Use of Allele-Specific FAIRE to Determine Functional Regulatory Polymorphism Using Large-Scale Genotyping Arrays

Following the widespread use of genome-wide association studies (GWAS), focus is turning towards identification of causal variants rather than simply genetic markers of diseases and traits. As a step towards a high-throughput method to identify genome-wide, non-coding, functional regulatory variants, we describe the technique of allele-specific FAIRE, utilising large-scale genotyping technology (FAIRE-gen) to determine allelic effects on chromatin accessibility and regulatory potential. FAIRE-gen was explored using lymphoblastoid cells and the 50,000 SNP Illumina CVD BeadChip. The technique identified an allele-specific regulatory polymorphism within NR1H3 (coding for LXR-α), rs7120118, coinciding with a previously GWAS-identified SNP for HDL-C levels. This finding was confirmed using FAIRE-gen with the 200,000 SNP Illumina Metabochip and verified with the established method of TaqMan allelic discrimination. Examination of this SNP in two prospective Caucasian cohorts comprising 15,000 individuals confirmed the association with HDL-C levels (combined beta = 0.016; p = 0.0006), and analysis of gene expression identified an allelic association with LXR-α expression in heart tissue. Using increasingly comprehensive genotyping chips and distinct tissues for examination, FAIRE-gen has the potential to aid the identification of many causal SNPs associated with disease from GWAS.     

Six novel susceptibility Loci for early-onset androgenetic alopecia and their unexpected association with common diseases

Androgenetic alopecia (AGA) is a highly heritable condition and the most common form of hair loss in humans. Susceptibility loci have been described on the X chromosome and chromosome 20, but these loci explain a minority of its heritable variance. We conducted a large-scale meta-analysis of seven genome-wide association studies for early-onset AGA in 12,806 individuals of European ancestry. While replicating the two AGA loci on the X chromosome and chromosome 20, six novel susceptibility loci reached genome-wide significance (p = 2.62×10⁻⁹–1.01×10⁻¹²). Unexpectedly, we identified a risk allele at 17q21.31 that was recently associated with Parkinson''s disease (PD) at a genome-wide significant level. We then tested the association between early-onset AGA and the risk of PD in a cross-sectional analysis of 568 PD cases and 7,664 controls. Early-onset AGA cases had significantly increased odds of subsequent PD (OR = 1.28, 95% confidence interval: 1.06–1.55, p = 8.9×10⁻³). Further, the AGA susceptibility alleles at the 17q21.31 locus are on the H1 haplotype, which is under negative selection in Europeans and has been linked to decreased fertility. Combining the risk alleles of six novel and two established susceptibility loci, we created a genotype risk score and tested its association with AGA in an additional sample. Individuals in the highest risk quartile of a genotype score had an approximately six-fold increased risk of early-onset AGA [odds ratio (OR) = 5.78, p = 1.4×10⁻⁸⁸]. Our results highlight unexpected associations between early-onset AGA, Parkinson''s disease, and decreased fertility, providing important insights into the pathophysiology of these conditions.     

Effect of Bednets and Indoor Residual Spraying on Spatio-Temporal Clustering of Malaria in a Village in South Ethiopia: A Longitudinal Study

Background

Understanding the spatio-temporal pattern of malaria transmission where prevention and control measures are in place will help to fine-tune strategies. The objective of this study was to assess the effect of mass distribution of bednets and indoor residual spraying (IRS) with insecticides on the spatio-temporal clustering of malaria in one malaria endemic village in south Ethiopia.

Methods

A longitudinal study was conducted from April 2009 to April 2011. The average population was 6631 in 1346 locations. We used active and passive searches for malaria cases for 101 weeks. SatScan v9.1.1 was used to identify statistically significant retrospective space–time clusters. A discrete Poisson based model was applied with the aim of identifying areas with high rates. PASW Statistics 18 was used to build generalized Poisson loglinear model.

Results

The total number of both types of malaria episodes was 622, giving 45.1 episodes per 1000 persons per year; among these, episodes of Plasmodium falciparum and vivax infection numbered 316 (22.9 per 1000 per year) and 306 (22.2 per 1000 per year), respectively. IRS with Dichlorodiphenyltrichloroethane (DDT) and later with Deltamethrin and free mass distribution of insecticide-treated nets (ITNs) were carried out during the study period. There was space–time clustering of malaria episodes at a household level. The spatio-temporal clustering of malaria was not influenced by free mass distribution of ITNs; however, the time-span of the spatio-temporal clustering of malaria cases ended after IRS with Deltamethrin. The presence of clusters on the south-east edge of the village was consistent with the finding of an increasing risk of acquiring malaria infection for individuals who lived closer to the identified vector breeding site.

Conclusion

The risk of getting malaria infection varied significantly within one village. Free mass distribution of ITNs did not influence the spatio-temporal clustering of malaria, but IRS might have eliminated malaria clustering.     

Specific leaf area as a superior predictor of changes in field layer abundance during forest succession

Question : How accurately can a suite of suggested functional traits predict plant species response to succession from semi‐open woodland to closed deciduous canopy forest? Location : Southeastern Sweden. Methods : Abundance of 46 field‐layer plant species in a temperate deciduous forest, measured as frequency of occupied plots, was estimated in 1961, 1970 and 2003. Abundance change over time across species was tested for correlations with functional traits and literature information on habitat preference. Results : Increase in abundance was positively correlated with specific leaf area (SLA), weakly negatively correlated with seed mass and not significantly correlated with plant height or start, peak and length of the flowering period. Change in abundance was correlated with the Ellenberg light indicator value, whereas no correlations were found with Ellenberg values for nitrogen, calcium and moisture, or forest preference according to the literature. Conclusions : SLA was a better predictor of how field layer plants responded to succession from semi‐open woodland to closed canopy forest than empirically‐derived measures of habitat preference. The same holds for SLA in relation to seed size, indicating that interactions in the established life‐cycle phase are more important than the recruitment phase for species response to succession.     

Crystallization of and preliminary X-ray data for bovine carbonic anhydrase III

Crystals of bovine carbonic anhydrase III have been grown in a solution of polyethylene glycol. The crystals are monoclinic, space group P2(1), with the unit cell parameters a = 50.6 A, b = 44.7 A, c = 56.9 A, and beta = 90.3 degrees. The asymmetric unit contains 1 molecule. The diffraction pattern extends beyond 2.0-A resolution.     

Renal 25-hydroxyvitamin D-3 1 alpha-hydroxylase in guinea-pig: activity variations during development and pregnancy

The renal 25-hydroxyvitamin D-3-1 alpha-hydroxylase (1 alpha-hydroxylase) activity and circulating levels of 1,25-dihydroxyvitamin D (1,25(OH)2D) were measured in pregnant guinea-pigs and their offspring. Serum levels of 1,25(OH)2D were significantly elevated in pregnant guinea-pigs but the renal enzyme activity was not different from non-pregnant animals. The fetal renal 1 alpha-hydroxylase activity was about 6-fold higher than the maternal level, whereas circulating 1,25(OH)2D was low. Treatment with pharmacological doses of 1,25(OH)2D3 increased circulating 1,25(OH)2D and depressed the renal 1 alpha-hydroxylases both in the mother and the fetus. In newborn guinea-pigs the enzyme activity was up to 10-times that seen in adults. It declined over the first 3 weeks, showing no difference between the sexes. In sexually mature animals the males had a significantly higher 1 alpha-hydroxylase activity than the female. However, this higher enzyme activity was not correlated to serum testosterone. Around the time the animals reached sexual maturity serum 1,25(OH)2D increased in both sexes. In the males this rise was correlated to an increase in serum testosterone. It is concluded that the maternal renal 1 alpha-hydroxylase activity is unchange in late pregnancy, compared to non-pregnant females. The data indicate that the fetus produces 1,25(OH)2D, and may contribute to the maternal circulating 1,25(OH)2D. The sex difference in 1 alpha-hydroxylase activity previously demonstrated is manifest at about the time of puberty.     

Taurine in the osmoregulation of the Brattleboro rat

The function of taurine in mammalian osmoregulation was studied in the Brattleboro rat with hereditary hypothalamic diabetes insipidus (DI). DI rats are chronically dehydrated because of their inability to synthesize vasopressin. One day of water deprivation did not affect the water balance in rats with normal vasopressin synthesis, whereas DI rats were markedly dehydrated and lost considerably body weight. Taurine content and 3H-taurine accumulation by platelets were significantly higher in DI rats, with a further increase after one day of water deprivation. In DI rats, water deprivation also evoked a clear taurine increase in skeletal muscle and in the brain. These findings indicate that taurine has an osmoregulatory function in mammals.     

Acetaldehyde levels during ethanol oxidation: a diet-induced change and its relation to liver aldehyde dehydrogenases and redox states.

3 different diets that had previously been observed to cause large differences in blood acetaldehyde levels of rats administered ethanol were compared with respect to their influence on liver enzymes metabolizing alcohol, on ethanol elimination and on the ethanol-induced changes in the hepatic content of metabolites that reflect the cytosolic or the mitochondrial redox state of the nicotine-amide dinucleotide couple. The results demonstrate that an unknown dietary factor affects the activity of liver aldehyde dehydrogenase, especially that of the low-K_m enzyme. It is suggested that these enzyme activity changes are reflected in the observed alterations in acetaldehyde levels, which in turn may be associated with the magnitude of the shift in the mitochondrial redox state during ethanol oxidation.