The impact of maternal plasma DNA fetal fraction on next generation sequencing tests for common fetal aneuploidies

Maternal plasma contains circulating cell-free DNA fragments originating from both the mother and the placenta. The proportion derived from the placenta is known as the fetal fraction. When measured between 10 and 20 gestational weeks, the average fetal fraction in the maternal plasma is 10% to 15% but can range from under 3% to over 30%. Screening performance using next-generation sequencing of circulating cell-free DNA is better with increasing fetal fraction and, generally, samples whose values are less than 3% or 4% are unsuitable. Three examples of the clinical impact of fetal fraction are discussed. First, the distribution of test results for Down syndrome pregnancies improves as fetal fraction increases, and this can be exploited in reporting patient results. Second, the strongest factor associated with fetal fraction is maternal weight; the false negative rate and rate of low fetal fractions are highest for women with high maternal weights. Third, in a mosaic, the degree of mosaicism will impact the performance of the test because it will reduce the effective fetal fraction. By understanding these aspects of the role of fetal fraction in maternal plasma DNA testing for aneuploidy, we can better appreciate the power and the limitations of this impressive new methodology. © 2013 John Wiley & Sons, Ltd.     

Swidden agriculture in a protected area: the Matsigenka native communities of Manu National Park, Peru

In this study, we investigate whether traditional swidden agriculture on nutrient-poor tropical soils can sustainably support a growing indigenous population within Manu National Park, Peru. Based on interviews with 50 Matsigenka farmers, as well as GPS mapping and field visits, we established the location and size of all 124 swidden gardens cultivated in 2000 and 2001. Using a GIS-based soil map of Manu Park, we identify the total extent of potential arable land (1) throughout the park zones currently available for Matsigenka habitation, and (2) within the vicinity of the two study communities. Taking into account current per capita garden size, cultivation and fallow practices, we calculate the maximum human carrying capacity of swidden agriculture for (1) all available park zones and (2) the immediate vicinity of the two current communities. Even given the second, highly limited scenario, the sustainable human carrying capacity is estimated to be 2,138 individuals, which is far higher than the current population of about 420 people. Thus, arable land does not appear to be a limiting factor for the growth of the indigenous population in Manu Park at the current time. Other possible limiting factors for population growth are identified and discussed. We conclude that a conservation policy of population stabilization around the current settlements is viable in that it will not result in reduced resource availability over the next few decades, and that the challenge is to identify and mitigate the forces causing population fissioning and spread. Readers should send their comments on this paper to BhaskarNath@aol.com within 3 months of publication of this issue.     

Regional planning acceptance by residents of Northern New York,USA

This study compares the effectiveness of two regional planning agencies in terms of public support for various planning activities. The Adirondack Park Agency and the Temporary State Commission on Tug Hill have fundamentally different approaches to planning. The Adirondack Park Agency has implemented a restrictive regulatory program with little citizen participation by Adirondack residents. The Tug Hill Commission has implemented an advisory and coordinating program with an emphasis on public input. Residents of two towns in each region were surveyed to determine environmental concern and support for regional planning activities. Respondents from both regions favored a planning agency that incorporates citizen input; controls air, water, and toxic waste pollution; and develops recreation areas. They strongly opposed an agency that regulates private land-use. Basic demographic characteristics and levels of environmental concern were similar in all four towns, but receptivity to various planning activities was consistently greater among residents of the Tug Hill Region. Paired comparisons of the four towns demonstrated no differences between towns of the same region and significant differences between towns of different regions. Public support for regional planning is greater in the Tug Hill Region than in the Adirondack Park.     

Assessing cancer incidence in a small community

Many small communities are concerned about health effects from environmental pollutants. One such community, Orwell, in Oswego County, New York, was investigated to determine if the level of cancer was significantly high in comparison to the county and the state. A pilot health study was administered among residents living in a defined area. Results of the survey demonstrated that cancer incidence was higher than both Oswego County and New York State, while cancer mortality was higher for men and lower for woman. A closer examination of the data showed that the way in which health surveys are usually analyzed may not be appropriate for small communities. In particular, some parametric statistics, such as chi-square analysis, might show significant differences between populations when standardized incidence and mortality rates are derived from small samples, yet standard deviations calculated from these data are so large as to cast doubt on the analysis. Researchers have discussed this problem theoretically, but empirical studies illustrating the difficulties have not heretofore appeared in the published literature. For health studies in small communities, greater consideration should be given to risk ratios and the implications of standard deviations.     

Niche separation in two species of hare. Metabolic costs of plant phenolics

Summary The distributions of mountain hare (Lepus timidus) and European hare (L. europaeus) overlap in central Sweden, but they occupy separate food niches in winter. In Scandinavia, the European hare is mainly a grazer while mountain hare is a predominant browser. Browse contain high amounts of secondary metabolites, such as phenols, compared to grass. This raises the question if the two hare species differ in their metabolic tolerance of plant phenols and that these differences influence their food choice.Phenolic excretion in urine increased significantly with phenolic intake in both species. Excretion of glucuronic acid conjugates, one of the major pathways of elimination of phenols in both hare species, is positively correlated to phenolic intake and excretion. However, the extent of excretion of phenolics by this route was different in the two species of hare. European hares excreted substantially more glucuronic acid per amount of phenolics than mountain hare. The phenols were metabolized to a larger extent in the mountain hare, indicating a higher detoxification capacity. From these results it is likely that European hare have a higher cost for the detoxification of plant phenols compared to mountain hare. This cost and negative effect on sodium balance when feeding on browse may prevent exploitation of forest habitats by European hares, whereas mountain hare are better able to do so.     

Efforts to Reduce Mortality to Hydroelectric Turbine-Passed Fish: Locating and Quantifying Damaging Shear Stresses

Severe fluid forces are believed to be a source of injury and mortality to fish that pass through hydroelectric turbines. A process is described by which laboratory bioassays, computational fluid dynamics models, and field studies can be integrated to evaluate the significance of fluid shear stresses that occur in a turbine. Areas containing potentially lethal shear stresses were identified near the stay vanes and wicket gates, runner, and in the draft tube of a large Kaplan turbine. However, under typical operating conditions, computational models estimated that these dangerous areas comprise less than 2% of the flow path through the modeled turbine. The predicted volumes of the damaging shear stress zones did not correlate well with observed fish mortality at a field installation of this turbine, which ranged from less than 1% to nearly 12%. Possible reasons for the poor correlation are discussed. Computational modeling is necessary to develop an understanding of the role of particular fish injury mechanisms, to compare their effects with those of other sources of injury, and to minimize the trial and error previously needed to mitigate those effects. The process we describe is being used to modify the design of hydroelectric turbines to improve fish passage survival.     

Development of environmental thresholds for nitrogen and phosphorus in streams

Inputs of nutrients (P and N) to freshwaters can cause excessive aquatic plant growth, depletion of oxygen, and deleterious changes in diversity of aquatic fauna. As part of a "National Agri-Environmental Standards Initiative," the Government of Canada committed to developing environmental thresholds for nutrients to protect ecological condition of agricultural streams. Analysis of data from >200 long-term monitoring stations across Canada and detailed ecological study at ~70 sites showed that agricultural land cover was associated with increased nutrient concentrations in streams and this, in turn, was associated with increased sestonic and benthic algal abundance, loss of sensitive benthic macroinvertebrate taxa, and an increase in benthic diatom taxa indicative of eutrophication. Chemical thresholds for N and P were defined by applying five approaches, employing either a predetermined percentile to a water chemistry data set or a relationship between water chemistry and land cover, to identify boundaries between minimally disturbed and impaired conditions. Comparison of these chemical thresholds with biological thresholds (derived from stressor-response relationships) produced an approach for rationalizing these two types of thresholds and deriving nutrient criteria. The resulting criteria were 0.01 to 0.03 mg L(-1) total P and 0.87-1.2 mg L(-1) total N for the Atlantic Maritime, 0.02 mg L(-1) total P and 0.21 mg L(-1) total N for the Montane Cordillera, ~0.03 mg L(-1) total P and ~1.1 mg L(-1) total N for the Mixedwood Plains, and ~0.10 mg L(-1) total P and 0.39-0.98 mg L(-1) total N for the interior prairies of Canada. Adoption of these criteria should result in greater likelihood of good ecological condition with respect to benthic algal abundance, diatom composition, and macroinvertebrate composition.     

Evaluation of Deposited Sediment and Macroinvertebrate Metrics Used to Quantify Biological Response to Excessive Sedimentation in Agricultural Streams

The objective of this study was to evaluate which macroinvertebrate and deposited sediment metrics are best for determining effects of excessive sedimentation on stream integrity. Fifteen instream sediment metrics, with the strongest relationship to land cover, were compared to riffle macroinvertebrate metrics in streams ranging across a gradient of land disturbance. Six deposited sediment metrics were strongly related to the relative abundance of Ephemeroptera, Plecoptera and Trichoptera and six were strongly related to the modified family biotic index (MFBI). Few functional feeding groups and habit groups were significantly related to deposited sediment, and this may be related to the focus on riffle, rather than reach-wide macroinvertebrates, as reach-wide sediment metrics were more closely related to human land use. Our results suggest that the coarse-level deposited sediment metric, visual estimate of fines, and the coarse-level biological index, MFBI, may be useful in biomonitoring efforts aimed at determining the impact of anthropogenic sedimentation on stream biotic integrity.