Detection of Pleiotropy through a Phenome-Wide Association Study (PheWAS) of Epidemiologic Data as Part of the Environmental Architecture for Genes Linked to Environment (EAGLE) Study

We performed a Phenome-wide association study (PheWAS) utilizing diverse genotypic and phenotypic data existing across multiple populations in the National Health and Nutrition Examination Surveys (NHANES), conducted by the Centers for Disease Control and Prevention (CDC), and accessed by the Epidemiological Architecture for Genes Linked to Environment (EAGLE) study. We calculated comprehensive tests of association in Genetic NHANES using 80 SNPs and 1,008 phenotypes (grouped into 184 phenotype classes), stratified by race-ethnicity. Genetic NHANES includes three surveys (NHANES III, 1999–2000, and 2001–2002) and three race-ethnicities: non-Hispanic whites (n = 6,634), non-Hispanic blacks (n = 3,458), and Mexican Americans (n = 3,950). We identified 69 PheWAS associations replicating across surveys for the same SNP, phenotype-class, direction of effect, and race-ethnicity at p<0.01, allele frequency >0.01, and sample size >200. Of these 69 PheWAS associations, 39 replicated previously reported SNP-phenotype associations, 9 were related to previously reported associations, and 21 were novel associations. Fourteen results had the same direction of effect across more than one race-ethnicity: one result was novel, 11 replicated previously reported associations, and two were related to previously reported results. Thirteen SNPs showed evidence of pleiotropy. We further explored results with gene-based biological networks, contrasting the direction of effect for pleiotropic associations across phenotypes. One PheWAS result was ABCG2 missense SNP rs2231142, associated with uric acid levels in both non-Hispanic whites and Mexican Americans, protoporphyrin levels in non-Hispanic whites and Mexican Americans, and blood pressure levels in Mexican Americans. Another example was SNP rs1800588 near LIPC, significantly associated with the novel phenotypes of folate levels (Mexican Americans), vitamin E levels (non-Hispanic whites) and triglyceride levels (non-Hispanic whites), and replication for cholesterol levels. The results of this PheWAS show the utility of this approach for exposing more of the complex genetic architecture underlying multiple traits, through generating novel hypotheses for future research.     

Characterization of an immunoglobulin binding protein homolog in the maize floury-2 endosperm mutant.

The maize b-70 protein is an endoplasmic reticulum protein overproduced in the floury-2 (fl2) endosperm mutant. The increase in b-70 levels in fl2 plants occurs during seed maturation and is endosperm specific. We have used amino acid sequence homology to identify b-70 as a homolog of mammalian immunoglobulin binding protein (BiP). Purified b-70 fractions contain two 75-kilodalton polypeptides with pl values of 5.3 and 5.4. Both 75-kilodalton polypeptides share several properties with BiP, including the ability to bind ATP and localization within the lumen of the endoplasmic reticulum. In addition, both b-70 polypeptides can be induced in maize cell cultures with tunicamycin treatment. Like BiP, the pl 5.3 form of b-70 is post-translationally modified by phosphorylation and ADP-ribosylation. However, modification of the pl 5.4 species was not detected in vitro or in vivo. Although the b-70 gene is unlinked to fl2, b-70 overproduction is positively correlated with the fl2 gene and is regulated at the mRNA level. In contrast, the fl2 allele negatively affects the accumulation of the major endosperm storage proteins. The physical similarity of b-70 to BiP and its association with abnormal protein accumulation in fl2 endoplasmic reticulum may reflect a biological function to mediate protein folding and assembly in maize endosperm.     

The contribution of crassulacean acid metabolism to the annual productivity of two aquatic vascular plants

Summary Net annual productivity and annual carbon budgets were determined for populations of Littorella uniflora var. americana and Isoetes macrospora in a mesotrophic and oligotrophic lake in northern Wisconsin, to assess the contribution of Crassulacean Acid Metabolism (CAM) to annual productivity of the species in their natural environment. Nocturnal carbon accumulation (CAM), daytime uptake of external CO₂ via the C₃ mechanism, and refixation of endogenously generated CO₂ from daytime respiration were the sources of carbon income. CAM activity as diurnal acid rhythms reached maxima of 89 to 182 eq·g^-1 leaf fresh weight for the various populations.Maximum rates of daytime ¹⁴C uptake ranged from 0.56 to 1.46 mg C·g^-1 leaf dry wt.·h^-1 for the study populations. Refixation of daytime respired CO₂ averaged 37% for the four populations. Carbon loss was due largely to dark respiration, during the day and night. Nocturnal carbon accumulation, daytime CO₂ uptake and 24-h dark respiration were of similar magnitude, indicating dark respiration was equivalent to 50% of gross photosynthesis.Net annual production was measured for each population by following leaf turnover. Turnover rates for the Littorella populations were 1.56 and 1.72·yr^-1, and for the Isoetes populations, 0.85 and 1.00·yr^-1. Measured net annual productivity and calculated net annual productivity (based on carbon exchange) agreed within an average of 12% for the four populations. While CAM activity was greater for the more productive population of each species, the results suggest that the contribution of CAM to annual productivity is greater for the less productive population of each species. CAM contributed 45 to 55% of the annual carbon gain for the study populations.     

Differential adherence of M line Biomphalaria glabrata hemocytes to Schistosoma mansoni and Echinostoma paraensei larvae, and experimental manipulation of hemocyte binding

The ability of M line strain Biomphalaria glabrata hemocytes to adhere to mother sporocysts (MS) of PR1 Schistosoma mansoni or to MS or daughter rediae (DR) of Echinostoma paraensei was studied using an in vitro hemocyte adherence assay. Hemocytes were significantly more likely to bind to S. mansoni MS than to E. paraensei MS or DR. Hemocyte adherence to E. paraensei MS or DR was significantly increased if glutaraldehyde-fixed larvae were used as targets. Also, E. paraensei MS pretreated with the lectin concanavalin A (Con A) were more likely to be bound by hemocytes than MS pretreated with Con A in the presence of the competing sugar, alpha-methyl mannoside. Pretreatment of hemocytes with Con A increased their ability to bind E. paraensei sporocysts, but the effect was small compared to that achieved by pretreatment of MS with Con A. The lectin probably did not function as a bridging molecule between hemocytes and MS but, rather, altered the MS surface in a way that facilitated adherence. Similarly, adherence to E. paraensei MS was significantly increased if the MS were pretreated with cell-free M line plasma prior to use in adherence assays. Our results indicate that the two parasites provoke fundamentally different responses from M line hemocytes in vitro and that the living tegument can be modified by host humoral factors and by lectins such that hemocyte binding is significantly increased.     

Ethyl-EPA in Alzheimer's disease--a pilot study

This pilot study of ethyl-eicosapentaenoate (ethyl-EPA) in the treatment of Alzheimer's disease aimed to estimate the magnitude of any change in measures of cognition during a 12-week treatment period. A simple linear design was used in which each patient had a baseline period of 12 weeks without treatment, followed by 12 weeks' treatment with ethyl-EPA. Blood samples were taken both before and after the treatment period to measure erythrocyte membrane fatty acids. Assessments comprised cognitive measures and visual analogue ratings of overall assessment of functioning. There was little difference between treatment and baseline periods in the rate of decline of efficacy measures, except for a small improvement in carer's visual analogue rating (P=0.02). It was concluded that it is unlikely there were any clinically important treatment effects of ethyl-EPA on cognition during the 12-week treatment period. A longer treatment period may be necessary to demonstrate efficacy of ethyl-EPA in this disorder.     

Fetal and maternal endocrine responses to exercise in the pregnant ewe

Maternal and fetal concentrations of plasma insulin, pancreatic glucagon, growth hormone (GH), corticosteroids and enteroglucagon, and of blood glucose and lactate, were measured in well-fed, late pregnant ewes before, during and after walking on a treadmill at 0.7 m.s-1, 10 degrees slope for 60 min. Exercise caused rapid and substantial increases in maternal concentrations of glucose, lactate, pancreatic glucagon and corticosteroids, smaller but significant decreases in levels of GH and enteroglucagon, and no change in insulin. With the exception of GH, concentrations of these maternal hormones had returned to pre-exercise levels within 20 min of stopping exercise. The exercise-induced maternal hyperglycaemia was associated with a proportionately similar, rapid increase in fetal blood glucose; fetal blood lactate and plasma corticosteroids also increased, but at slower rates and other fetal hormone concentrations were unchanged. During recovery there was a rapid increase in fetal insulin levels. The results are discussed in terms of the regulation of exercise-induced changes in maternal energy metabolism, and fetal metabolic and hormonal sensitivity to these changes.