Promises,pitfalls and practicalities of prenatal whole exome sequencing

Prenatal genetic diagnosis provides information for pregnancy and perinatal decision-making and management. In several small series, prenatal whole exome sequencing (WES) approaches have identified genetic diagnoses when conventional tests (karyotype and microarray) were not diagnostic. Here, we review published prenatal WES studies and recent conference abstracts. Thirty-one studies were identified, with diagnostic rates in series of five or more fetuses varying between 6.2% and 80%. Differences in inclusion criteria and trio versus singleton approaches to sequencing largely account for the wide range of diagnostic rates. The data suggest that diagnostic yields will be greater in fetuses with multiple anomalies or in cases preselected following genetic review. Beyond its ability to improve diagnostic rates, we explore the potential of WES to improve understanding of prenatal presentations of genetic disorders and lethal fetal syndromes. We discuss prenatal phenotyping limitations, counselling challenges regarding variants of uncertain significance, incidental and secondary findings, and technical problems in WES. We review the practical, ethical, social and economic issues that must be considered before prenatal WES could become part of routine testing. Finally, we reflect upon the potential future of prenatal genetic diagnosis, including a move towards whole genome sequencing and non-invasive whole exome and whole genome testing. © 2017 John Wiley & Sons, Ltd.     

Development and Application of Critical,Target and Monitoring Loads for the Management of Acid Deposition in Alberta,Canada

The Alberta, Canada acid deposition management framework, based upon the application of critical, target and monitoring loads, is described. This framework is the culmination of four years work by stakeholders brought together within Alberta's Clean Air Strategic Alliance (CASA). The elements of the framework include scientific aspects of measurement, model estimation, and monitoring of acid deposition, assessment of receptor sensitivity, and management processes to reduce emissions and deposition (should reductions become necessary). All loads are applied to grid cells measuring 1°latitude × 1° longitude, with each cell being categorized as sensitive, moderately sensitive or of low sensitivity on the basis of the sensitivities of the soil and water systems within the cell. Critical loads have been set at 0.25, 0.50 and 1.00 keq H⁺ ha^-1 yr^-1 for grid cells that are categorized as sensitive, moderately sensitive, and of low sensitivity, respectively. Target loads, the environmental management objectives, have been set at 0.22, 0.45, and 0.90 keq H⁺ ha^-1 yr^-1, and monitoring loads, a new concept in acid deposition management, have been set at 0.17, 0.35 and 0.70 keq H⁺ ha^-1 yr^-1 for the three sensitivity classes. When model prediction indicates that deposition may be exceeding the monitoring load, deposition monitoring and receptor sensitivity studies are to be initiated to confirm the deposition model prediction, and to ensure that the sensitivity of the recipient systems is understood. In this manner, management actions that occur in the event of a target load exceedance will be based upon receptor sensitivity and deposition data rather than upon model prediction alone. A process for stakeholder involvement in the evaluation of the framework and its application in long-term, long-range management of emissions and deposition is also included within the framework.     

Land-cover change within and around protected areas in a biodiversity hotspot

The landscape surrounding protected areas influences their ability to maintain ecosystem functions and achieve conservation goals. As anthropogenic intensification continues, it is important to monitor land-use and land-cover change in and around protected areas. We measure land-cover change surrounding protected areas in the Maputaland-Pondoland-Albany Biodiversity hotspot from the 1980s to present. Using Landsat imagery, we classified land cover within and around each protected area. Agricultural land uses were increasing and often directly border protected area boundaries. Human settlements increased around every protected area, potentially increasing human activity along the edges of protected areas and threatening their ecological integrity. Urban expansion around protected areas varied but increased as much as 10%. Woody vegetation cover varied both within and around protected areas with possible evidence of deforestation and shrub encroachment throughout the hotspot. We recommend monitoring land cover across southeastern Africa to better understand regional trends in land-use impacts to protected areas.     

Plant growth rates and seed size: a re-evaluation

Small-seeded plant species are often reported to have high relative growth rate or RGR. However, because RGR declines as plants grow larger, small-seeded species could achieve higher RGR simply by virtue of their small size. In contrast, size-standardized growth rate or SGR factors out these size effects. Differences in SGR can thus only be due to differences in morphology, allocation, or physiology. We used nonlinear regression to calculate SGR for comparison with RGR for 10 groups of species spanning a wide range of life forms. We found that RGR was negatively correlated with seed mass in nearly all groups, but the relationship between SGR and seed mass was highly variable. We conclude that small-seeded species only sometimes possess additional adaptations for rapid growth over and above their general size advantage.     

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.     

Computer-based training for safety: comparing methods with older and younger workers

INTRODUCTION: Computer-based safety training is becoming more common and is being delivered to an increasingly aging workforce. Aging results in a number of changes that make it more difficult to learn from certain types of computer-based training. Instructional designs derived from cognitive learning theories may overcome some of these difficulties. METHODS: Three versions of computer-based respiratory safety training were shown to older and younger workers who then took a high and a low level learning test. RESULTS: Younger workers did better overall. Both older and younger workers did best with the version containing text with pictures and audio narration. DISCUSSION: Computer-based training with pictures and audio narration may be beneficial for workers over 45 years of age. IMPACT ON INDUSTRY: Computer-based safety training has advantages but workers of different ages may benefit differently. Computer-based safety programs should be designed and selected based on their ability to effectively train older as well as younger learners.     

Foraging areas differentially affect reproductive output and interpretation of trends in abundance of loggerhead turtles

Diet items and habitat constitute some of the environmental resources that may be used differently by individuals within a population. Long-term fidelity by individuals to particular resources exemplifies individual specialization, a phenomenon that is becoming increasingly recognized across a wide range of species. Less is understood about the consequences of such specialization. Here, we investigate the effects of differential foraging ground use on reproductive output in 183 loggerhead sea turtles (Caretta caretta) nesting at Wassaw Island, Georgia (31.89°N, 80.97°W), between 2004 and 2011 with resulting possible fitness effects. Stable isotope analysis was used to assign the adult female loggerheads to one of three foraging areas in the Northwest Atlantic Ocean. Our data indicate that foraging area preference influences the size, fecundity, and breeding periodicity of adult female loggerhead turtles. We also found that the proportion of turtles originating from each foraging area varied significantly among the years examined. The change in the number of nesting females across the years of the study was not a result of uniform change from all foraging areas. We develop a novel approach to assess differential contributions of various foraging aggregations to changes in abundance of a sea turtle nesting aggregation using stable isotopes. Our approach can provide an improved understanding of the influences on the causes of increasing or decreasing population trends and allow more effective monitoring for these threatened species and other highly migratory species.     

High degree of paternity loss in a species with alternative reproductive tactics

In many mating systems, males adopt alternative reproductive tactics (ARTs) to maximize reproductive success. In fishes, guarding males often invest more energy into courtship, defense, and paternal care, whereas cuckolding males forego such costs and steal fertilizations by releasing their sperm in the nest of a guarding male. These two tactics have been documented in the plainfin midshipman fish (Porichthys notatus), yet the relative reproductive success of the guarding and cuckolding male tactics remains unknown. In this study, we used microsatellite markers to determine the level of paternity of the guarding type I males. We explored how paternity varied with male phenotype and across the breeding season. Our results revealed the lowest documented levels of paternity in a species with obligate paternal care. Although paternity remained consistently low, it did increase as the breeding season progressed. Male body size did not significantly predict paternity. The low paternity in this species may be explained, in part, by aspects of their reproductive ecology including the duration of parental care period, limited nest availability and competition for nests, as well as the occurrence of nest takeovers. Overall, our findings contribute to the understanding of the ultimate factors underlying ARTs in this species and highlight the importance of investigating reproductive success across the entire breeding season.     

Temporal, spatial, and body size effects on growth rates of loggerhead sea turtles (Caretta caretta) in the Northwest Atlantic

In response to a call from the US National Research Council for research programs to combine their data to improve sea turtle population assessments, we analyzed somatic growth data for Northwest Atlantic (NWA) loggerhead sea turtles (Caretta caretta) from 10 research programs. We assessed growth dynamics over wide ranges of geography (9–33°N latitude), time (1978–2012), and body size (35.4–103.3 cm carapace length). Generalized additive models revealed significant spatial and temporal variation in growth rates and a significant decline in growth rates with increasing body size. Growth was more rapid in waters south of the USA (<24°N) than in USA waters. Growth dynamics in southern waters in the NWA need more study because sample size was small. Within USA waters, the significant spatial effect in growth rates of immature loggerheads did not exhibit a consistent latitudinal trend. Growth rates declined significantly from 1997 through 2007 and then leveled off or increased. During this same interval, annual nest counts in Florida declined by 43 % (Witherington et al. in Ecol Appl 19:30–54, 2009) before rebounding. Whether these simultaneous declines reflect responses in productivity to a common environmental change should be explored to determine whether somatic growth rates can help interpret population trends based on annual counts of nests or nesting females. Because of the significant spatial and temporal variation in growth rates, population models of NWA loggerheads should avoid employing growth data from restricted spatial or temporal coverage to calculate demographic metrics such as age at sexual maturity.