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.

     

A plasma display window?-The shifting baseline problem in a technologically mediated natural world

Humans will continue to adapt to an increasingly technological world. But are there costs to such adaptations in terms of human well being? Toward broaching this question, we investigated physiological effects of experiencing a HDTV quality real-time view of nature through a plasma display “window.” In an office setting, 90 participants (30 per group) were exposed either to (a) a glass window that afforded a view of a nature scene, (b) a plasma window that afforded a real-time HDTV view of essentially the same scene, or (c) a blank wall. Results showed that in terms of heart rate recovery from low-level stress the glass window was more restorative than a blank wall; in turn, a plasma window was no more restorative than a blank wall. Moreover, when participants spent more time looking at the glass window, their heart rate tended to decrease more rapidly; that was not the case with the plasma window. Discussion focuses on how the purported benefits of viewing nature may be attenuated by a digital medium.     

Assessing alternative aquaculture technologies: life cycle assessment of salmonid culture systems in Canada

This study employed life cycle assessment (LCA) to quantify and compare the potential environmental impacts of culturing salmonids in a conventional marine net-pen system with those of three reportedly environmentally-friendly alternatives; a marine floating bag system; a land-based saltwater flow-through system; and a land-based freshwater recirculating system. Results of the study indicate that while the use of these closed-containment systems may reduce the local ecological impacts typically associated with net-pen salmon farming, the increase in material and energy demands associated with their use may result in significantly increased contributions to several environmental impacts of global concern, including global warming, non-renewable resource depletion, and acidification. It is recommended that these unanticipated impacts be carefully considered in further assessments of the sustainability of closed-containment systems and in ongoing efforts to develop and employ these technologies on a larger scale.     

Predator diversity and identity drive interaction strength and trophic cascades in a food web

Declining predator diversity may drastically affect the biomass and productivity of herbivores and plants. Understanding how changes in predator diversity can propagate through food webs to alter ecosystem function is one of the most challenging ecological research topics today. We studied the effects of predator removal in a simple natural food web in the Sierra Nevada mountains of California (USA). By excluding the predators of the third trophic level of a food web in a full-factorial design, we monitored cascading effects of varying predator diversity and composition on the herbivorous beetle Chrysomela aeneicollis and the willow Salix orestera, which compose the first and second trophic levels of the food web. Decreasing predator diversity increased herbivore biomass and survivorship, and consequently increased the amount of plant biomass consumed via a trophic cascade. Despite this simple linear mean effect of diversity on the strength of the trophic cascade, we found additivity, compensation, and interference in the effects of multiple predators on herbivores and plants. Herbivore survivorship and predator-prey interaction strengths varied with predator diversity, predator identity, and the identity of coexisting predators. Additive effects of predators on herbivores and plants may have been driven by temporal niche separation, whereas compensatory effects and interference occurred among predators with a similar phenology. Together, these results suggest that while the general trends of diversity effects may appear linear and additive, other information about species identity was required to predict the effects of removing individual predators. In a community that is not temporally well-mixed, predator traits such as phenology may help predict impacts of species loss on other species. Information about predator natural history and food web structure may help explain variation in predator diversity effects on trophic cascades and ecosystem function.     

Interannual variability of growth and reproduction in Bursera simaruba: the role of allometry and resource variability

Plants are expected to differentially allocate resources to reproduction, growth, and survival in order to maximize overall fitness. Life history theory predicts that the allocation of resources to reproduction should occur at the expense of vegetative growth. Although it is known that both organism size and resource availability can influence life history traits, few studies have addressed how size dependencies of growth and reproduction and variation in resource supply jointly affect the coupling between growth and reproduction. In order to understand the relationship between growth and reproduction in the context of resource variability, we utilize a long-term observational data set consisting of 670 individual trees over a 10-year period within a local population of Bursera simaruba (L.) Sarg. We (1) quantify the functional form and variability in the growth-reproduction relationship at the population and individual-tree level and (2) develop a theoretical framework to understand the allometric dependence of growth and reproduction. Our findings suggest that the differential responses of allometric growth and reproduction to resource availability, both between years and between microsites, underlie the apparent relationship between growth and reproduction. Finally, we offer an alternative approach for quantifying the relationship between growth and reproduction that accounts for variation in allometries.     

Insects mediate the effects of propagule supply and resource availability on a plant invasion

Invasive species are a global threat to biodiversity and the functioning of natural ecosystems. Here, we report on a two-year experiment aimed at elucidating the combined and relative effects of three key controls on plant invasions: propagule supply, soil nitrogen (N) availability, and herbivory by native insects. We focus on the exotic species Lespedeza cuneata, a Rank 1 invasive species. Propagule supply and soil N-availability interacted to control the density and foliar cover of L. cuneata. In low N plots, density and foliar cover of L. cuneata were higher in the propagule addition plots than in the plots to which propagules were not added. Surprisingly, this interaction was significant only when the abundance of herbivores was experimentally reduced. This experiment provides evidence that native insect herbivores mediate the interactive effects of propagule supply and resources on invasion by a widespread invasive plant species.     

Modeling and interpreting bioavailability of organic contaminant mixtures in subsurface environments

Bioavailability often controls the fate of organic contaminants in surface and subsurface aquatic environments. Bioavailability can be limited by sorption, mass transfer, and intrinsic biodegradation potential and can be further altered by the presence of other compounds. This paper reviews current perspectives on the processes influencing subsurface contaminant bioavailability, how these processes are modeled, and how the relative role of the various processes can be assessed through bioavailability indices. Although these processes are increasingly well understood, the use of sophisticated models and indices often are precluded by an inability to estimate the many parameters that are associated with complex models. Nonetheless, the proper representation of sorption, mass transfer, biodegradation, and co-solute effects can be critical in predicting bio-attenuation. The influence of these processes on contaminant fate is illustrated with numerical simulations for the simultaneous degradation of toluene (growth substrate) and trichloroethylene (nongrowth cometabolite) in hypothetical, aerobic, solid-water systems. The results show how the relative impacts on contaminant fate of the model's various component processes depends upon system conditions, including co-solute concentrations. Slow biodegradation rates increase the inhibition effects of a cometabolite and suppress the rate enhancement effects of a growth substrate. Irrespective of co-solute effects, contaminant fate is less sensitive to biodegradation processes in systems with strong sorption and slow desorption rates. Bioavailability indices can be used to relate these findings and to help identify appropriate modeling simplifications. In general, however, there remains a need to redefine such indices in order that bioavailability concepts can be better incorporated into site characterization, remediation design, and regulatory oversight.     

Effect of neem limonoids on lactate dehydrogenase (LDH) of the rice leaffolder, Cnaphalocrocis medinalis (Guenée) (Insecta: Lepidoptera: Pyralidae)

Neem is derived from the neem tree Azadirachta indica A. Juss. (Meliaceae), and its primary insecticidal component is the tetranortriterpenoid azadirachtin and other limonoids. The effect of neem limonoids azadirachtin, salannin, deacetylgedunin, gedunin, 17-hydroxyazadiradione and deacetylnimbin on enzyme lactate dehydrogenase (LDH) activity of the rice leaffolder (RLF) Cnaphalocrocis medinalis (Lepidoptera: Pyralidae) larvae was investigated. There was a decrease in enzyme activity relative to the control at all concentrations tested. When fed a diet of rice leaves treated with neem limonoids in bioassays, gut tissue enzyme, LDH levels in rice leaffolder larvae are affected. These results indicate neem limonoids affect LDH activity. These effects are most pronounced in early instar larvae. Azadirachtin was the most potent in of all the limonoids in all experiments indicating strong enzyme inhibition. Clear dose-response relationships were established with respect to LDH activity.     

Diel and tidal cycles regulate larval dynamics in salt marshes and mangrove forests

Variation in the release and recruitment of larvae of estuarine invertebrates affects the distribution and abundance of adults, as well as trophic interactions in both the plankton and the benthos. Larval release and supply are often timed to environmental cycles such as the diel and tidal cycles. Here, we determined using plankton tows whether the abundance of larvae spanning salt marsh and mangrove habitats across the intertidal landscape varied with diel and tidal cycles. Using three different sampling designs across two sites and within each of two estuaries over a 12-month period, we covered a range of spatial and temporal scales. This allowed us to test the general prediction that densities of meroplankton in the water column would be greater during nocturnal ebb tides than during other phases of the diel or tidal cycle. As predicted, nocturnal ebb tides yielded the highest densities of meroplanktonic larvae and were dominated by first-stage crab zoeae and this finding was most pronounced in the salt marsh. Throughout the course of the year, greater numbers of meroplankters consistently occurred during the ebb tide compared with the flood tide. The densities of other taxa (e.g. gastropods and polychaetes) showed no clear trends with diel or tidal cycles. This study highlights the effects of these pervasive physical cycles on the timing of larval release and supply in the salt marsh–mangrove complex, and emphasises their contribution to the trophic interactions and the dynamics of benthic populations within estuaries.