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.     

Repellent scent-marking of flowers by a guild of foraging bumblebees (Bombus spp.)

We have found that foraging bumblebees (Bombus hortorum, B. pascuorum, B. pratorum and B.␣terrestris) not only avoid flowers of Symphytum officinale that have recently been visited by conspecifics but also those that have been recently visited by heterospecifics. We propose that the decision whether to reject or accept a flower is influenced by a chemical odour that is left on the corolla by a forager, which temporarily repels subsequent foragers. Honeybees and carpenter bees have previously been shown to use similar repellent forage-marking scents. We found that flowers were repellent to other bumblebee foragers for approximately 20 min and also that after this time nectar levels in S. officinale flowers had largely replenished. Thus bumblebees could forage more efficiently by avoiding flowers with low rewards. Flowers to which extracts of tarsal components were applied were more often rejected by wild B. terrestris workers than flowers that had head extracts applied, which in turn were more often rejected than flowers that had body extracts applied. Extracts from four Bombus species were equally repellent to foragers. The sites of production of the repellent scent and its evolutionary origins are discussed. Received: 24 November 1997 / Accepted after revision: 8 March 1998     

Influence of fish size and sex on mercury/PCB concentration: importance for fish consumption advisories

Fish advisories for polychlorinated biphenyls (total-PCBs) and mercury are often given on a length-specific basis and fish sex is usually not considered. The relationship between concentration and length is well established for mercury, however its suitability for total-PCBs and the influence of sex over the large scale covered by most monitoring programs is not well known. Here we use what is perhaps the largest consistent sport fish contaminant dataset to evaluate the relationship between total-PCB/mercury and length and sex. We evaluated seven of the most commonly consumed fishes from the Canadian Great Lakes and two Ontario (Canada) inland lakes. For mercury, the relationship between concentration and length was significant (p<0.05) in most fish species and locations. For total-PCB, this relationship was also generally significant in Chinook salmon and lake trout, which are the species with the most advisories for this compound. In contrast, significant relationships were found less often for whitefish, northern pike, smallmouth bass, walleye, and especially yellow perch. However, mercury usually drives fish consumption advisories for these species. Overall, our results support the protocol of issuing contaminant advice on a length-specific basis in fish monitoring programs with reasonable confidence when at least a moderate number of samples over the natural size range of a species are included in the analysis. Sex differences were common for walleye (males>females, p<0.05) but not other species, suggesting that an equal number of male and female walleye should be used in deriving fish advisories for walleye.     

Targeting vulnerability after the 2005 earthquake: Pakistan's Livelihood Support Cash Grants programme

The 7.6 magnitude (Richter scale) earthquake that struck northern Pakistan on 8 October 2005 was devastating. This paper gauges success in targeting vulnerable families during the transition from relief to reconstruction through cash assistance provided by the Livelihood Support Cash Grants (LSCG) programme. Families without a male member, with a disabled male member aged between 18 and 60 years or with more than five children, defined as vulnerable, were provided with USD 50 per month for six months via a bank transfer. The LSCG scheme enrolled around 750,000 families and selected 267,402 vulnerable families to whom it disbursed a total of USD 86.95 million. Using a community‐based survey, this paper assesses leakage and under‐coverage (exclusion). Approximately 30 per cent of families received the cash grant. However, only one in two was eligible for the benefit, and one in two deserving families was excluded. This is a matter of grave concern.     

Inequalities in exposure and awareness of flood risk in England and Wales

This paper explores the environmental inequalities of living in the floodplains of England and Wales and the differences in flood awareness of those 'at risk'. An area comparison is made between an etic, objective flood risk exposure, and an emic, subjective perception of that risk by social class. In all areas except the Midlands, the working classes were more likely to reside in the floodplains; the greatest exposure inequality is seen in the North East and Anglian regions. Flood awareness in the Anglian regions was much lower than average, but there were no significant class differences. In the Thames region, despite equal flood risk exposure between classes, the most deprived displayed the least awareness of flood risk. In the North East, inequalities in the distribution of flood risk exposure accompanied inequalities in perception, resulting in the least aware and most deprived experiencing the greatest flood risk.     

Agricultural opportunities to mitigate greenhouse gas emissions

Agriculture is a source for three primary greenhouse gases (GHGs): CO(2), CH(4), and N(2)O. It can also be a sink for CO(2) through C sequestration into biomass products and soil organic matter. We summarized the literature on GHG emissions and C sequestration, providing a perspective on how agriculture can reduce its GHG burden and how it can help to mitigate GHG emissions through conservation measures. Impacts of agricultural practices and systems on GHG emission are reviewed and potential trade-offs among potential mitigation options are discussed. Conservation practices that help prevent soil erosion, may also sequester soil C and enhance CH(4) consumption. Managing N to match crop needs can reduce N(2)O emission and avoid adverse impacts on water quality. Manipulating animal diet and manure management can reduce CH(4) and N(2)O emission from animal agriculture. All segments of agriculture have management options that can reduce agriculture's environmental footprint.