Evaluation and classification of severity for 176 genes on an expanded carrier screening panel

Background

Disease severity is important when considering genes for inclusion on reproductive expanded carrier screening (ECS) panels. We applied a validated and previously published algorithm that classifies diseases into four severity categories (mild, moderate, severe, and profound) to 176 genes screened by ECS. Disease traits defining severity categories in the algorithm were then mapped to four severity-related ECS panel design criteria cited by the American College of Obstetricians and Gynecologists (ACOG).

Methods

Eight genetic counselors (GCs) and four medical geneticists (MDs) applied the severity algorithm to subsets of 176 genes. MDs and GCs then determined by group consensus how each of these disease traits mapped to ACOG severity criteria, enabling determination of the number of ACOG severity criteria met by each gene.

Results

Upon consensus GC and MD application of the severity algorithm, 68 (39%) genes were classified as profound, 71 (40%) as severe, 36 (20%) as moderate, and one (1%) as mild. After mapping of disease traits to ACOG severity criteria, 170 out of 176 genes (96.6%) were found to meet at least one of the four criteria, 129 genes (73.3%) met at least two, 73 genes (41.5%) met at least three, and 17 genes (9.7%) met all four.

Conclusion

This study classified the severity of a large set of Mendelian genes by collaborative clinical expert application of a trait-based algorithm. Further, it operationalized difficult to interpret ACOG severity criteria via mapping of disease traits, thereby promoting consistency of ACOG criteria interpretation.

     

Nestling rearing is antioxidant demanding in female barn swallows (Hirundo rustica)

Reproduction is a demanding activity, since organisms must produce and, in some cases, protect and provision their progeny. Hence, a central tenet of life-history theory predicts that parents have to trade parental care against body maintenance. One physiological cost thought to be particularly important as a modulator of such trade-offs is oxidative stress. However, evidence in favour of the hypothesis of an oxidative cost of reproduction is contradictory. In this study, we manipulated the brood size of wild barn swallows Hirundo rustica soon after hatching of their nestlings to test whether an increase in nestling rearing effort translates into an increased oxidative damage and a decreased antioxidant protection at the end of the nestling rearing period. We found that, while plasma oxidative damage was unaffected by brood size enlargement, females rearing enlarged broods showed a decrease in plasma non-enzymatic antioxidants during the nestling rearing period. This was not the case among females rearing reduced broods and among males assigned to either treatment. Moreover, individuals with higher plasma oxidative damage soon after the brood size manipulation had lower plasma non-enzymatic antioxidants at the end of the nestling rearing period, suggesting that non-enzymatic antioxidants were depleted to buffer the negative effects of high oxidative damage. Our findings point to antioxidant depletion as a potential mechanism mediating the cost of reproduction among female birds.     

Methanesulphonic acid (MSA) stratigraphy from a Talos Dome ice core as a tool in depicting sea ice changes and southern atmospheric circulation over the previous 140 years

Firn core methanesulphonic acid (MSA) stratigraphy from Talos Dome (East Antarctica) was compared with anomalies of the satellite-measured sea ice extent (1973–1995) in the Ross Sea and Wilkes Land oceanic sector. In spite of the sparseness of sea ice data, the MSA maxima fit with many positive sea ice anomalies in the Ross Sea. This evidence suggests that marine biogenic activity enhanced by large sea ice cover is an important, but not exclusive, factor in controlling MSA concentration in snow precipitation at Talos Dome. Other than source intensity, differences in regional atmospheric transport mechanisms affect the arrival of MSA-rich aerosol at Talos Dome. To clarify the role of transport processes in bringing biogenic aerosol to Talos Dome, a spectral analysis was applied to the MSA, SOI (South Oscillation Index), and SAM (Southern Annular Mode) record. Synchronicity or phase shift between the chemical signature and atmospheric circulation modes were tested. The variations in the MSA profile have a periodicity of 6.9, 4.9, 3.5, and 2.9 years. The 6.9 and 2.9 year periodicities show a strong positive correlation and are synchronous with corresponding SOI periodicity. This variability could be related to an increase in MSA source intensity (by dimethylsulphide from phytoplanktonic activity) linked to the sea ice extent in the Ross Sea area, but also to an increased strength in transport processes. Both of these factors are correlated with La Niña events (SOI positive values). Furthermore, SAM positive values are related to an increased sea ice extent in the Ross Sea sector and show two main periodicities 3.3 and 3.8 years. These periodicities determine the MSA variability at 3.5 years. However, the effect of intensification of the polar vortex and the consequent reduction in transport process intensity, which reduce the delivery of air masses enriched in MSA from oceanic areas to Talos Dome, make the effect of the SAM on the MSA concentration at Talos Dome less active than the SOI. In this way, snow deposition at the Talos Dome records larger MSA concentration by the combined effects of increased source emissions and more efficient transport processes. The MSA record from Talos Dome can therefore be considered a reliable proxy of sea ice extent when the effect of changes in transport processes in this region of Antarctica is considered. Over the previous 140 years, these conditions occur with a periodicity of 6.9 years.     

Anguilliform larvae collected off North Carolina

The distinctive larval stage of eels (leptocephalus) facilitates dispersal through prolonged life in the open ocean. Leptocephali are abundant and diverse off North Carolina, yet data on distributions and biology are lacking. The water column (from surface to 1,293 m) was sampled in or near the Gulf Stream off Cape Hatteras, Cape Lookout, and Cape Fear, North Carolina during summer through fall of 1999–2005, and leptocephali were collected by neuston net, plankton net, Tucker trawl, and dip net. Additional samples were collected nearly monthly from a transect across southern Onslow Bay, North Carolina (from surface to 91 m) from April 2000 to December 2001 by bongo and neuston nets, Methot frame trawl, and Tucker trawl. Overall, 584 tows were completed, and 224 of these yielded larval eels. The 1,295 eel leptocephali collected (combining all methods and areas) represented at least 63 species (nine families). Thirteen species were not known previously from the area. Dominant families for all areas were Congridae (44% of individuals, 11 species), Ophichthidae (30% of individuals, 27 species), and Muraenidae (22% of individuals, ten species). Nine taxa accounted for 70% of the overall leptocephalus catches (in order of decreasing abundance): Paraconger caudilimbatus (Poey), Gymnothorax ocellatus Agassiz complex, Ariosoma balearicum (Delaroche), Ophichthus gomesii (Castelnau), Callechelys muraena Jordan and Evermann, Letharchus aliculatus McCosker, Rhynchoconger flavus (Goode and Bean), Ophichthus cruentifer (Goode and Bean), Rhynchoconger gracilior (Ginsburg). The top three species represented 52% of the total eel larvae collected. Most leptocephali were collected at night (79%) and at depths > 45 m. Eighty percent of the eels collected in discrete depth Tucker trawls at night ranged from mean depths of 59–353 m. A substantial number (38% of discrete depth sample total) of larval eels were also collected at the surface (neuston net) at night. Daytime leptocephalus distributions were less clear partly due to low catches and lower Tucker trawl sampling effort. While net avoidance may account for some of the low daytime catches, an alternative explanation is that many species of larval eels occur during the day at depths > 350 m. Larvae of 21 taxa of typically shallow water eels were collected at depths > 350 m, but additional discrete depth diel sampling is needed to resolve leptocephalus vertical distributions. The North Carolina adult eel fauna (estuary to at least 2,000 m) consists of 51 species, 41% of which were represented in these collections. Many species of leptocephali collected are not yet known to have juveniles or adults established in the South Atlantic Bight or north of Cape Hatteras. Despite Gulf Stream transport and a prolonged larval stage, many of these eel leptocephali may not contribute to their respective populations.     

Chihuahuan Desert kangaroo rats: nonlinear effects of population dynamics, competition, and rainfall

Using long-term data on two kangaroo rats in the Chihuahuan Desert of North America, we fitted logistic models including the exogenous effects of seasonal rainfall patterns. Our aim was to test the effects of intraspecific interactions and seasonal rainfall in explaining and predicting the numerical fluctuations of these two kangaroo rats. We found that logistic models fit both data sets quite well; Dipodomys merriami showed lower maximum per capita growth rates than Dipodomys ordii, and in both cases logistic models were nonlinear. Summer rainfall appears to be the most important exogenous effect for both rodent populations; models including this variable were able to predict independent data better than models including winter rainfall. D. merriami was also negatively affected by another kangaroo rat (Dipodomys spectabilis), consistent with previous experimental evidence. We hypothesized that summer rainfall influences the carrying capacity of the environment by affecting seed availability and the intensity of intraspecific competition.     

Limited salvage logging effects on forest regeneration after moderate-severity windthrow.

Recent conceptual advances address forest response to multiple disturbances within a brief time period, providing an ideal framework for examining the consequences of natural disturbances followed by anthropogenic management activities. The combination of two or more disturbances in a short period may produce "ecological surprises," and models predict a threshold of cumulative disturbance severity above which forest composition will be drastically altered and regeneration may be impaired. Salvage logging (the harvesting of timber after natural disturbances; also called "salvaging" or "sanitary logging") is common, but there have been no tests of the manner in which salvaging after natural wind disturbance affects woody plant regeneration. Here we present findings from three years after a moderate-severity wind disturbance in west-central Tennessee, USA. We compare two unsalvaged sites and two sites that had intermediate-intensity salvaging. Our approach demonstrates the calculation of cumulative severity measures, which combine natural windthrow severity and anthropogenic tree cutting and removal, on a plot-by-plot basis. Seedling/sapling density and species richness were not influenced by cumulative disturbance severity, but species diversity showed a marginal increase with increasing cumulative severity. The amount of compositional change (from predisturbance trees to post-disturbance seedlings/saplings) increased significantly with cumulative severity of disturbance but showed no evidence of thresholds within the severity range examined. Overall, few deleterious changes were evident in these sites. Moderate-severity natural disturbances followed by moderate-intensity salvaging may have little detrimental effect on forest regeneration and diversity in these systems; the ecological surprises and threshold compositional change are more likely after combinations of natural and anthropogenic disturbances that have a much greater cumulative severity.     

Stormwater treatment: examples of computational fluid dynamics modeling

Control of rainfall-runoff particulate matter (PM) and PM-bound chemical loads is challenging; in part due to the wide gradation of PM complex geometries of many unit operations and variable flow rates. Such challenges and the expense associated with resolving such challenges have led to the relatively common examination of a spectrum of unit operations and processes. This study applies the principles of computational fluid dynamics (CFD) to predict the particle and pollutant clarification behavior of these systems subject to dilute multiphase flows, typical of rainfall-runoff, within computationally reasonable limits, to a scientifically acceptable degree of accuracy. The Navier-Stokes (NS) system of nonlinear partial differential equations for multiphase hydrodynamics and separation of entrained particles are solved numerically over the unit operation control volume with the boundary and initial conditions defined and then solved numerically until the desired convergence criteria are met. Flow rates examined are scaled based on sizing of common unit operations such as hydrodynamic separators (HS), wet basins, or filters, and are examined from 1 to 100 percent of the system maximum hydraulic operating flow rate. A standard turbulence model is used to resolve flow, and a discrete phase model (DPM) is utilized to examine the particle clarification response. CFD results closely follow physical model results across the entire range of flow rates. Post-processing the CFD predictions provides an in-depth insight into the mechanistic behavior of unit operations by means of three dimensional (3-D) hydraulic profiles and particle trajectories. Results demonstrate the role of scour in the rapid degradation of unit operations that are not maintained. Comparisons are provided between measured and CFD modeled results and a mass balance error is identified. CFD is arguably the most powerful tool available for our profession since continuous simulation modeling.     

Stable isotopes identify age- and sex-specific dietary partitioning and foraging habitat segregation in southern giant petrels breeding in Antarctica and southern Patagonia

We examined the isotopic signatures (δ¹³C, δ¹⁵N) of adult body feathers from southern giant petrels Macronectes giganteus collected at two breeding colonies in Antarctica (Potter Peninsula and Cape Geddes) and one in southern Patagonia (Observatorio Island), as well as in whole blood collected from adults of both sexes at each Antarctic colonies and from chicks at Potter Peninsula. As body feather moult is a continuous process in giant petrels, feathers provide an integrated annual signal of an adult’s diets and foraging habitats. In contrast, the stable isotope values of adult and chick blood are reflective of their diets during the breeding season. We found that sex-specific dietary segregation in adults breeding in Antarctica was notable during the breeding season (blood samples) but absent when examined across the entire year (feather samples). In addition, blood stable isotope values differed between chicks and adults, indicating that adults provision their offspring with a relatively higher amount of penguin and seal prey that what they consume themselves. This finding confirms previous work that suggests that chicks are preferentially fed with prey of presumably higher nutritional value such as carrion. Finally, based on isotopic differences between major oceanographic zones in the Southern Ocean, our data indicate population-specific differences in foraging distribution, with Antarctic populations move seasonally between Antarctic and subantarctic zones, while Patagonian populations likely forage in subtropical waters and in continental shelf habitats year-round.     

Invasive species impacts on ecosystem structure and function: A comparison of the Bay of Quinte, Canada, and Oneida Lake, USA, before and after zebra mussel invasion

As invasion rates of exotic species increase, an ecosystem level understanding of their impacts is imperative for predicting future spread and consequences. We have previously shown that network analyses are powerful tools for understanding the effects of exotic species perturbation on ecosystems. We now use the network analysis approach to compare how the same perturbation affects another ecosystem of similar trophic status. We compared food web characteristics of the Bay of Quinte, Lake Ontario (Canada), to previous research on Oneida Lake, New York (USA) before and after zebra mussel (Dreissena polymorpha) invasion. We used ecological network analysis (ENA) to rigorously quantify ecosystem function through an analysis of direct and indirect food web transfers. We used a social network analysis method, cohesion analysis (CA), to assess ecosystem structure by organizing food web members into subgroups of strongly interacting predators and prey. Together, ENA and CA allowed us to understand how food web structure and function respond simultaneously to perturbation. In general, zebra mussel effects on the Bay of Quinte, when compared to Oneida Lake, were similar in direction, but greater in magnitude. Both systems underwent functional changes involving focused flow through a small number of taxa and increased use of benthic sources of production; additionally, both systems structurally changed with subgroup membership changing considerably (33% in Oneida Lake) or being disrupted entirely (in the Bay of Quinte). However, the response of total ecosystem activity (as measured by carbon flow) differed between both systems, with increasing activity in the Bay of Quinte, and decreasing activity in Oneida Lake. Thus, these analyses revealed parallel effects of zebra mussel invasion in ecosystems of similar trophic status, yet they also suggested that important differences may exist. As exotic species continue to disrupt the structure and function of our native ecosystems, food web network analyses will be useful for understanding their far-reaching effects.