-38-fold), which illustrated that the soils differed widely in the expression of Mo toxicity. Toxicity thresholds based on soil solution Mo narrowed the variation among soils compared to thresholds based on added Mo concentrations. We conclude that plant bioavailability of Mo in soil depends on Mo solubility, but this alone did not decrease the variability in observed toxicity enough to be used in risk assessment and that other soil properties influencing Mo toxicity to plants need to be considered.     

Quantification of ionophores in aged poultry litter using liquid chromatography tandem mass spectrometry

Veterinary anticoccidials, biochemically known as ionophores, are widely used in poultry feed at therapeutic levels to treat Coccidiosis and at sub-therapeutic levels for growth- promotion. Commonly used ionophores in the US poultry industry are monensin, salinomycin, lasalocid and narasin. There is an increasing concern regarding the persistence of these anticoccidials in the environment. However, little attention has been directed to methods development for quantitatively measuring ionophores in complex environmental matrices such as poultry litters that are land applied. Here, we describe a rapid and sensitive liquid chromatography tandem mass spectrometry (LC-MS/MS)-based method developed for simultaneous quantification of monensin, lasalocid, salinomycin, and narasin in aged poultry litter samples. Results show significant level of monensin (97.8 ± 3.2?μg kg(-1)), lasalocid (19.2 ± 6.6?μg kg(-1)), salinomycin (70 ± 2.7?μg kg(-1)) and narasin (57.3 ± 2.6?μg kg(-1)) in poultry litter stored for over three years at < 5°C. Our findings indicate that even after several years of unmanaged storage of poultry litter, ionophores may continue to persist in this matrix, raising the possibility of prolonged release into the environment.     

Cadmium content of wheat grain from a long-term field experiment with sewage sludge

Grain Cd concentrations were determined in the wheat (Triticum aestivum L.) cultivars Soissons, Brigadier, and Hereward grown in 1994,1996, and 1999, respectively, in soils of a long-term field experiment to which sewage sludges contaminated with Zn, Cu, Ni, or Cr had previously been added. Soil pore water soluble Cd and free Cd2+ increased linearly with increasing total soil Cd (R2=0.82 and 0.84, respectively; P<0.001). Similarly, soil pore water free Cd2+ increased linearly with increasing soil pore water soluble Cd (R2=0.98; P<0.001). There was no evidence of a plateau in soil pore water Cd concentrations with increasing soil Cd concentrations. Grain Cd concentrations were significantly correlated with total soil Cd (P<0.001), soil pore water Cd (P<0.001), and free Cd2+ (P<0.001). A slight curvilinear relationship between grain Cd and soil Cd was apparent, but there was no plateau, even at the maximum soil Cd concentration of about 2.7 mg kg(-1). The relationship between soil pore water Cd and grain Cd was linear for all three cultivars. The slopes were in the order 1994 > 1996 > 1999, with more Cd being taken up into the grain by Soissons grown in 1994, and least by Hereward grown in 1999. For Soissons, Cd concentration in the grain greater than the EU limit (0.24 mg kg(-1) dry wt.) occurred at soil Cd less than the current UK limit of 3 mg kg(-1) for soils receiving sewage sludge. In contrast, for Brigadier and Hereward, grain Cd concentrations were near to and less than the EU limit, respectively, at soil Cd concentrations of 3 mg kg(-1).     

The dynamics of arsenic in four paddy fields in the Bengal delta

Irrigation with arsenic contaminated groundwater in the Bengal Delta may lead to As accumulation in the soil and rice grain. The dynamics of As concentration and speciation in paddy fields during dry season (boro) rice cultivation were investigated at 4 sites in Bangladesh and West Bengal, India. Three sites which were irrigated with high As groundwater had elevated As concentrations in the soils, showing a significant gradient from the irrigation inlet across the field. Arsenic concentration and speciation in soil pore water varied temporally and spatially; higher As concentrations were associated with an increasing percentage of arsenite, indicating a reductive mobilization. Concentrations of As in rice grain varied by 2-7 fold within individual fields and were poorly related with the soil As concentration. A field site employing alternating flooded-dry irrigation produced the lowest range of grain As concentration, suggesting a lower soil As availability caused by periodic aerobic conditions.     

Estimates of ambient background concentrations of trace metals in soils for risk assessment

Site-specific or soil type-specific ambient background concentrations (ABCs) of trace metals in soils are needed for risk assessment. We investigated three different methods for estimating ABCs in soils using a dataset of 5691 soil samples from England and Wales. The concentrations of Co, Cr and Ni were strongly associated with Al and Fe, and multiple regressions explained 62-85% of their variation, and Al and Fe can therefore be used to predict ABCs for these metals. Soil texture had a major influence on the concentrations of Cd, Co, Cr, Cu, Ni and Zn, and the medians were 3-5 fold higher in clayey than in sandy soils. This was used to predict texture-specific ABCs. Lead concentration was higher in acidic peaty soils than in other soils. A probability graph method was used to estimate ABC for Pb in a population of relatively uncontaminated soils. Potential applications of ABCs are discussed.     

Spring leaf flush in aspen (Populus tremuloides) clones is altered by long-term growth at elevated carbon dioxide and elevated ozone concentration

Early spring leaf out is important to the success of deciduous trees competing for light and space in dense forest plantation canopies. In this study, we investigated spring leaf flush and how long-term growth at elevated carbon dioxide concentration ([CO₂]) and elevated ozone concentration ([O₃]) altered leaf area index development in a closed Populus tremuloides (aspen) canopy. This work was done at the Aspen FACE experiment where aspen clones have been grown since 1997 in conditions simulating the [CO₂] and [O₃] predicted for ∼2050. The responses of two clones were compared during the first month of spring leaf out when CO₂ fumigation had begun, but O₃ fumigation had not. Trees in elevated [CO₂] plots showed a stimulation of leaf area index (36%), while trees in elevated [O₃] plots had lower leaf area index (−20%). While individual leaf area was not significantly affected by elevated [CO₂], the photosynthetic operating efficiency of aspen leaves was significantly improved (51%). There were no significant differences in the way that the two aspen clones responded to elevated [CO₂]; however, the two clones responded differently to long-term growth at elevated [O₃]. The O₃-sensitive clone, 42E, had reduced individual leaf area when grown at elevated [O₃] (−32%), while the tolerant clone, 216, had larger mature leaf area at elevated [O₃] (46%). These results indicate a clear difference between the two clones in their long-term response to elevated [O₃], which could affect competition between the clones, and result in altered genotypic composition in future atmospheric conditions.     

Effect of soil characteristics on Cd uptake by the hyperaccumulator Thlaspi caerulescens

The influence of soil characteristics on the phytoremediation potential of Thlaspi caerulescens is not well understood. We investigated the effect of soil pH and Cd concentration on plant Cd uptake on one soil type, and the variation in Cd uptake using a range of field contaminated soils. On soils with total Cd concentrations of 0.6-3.7 mg kg(-1), T. caerulescens (the Ganges ecotype) produced greater biomass in the pH range 5.1-7.6 than at pH 4.4. The highest plant Cd concentration (236 mg kg(-1)) and Cd uptake (228 microg pot(-1)) were observed at pH 5.1. On soils with total Cd concentrations of 2.6-314.8 mg kg(-1), shoot Cd concentrations were 10.9-1,196 mg kg(-1). Multiple regression analysis indicated that higher Cd in soil, low pH (within the range of >5) and coarser texture were associated with higher Cd concentration and Cd uptake by T. caerulescens.     

Field evaluation of in situ remediation of a heavy metal contaminated soil using lime and red-mud

We evaluated the effectiveness of lime and red mud (by-product of aluminium manufacturing) to reduce metal availability to Festuca rubra and to allow re-vegetation on a highly contaminated brown-field site. Application of both lime and red mud (at 3 or 5%) increased soil pH and decreased metal availability. Festuca rubra failed to establish in the control plots, but grew to a near complete vegetative cover on the amended plots. The most effective treatment in decreasing grass metal concentrations in the first year was 5% red mud, but by year two all amendments were equally effective. In an additional pot experiment, P application in combination with red mud or lime decreased the Pb concentration, but not total uptake of Pb in Festuca rubra compared to red mud alone. The results show that both red mud and lime can be used to remediate a heavily contaminated acid soil to allow re-vegetation.     

Geostatistical analyses and hazard assessment on soil lead in Silvermines area, Ireland

Spatial distribution and hazard assessment of soil lead in the mining site of Silvermines, Ireland, were investigated using statistics, geostatistics and geographic information system (GIS) techniques. Positively skewed distribution and possible outlying values of Pb and other heavy metals were observed. Box-Cox transformation was applied in order to achieve normality in the data set and to reduce the effect of outliers. Geostatistical analyses were carried out, including calculation of experimental variograms and model fitting. The ordinary point kriging estimates of Pb concentration were mapped. Kriging standard deviations were regarded as the standard deviations of the interpolated pixel values, and a second map was produced, that quantified the probability of Pb concentration higher than a threshold value of 1000 mg/kg. These maps provide valuable information for hazard assessment and for decision support.