Development and validation of a computational method for assessment of missense variants in hypertrophic cardiomyopathy

Assessing the significance of novel genetic variants revealed by DNA sequencing is a major challenge to the integration of genomic techniques with medical practice. Many variants remain difficult to classify by traditional genetic methods. Computational methods have been developed that could contribute to classifying these variants, but they have not been properly validated and are generally not considered mature enough to be used effectively in a clinical setting. We developed a computational method for predicting the effects of missense variants detected in patients with hypertrophic cardiomyopathy (HCM). We used a curated clinical data set of 74 missense variants in six genes associated with HCM to train and validate an automated predictor. The predictor is based on support vector regression and uses phylogenetic and structural features specific to genes involved in HCM. Ten-fold cross validation estimated our predictor's sensitivity at 94% (95% confidence interval: 83%-98%) and specificity at 89% (95% confidence interval: 72%-100%). This corresponds to an odds ratio of 10 for a prediction of pathogenic (95% confidence interval: 4.0-infinity), or an odds ratio of 9.9 for a prediction of benign (95% confidence interval: 4.6-21). Coverage (proportion of variants for which a prediction was made) was 57% (95% confidence interval: 49%-64%). This performance exceeds that of existing methods that are not specifically designed for HCM. The accuracy of this predictor provides support for the clinical use of automated predictions alongside family segregation and population frequency data in the interpretation of new missense variants and suggests future development of similar tools for other diseases.     

Dental handpiece contamination: a proteomics and surface analysis approach

Dental handpieces (DHPs) become biofouled internally with patient derived material that is difficult to access for removal and inactivation. This study undertook a quantitative and qualitative investigation of protein contamination of internal components from three different types of DHP: the turbine, slow speed contra-angle and surgical. Eluates from the high speed turbine, low speed spray channels and surgical gear were assayed for protein using an orthophthaldehyde assay. Eluates concentrated by Amicon ultrafiltration were also analysed by SDS-PAGE, mass spectroscopy, Western blotting and ELISA. The surfaces of handpiece components were also investigated by SEM, EFSCAN and EDAX microscopy. Surgical gears contained highest levels of protein (403?μg), followed by low speed spray channels (17.7?μg) and the high speed turbine (<5?μg). Mass spectroscopy of surgical gears demonstrated mostly serum derived proteins. Decontamination of the DHPs using an automated washer disinfector and handpiece irrigator showed a significant reduction in residual protein levels.     

The Parasitic Eyeworm Oxyspirura petrowi as a Possible Cause of Decline in the Threatened Lesser Prairie-Chicken (Tympanuchus pallidicinctus)

Lesser prairie-chickens (Tympanuchus pallidicinctus) have been declining range wide since the early 1900''s despite efforts to establish conservation and improve their habitat. In early 2014, the lesser prairie-chicken was listed as a threatened species under the U.S Endangered Species Act and the need to find out why they are declining is more important than ever. Nine hunter shot lesser prairie-chickens were donated and sampled for the presence or absence of the eyeworm Oxyspirura petrowi, a known parasite that can cause damage to the eye of its host, and common environmental contaminants. Eyeworm infection was found in 7 of 9 birds (78% infection rate) with an infection range between 0–16 O. petrowi per bird. Breast, liver, and fat tissue samples from the lesser prairie-chickens were analyzed for the frequency of 20 organochlorine pesticides. Femurs and livers were also tested on these birds for metal contaminants. Pesticides were found in several samples above the detection limits but were still in the low ng/g range. Notable was the ubiquitous presence of endrin aldehyde across all tissues. One femur showed 5.66 µg/g of lead (Pb) but this is still relatively low. No liver samples had elevated mercury (Hg) above detection limits. The presence of these organochlorines is consistent with the historic use of pesticides in this region. With pesticide and metals found in such low levels and parasitic nematode infections at rather high levels, it is recommended that these parasites be further evaluated as a contributing factor to the decline of the lesser prairie-chicken.     

Fine structure of cytoplasmic inclusions of some methylotrophic bacteria from plant surfaces

Five strains of pink-pigmented, facultatively methylotrophic bacteria (PPFM) isolated from plant surfaces and grown in different carbon sources, were fixed, embedded and sectioned for examination with the electron microscope. The strains studied represented the two mainsub-groups, those that can use carbohydrates and those that can not use carbohydrates as a sole carbon and energy source. All of the isolates examined, produced crystalloid inclusions, internal membranous vesicles and internal membranous sheets although the number of cells with inclusions, varied with the carbon source and specific strain. Polybetahydroxybutyrate and polyphosphate bodies were observed in all strains, with all carbon sources used for growing cells which includes methanol, formate and glycerol. Isolates that could use glucose accumulated polyglucoside granules but not when other carbon sources were provided. The relationship of these inclusions to growth conditions is discussed.     

South African mouse shrews (<Emphasis Type="Italic">Myosorex</Emphasis>) feel the heat: using species distribution models (SDMs) and IUCN Red List criteria to flag extinction risks due to climate change

Five species of mouse or forest shrews (Myosorex) are endemic to South Africa, Lesotho and Swaziland, four of which (Myosorex varius, Myosorex cafer, Myosorex longicaudatus and Myosorex cf. tenuis) are associated with montane or temperate grassland, fynbos and/or forest habitats while a fifth (Myosorex sclateri) is associated with lowland subtropical forests. Due to their small size, specialised habitat, low dispersal capacity, high metabolism and sensitivity to temperature extremes, we predicted that, particularly for montane species, future climate change should have a negative impact on area of occupancy (AOO) and ultimately extinction risks. Species distribution models (SDMs) indicated general declines in AOO of three species by 2050 under the A1b and A2 climate change scenarios (M. cafer, M. varius, M. longicaudatus) while two species (M. sclateri and M. cf. tenuis) remained unchanged (assuming no dispersal) or increased their AOO (assuming dispersal). While temperate species such as M. varius appear to be limited by temperature maxima (preferring cooler temperatures), the subtropical species M. sclateri appears to be limited by temperature minima (preferring warmer temperatures). Evidence for declines in AOO informed the uplisting (to a higher category of threat) of the Red List status of four Myosorex species to either vulnerable or endangered as part of a separate regional International Union for Conservation of Nature (IUCN) Red List assessment.     

A general method for purification of deoxycytidine kinase.

Deoxycytidine kinase from a variety of animal tissues binds to Cibacron Blue 3G-A coupled to Sepharose CL-6B. The enzyme can be selectively eluted with ATP to yield single-step purifications of 17-89-fold. The affinity adsorbent is re-usable.     

Plant carbon allocation drives turnover of old soil organic matter in permafrost tundra soils

Carbon cycle feedbacks from permafrost ecosystems are expected to accelerate global climate change. Shifts in vegetation productivity and composition in permafrost regions could influence soil organic carbon (SOC) turnover rates via rhizosphere (root zone) priming effects (RPEs), but these processes are not currently accounted for in model predictions. We use a radiocarbon (bomb‐¹⁴C) approach to test for RPEs in two Arctic tall shrubs, alder (Alnus viridis (Chaix) DC.) and birch (Betula glandulosa Michx.), and in ericaceous heath tundra vegetation. We compare surface CO₂ efflux rates and ¹⁴C content between intact vegetation and plots in which below‐ground allocation of recent photosynthate was prevented by trenching and removal of above‐ground biomass. We show, for the first time, that recent photosynthate drives mineralization of older (>50 years old) SOC under birch shrubs and ericaceous heath tundra. By contrast, we find no evidence of RPEs in soils under alder. This is the first direct evidence from permafrost systems that vegetation influences SOC turnover through below‐ground C allocation. The vulnerability of SOC to decomposition in permafrost systems may therefore be directly linked to vegetation change, such that expansion of birch shrubs across the Arctic could increase decomposition of older SOC. Our results suggest that carbon cycle models that do not include RPEs risk underestimating the carbon cycle feedbacks associated with changing conditions in tundra regions.     

Serum Iron Levels and the Risk of Parkinson Disease: A Mendelian Randomization Study

Background

Although levels of iron are known to be increased in the brains of patients with Parkinson disease (PD), epidemiological evidence on a possible effect of iron blood levels on PD risk is inconclusive, with effects reported in opposite directions. Epidemiological studies suffer from problems of confounding and reverse causation, and mendelian randomization (MR) represents an alternative approach to provide unconfounded estimates of the effects of biomarkers on disease. We performed a MR study where genes known to modify iron levels were used as instruments to estimate the effect of iron on PD risk, based on estimates of the genetic effects on both iron and PD obtained from the largest sample meta-analyzed to date.

Methods and Findings

We used as instrumental variables three genetic variants influencing iron levels, HFE rs1800562, HFE rs1799945, and TMPRSS6 rs855791. Estimates of their effect on serum iron were based on a recent genome-wide meta-analysis of 21,567 individuals, while estimates of their effect on PD risk were obtained through meta-analysis of genome-wide and candidate gene studies with 20,809 PD cases and 88,892 controls. Separate MR estimates of the effect of iron on PD were obtained for each variant and pooled by meta-analysis. We investigated heterogeneity across the three estimates as an indication of possible pleiotropy and found no evidence of it. The combined MR estimate showed a statistically significant protective effect of iron, with a relative risk reduction for PD of 3% (95% CI 1%–6%; p = 0.001) per 10 µg/dl increase in serum iron.

Conclusions

Our study suggests that increased iron levels are causally associated with a decreased risk of developing PD. Further studies are needed to understand the pathophysiological mechanism of action of serum iron on PD risk before recommendations can be made. Please see later in the article for the Editors'' Summary