All-in-one whole exome sequencing strategy with simultaneous copy number variant,single nucleotide variant and absence-of-heterozygosity analysis in fetuses with structural ultrasound anomalies: A 1-year experience

Objective

We performed a 1-year evaluation of a novel strategy of simultaneously analyzing single nucleotide variants (SNVs), copy number variants (CNVs) and copy-number-neutral Absence-of-Heterozygosity from Whole Exome Sequencing (WES) data for prenatal diagnosis of fetuses with ultrasound (US) anomalies and a non-causative QF-PCR result.

Methods

After invasive diagnostics, whole exome parent-offspring trio-sequencing with exome-wide CNV analysis was performed in pregnancies with fetal US anomalies and a non-causative QF-PCR result (WES-CNV). On request, additional SNV-analysis, restricted to (the) requested gene panel(s) only (with the option of whole exome SNV-analysis afterward) was performed simultaneously (WES-CNV/SNV) or as rapid SNV-re-analysis, following a normal CNV analysis.

Results

In total, 415 prenatal samples were included. Following a non-causative QF-PCR result, WES-CNV analysis was initially requested for 74.3% of the chorionic villus (CV) samples and 45% of the amniotic fluid (AF) samples. In case WES-CNV analysis did not reveal a causative aberration, SNV-re-analysis was requested in 41.7% of the CV samples and 17.5% of the AF samples. All initial analyses could be finished within 2 weeks after sampling. For SNV-re-analysis during pregnancy, turn-around-times (TATs) varied between one and 8 days.

Conclusion

We show a highly efficient all-in-one WES-based strategy, with short TATs, and the option of rapid SNV-re-analysis after a normal CNV result.     

Environmental Dependency of Inbreeding Depression: Implications for Conservation Biology

Inbreeding depression is environmentally dependent, such that a population may suffer from inbreeding depression in one environment but not another. We examined the phenotypic responses of 35 inbred ( F = 0.672) lineages of the red flour beetle Tribolium castaneum in two different climatic environments. We found a significant environmental effect on males but not females. More important, we found that the rank fitness order of lineages differs between environments; lineages of high fitness in one environment may have low fitness in another environment. This change in rank is evident in a significant genotype-by-environment interaction for inbreeding depression for both females and males. These results suggest that even if we know the average environmental effect of inbreeding depression in a population, for any particular lineage measurements of inbreeding depression in one environment may not predict the level of inbreeding depression in another environment. Conservation biologists need to be aware of the environmental dependency of inbreeding depression when planning wildlife refuges or captive propagation programs for small populations. Ideally, captive propagation programs should maintain separate lineages for release efforts. Refuge design programs should consider maintaining a range of habitat types.     

Adsorption of As(III) versus As(V) from aqueous solutions by cerium-loaded volcanic rocks

Environmental Science and Pollution Research - Contamination of drinking water with arsenic causes severe health problems in various world regions. Arsenic exists predominantly as As(III) and As(V)...     

Development of a distance-to-roadway proximity metric to compare near-road pollutant levels to a central site monitor

The primary objective of the Detroit Exposure and Aerosol Research Study (DEARS) was to compare air pollutant concentrations measured at various neighborhoods, or exposure monitoring areas (EMAs), throughout a major metropolitan area to levels measured at a central site or community monitor. One of the EMAs was located near a busy freeway (annual average daily traffic (AADT) of ～130,000) so that impacts of mobile sources could be examined. Air pollution concentrations from the roadway-proximate sites were compared to the central site monitor. The volatile organic compounds (VOCs) selected (benzene, toluene, ethylbenzene, m,p- and o-xylene, 1,3 butadiene, 1,3,5-trimethylbenzene and 4-ethyltoluene) are typically associated with mobile sources. Gradients were also evident that demonstrated the amplification of pollutant levels near the roadway compared to the community monitor. A novel distance-to-roadway proximity metric was developed to plot the measurements and model these gradients. Effective distance represents the actual distance an air parcel travels from the middle of a roadway to a site and varies as a function of wind direction, whereas perpendicular distance is a fixed distance oriented normal to the roadway. Perpendicular distance is often used as a proxy for exposures to traffic emissions in epidemiological studies.Elevated concentrations of all the compounds were found for both a summer and winter season. Effective distance was found to be a statistically significant (p < 0.05) univariate predictor for concentrations of toluene, ethylbenzene, m,p-xylene and o-xylene for summer 2005. For each of these pollutants, effective distance yielded lower p-values than the corresponding perpendicular distance models, and model fit improved. Results demonstrate that this near-road EMA had elevated levels of traffic-related VOCs compared to the community monitor, and that effective distance was a more accurate predictor of the degree to which they were elevated as a function of distance. Effective distance produced a range of distance-to-roadway values for a single site based on wind direction, thus increasing the number and range of values that could be used to plot and predict relative differences in pollutant concentrations between two sites.     

Investigation of Selective Catalytic Reduction Impact on Mercury Speciation under Simulated NOx Emission Control Conditions

Abstract

Selective catalytic reduction (SCR) technology increasingly is being applied for controlling emissions of nitrogen oxides (NO_x) from coal-fired boilers. Some recent field and pilot studies suggest that the operation of SCR could affect the chemical form of mercury (Hg) in coal combustion flue gases. The speciation of Hg is an important factor influencing the control and environmental fate of Hg emissions from coal combustion. The vanadium and titanium oxides, used commonly in the vanadia-titania SCR catalyst for catalytic NO_x reduction, promote the formation of oxidized mercury (Hg²⁺).

The work reported in this paper focuses on the impact of SCR on elemental mercury (Hg⁰) oxidation. Bench-scale experiments were conducted to investigate Hg⁰ oxidation in the presence of simulated coal combustion flue gases and under SCR reaction conditions. Flue gas mixtures with different concentrations of hydrogen chloride (HCl) and sulfur dioxide (SO₂) for simulating the combustion of bituminous coals and subbituminous coals were tested in these experiments. The effects of HCl and SO₂ in the flue gases on Hg⁰ oxidation under SCR reaction conditions were studied. It was observed that HCl is the most critical flue gas component that causes conversion of Hg⁰ to Hg²⁺ under SCR reaction conditions. The importance of HCl for Hg⁰ oxidation found in the present study provides the scientific basis for the apparent coal-type dependence observed for Hg⁰ oxidation occurring across the SCR reactors in the field.     

Influence of Sampling Frequency on Estimation of Annual Total Phosphorus and Total Suspended Solids Loads1

Abstract: The determination of sediment and nutrient loads is typically based on the collection and analysis of grab samples. The frequency and regularity of traditional sampling may not provide representation of constituent loading, particularly in systems with flashy hydrology. At two sites in the Little Bear River, Utah, continuous, high‐frequency turbidity was used with surrogate relationships to generate estimates of total phosphorus and total suspended solids concentrations, which were paired with discharge to estimate annual loads. The high frequency records were randomly subsampled to represent hourly, daily, weekly, and monthly sampling frequencies and to examine the effects of timing, and resulting annual load estimates were compared to the reference loads. Higher frequency sampling resulted in load estimates that better approximated the reference loads. The degree of bias was greater at the more hydrologically responsive site in the upper watershed, which required a higher sampling frequency than the lower watershed site to achieve the same level of accuracy in estimating the reference load. The hour of day and day of week of sampling impacted load estimation, depending on site and hydrologic conditions. The effects of sampling frequency on the determination of compliance with a water quality criterion were also examined. These techniques can be helpful in determining necessary sampling frequency to meet the objectives of a water quality monitoring program.     

Linking sustainable consumption and production: The government role

Achieving sustainable development depends on comprehensive approaches which integrate consumption and production initiatives. At present, sustainable consumption is being overemphasized to the neglect of the more important production side. This paper examines the role of governments in promoting sustainable consumption and production to identify gaps in national schemes which reduce their overall effectiveness. Public policy tools promoting sustainable consumption and production are discussed in terms of whether they are aimed at correcting: 1) market failures (regulations, taxes, subsidies); or 2) systems failures (labels, communications, education, public procurement). The challenge for governments is to link sustainable consumption initiatives to policies aimed at increasing the sustainability of production in the private sector in both their national and international dimensions. In this way, governments can enlist the aid of consumers in pushing producers towards sustainability and to achieve the ultimate goal of sustainable development.     

An assessment of hydraulic containment to control vertical DNAPL migration

Because of increased awareness and knowledge about their behavior, dense nonaqueous phase liquids (DNAPLs) are being detected at an increasing frequency at hazardous and solid waste land disposal units. Remedial systems at sites containing DNAPLs need to be designed to address the specific problems presented by DNAPLs. Because of their physical properties, DNAPLs migrate downward and are difficult to remove using conventional recovery methods. Groundwater pumping schemes can be designed to hydraulically contain this vertical migration. The purpose of this article is to present an approach for evaluating the potential to halt the vertical migration of DNAPLs using hydraulic control. Detailed groundwater flow modeling of a group of waste basins indicates that groundwater pumping in low-permeability sands can impose the upward hydraulic gradients required to stop downward DNAPL movement. However, a recovery well system located around the perimeter of the waste basins will not impose the required gradients over a sufficiently large area to effectively contain DNAPLs under the basins because the distribution of vertical gradients that could stop DNAPLs extends only about fifty to sixty feet from the wells. Additional modeling indicates that horizontal recovery wells located directly under the basins can contain the vertical migration of DNAPLs.