Genotype-informed estimation of risk of coronary heart disease based on genome-wide association data linked to the electronic medical record

<p>Abstract</p> <p>Background</p> <p>Susceptibility variants identified by genome-wide association studies (GWAS) have modest effect sizes. Whether such variants provide incremental information in assessing risk for common 'complex' diseases is unclear. We investigated whether measured and imputed genotypes from a GWAS dataset linked to the electronic medical record alter estimates of coronary heart disease (CHD) risk.</p> <p>Methods</p> <p>Study participants (<it>n </it>= 1243) had no known cardiovascular disease and were considered to be at high, intermediate, or low 10-year risk of CHD based on the Framingham risk score (FRS) which includes age, sex, total and HDL cholesterol, blood pressure, diabetes, and smoking status. Of twelve SNPs identified in prior GWAS to be associated with CHD, four were genotyped in the participants as part of a GWAS. Genotypes for seven SNPs were imputed from HapMap CEU population using the program MACH. We calculated a multiplex genetic risk score for each patient based on the odds ratios of the susceptibility SNPs and incorporated this into the FRS.</p> <p>Results</p> <p>The mean (SD) number of risk alleles was 12.31 (1.95), range 6-18. The mean (SD) of the weighted genetic risk score was 12.64 (2.05), range 5.75-18.20. The CHD genetic risk score was not correlated with the FRS (<it>P </it>= 0.78). After incorporating the genetic risk score into the FRS, a total of 380 individuals (30.6%) were reclassified into higher-(188) or lower-risk groups (192).</p> <p>Conclusion</p> <p>A genetic risk score based on measured/imputed genotypes at 11 susceptibility SNPs, led to significant reclassification in the 10-y CHD risk categories. Additional prospective studies are needed to assess accuracy and clinical utility of such reclassification.</p

The individual-cell-based cryo-chip for the cryopreservation, manipulation and observation of spatially identifiable cells. I: Methodology

<p>Abstract</p> <p>Background</p> <p>Cryopreservation is the only widely applicable method of storing vital cells for nearly unlimited periods of time. Successful cryopreservation is essential for reproductive medicine, stem cell research, cord blood storage and related biomedical areas. The methods currently used to retrieve a specific cell or a group of individual cells with specific biological properties after cryopreservation are quite complicated and inefficient.</p> <p>Results</p> <p>The present study suggests a new approach in cryopreservation, utilizing the Individual Cell-based Cryo-Chip (i3C). The i3C is made of materials having appropriate durability for cryopreservation conditions. The core of this approach is an array of picowells, each picowell designed to maintain an individual cell during the severe conditions of the freezing - thawing cycle and accompanying treatments. More than 97% of cells were found to retain their position in the picowells throughout the entire freezing - thawing cycle and medium exchange. Thus the comparison between pre-freezing and post-thawing data can be achieved at an individual cell resolution. The intactness of cells undergoing slow freezing and thawing, while residing in the i3C, was found to be similar to that obtained with micro-vials. However, in a fast freezing protocol, the i3C was found to be far superior.</p> <p>Conclusions</p> <p>The results of the present study offer new opportunities for cryopreservation. Using the present methodology, the cryopreservation of individual identifiable cells, and their observation and retrieval, at an individual cell resolution become possible for the first time. This approach facilitates the correlation between cell characteristics before and after the freezing - thawing cycle. Thus, it is expected to significantly enhance current cryopreservation procedures for successful regenerative and reproductive medicine.</p

Seventh to eleventh century CE glass from Northern Italy: between continuity and innovation

Previous analytical studies show that most of Northern Italian glass has been heavily recycled and that mixing of natron and plant ash glass was occurring (Verità and Toninato 1990; Verità et al. 2002; Uboldi and Verità 2003; Andreescu-Treadgold and Henderson 2006; Silvestri and Marcante 2011). The re-use of “old Roman glass” has been interpreted as stagnation in glass trade from the primary production areas. However, the reintroduction of plant ash glass on sites such as Torcello, Nogara, and in Lombardy at the same time as it was reintroduced in the Levant, strongly indicates long-distance contacts with the Levant at least from the eighth century CE. This paper addresses the key issue of recycling by focusing on the compositional nature of glass traded and reworked in Northern Italy after the seventh century CE set in a broad Mediterranean context by analysing major, minor, and trace elements in eighty-nine glass samples (seventh to the eleventh century AD) from the glass workshop of Piazza XX Settembre, Comacchio. Five major previously proposed compositional groups of glass have been identified from Comacchio (Levantine Apollonia and Jalame types, HIMT, Foy-2, and plant ash glass). The impact of recycling and mixing practices in Comacchio glass is also discussed with the help of known recycling markers and selected ratios (major and trace elements). The mixing between Levantine, HIMT, and plant ash glass is highlighted and end-members of potential natron to natron mixing compositional groups have been identified. The compositional nature of plant ash glass from Northern Italy is discussed in light of their trace element content and production areas

Do sexist mothers change more diapers? Ambivalent sexism, maternal gatekeeping and the division of childcare

This study examined the role of ambivalent sexist ideologies in the division of childcare responsibilities. It proposed maternal gatekeeping as a mediator through which hostile sexist attitudes toward men and women facilitate gendered division of childcare. A sample of 207 mothers with at least one child aged 6 years or younger completed extensive questionnaires. As hypothesized, the mother’s hostile sexist attitudes toward men and women were positively related to maternal gatekeeping tendencies. Gatekeeping, in turn, was related to the mother’s greater time investment in childcare and greater share of childcare tasks relative to the father. Finally, hostile sexist attitudes toward men and women had an indirect effect on the mother’s hours of care and relative share of childcare tasks, mediated though maternal gatekeeping. The findings underscore the importance of investigating the mechanisms through which sexist ideologies are translated into daily behaviors that help maintain a gendered social structure. They may be utilized to inform parenting interventions aimed at increasing collaborative family work and fathers’ participation

Glass groups, glass supply and recycling in late Roman Carthage

Carthage played an important role in maritime exchange networks during the Roman and late antique periods. One hundred ten glass fragments dating to the third to sixth centuries CE from a secondary deposit at the Yasmina Necropolis in Carthage have been analysed by electron microprobe analysis (EPMA) to characterise the supply of glass to the city. Detailed bivariate and multivariate data analysis identified different primary glass groups and revealed evidence of extensive recycling. Roman mixed antimony and manganese glasses with MnO contents in excess of 250 ppm were clearly the product of recycling, while iron, potassium and phosphorus oxides were frequent contaminants. Primary glass sources were discriminated using TiO2 as a proxy for heavy minerals (ilmenite/spinel), Al2O3 for feldspar and SiO2 for quartz in the glassmaking sands. It was thus possible to draw conclusions about the chronological and geographical attributions of the primary glass types. Throughout much of the period covered in this study, glassworkers in Carthage utilised glass from both Egyptian and Levantine sources. Based on their geochemical characteristics, we conclude that Roman antimony and Roman manganese glasses originated from Egypt and the Levant, respectively, and were more or less simultaneously worked at Carthage in the fourth century as attested by their mixed recycling (Roman Sb-Mn). In the later fourth and early fifth centuries, glasses from Egypt (HIMT) and the Levant (two Levantine I groups) continued to be imported to Carthage, although the Egyptian HIMT is less well represented at Yasmina than in many other late antique glass assemblages. In contrast, in the later fifth and sixth centuries, glass seems to have been almost exclusively sourced from Egypt in the form of a manganese-decolourised glass originally described and characterised by Foy and colleagues (2003). Hence, the Yasmina assemblage testifies to significant fluctuations in the supply of glass to Carthage that require further attention

Differential lipid dependence of the function of bacterial sodium channels

The lipid bilayer is important for maintaining the integrity of cellular compartments and plays a vital role in providing the hydrophobic and charged interactions necessary for membrane protein structure, conformational flexibility and function. To directly assess the lipid dependence of activity for voltage-gated sodium channels, we compared the activity of three bacterial sodium channel homologues (NaChBac, NavMs, and NavSp) by cumulative 22Na+ uptake into proteoliposomes containing a 3:1 ratio of 1-palmitoyl 2-oleoyl phosphatidylethanolamine and different “guest” glycerophospholipids. We observed a unique lipid profile for each channel tested. NavMs and NavSp showed strong preference for different negatively-charged lipids (phosphatidylinositol and phosphatidylglycerol, respectively), whilst NaChBac exhibited a more modest variation with lipid type. To investigate the molecular bases of these differences we used synchrotron radiation circular dichroism spectroscopy to compare structures in liposomes of different composition, and molecular modeling and electrostatics calculations to rationalize the functional differences seen. We then examined pore-only constructs (with voltage sensor subdomains removed) and found that in these channels the lipid specificity was drastically reduced, suggesting that the specific lipid influences on voltage-gated sodium channels arise primarily from their abilities to interact with the voltage-sensing subdomains

Polymorphisms in the Estrogen Receptor 1 and Vitamin C and Matrix Metalloproteinase Gene Families Are Associated with Susceptibility to Lymphoma

BACKGROUND: Non-Hodgkin lymphoma (NHL) is the fifth most common cancer in the U.S. and few causes have been identified. Genetic association studies may help identify environmental risk factors and enhance our understanding of disease mechanisms. METHODOLOGY/PRINCIPAL FINDINGS: 768 coding and haplotype tagging SNPs in 146 genes were examined using Illumina GoldenGate technology in a large population-based case-control study of NHL in the San Francisco Bay Area (1,292 cases 1,375 controls are included here). Statistical analyses were restricted to HIV- participants of white non-Hispanic origin. Genes involved in steroidogenesis, immune function, cell signaling, sunlight exposure, xenobiotic metabolism/oxidative stress, energy balance, and uptake and metabolism of cholesterol, folate and vitamin C were investigated. Sixteen SNPs in eight pathways and nine haplotypes were associated with NHL after correction for multiple testing at the adjusted q<0.10 level. Eight SNPs were tested in an independent case-control study of lymphoma in Germany (494 NHL cases and 494 matched controls). Novel associations with common variants in estrogen receptor 1 (ESR1) and in the vitamin C receptor and matrix metalloproteinase gene families were observed. Four ESR1 SNPs were associated with follicular lymphoma (FL) in the U.S. study, with rs3020314 remaining associated with reduced risk of FL after multiple testing adjustments [odds ratio (OR) = 0.42, 95% confidence interval (CI) = 0.23-0.77) and replication in the German study (OR = 0.24, 95% CI = 0.06-0.94). Several SNPs and haplotypes in the matrix metalloproteinase-3 (MMP3) and MMP9 genes and in the vitamin C receptor genes, solute carrier family 23 member 1 (SLC23A1) and SLC23A2, showed associations with NHL risk. CONCLUSIONS/SIGNIFICANCE: Our findings suggest a role for estrogen, vitamin C and matrix metalloproteinases in the pathogenesis of NHL that will require further validation

Genome-Wide Meta-Analysis Identifies Regions on 7p21 (AHR) and 15q24 (CYP1A2) As Determinants of Habitual Caffeine Consumption

We report the first genome-wide association study of habitual caffeine intake. We included 47,341 individuals of European descent based on five population-based studies within the United States. In a meta-analysis adjusted for age, sex, smoking, and eigenvectors of population variation, two loci achieved genome-wide significance: 7p21 (P = 2.4×10−19), near AHR, and 15q24 (P = 5.2×10−14), between CYP1A1 and CYP1A2. Both the AHR and CYP1A2 genes are biologically plausible candidates as CYP1A2 metabolizes caffeine and AHR regulates CYP1A2

Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption.

Coffee, a major dietary source of caffeine, is among the most widely consumed beverages in the world and has received considerable attention regarding health risks and benefits. We conducted a genome-wide (GW) meta-analysis of predominately regular-type coffee consumption (cups per day) among up to 91 462 coffee consumers of European ancestry with top single-nucleotide polymorphisms (SNPs) followed-up in ~30 062 and 7964 coffee consumers of European and African-American ancestry, respectively. Studies from both stages were combined in a trans-ethnic meta-analysis. Confirmed loci were examined for putative functional and biological relevance. Eight loci, including six novel loci, met GW significance (log10Bayes factor (BF)&gt;5.64) with per-allele effect sizes of 0.03-0.14 cups per day. Six are located in or near genes potentially involved in pharmacokinetics (ABCG2, AHR, POR and CYP1A2) and pharmacodynamics (BDNF and SLC6A4) of caffeine. Two map to GCKR and MLXIPL genes related to metabolic traits but lacking known roles in coffee consumption. Enhancer and promoter histone marks populate the regions of many confirmed loci and several potential regulatory SNPs are highly correlated with the lead SNP of each. SNP alleles near GCKR, MLXIPL, BDNF and CYP1A2 that were associated with higher coffee consumption have previously been associated with smoking initiation, higher adiposity and fasting insulin and glucose but lower blood pressure and favorable lipid, inflammatory and liver enzyme profiles (P&lt;5 × 10-8).Our genetic findings among European and African-American adults reinforce the role of caffeine in mediating habitual coffee consumption and may point to molecular mechanisms underlying inter-individual variability in pharmacological and health effects of coffee

Perceived quality of life among caregivers of children with a childhood-onset dystrophinopathy: a double ABCX model of caregiver stressors and perceived resources

Background: Duchenne and Becker muscular dystrophies, collectively referred to as dystrophinopathies, are recessive X-linked disorders characterized by progressive muscle weakness and ultimately cardiac and respiratory failure. Immediate family members are often primary caregivers of individuals with a dystrophinopathy. Methods: We explored the impact of this role by inviting primary caregivers (n = 209) of males diagnosed with childhood-onset dystrophinopathy who were identified by the Muscular Dystrophy Surveillance, Tracking, and Research Network (MD STARnet) to complete a mailed questionnaire measuring perceived social support and stress, spirituality, and family quality of life (FQoL). Bivariate and multivariate analyses examined associations between study variables using the Double ABCX model as an analytic framework. Results: Higher stressor pile-up was associated with lower perceived social support (r = -0.29, p 0.05). FQoL was positively associated with all support measures (correlations ranged from: 0.25 to 0.58, p-values 0.01-0.001) and negatively associated with perceived stress and control (r = -0.49, p <.001). The association between stressor pile-up and FQoL was completely mediated through global perceived social support, supportive family relationships, and perceived stress and control; supportive non-family relationships did not remain statistically significant after controlling for other mediators. Conclusions: Findings suggest caregiver adaptation to a dystrophinopathy diagnosis can be optimized by increased perceived control, supporting family resources, and creation of a healthy family identity. Our findings will help identify areas for family intervention and guide clinicians in identifying resources that minimize stress and maximize family adaptation.CDC [5U01DD000831, 5U01DD000187, 5U01DD000189, 5U01DD000191, 5U01DD000190]This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]