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.     

Conservation Prioritization Using GAP Data

Data collected by the Gap Analysis Program in the state of Idaho (U.S.A.) are used to prioritize the selection of locations for conservation action and research. Set coverage and integer programming algorithms provide a sequence of localities that maximize the number of species or vegetation classes represented at each step. Richness maps of vegetation cover class diversity, terrestrial vertebrate species diversity ("hot spot analysis"), endangered, threatened, and candidate species diversity, and unprotected vertebrate species diversity ("gap analysis"), when prioritized, show a rapid accumulation of species as more localities are chosen for terrestrial vertebrates and unprotected vertebrates. Gap analysis identifies four target areas ("gaps") that include 79 of the 83 vertebrate species not currently protected. Accumulation of vegetation cover classes and endangered, threatened, and candidate species is much slower. Sweep analysis is used to determine how well prioritizing on one component of diversity accumulates other components. Endangered, threatened, and candidate species do not sweep total vertebrates as well as unprotected vertebrates do, but are better than vegetation classes. Total vertebrates sweep endangered, threatened, and candidate species better than unprotected vertebrates do, which in turn are better than vegetation classes. We emphasize that prioritization must be part of conservation efforts at multiple scales and that prioritization points out important localities where more detailed work mast be undertaken.     

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.     

Application of agroforestry business models to tropical peatland restoration

Indonesia is home to around 45% of the world’s tropical peatlands which continue to be degraded on a large scale by deforestation, drainage and fire, contributing massively to global GHG emissions. Approaches to restoring the peat–water balance and reducing emissions in peat hydrological units, through managing them based either on full protection or large-scale commercial production, have generally failed to address environmental and local community needs. We present published and unpublished findings pointing to the need for an integrated peatland protection and restoration strategy based first on raising water levels in degraded (drained) peatlands and maintaining them in forested peatlands, thus, reducing GHG emissions. Second, the strategy incorporates ecologically sound agroforestry business models that strengthen livelihoods of smallholders and so sustain their interest in sustainably managing the peatlands. In this paper, we focus on the second element of this strategy in Indonesia. Eight agroforestry business models are proposed based on their merits to attract both smallholders and commercial investors as well as their compatibility with hydrological rehabilitation of the peatlands. While financial returns on investment will vary across sites and countries, our analysis indicates that some models can be profitable over both short and longer time periods with relatively low levels of investment risk.     

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.     

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.