Fetal fraction and noninvasive prenatal testing: What clinicians need to know

The fetal fraction (FF) is a function of both biological factors and bioinformatics algorithms used to interpret DNA sequencing results. It is an essential quality control component of noninvasive prenatal testing (NIPT) results. Clinicians need to understand the biological influences on FF to be able to provide optimal post-test counseling and clinical management. There are many different technologies available for the measurement of FF. Clinicians do not need to know the details behind the bioinformatics algorithms of FF measurements, but they do need to appreciate the significant variations between the different sequencing technologies used by different laboratories. There is no universal FF threshold that is applicable across all platforms and there have not been any differences demonstrated in NIPT performance by sequencing platform or method of FF calculation. Importantly, while FF should be routinely measured, there is not yet a consensus as to whether it should be routinely reported to the clinician. The clinician should know what to expect from a standard test report and whether reasons for failed NIPT results are revealed. Emerging solutions to the challenges of samples with low FF should reduce rates of failed NIPT in the future. In the meantime, having a “plan B" prepared for those patients for whom NIPT is unsuccessful is essential in today's clinical practice.     

Effects of road age on the structure of roadside vegetation in south-eastern Australia

In many agricultural landscapes, roadside (or road verge) environments provide important refuge for threatened native species and ecosystems, and are often selected as benchmark sites to guide restoration activities. However few studies have investigated potential temporal variability in roadside vegetation conditions. In this paper we used archived cadastral maps to determine road age and examine potential variability in roadside vegetation structures in a typical rural landscape in south-eastern Australia. We found significant differences in the density of mature trees for road segments in different road-age categories. The oldest roads (<1870s) were characterized by having the greatest density of large hollow-bearing Eucalyptus trees, but few native conifer trees or shrubs. Roads surveyed when broad-scale clearing commenced (1870–1879), and not the oldest roads, were found to be more intact in terms of the density of large pre-settlement trees, range of tree stem-size classes and overall shrub diversity. By contrast, the youngest roads (post-1900s) had the greatest number of native conifer trees, but few shrubs or large Eucalyptus trees. As a result, roads of different ages had different densities of hollow-bearing trees, which is discussed in terms of past land-use legacies. These results have important implications for selecting roadsides as benchmark sites for restoration activities, and highlight the critical importance of roadsides to conserving native biota in agricultural landscapes.     

Conservation value of an exotic species: the case of coconuts on the Kayapo indigenous lands, south-eastern Amazonia

In a meeting between FUNAI (the Brazilian Indian National Foundation) and the Kayapo in the Kayapo village of Aukre, in October 2005, the Kayapo Indians requested support to increase the culture of coconuts (Cocos nucifera) in their lands. The introduction of exotic species is a cause of biological diversity loss throughout the world. However, this is by no means applicable to all kinds of exotic species. We argue that the culture of coconuts may actually be a useful tool for the conservation of this country’s indigenous lands, despite criticism to the contrary. It may also be useful as source for raw material for the indigenous people who are presently experiencing a population boom. For the Kayapo of south-eastern Amazonia, such a demographic explosion, coupled with their increasing dependence on money to purchase industrialized goods, tend to substantially increase the pressure on their lands, which still contain a substantial amount of well-preserved seasonally-dry Amazonian forests. We investigated the actual economic relevance of coconuts for the Kayapo by measuring human and coconut populations and found that this exotic palm is not important for the subsistence of these Indians, due to coconut scarcity, and that such importance is not forthcoming. In the Amazon, coconuts may be particularly useful for the Indians’ nutrition due to the high energetic value of the solid endosperm of the mature fruit. Therefore, given the importance of indigenous lands for the conservation of the Amazonian forests, the encouragement of subsistence coconut cultures in indigenous lands is defensible as a measure for the conservation of biodiversity.     

Food availability and physiological state of sea urchin larvae (<Emphasis Type="Italic">Strongylocentrotus purpuratus</Emphasis>)

Food availability is highly variable in the ocean. Many species of marine invertebrates have a larval form that depends upon exogenous nutrients for growth, yet there are few biochemical and physiological indices for determining changes in the nutritional status of larvae. In this study, the effects of food availability on biochemical compositions and metabolic processes of larvae of the sea urchin, Strongylocentrotus purpuratus, were determined. Larvae were cultured under different food concentrations (fed-to-excess and unfed) and a suite of biological processes assayed, ranging from measurements at the level of the whole organism to that of specific molecules. These data were normalized to DNA content (an index of cell number) to allow comparisons of physiological rates in larvae of different sizes. Changes in the following were measured during larval growth: free amino acid pool, protein, lipid classes (cholesterol, free fatty acids, hydrocarbons, phospholipids, triacylglycerol), enzyme activities (Na⁺, K⁺-ATPase and citrate synthase), and respiration rates. In growing larvae, the two key components that showed differential cell-specific content relative to unfed larvae were glycine in the free amino acid pool and phospholipids. Additionally, several lipid classes were detectable only in fed larvae (cholesterols, free fatty acids, and hydrocarbons). While triacylglycerols were present in eggs and utilized during pre-feeding development, they were not re-accumulated at detectable levels in feeding larvae. Respiration rates, protein content, and enzyme activities were all similar on a cell-specific basis, showing that these variables did not provide useful indices of differences in physiological state between fed and unfed larvae. In contrast, measurements of the cell-specific content of glycine and certain lipid classes did provide useful indices of physiological state of larvae. Application of these indices could potentially allow for determinations of nutritional state of larvae in the ocean.     

Increased nuchal translucency after low-risk noninvasive prenatal testing: What should we tell prospective parents?

Three decades ago, the observation that first trimester fetuses with excess fluid accumulation at the back of the neck were more likely to be aneuploid, gave rise to a new era of prenatal screening. The nuchal translucency (NT) measurement in combination with serum biomarkers and maternal age, resulted in the first trimester combined screening (FTCS) program. The introduction of noninvasive prenatal testing (NIPT) over the past decade has introduced the option for parents to receive highly sensitive and specific screening information for common trisomy from as early as 10 weeks gestation, altering the traditional pathway FTCS pathway. The retention of the 11–13-week NT ultrasound remains important in the detection of structural anomalies; however, the optimal management of pregnancies with a low-risk NIPT result and an isolated increased NT measurement in an era of advanced genomic testing options is a new dilemma for clinicians. For parents, the prolonged period between the initial diagnosis in first trimester, and prognostic information at each successive stage of investigations up to 22–24 weeks, can be emotionally challenging. This article addresses the common questions from parents and clinicians as they navigate the uncertainty of having a fetus diagnosed with an increased NT after a low-risk NIPT result and presents suggested approaches to management.