Mining the LIPG allelic spectrum reveals the contribution of rare and common regulatory variants to HDL cholesterol

Genome-wide association studies (GWAS) have successfully identified loci associated with quantitative traits, such as blood lipids. Deep resequencing studies are being utilized to catalogue the allelic spectrum at GWAS loci. The goal of these studies is to identify causative variants and missing heritability, including heritability due to low frequency and rare alleles with large phenotypic impact. Whereas rare variant efforts have primarily focused on nonsynonymous coding variants, we hypothesized that noncoding variants in these loci are also functionally important. Using the HDL-C gene LIPG as an example, we explored the effect of regulatory variants identified through resequencing of subjects at HDL-C extremes on gene expression, protein levels, and phenotype. Resequencing a portion of the LIPG promoter and 5' UTR in human subjects with extreme HDL-C, we identified several rare variants in individuals from both extremes. Luciferase reporter assays were used to measure the effect of these rare variants on LIPG expression. Variants conferring opposing effects on gene expression were enriched in opposite extremes of the phenotypic distribution. Minor alleles of a common regulatory haplotype and noncoding GWAS SNPs were associated with reduced plasma levels of the LIPG gene product endothelial lipase (EL), consistent with its role in HDL-C catabolism. Additionally, we found that a common nonfunctional coding variant associated with HDL-C (rs2000813) is in linkage disequilibrium with a 5' UTR variant (rs34474737) that decreases LIPG promoter activity. We attribute the gene regulatory role of rs34474737 to the observed association of the coding variant with plasma EL levels and HDL-C. Taken together, the findings show that both rare and common noncoding regulatory variants are important contributors to the allelic spectrum in complex trait loci.     

Mapping QTLs for Plant Phenology and Production Traits Using Indica Rice (Oryza sativa L.) Lines Adapted to Rainfed Environment

Drought is a major abiotic stress limiting rice production and yield stability in rainfed ecosystems. Identifying quantitative trait loci (QTL) for rice yield and yield components under water limited environments will help to develop drought resilient cultivars using marker assisted breeding (MAB) strategy. A total of 232 recombinant inbred lines of IR62266/Norungan were used to map QTLs for plant phenology and production traits under rainfed condition in target population of environments. A total of 79 QTLs for plant phenology and production traits with phenotypic variation ranging from 4.4 to 72.8% were detected under non-stress and drought stress conditions across two locations. Consistent QTLs for phenology and production traits were detected across experiments and water regimes. The QTL region, RM204-RM197-RM217 on chromosome 6 was linked to days to 50% flowering and grain yield per plant under both rainfed and irrigated conditions. The same genomic region, RM585-RM204-RM197 was also linked to harvest index under rainfed condition with positive alleles from Norungan, a local landrace. QTLs for plant production and drought resistance traits co-located near RM585-RM204-RM197-RM217 region on chromosome 6 in several rice genotypes. Thus with further fine mapping, this region may be useful as a candidate QTL for MAB, map-based cloning of genes and functional genomics studies for rainfed rice improvement.     

Modeling the potential global distribution of suitable habitat for the biological control agent Heterorhabditis indica

Entomopathogenic nematode (EPN) Heterorhabditis indica is a promising biocontrol candidate. Despite the acknowledged importance of EPN in pest control, no extensive data sets or maps have been developed on their distribution at global level. This study is the first attempt to generate Ecological Niche Models (ENM) for H. indica and its global Habitat Suitability Map (HSM) for H. indica to generate biogeographical information and predicts its global geographical range and help identify of prospective areas for its exploration and to help identify the suitable release areas for biocontrol purpose. The aim of the modeling exercise was to access the influence of temperature and soil moisture on the biogeographical patterns of H. indica at the global level. Global Heterorhabditis indica ecosystems. CLIMEX software was used to model the distribution of H. indica and assess the influence of environmental variable on its global distribution. In total, 162 records of H. indica occurrence from 27 countries over 25 years were combined to generate the known distribution data. The model was further fine‐tuned using the direct experimental observations of the H. indica''s growth response to temperature and soil moisture. Model predicts that much of the tropics and subtropics have suitable climatic conditions for H. indica. It further predicts that H. indica distribution can extend into warmer temperate climates. Examination of the model output, predictions maps at a global level indicate that H. indica distribution may be limited by cold stress, heat stress, and dry stresses in different areas. However, cold stress appears to be the major limiting factor. This study highlighted an efficient way to construct HSM for EPN potentially useful in the search/release of target species in new locations. The study showed that H. indica which is known as warm adapted EPN generally found in tropics and subtropics can potentially establish itself in warmer temperate climates as well. The model can also be used to decide the release timing of EPN by adjusting with season for maximum growth. The model developed in this study clearly identified the value and potential of Habitat Suitability Map (HSM) in planning of future surveys and application of H. indica.     

Length‐weight relationships of four snowtrout species from the Kashmir Valley in India

Length–weight relationships (LWR) are presented for one species of the genus Schizopyge [S. curvifrons (Heckel, 1838)] and three species of the genus Schizothorax [S. esocinus (Heckel, 1838), S. labiatus (McClelland, 1842) and S. plagiostomus (Heckel, 1838)] from different water bodies of the Kashmir Valley, India. A total of 774 specimens were sampled and measured from January to November 2011. No information regarding LWRs of these species was available in FishBase.     

C. elegans mutant identification with a one-step whole-genome-sequencing and SNP mapping strategy

Whole-genome sequencing (WGS) is becoming a fast and cost-effective method to pinpoint molecular lesions in mutagenized genetic model systems, such as Caenorhabditis elegans. As mutagenized strains contain a significant mutational load, it is often still necessary to map mutations to a chromosomal interval to elucidate which of the WGS-identified sequence variants is the phenotype-causing one. We describe here our experience in setting up and testing a simple strategy that incorporates a rapid SNP-based mapping step into the WGS procedure. In this strategy, a mutant retrieved from a genetic screen is crossed with a polymorphic C. elegans strain, individual F2 progeny from this cross is selected for the mutant phenotype, the progeny of these F2 animals are pooled and then whole-genome-sequenced. The density of polymorphic SNP markers is decreased in the region of the phenotype-causing sequence variant and therefore enables its identification in the WGS data. As a proof of principle, we use this strategy to identify the molecular lesion in a mutant strain that produces an excess of dopaminergic neurons. We find that the molecular lesion resides in the Pax-6/Eyeless ortholog vab-3. The strategy described here will further reduce the time between mutant isolation and identification of the molecular lesion.     

Conformation and vasoreactivity of VIP in phospholipids: effects of calmodulin

The purpose of this study was to determine the conformation and vasorelaxant effects of vasoactive intestinal peptide (VIP) self-associated with sterically stabilized phospholipid micelles (SSM) and whether calmodulin modulates both of these processes. Circular dichroism spectroscopy revealed that VIP is unordered in aqueous solution at room temperature but assumes appreciable α helix conformation in SSM. This conformational transition was amplified at 37°C and by a low concentration of calmodulin (0.1 nM). Suffusion of VIP in SSM elicited significant time- and concentration-dependent potentiation of vasodilation relative to that elicited by aqueous VIP in the in situ hamster cheek pouch (P < 0.05). This response was significantly potentiated by calmodulin (0.1 nM). Collectively, these data indicate that exogenous calmodulin interacts with VIP in SSM to elicit conformational transition of VIP molecule from a predominantly random coil in aqueous environment to α helix in SSM. This process is associated with potentiation and prolongation of VIP-induced vasodilation in the in situ peripheral microcirculation.     

Novel Loci Associated with Increased Risk of Sudden Cardiac Death in the Context of Coronary Artery Disease

Background

Recent genome-wide association studies (GWAS) have identified novel loci associated with sudden cardiac death (SCD). Despite this progress, identified DNA variants account for a relatively small portion of overall SCD risk, suggesting that additional loci contributing to SCD susceptibility await discovery. The objective of this study was to identify novel DNA variation associated with SCD in the context of coronary artery disease (CAD).

Methods and Findings

Using the MetaboChip custom array we conducted a case-control association analysis of 119,117 SNPs in 948 SCD cases (with underlying CAD) from the Oregon Sudden Unexpected Death Study (Oregon-SUDS) and 3,050 controls with CAD from the Wellcome Trust Case-Control Consortium (WTCCC). Two newly identified loci were significantly associated with increased risk of SCD after correction for multiple comparisons at: rs6730157 in the RAB3GAP1 gene on chromosome 2 (P = 4.93×10⁻¹², OR = 1.60) and rs2077316 in the ZNF365 gene on chromosome 10 (P = 3.64×10⁻⁸, OR = 2.41).

Conclusions

Our findings suggest that RAB3GAP1 and ZNF365 are relevant candidate genes for SCD and will contribute to the mechanistic understanding of SCD susceptibility.