Do recent US Supreme Court rulings on patenting of genes and genetic diagnostics affect the practice of genetic screening and diagnosis in prenatal and reproductive care?

Thousands of patents have been awarded that claim human gene sequences and their uses, and some have been challenged in court. In a recent high-profile case, Association for Molecular Pathology, et al. v. Myriad Genetics, Inc., et al., the US Supreme Court ruled that genes are natural occurring substances and therefore not patentable through ‘composition of matter’ claims. The consequences of this ruling will extend well beyond ending Myriad's monopoly over BRCA testing and may affect similar monopolies of other commercial laboratories for tests involving other genes. It could also simplify intellectual property issues surrounding genome-wide clinical sequencing, which can generate results for genes covered by intellectual property. Non-invasive prenatal testing (NIPT) for common aneuploidies using cell-free fetal (cff) DNA in maternal blood is currently offered through commercial laboratories and is also the subject of ongoing patent litigation. The recent Supreme Court decision in the Myriad case has already been invoked by a lower district court in NIPT litigation and resulted in invalidation of primary claims in a patent on currently marketed cffDNA-based testing for chromosomal aneuploidies. © 2014 John Wiley & Sons, Ltd.     

Geometry of Zn(II) complexes with dissolved organic matter: X-ray studies at variable pH

The structure of Zn(II) complexes with dissolved organic matter (DOM) is an important consideration in developing molecular-level models of Zn(II) speciation, but recent reports favoring the tetrahedral geometry differ from earlier findings that geometry was largely octahedral. In general, the presence of thiolate ligands favors the tetrahedral geometry, while O and N ligands favor the octahedral geometry. This work presents extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) spectroscopic results, indicating an octahedral geometry over the pH range of 5–9 for a freshwater DOM isolate. Changes in XANES derivatives as a function of pH can be explained in terms of ligand protonation and/or changing ligand groups. Tetrahedral Zn(II)–DOM geometry may be restricted to binding environments containing thiol groups.     

Metabolic suppression in thecosomatous pteropods as an effect of low temperature and hypoxia in the eastern tropical North Pacific

Many pteropod species in the eastern tropical North Pacific Ocean migrate vertically each day, transporting organic matter and respiratory carbon below the thermocline. These migrations take species into cold (15–10°?C) hypoxic water (<20?μmol O₂ kg^?1) at depth. We measured the vertical distribution, oxygen consumption and ammonia excretion for seven species of pteropod, some of which migrate and some which remain in oxygenated surface waters throughout the day. Within the upper 200?m of the water column, changes in water temperature result in a?~60–75?% reduction in respiration for most species. All three species tested under hypoxic conditions responded to low O₂ with an additional?~35–50?% reduction in respiratory rate. Combined, low temperature and hypoxia suppress the metabolic rate of pteropods by?~80–90?%. These results shed light on the ways in which expanding regions of hypoxia and surface ocean warming may impact pelagic ecology.     

Multi-scale marine biodiversity patterns inferred efficiently from habitat image processing

Cost-effective proxies of biodiversity and species abundance, applicable across a range of spatial scales, are needed for setting conservation priorities and planning action. We outline a rapid, efficient, and low-cost measure of spectral signal from digital habitat images that, being an effective proxy for habitat complexity, correlates with species diversity and requires little image processing or interpretation. We validated this method for coral reefs of the Great Barrier Reef (GBR), Australia, across a range of spatial scales (1 m to 10 km), using digital photographs of benthic communities at the transect scale and high-resolution Landsat satellite images at the reef scale. We calculated an index of image-derived spatial heterogeneity, the mean information gain (MIG), for each scale and related it to univariate (species richness and total abundance summed across species) and multivariate (species abundance matrix) measures of fish community structure, using two techniques that account for the hierarchical structure of the data: hierarchical (mixed-effect) linear models and distance-based partial redundancy analysis. Over the length and breadth of the GBR, MIG alone explained up to 29% of deviance in fish species richness, 33% in total fish abundance, and 25% in fish community structure at multiple scales, thus demonstrating the possibility of easily and rapidly exploiting spatial information contained in digital images to complement existing methods for inferring diversity and abundance patterns among fish communities. Thus, the spectral signal of unprocessed remotely sensed images provides an efficient and low-cost way to optimize the design of surveys used in conservation planning. In data-sparse situations, this simple approach also offers a viable method for rapid assessment of potential local biodiversity, particularly where there is little local capacity in terms of skills or resources for mounting in-depth biodiversity surveys.     

Niche complementarity due to plasticity in resource use: plant partitioning of chemical N forms

Niche complementarity, in which coexisting species use different forms of a resource, has been widely invoked to explain some of the most debated patterns in ecology, including maintenance of diversity and relationships between diversity and ecosystem function. However, classical models assume resource specialization in the form of distinct niches, which does not obviously apply to the broadly overlapping resource use in plant communities. Here we utilize an experimental framework based on competition theory to test whether plants partition resources via classical niche differentiation or via plasticity in resource use. We explore two alternatives: niche preemption, in which individuals respond to a superior competitor by switching to an alternative, less-used resource, and dominant plasticity, in which superior competitors exhibit high resource use plasticity and shift resource use depending on the competitive environment. We determined competitive ability by measuring growth responses with and without neighbors over a growing season and then used 15N tracer techniques to measure uptake of different nitrogen (N) forms in a field setting. We show that four alpine plant species of differing competitive abilities have statistically indistinguishable uptake patterns (nitrate > ammonium > glycine) in their fundamental niche (without competitors) but differ in whether they shift these uptake patterns in their realized niche (with competitors). Competitively superior species increased their uptake of the most available N form, ammonium, when in competition with the rarer, competitively inferior species. In contrast, the competitively inferior species did not alter its N uptake pattern in competition. The existence of plasticity in resource use among the dominant species provides a mechanism that helps to explain the manner by which plant species with broadly overlapping resource use might coexist.     

Photosynthetic resource-use efficiency and demographic variability in desert winter annual plants

We studied a guild of desert winter annual plants that differ in long-term variation in per capita reproductive success (lb, the product of per capita survival from germination to reproduction, l, times per capita reproduction of survivors, b) to relate individual function to population and community dynamics. We hypothesized that variation in lb should be related to species' positions along a trade-off between relative growth rate (RGR) and photosynthetic water-use efficiency (WUE) because lb is a species-specific function of growing-season precipitation. We found that demographically variable species have greater RGR and greater leaf carbon isotope discrimination (Delta, a proxy inversely related to WUE). We examined leaf nitrogen and photosynthetic characteristics and found that, in this system, variation in Delta is a function of photosynthetic demand rather than stomatal regulation of water loss. The physiological characteristics that result in low Delta in some species may confer greater photosynthetic performance during the reliably moist but low temperature periods that immediately follow winter rainfall in the Sonoran Desert or alternatively during cool periods of the day or early growing season. Conversely, while species with high Delta and high RGR exhibit low leaf N, they have high biomass allocation to canopy leaf area display. Such trait associations may allow for greater performance during the infrequent conditions where high soil moisture persists into warmer conditions, resulting in high demographic variance. Alternatively, high variance could arise from specialization to warm periods of the day or season. Population dynamic buffering via stress tolerance (low RGR and Delta) correlates negatively with buffering via seed banks, as predicted by bet-hedging theory. By merging analyses of population dynamics with functional trait relationships, we develop a deeper understanding of the physiological, ecological, and evolutionary mechanisms involved in population and community dynamics.     

Plant uptake of inorganic and organic nitrogen: neighbor identity matters

The importance of interspecific competition as a cause of resource partitioning among species has been widely assumed but rarely tested. Using neighbor removals in combination with 15N tracer additions in the field, we examined variation among three alpine species in the uptake of 15N-NH4+, 15N-NO3-, and 15N-13C-[2]-glycine in intact neighborhoods, when paired with a specific neighbor, and when all neighbors were removed. Species varied in the capacity to take up 15N-labeled NH4+, NO3-, and glycine in intact neighborhoods and in interspecific pairs. When interspecific neighbor pairs were compared with no neighbor controls, neighbors reduced 15N uptake in target species by as much as 50%, indicating competition for N. Furthermore, neighbor identity influenced the capacity of species to take up different forms of N. Thus, competition within interspecific neighbor pairs often caused reduced uptake of a particular form of N, as well as shifts to uptake of an alternative form of N. Such shifts in resource use as a result of competition are an implicit assumption in studies of resource partitioning but have rarely been documented. Our study suggests that plasticity in the uptake of different forms of N may be a mechanism by which cooccurring plants reduce competition for N.     

Determinants of seed removal distance by scatter-hoarding rodents in deciduous forests

Scatter-hoarding rodents should space food caches to maximize cache recovery rate (to minimize loss to pilferers) relative to the energetic cost of carrying food items greater distances. Optimization models of cache spacing make two predictions. First, spacing of caches should be greater for food items with greater energy content. Second, the mean distance between caches should increase with food abundance. However, the latter prediction fails to account for the effect of food abundance on the behavior of potential pilferers or on the ability of caching individuals to acquire food by means other than recovering their own caches. When considering these factors, shorter cache distances may be predicted in conditions of higher food abundance. We predicted that seed caching distances would be greater for food items of higher energy content and during lower ambient food abundance and that the effect of seed type on cache distance variation would be lower during higher food abundance. We recorded distances moved for 8636 seeds of five seed types at 15 locations in three forested sites in Pennsylvania, USA, and 29 forest fragments in Indiana, U.S.A., across five different years. Seed production was poor in three years and high in two years. Consistent with previous studies, seeds with greater energy content were moved farther than less profitable food items. Seeds were dispersed less far in seed-rich years than in seed-poor years, contrary to predictions of conventional models. Interactions were important, with seed type effects more evident in seed-poor years. These results suggest that, when food is superabundant, optimal cache distances are more strongly determined by minimizing energy cost of caching than by minimizing pilfering rates and that cache loss rates may be more strongly density-dependent in times of low seed abundance.