Spoiling the Whole Bunch: Quality Control Aimed at Preserving the Integrity of High-Throughput Genotyping

False-positive or false-negative results attributable to undetected genotyping errors and confounding factors present a constant challenge for genome-wide association studies (GWAS) given the low signals associated with complex phenotypes and the noise associated with high-throughput genotyping. In the context of the genetics of kidneys in diabetes (GoKinD) study, we identify a source of error in genotype calling and demonstrate that a standard battery of quality-control (QC) measures is not sufficient to detect and/or correct it. We show that, if genotyping and calling are done by plate (batch), even a few DNA samples of marginally acceptable quality can profoundly alter the allele calls for other samples on the plate. In turn, this leads to significant differential bias in estimates of allele frequency between plates and, potentially, to false-positive associations, particularly when case and control samples are not sufficiently randomized to plates. This problem may become widespread as investigators tap into existing public databases for GWAS control samples. We describe how to detect and correct this bias by utilizing additional sources of information, including raw signal-intensity data.     

Rate of Synthesis of Polyadenylate-Containing Ribonucleic Acid During the Yeast Cell Cycle

The rate of synthesis of polyadenylate-containing ribonucleic acid is constant throughout the cell cycle of Saccharomyces cerevisiae.     

The stimulatory effect of testosterone propionate and 17β-estradiol on 5′-methylthioadenosine phosphorylase activity in rat target tissues

The effect of castration and subsequent administration of 17β-estradiol and testosterone propionate on 5′-methylthioadenosine phosphorylase activity in rat target tissues was studied. Castration 34 days earlier resulted in a 95 reduction in ventral prostate 5′-methylthioadenosine phosphorylase activity and 16 days earlier in a 67% reduction in uterine 5′-methylthiodenosine phosphorylase activity. Four days of testosterone propionate administration stimulated ventral prostate 5′-methylhioadenosine phosphorylase activity 32% above castrate levels, which represented more than 50% of the intact control levels. 17β-Estradiol on the other hand stimulated uterine 5′-methylthioadenosine phosphorylase activity of 35% above castrate controls within 24h and with 3 days of continuous hormone treatment to within 97% of the intact control levels. However, castration and subsequent 17β-estradiol administration did not affect 5′-methylthioadenosine phosphorylase activity in rat liver and lung. Both prostate and uterine 5′-methylthioadenosine phosphorylase were shown to metabolize 5′-methylthioadenosine to 5′-methylthioribose through a 5′-methythiribose 1-phosphate intermediate. The data suggest that 5′-methylthioadenosine is not allowed to accumulate in rat target tissues even under conditions which are known to stimulate polyamine synthesis.     

FIELD STUDIES ON THE GIANT KELP NEREOCYSTIS1,2

An intertidal population of Nereocystis luetkeana was investigated in the field, and techniques for measuring sporophyte growth were developed. Primary regions of growth in plants prior to reproductive maturity were located in the bases of the blades, upper stipe, and holdfast. After reproductive areas on blades appeared, growth was confined to 2 major regions: the blade bases and the junction between lower stipe and holdfast where new holdfast haptera were produced. Complete deblading halted growth at whatever stage the plants had attained at the time of the operation but did not kill the plants. Partial deblading resulted in low but measurable growth rates in the blade bases. The data presented suggest that the function of the blades is twofold: they bear reproductive structures in the mature plants and. they may provide, materials used, in rapidly growing regions.     

Social Factors and Leukocyte DNA Methylation of Repetitive Sequences: The Multi-Ethnic Study of Atherosclerosis

Epigenetic changes are a potential mechanism contributing to race/ethnic and socioeconomic disparities in health. However, there is scant evidence of the race/ethnic and socioeconomic patterning of epigenetic marks. We used data from the Multi-Ethnic Study of Atherosclerosis Stress Study (N = 988) to describe age- and gender- independent associations of race/ethnicity and socioeconomic status (SES) with methylation of Alu and LINE-1 repetitive elements in leukocyte DNA. Mean Alu and Line 1 methylation in the full sample were 24% and 81% respectively. In multivariable linear regression models, African-Americans had 0.27% (p<0.01) and Hispanics 0.20% (p<0.05) lower Alu methylation than whites. In contrast, African-Americans had 0.41% (p<0.01) and Hispanics 0.39% (p<0.01) higher LINE-1 methylation than whites. These associations remained after adjustment for SES. In addition, a one standard deviation higher wealth was associated with 0.09% (p<0.01) higher Alu and 0.15% (p<0.01) lower LINE-1 methylation in age- and gender- adjusted models. Additional adjustment for race/ethnicity did not alter this pattern. No associations were observed with income, education or childhood SES. Our findings, from a large community-based sample, suggest that DNA methylation is socially patterned. Future research, including studies of gene-specific methylation, is needed to understand better the opposing associations of Alu and LINE-1 methylation with race/ethnicity and wealth as well as the extent to which small methylation changes in these sequences may influence disparities in health.