Non-invasive fetal genotyping for maternal alleles with droplet digital PCR: A comparative study of analytical approaches

Objectives

To develop a flexible droplet digital PCR (ddPCR) workflow to perform non-invasive prenatal diagnosis via relative mutation dosage (RMD) for maternal pathogenic variants with a range of inheritance patterns, and to compare the accuracy of multiple analytical approaches.

Methods

Cell free DNA (cfDNA) was tested from 124 archived maternal plasma samples: 88 cases for sickle cell disease and 36 for rare Mendelian conditions. Three analytical methods were compared: sequential probability ratio testing (SPRT), Bayesian and z-score analyses.

Results

The SPRT, Bayesian and z-score analyses performed similarly well with correct prediction rates of 96%, 97% and 98%, respectively. However, there were high rates of inconclusive results for each cohort, particularly for z-score analysis which was 31% overall. Two samples were incorrectly classified by all three analytical methods; a false negative result predicted for a fetus affected with sickle cell disease and a false positive result predicting the presence of an X-linked IDS variant in an unaffected fetus.

Conclusions

ddPCR can be applied to RMD for diverse conditions and inheritance patterns, but all methods carry a small risk of erroneous results. Further evaluation is required both to reduce the rate of inconclusive results and explore discordant results in more detail.     

Toxicity of carbaryl,diquat dibromide,and fluoranthene,individually and in mixture,to larval grass shrimp,Palaemonetes pugio

This study examined the toxicity of two pesticides (carbaryl and diquat dibromide) and one polycyclic aromatic hydrocarbon (fluoranthene), both singly and in mixture, to grass shrimp larvae (Palaemonetes pugio). These three chemicals are all present in coastal environments and can easily enter estuarine ecosystems. Fluoranthene was the most toxic chemical with a 96-h LC₅₀ value of 32.45 μ g/L, followed by carbaryl (43.02 μ g/L) and diquat dibromide (1624 μ g/L). In the chemical mixture tests, the binary carbaryl/diquat dibromide mixture and the ternary carbaryl/diquat dibromide/fluoranthene mixture had additive results.     

Brazil's Electric Power Choices and Their Corresponding Carbon Emissions Implications

This study analyzes the options for meeting power demand in the Brazilianpower sector through the year 2015. Three policy cases are constructedto test economic and environmental policy measures against a baseline:advanced technologies scenario, environmental control scenario and carbon(C) elimination scenario. Least-cost modeling simulated these scenarios throughchanges in emissions fees and caps, costs for advanced technologies,demand side efficiency, and clean energy supplies. Results show that, in theabsence of alternative policies, new additions to Brazil's electric powersector will shift rapidly from hydroelectricity to combined-cycle natural gasplants. When the cost of environmental impacts are incorporated in theprice of power, the least-cost mix of electric power generation technologycould change in other ways. In all scenarios, energy efficiency andcogeneration play an important role in the least-cost power solution. Savingelectricity through increased efficiency offsets the needs for new supply andhas enormous potential in Brazil's industrial sector. Efficiency also reducesthe environmental burden associated with electricity production andtransmission, without compromising the quality of the services demandedby end users. Interesting enough, carbon dioxide (CO₂) emissions will remainrelatively low under almost every conceivable scenario.     

“At the water's edge”: community voices on climate change

The photovoice research project, “At the water's edge”, which gives voice to communities exploring the threats and impact of climate change and rising sea levels on coastal communities, was conducted during an environmental art symposium in the Noosa Biosphere Reserve, Australia in June 2009. Photos by participants illustrated both local and global threats and reflected psychological tension between global and local action. This research partnership with the local people demonstrated an innovative visualisation technique which can be used to collaboratively build capacity and consensus about adaptation to climate change. It also contributed to the Biosphere Reserve's educational and cultural aims in relation to climate change.     

Phosphorus retention mechanisms of a water treatment residual

Water treatment residuals (WTRs) are a by-product of municipal drinking water treatment plants and can have the capacity to adsorb tremendous amounts of P. Understanding the WTR phosphorus adsorption process is important for discerning the mechanism and tenacity of P retention. We studied P adsorbing mechanism(s) of an aluminum-based [Al2(SO4)3 x 14H2O] WTR from Englewood, CO. In a laboratory study, we shook mixtures of P-loaded WTR for 1 to 211 d followed by solution pH analysis, and solution Ca, Al, and P analysis via inductively coupled plasma atomic emission spectroscopy. After shaking periods, we also examined the solids fraction by X-ray diffraction (XRD) and electron microprobe analysis using wavelength dispersive spectroscopy (EMPA-WDS). The shaking results indicated an increase in pH from 7.2 to 8.2, an increase in desorbed Ca and Al concentrations, and a decrease in desorbed P concentration. The pH and desorbed Ca concentration increases suggested that CaCO3 controlled Ca solubility. Increased desorbed Al concentration may have been due to Al(OH)4 formation. Decreased P content, in conjunction with the pH increase, was consistent with calcium phosphate formation or precipitation. The system appeared to be undersaturated with respect to dicalcium phosphate (DCP; CaHPO4) and supersaturated with respect to octacalcium phosphate [OCP; Ca4H(PO4)3 x 2.5H2O]. The Ca and Al increases, as well as OCP formation, were supported by MINTEQA2 modeling. The XRD and EMPA-WDS results for all shaking times, however, suggested surface P chemisorption as an amorphous Al-P mineral phase.     

Impervious Surface Area as a Predictor of the Effects of Urbanization on Stream Insect Communities in Maine, U.S.A.

The influence of urbanization on stream insect communities was determined by comparing physical, chemical, and biological characteristics of streams draining 20 catchments with varyinglevels of urban land-cover in Maine (U.S.A). Percent total impervious surface area (PTIA), which was used to quantify urbanland-use, ranged from 1–31% among the study catchments.Taxonomic richness of stream insect communities showed an abruptdecline as PTIA increased above 6%. Streams draining catchmentswith PTIA < 6% had the highest levels of both total insect and EPT (Ephemeroptera + Plecoptera + Trichoptera) taxonomic richness. These streams contained insect communities with a totalrichness averaging 33 taxa in fall and 31 taxa in spring; EPT richness ranged from an average of 15 taxa in fall and 13 taxa inspring. In contrast, none of the streams draining catchments with6–27% PTIA had a total richness > 18 taxa or an EPT richness> 6 taxa. Insect communities in streams with PTIA > 6% were characterized by the absence of pollution-intolerant taxa. The distribution of more pollution-tolerant taxa (e.g.Acerpenna (Ephemeroptera); Paracapnia, Allocapnia (Plecoptera); Optioservus, Stenelmis (Coleoptera); Hydropsyche, Cheumatopsyche (Trichoptera)), however, showed little relation to PTIA. In contrast to the apparent threshold relationship between PTIA and insect taxonomic richness, both habitat qualityand water quality tended to decline as linear functions of PTIA.Our results indicate that, in Maine, an abrupt change in stream insect community structure occurs at a PTIA above a threshold ofapproximately 6% of total catchment area. The measurement of PTIA may provide a valuable tool for predicting thresholds for adverse effects of urbanization on the health of headwater streams in Maine.     

Optimizing conservation in species-specific agricultural landscapes

Recovery of grassland birds in agricultural landscapes is a global imperative. Agricultural landscapes are complex, and the value of resource patches may vary substantially among species. The spatial extent at which landscape features affect populations (i.e., scale of effect) may also differ among species. There is a need for regional-scale conservation planning that considers landscape-scale and species-specific responses of grassland birds to environmental change. We developed a spatially explicit approach to optimizing grassland conservation in the context of species-specific landscapes and prioritization of species recovery and applied it to a conservation program in Kentucky (USA). We used a hierarchical distance-sampling model with an embedded scale of effect predictor to estimate the relationship between landscape structure and abundance of eastern meadowlarks (Sturnella magna), field sparrows (Spizella pusilla), and northern bobwhites (Colinus virginianus). We used a novel spatially explicit optimization procedure rooted in multi-attribute utility theory to design alternative conservation strategies (e.g., prioritize only northern bobwhite recovery or assign equal weight to each species’ recovery). Eastern meadowlarks and field sparrows were more likely to respond to landscape-scale resource patch adjacencies than landscape-scale patch densities. Northern bobwhite responded to both landscape-scale resource patch adjacencies and densities and responded strongly to increased grassland density. Effects of landscape features on local abundance decreased as distance increased and had negligible influence at 0.8 km for eastern meadowlarks (0.7–1.2 km 95% Bayesian credibility intervals [BCI]), 2.5 km for field sparrows (1.5–5.8 km 95% BCI), and 8.4 km for bobwhite (6.4–26 km 95% BCI). Northern bobwhites were predicted to benefit greatly from future grassland conservation regardless of conservation priorities, but eastern meadowlark and field sparrow were not. Our results suggest similar species can respond differently to broad-scale conservation practices because of species-specific, distance-dependent relationships with landscape structure. Our framework is quantitative, conceptually simple, customizable, and predictive and can be used to optimize conservation in heterogeneous ecosystems while considering landscape-scale processes and explicit prioritization of species recovery.     

Relating characteristics of global biodiversity targets to reported progress

To inform governmental discussions on the nature of a revised Strategic Plan for Biodiversity of the Convention on Biological Diversity (CBD), we reviewed the relevant literature and assessed the framing of the 20 Aichi Biodiversity Targets in the current strategic plan. We asked international experts from nongovernmental organizations, academia, government agencies, international organizations, research institutes, and the CBD to score the Aichi Targets and their constituent elements against a set of specific, measurable, ambitious, realistic, unambiguous, scalable, and comprehensive criteria (SMART based, excluding time bound because all targets are bound to 2015 or 2020). We then investigated the relationship between these expert scores and reported progress toward the target elements by using the findings from 2 global progress assessments (Global Biodiversity Outlook and the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services). We analyzed the data with ordinal logistic regressions. We found significant positive relationships (p < 0.05) between progress and the extent to which the target elements were perceived to be measurable, realistic, unambiguous, and scalable. There was some evidence of a relationship between progress and specificity of the target elements, but no relationship between progress and ambition. We are the first to show associations between progress and the extent to which the Aichi Targets meet certain SMART criteria. As negotiations around the post-2020 biodiversity framework proceed, decision makers should strive to ensure that new or revised targets are effectively structured and clearly worded to allow the translation of targets into actionable policies that can be successfully implemented nationally, regionally, and globally.     

Landscape-level impact of tropical forest loss and fragmentation on bird occurrence in eastern Guatemala

Tropical forest destruction and fragmentation of habitat patches may reduce population persistence at the landscape level. Given the complex nature of simultaneously evaluating the effects of these factors on biotic populations, statistical presence/absence modelling has become an important tool in conservation biology. This study uses logistic regression to evaluate the independent effects of tropical forest cover and fragmentation on bird occurrence in eastern Guatemala. Logistic regression models were constructed for 10 species with varying response to habitat alteration. Predictive variables quantified forest cover, fragmentation and their interaction at three different radii (200, 500 and 1000 m scales) of 112 points where presence of target species was determined. Most species elicited a response to the 1000 m scale, which was greater than most species’ reported territory size. Thus, their presence at the landscape scale is probably regulated by extra-territorial phenomena, such as dispersal. Although proportion of forest cover was the most important predictor of species’ presence, there was strong evidence of area-independent and -dependent fragmentation effects on species presence, results that contrast with other studies from northernmost latitudes. Species’ habitat breadth was positively correlated with AIC model values, indicating a better fit for species more restricted to tropical forest. Species with a narrower habitat breadth also elicited stronger negative responses to forest loss. Habitat breadth is thus a simple measure that can be directly related to species’ vulnerability to landscape modification. Model predictive accuracy was acceptable for 4 of 10 species, which were in turn those with narrower habitat breadths.     

Sympatry of distinct mitochondrial DNA lineages in a copepod inhabiting estuarine creeks in the southeastern USA

The population genetic structure of the meiobenthic harpacticoid copepod Microarthridion littorale (Poppe) was examined with a geographic survey of a 348 bp fragment of the mitochondrial cytochrome b gene. Copepods were collected from ten locations on the coast from North Carolina to Georgia, USA, from January 1997 to November 1998. Sequence divergence among 198 individuals was as much as 4.3%, and three divergent mitochondrial clades were uncovered that differed by six to nine nucleotide changes. A rapid assay was developed to distinguish among mitochondrial clades, and an additional 333 specimens were surveyed. The three lineages co-occurred in seven of ten sampling locations. Data analyses were carried out separately for individuals assayed by DNA sequencing as well as for a combined data set that included individuals typed by restriction endonuclease digestion. An analysis of molecular variance indicated that a significant proportion of the total genetic variance could be partitioned among populations, although no significant correlation between geographical and genetic distance was detected.