Delivering an accredited non-invasive prenatal diagnosis service for monogenic disorders and recommendations for best practice

The identification of cell-free fetal DNA circulating in maternal blood combined with technological developments, in particular next-generation sequencing, is enabling the development of safer prenatal diagnosis. While this technology has been widely applied as a highly sensitive screening test for aneuploidy, there has been relatively little clinical application for the diagnosis of monogenic disorders. In the UK, we have established non-invasive prenatal diagnosis (NIPD) as a clinical service for a range of inherited disorders. The results from NIPD do not require confirmation by invasive testing and are welcomed by patients and health professionals alike. Here, we describe the technical approaches used, current practice and outline recommendations for best practice when delivering an NIPD service from an accredited laboratory. © 2017 John Wiley & Sons, Ltd.     

Evaluation of a Regional Monitoring Program’s Statistical Power to Detect Temporal Trends in Forest Health Indicators

Forests are socioeconomically and ecologically important ecosystems that are exposed to a variety of natural and anthropogenic stressors. As such, monitoring forest condition and detecting temporal changes therein remain critical to sound public and private forestland management. The National Parks Service’s Vital Signs monitoring program collects information on many forest health indicators, including species richness, cover by exotics, browse pressure, and forest regeneration. We applied a mixed-model approach to partition variability in data for 30 forest health indicators collected from several national parks in the eastern United States. We then used the estimated variance components in a simulation model to evaluate trend detection capabilities for each indicator. We investigated the extent to which the following factors affected ability to detect trends: (a) sample design: using simple panel versus connected panel design, (b) effect size: increasing trend magnitude, (c) sample size: varying the number of plots sampled each year, and (d) stratified sampling: post-stratifying plots into vegetation domains. Statistical power varied among indicators; however, indicators that measured the proportion of a total yielded higher power when compared to indicators that measured absolute or average values. In addition, the total variability for an indicator appeared to influence power to detect temporal trends more than how total variance was partitioned among spatial and temporal sources. Based on these analyses and the monitoring objectives of the Vital Signs program, the current sampling design is likely overly intensive for detecting a 5 % trend·year^?1 for all indicators and is appropriate for detecting a 1 % trend·year^?1 in most indicators.     

The Role of Women in Water Management and Conflict Resolution in Marsabit,Kenya

We employed qualitative methods to explore how conflict over water collection and use impacts women, and the role that women play in water management and conflict resolution in Marsabit, Kenya. Conflicts between domestic and livestock water led to insufficient water for domestic use and intra-household conflict. Women’s contributions to water management were valued, especially through informal initiatives, though involvement in statutory water management committees was not culturally appropriate. Promoting culturally appropriate ways to involve women in water management, rather than merely increasing the percentage of women on water committee, may reduce conflicts and increase women’s access to domestic water supplies.     

PCB 105-induced ultrastructural alterations in the rat liver: A stereological study

Liver alterations were stereologically determined in five groups, each of 10 male and female Sprague–Dawley weanling rats fed PCB 105 (2,3,3′,4,4′-pentachlorobiphenyl) for 13 weeks at concentrations of 0.05, 0.5, 5, and 50?ppm mixed with corn oil. Animals from two groups receiving the oil in diets served as controls for each gender. A significant increase in mean volume fraction (VF) of smooth endoplasmic reticulum (SER) profiles was estimated in hepatocytes of female rats in 0.5, 5, and 50?ppm groups. A significant decrease in VF of mitochondria in female rats at 50?ppm was detected. In addition, a decrease in VF of lipid droplets was measured in female rats at 0.5, 5, and 50?ppm groups. No difference was found in VF of rough endoplasmic reticulum (RER) cisternae, and peroxisome profiles at any concentration of the PCB in either male or female animals as compared to baseline values from controls. A significant elevation of baseline VF for RER in female rats was detected in comparison with males. In the present study, no observable adverse effect level (NOAEL) for PCB 105 was estimated at <0.5?ppm for hepatocyte alterations in female Sprague–Dawley rats.     

Evaluation of a diode laser based photoacoustic instrument combined with preconcentration sampling for measuring surface–atmosphere exchange of ammonia with the aerodynamic gradient method

We present here a novel instrument for measuring surface–atmosphere exchange fluxes of ammonia. The instrument is the upgraded version of a recently developed near-infrared diode laser based photoacoustic ammonia concentration monitoring instrument, i.e. the original instrument is supplemented with two additional sampling lines, an appropriate gas handling system and an advanced software controlling gradient measurements. As a result of these developments, ammonia concentration can be measured simultaneously at three different heights above the ground and ammonia fluxes can be calculated from these data using the aerodynamic gradient method. The instrument operates fully automatically, requires minimal maintenance and has a temperature controlled, waterproof housing which makes it suitable for measurements even under harsh field conditions. Preliminary tests on stability and accuracy were carried out during two two-week field measurement campaigns, with the three sampling inlets being placed at the same height together with the inlet of a reference instrument. The readings of the three channels agreed well (with correlation coefficients above 0.96). Comparison to reference instruments showed good stability of the photoacoustic instrument, there was no measurable zero-drift or change in sensitivity during the tests. Flux measurements were carried out during a three-week field campaign in southern Scotland over fertilized grassland with reference to a wet-chemical AMANDA instrument in gradient configuration. Ammonia fluxes calculated from the data of the two instruments agreed well. Fluxes up to 2500 ng m^?2 s^?1 were observed after fertilization. The minimum detectable ammonia flux was calculated on the basis of “virtual ammonia fluxes”, from measurements carried out with all inlets at the same height and was found to be ±60 ng m^?2 s^?1 which ensures reliable measurements above intensively managed grasslands or agricultural fields.     

Index models to evaluate the risk of phosphorus and nitrogen loss at catchment scales

This paper investigates index models as a tool to estimate the risk of N and P source strengths and loss at the catchment scale. The index models assist managers in improving the focus of remediation actions that reduce nutrient delivery to waterbodies. N and P source risk factors (e.g. soil nutrient concentrations) and transport risk factors (e.g. distance-to-streams) are used to determine the overall risk of nutrient loss for a case study in the Tuross River catchment of coastal southeast Australia. In the development of the N index model for Tuross, particulate N was considered important based on the observed event water quality data. In contrast to previous N index models, erosion and contributing distance were therefore included in the Tuross River catchment N index. Event-based water quality monitoring, and soil information, or in data-poor catchments conceptual understanding, are essential to represent catchment-scale processes. The techniques have high applicability in other catchments, and are complementary to other modelling techniques such as process-based semi-distributed modelling. Index models generally provide much more detailed spatial resolution than fully- or semi-distributed conceptual modelling approaches. Semi-distributed models can be used to quantify nutrient loads and provide overall direction to set the broad focus of management. Index models can then be used to refine on-the-ground investigations and investment priorities. In this way semi-distributed models can be combined with index models to provide a set of powerful tools to influence management decisions and outcomes.     

Comparing the impacts of mitigation and non-mitigation on mountain pine beetle populations

Mountain pine beetles, Dendroctonus ponderosae (Hopkins) attack and can ultimately kill individuals and groups of pine trees, specifically lodgepole pine (Pinus contorta Dougl. ex. Loud var. latifolia Engl.). In British Columbia, beetle attack has increased from 164 000 ha in 1999 to over 13 million ha in 2008. Mitigation efforts can play a key role in addressing the impact beetle infestations can have on the forested landscape. In this research, the impact of mitigation on a mountain pine beetle infestation is examined within a network of 28 research plots where sanitation harvesting was completed (10 mitigated plots) and not completed (18 unmitigated plots). Three forest stand level modelling scenarios which predict the number of attacked trees, based on current infestation within the plots, were utilized to compare the differences between mitigated and non-mitigated plots. In the first scenario in the non-mitigated plots, 125 trees were infested after 10 years, while in the mitigated plots no trees were infested in the same time period. The second scenario indicates the level of mitigation required to suppress beetle infestations where the proportion of mitigated trees was calculated for each plot by counting the residual attack and the number of mitigated trees. The average mitigation rate over all plots of 43% (range 0–100%) is not sufficient to provide control. In the non-mitigated plots, the average population expansion rate was 5 (range of 0–18) which requires a detection accuracy of 74% to reliably detect infestation. The third scenario estimated the length of time required for ongoing detection, monitoring, and mitigation to bring an infestation under control. If mitigation efforts were maintained at the current rate of 43%, the beetle population would not be adequately controlled. However, when aided by continued detection and monitoring of attacked trees, mitigation rates greater than 50% are sufficient to control infestations, especially with persistent implementation, aided by continued detection and monitoring of infested trees.     

Sex-specific effects of the local social environment on juvenile post-fledging dispersal in great tits

An individual’s decision to disperse from the natal habitat can affect its future fitness prospects. Especially in species with sex-biased dispersal, we expect the cost–benefit balance for dispersal to vary according to the social environment (e.g., local sex ratio and density). However, little is known about the social factors affecting dispersal decisions and about the temporal and spatial patterns of the dispersal process. In our study, we investigated experimentally the effects of the social environment on post-fledging dispersal of juvenile great tits by simultaneously manipulating the density and sex ratio of fledglings within forest plots. We expected young females in the post-fledging period mainly to compete for resources related to food and, as they are subordinate to males, we predicted higher female dispersal from male-biased plots. Juvenile males compete for vacant territories already in late summer and autumn; thus, we predicted increased male dispersal from high density and male-biased plots. We found that juvenile females had a higher probability to leave male-biased plots and had dispersed further from male-biased plots in the later post-fledging phase when juvenile males start to become territorial and more aggressive. Juvenile males were least likely to leave male-biased plots and had smallest dispersal distances from female-biased plots early after fledging. The results suggest that the social environment differentially affected the costs and benefits of philopatry for male and female juveniles. The local sex ratio of individuals is thus an important social trait to be considered for understanding sex-specific dispersal processes.