METAL: fast and efficient meta-analysis of genomewide association scans

Summary: METAL provides a computationally efficient tool for meta-analysis of genome-wide association scans, which is a commonly used approach for improving power complex traits gene mapping studies. METAL provides a rich scripting interface and implements efficient memory management to allow analyses of very large data sets and to support a variety of input file formats

Biosorption of Cadmium by Mangrove-Derived Cyanobacteria (Gloeocapsa sp ARKK3)

Dried microbial biomass of Gloeocapsa sp. Trichoderma, and Thrustochytrids used as bioadsorbent for the removal of cadmium in the artificial sewage. Among the three species the maximum adsorption recorded in Gloeocapsa sp. biomass. For the augmentation of cadmium removal in sewage, adsorption process conditions was statistically optimized by the method of response surface methodology (RSM) and adsorption kinetics also studied. The important factors of temperature, pH, adsorbent dosage and processing time were selected for optimization, and it was done with 30 experimental cycles derived from centre composite design (CCD). The statistical optimization reveled that optimized condition for cadmium removal was pH 9, temperature 40ºC, adsorbent dosage 0.6 mg.l-1 and 60 minutes. Finally in this condition was experimentally proved with yield of cadmium removal of 92.9 % under statistically optimized condition. In the case of the adsorption kinetic Gloeocapsa sp. biomass showed a significant adsorption capacity of qmax-56.96 (mg.g-1). The present study concluded that the microbial dried biomass derived from marine Gloeocapsa sp. was a potent source for the removal of the cadmium in the sewage waste water

Efficacy of new herbicide (bispyribac sodium 10% SC) against different weed flora, nutrient uptake in rice and their residual effects on succeeding crop of green gram under zero tillage

Field experiment was conducted in the wetland farms of Tamil Nadu Agricultural University, Coimbatore during rabi season (August to February) of 2011-12 to evaluate the herbicide (Bispyribac sodium 10% SC) on weed control and their nutrient management in direct seeded lowland rice. The experiment was laid out in a Randomized Block Design (RBD) with three replications. The results revealed that Early Post Emergence (EPOE) application of bispyribac sodium 10% SC 40 g ha-1 recorded higher weed control efficiency and lesser weed density, nutrient uptake at reproductive stage of the crop. Different weed management practices imposed on rice crop did not affect the germination of succeeding green gram

Efficacy of Preserving Sea Foods Using Marine Lactobacillus

Scombroid food poisoning is a food borne illness that results from eating spoiled (decayed) fish. Histamine is the causative agent of scombroid poisoning, a food borne chemical intoxication. Histamine is one of the main biogenic amines and it is heterocyclic and biologically active primary amine, formed post-mortem in the muscles of scombroid and   non-scombroid fish. The present study was carried out to isolate histamine-producing bacteria from a local fish and to test antibacterial activity of mangrove isolates of Lactobacillus species against the histamine producing bacteria. Fresh tuna fish (Euthinus affinis) obtained from   Parangipettai coast and they were divided in to three groups. One group of the fish samples were stored directly and another two group of the fish  samples were dipped in cold distilled water containing bacteriocin of   Lactobacillus sp. and partially purified bacteriocin (10 ml, 1% v/v) respectively. The fish samples, after treatment were stored at 5, 15, 20 and 25 0C for the period of 24, 48, 72 and 96 h, respectively. Histamine quantification was performed at an interval of 24 h for four days. According to the results obtained it was proved that mangrove isolates of  Lactobacillus species having high antimicrobial activity against histamine-producing bacteria which is responsible for spoilage of sea foods

Microstructural characterization of friction stir welded AA5083 aluminum alloy joints

The objective of the current work is to apply Taguchi L9 orthogonal array to enhance the welding process factors for friction stir welding (FSW) of AA5083 aluminium alloy plates. Using a randomized procedure, the Taguchi orthogonal array was implemented to identify the FSW process parameters such as the rotating speed of the tool, welding speed, and tilting angle of the tool. The optimum welding parameters for the ultimate tensile strength and hardness of the joints were predicted and the individual rank of each process parameter on the ultimate tensile strength and hardness of the friction stir weld was assessed by investigative ANOVA results and the S/N ratio (signal-to- noise ratio). The most desirable rotational speed of the tool, welding speed and tilting angle of the tool were 600 rev. per. min, 70 millimeter/min and 1o appropriately for the ultimate eluting strength and 600 rev. per. min, 80 millimeter/min and 1o correspondingly for summit joint hardness. The outcomes of Analysis of Variance (ANOVA) designated that the tilting angle of the tool has the higher statistical effect succeeded by the welding velocity and rotational speed of the tool. Furthermore, metallurgical properties of the weld cross-sections were investigated by using optical microscope (OM), scanning electron microscope (SEM), energy dispersive spectroscopy (EDS) analysis. The microstructure of the stir zone reveals finer grain structure, directed to the higher hardness, which gives rise to higher tensile strength

Genome-Wide Association with Select Biomarker Traits in the Framingham Heart Study

BACKGROUND: Systemic biomarkers provide insights into disease pathogenesis, diagnosis, and risk stratification. Many systemic biomarker concentrations are heritable phenotypes. Genome-wide association studies (GWAS) provide mechanisms to investigate the genetic contributions to biomarker variability unconstrained by current knowledge of physiological relations. METHODS: We examined the association of Affymetrix 100K GeneChip single nucleotide polymorphisms (SNPs) to 22 systemic biomarker concentrations in 4 biological domains: inflammation/oxidative stress; natriuretic peptides; liver function; and vitamins. Related members of the Framingham Offspring cohort (n = 1012; mean age 59 ± 10 years, 51% women) had both phenotype and genotype data (minimum-maximum per phenotype n = 507–1008). We used Generalized Estimating Equations (GEE), Family Based Association Tests (FBAT) and variance components linkage to relate SNPs to multivariable-adjusted biomarker residuals. Autosomal SNPs (n = 70,987) meeting the following criteria were studied: minor allele frequency ≥ 10%, call rate ≥ 80% and Hardy-Weinberg equilibrium p ≥ 0.001. RESULTS: With GEE, 58 SNPs had p < 10-6: the top SNPs were rs2494250 (p = 1.00*10-14) and rs4128725 (p = 3.68*10-12) for monocyte chemoattractant protein-1 (MCP1), and rs2794520 (p = 2.83*10-8) and rs2808629 (p = 3.19*10-8) for C-reactive protein (CRP) averaged from 3 examinations (over about 20 years). With FBAT, 11 SNPs had p < 10-6: the top SNPs were the same for MCP1 (rs4128725, p = 3.28*10-8, and rs2494250, p = 3.55*10-8), and also included B-type natriuretic peptide (rs437021, p = 1.01*10-6) and Vitamin K percent undercarboxylated osteocalcin (rs2052028, p = 1.07*10-6). The peak LOD (logarithm of the odds) scores were for MCP1 (4.38, chromosome 1) and CRP (3.28, chromosome 1; previously described) concentrations; of note the 1.5 support interval included the MCP1 and CRP SNPs reported above (GEE model). Previous candidate SNP associations with circulating CRP concentrations were replicated at p < 0.05; the SNPs rs2794520 and rs2808629 are in linkage disequilibrium with previously reported SNPs. GEE, FBAT and linkage results are posted at . CONCLUSION: The Framingham GWAS represents a resource to describe potentially novel genetic influences on systemic biomarker variability. The newly described associations will need to be replicated in other studies.National Heart, Lung, and Blood Institute's Framingham Heart Study (N01-HC25195); National Institutes of Health National Center for Research Resources Shared Instrumentation grant (1S10RR163736-01A1); National Institutes of Health (HL064753, HL076784, AG028321, HL71039, 2 K24HL04334, 1K23 HL083102); Doris Duke Charitable Foundation; American Diabetes Association Career Developement Award; National Center for Research Resources (GCRC M01-RR01066); US Department of Agriculture Agricultural Research Service (58-1950-001, 58-1950-401); National Institute of Aging (AG14759

Genetic Differences between the Determinants of Lipid Profile Phenotypes in African and European Americans: The Jackson Heart Study

Genome-wide association analysis in populations of European descent has recently found more than a hundred genetic variants affecting risk for common disease. An open question, however, is how relevant the variants discovered in Europeans are to other populations. To address this problem for cardiovascular phenotypes, we studied a cohort of 4,464 African Americans from the Jackson Heart Study (JHS), in whom we genotyped both a panel of 12 recently discovered genetic variants known to predict lipid profile levels in Europeans and a panel of up to 1,447 ancestry informative markers allowing us to determine the African ancestry proportion of each individual at each position in the genome. Focusing on lipid profiles—HDL-cholesterol (HDL-C), LDL-cholesterol (LDL-C), and triglycerides (TG)—we identified the lipoprotein lipase (LPL) locus as harboring variants that account for interethnic variation in HDL-C and TG. In particular, we identified a novel common variant within LPL that is strongly associated with TG (p = 2.7×10−6) and explains nearly 1% of the variability in this phenotype, the most of any variant in African Americans to date. Strikingly, the extensively studied “gain-of-function” S447X mutation at LPL, which has been hypothesized to be the major determinant of the LPL-TG genetic association and is in trials for human gene therapy, has a significantly diminished strength of biological effect when it is found on a background of African rather than European ancestry. These results suggest that there are other, yet undiscovered variants at the locus that are truly causal (and are in linkage disequilibrium with S447X) or that work synergistically with S447X to modulate TG levels. Finally, we find systematically lower effect sizes for the 12 risk variants discovered in European populations on the African local ancestry background in JHS, highlighting the need for caution in the use of genetic variants for risk assessment across different populations

Relationship between moderate-to-vigorous physical activity, abdominal fat and immunometabolic markers in postmenopausal women

AbstractObjectsTo assess the burden of levels of physical activity, non-esterified fatty acids (NEFA), triacylglycerol and abdominal fat on the immunometabolic profile of postmenopausal women.Study designForty-nine postmenopausal women [mean age 59.43 (standard deviation 5.61) years] who did not undertake regular physical exercise participated in this study. Body composition was assessed using dual-energy X-ray absorptiometry, and levels of NEFA, tumour necrosis factor-α, adiponectin, insulin and triacylglycerol were assessed using fasting blood samples. The level of physical activity was assessed using an accelerometer (Actigraph GTX3x), and reported as counts/min, time spent undertaking sedentary activities and time spent undertaking moderate-to-vigorous physical activity (MVPA). The following conditions were considered to be risk factors: (i) sedentary lifestyle (<150min of MVPA per week); (ii) high level (above median) of abdominal fat; and (iii) hypertriacylglycerolaemia (<150mg/dl of triacylglycerol).ResultsIn comparison with active women, sedentary women had higher levels of body fat (%) (p=0.041) and NEFA (p=0.064). Women with higher levels of abdominal fat had impaired insulin resistance (HOMA-IR) (p=0.016) and spent more time undertaking sedentary activities (p=0.043). Moreover, the women with two risk factors or more had high levels of NEFA and HOMA-IR (p<0.05), as well as an eight-fold higher risk of a high level of NEFA, independent of age (p<0.05). No significant relationship was found between levels of physical activity, abdominal fat, tumour necrosis factor-α and adiponectin (p>0.05).ConclusionPostmenopausal women with a combination of hypertriacylglycerolaemia, a high level of abdominal fat and a sedentary lifestyle are more likely to have metabolic disturbances

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals.

Large-scale deep-coverage whole-genome sequencing (WGS) is now feasible and offers potential advantages for locus discovery. We perform WGS in 16,324 participants from four ancestries at mean depth &gt;29X and analyze genotypes with four quantitative traits-plasma total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol, and triglycerides. Common variant association yields known loci except for few variants previously poorly imputed. Rare coding variant association yields known Mendelian dyslipidemia genes but rare non-coding variant association detects no signals. A high 2M-SNP LDL-C polygenic score (top 5th percentile) confers similar effect size to a monogenic mutation (~30 mg/dl higher for each); however, among those with severe hypercholesterolemia, 23% have a high polygenic score and only 2% carry a monogenic mutation. At these sample sizes and for these phenotypes, the incremental value of WGS for discovery is limited but WGS permits simultaneous assessment of monogenic and polygenic models to severe hypercholesterolemia