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.     

Loss of T cell antigen recognition arising from changes in peptide and major histocompatibility complex protein flexibility: implications for vaccine design

Modification of the primary anchor positions of antigenic peptides to improve binding to major histocompatibility complex (MHC) proteins is a commonly used strategy for engineering peptide-based vaccine candidates. However, such peptide modifications do not always improve antigenicity, complicating efforts to design effective vaccines for cancer and infectious disease. Here we investigated the MART-1(27-35) tumor antigen, for which anchor modification (replacement of the position two alanine with leucine) dramatically reduces or ablates antigenicity with a wide range of T cell clones despite significantly improving peptide binding to MHC. We found that anchor modification in the MART-1(27-35) antigen enhances the flexibility of both the peptide and the HLA-A*0201 molecule. Although the resulting entropic effects contribute to the improved binding of the peptide to MHC, they also negatively impact T cell receptor binding to the peptide·MHC complex. These results help explain how the "anchor-fixing" strategy fails to improve antigenicity in this case, and more generally, may be relevant for understanding the high specificity characteristic of the T cell repertoire. In addition to impacting vaccine design, modulation of peptide and MHC flexibility through changes to antigenic peptides may present an evolutionary strategy for the escape of pathogens from immune destruction.     

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 functional and numerical response of Typhlodromips swirskii (Acari: Phytoseiidae) to the factitious prey Suidasia medanensis (Acari: Suidasidae) in the context of a breeding sachet

The whitefly and thrips predator Typhlodromips swirskii (Athias-Henriot) (Acari: Phytoseiidae) can be reared on the factitious astigmatid mite Suidasia medanensis (Oudemans) (Acari: Suidasiidae). The predator–prey relationship allows the system to be incorporated into a breeding sachet which releases predators into a crop over several weeks ensuring predator presence on arrival of the target pests and increased predator numerical response on the crop through immigration from the breeding sachet. This study investigated whether the prey preference and functional and numerical response of T. swirskii to different development stages of S. medanensis can provide understanding of the predator–prey interactions sustaining such a breeding sachet. T. swirskii elicited a strong preference to egg stages of S. medanensis, exhibited a Type II functional response and increased oviposition rate with increasing prey density. The relevance of these attributes to a balanced breeding sachet is discussed.     

The Burden Attributable to Mental and Substance Use Disorders as Risk Factors for Suicide: Findings from the Global Burden of Disease Study 2010

Background

The Global Burden of Disease Study 2010 (GBD 2010) identified mental and substance use disorders as the 5^th leading contributor of burden in 2010, measured by disability adjusted life years (DALYs). This estimate was incomplete as it excluded burden resulting from the increased risk of suicide captured elsewhere in GBD 2010''s mutually exclusive list of diseases and injuries. Here, we estimate suicide DALYs attributable to mental and substance use disorders.

Methods

Relative-risk estimates of suicide due to mental and substance use disorders and the global prevalence of each disorder were used to estimate population attributable fractions. These were adjusted for global differences in the proportion of suicide due to mental and substance use disorders compared to other causes then multiplied by suicide DALYs reported in GBD 2010 to estimate attributable DALYs (with 95% uncertainty).

Results

Mental and substance use disorders were responsible for 22.5 million (14.8–29.8 million) of the 36.2 million (26.5–44.3 million) DALYs allocated to suicide in 2010. Depression was responsible for the largest proportion of suicide DALYs (46.1% (28.0%–60.8%)) and anorexia nervosa the lowest (0.2% (0.02%–0.5%)). DALYs occurred throughout the lifespan, with the largest proportion found in Eastern Europe and Asia, and males aged 20–30 years. The inclusion of attributable suicide DALYs would have increased the overall burden of mental and substance use disorders (assigned to them in GBD 2010 as a direct cause) from 7.4% (6.2%–8.6%) to 8.3% (7.1%–9.6%) of global DALYs, and would have changed the global ranking from 5^th to 3^rd leading cause of burden.

Conclusions

Capturing the suicide burden attributable to mental and substance use disorders allows for more accurate estimates of burden. More consideration needs to be given to interventions targeted to populations with, or at risk for, mental and substance use disorders as an effective strategy for suicide prevention.     

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.