Protein Phosphatase 2A and Cdc7 Kinase Regulate the DNA Unwinding Element-binding Protein in Replication Initiation

The DNA unwinding element (DUE)-binding protein (DUE-B) binds to replication origins coordinately with the minichromosome maintenance (MCM) helicase and the helicase activator Cdc45 in vivo, and loads Cdc45 onto chromatin in Xenopus egg extracts. Human DUE-B also retains the aminoacyl-tRNA proofreading function of its shorter orthologs in lower organisms. Here we report that phosphorylation of the DUE-B unstructured C-terminal domain unique to higher organisms regulates DUE-B intermolecular binding. Gel filtration analyses show that unphosphorylated DUE-B forms multiple high molecular weight (HMW) complexes. Several aminoacyl-tRNA synthetases and Mcm2–7 proteins were identified by mass spectrometry of the HMW complexes. Aminoacyl-tRNA synthetase binding is RNase A sensitive, whereas interaction with Mcm2–7 is nuclease resistant. Unphosphorylated DUE-B HMW complex formation is decreased by PP2A inhibition or direct DUE-B phosphorylation, and increased by inhibition of Cdc7. These results indicate that the state of DUE-B phosphorylation is maintained by the equilibrium between Cdc7-dependent phosphorylation and PP2A-dependent dephosphorylation, each previously shown to regulate replication initiation. Alanine mutation of the DUE-B C-terminal phosphorylation target sites increases MCM binding but blocks Cdc45 loading in vivo and inhibits cell division. In egg extracts alanine mutation of the DUE-B C-terminal phosphorylation sites blocks Cdc45 loading and inhibits DNA replication. The effects of DUE-B C-terminal phosphorylation reveal a novel S phase kinase regulatory mechanism for Cdc45 loading and MCM helicase activation.     

Microbial profiles, in vitro gas production and dry matter digestibility based on various ratios of roughage to concentrate

The study assessed the effects of different roughage to concentrate ratios on enteric methane production, rumen fermentation and microbial counts. These ratios were 80:20, 50:50, and 20:80 for diets 1, 2, and 3, respectively. No significant differences were observed in total gas production among diets; however, methane emissions increased (P?<?0.05) with increased roughage in diet. The pH was greater (P?<?0.05) in diet 1 compared to diets 2 and 3 (6.38 vs 6.17 and 6.07). In vitro dry matter digestibility increased with decreased roughage ratios (47.67, 61.67, 67.33 % for diets 1, 2 and 3, respectively). Similarly, total volatile fatty acids (mM/100 mL) also increased with decreased roughage ratios [diet 1 (5.38); diet 2 (6.30); diet 3 (7.37)]. Methanogen counts, total bacterial counts and protozoal counts were lower (P?<?0.05) in diet 3 compared to diet 1 and 2. However, total fungal counts were higher in diet 1 compared to diet 2 and 3. The results indicate that methane emission, enteric fermentation patterns, and change in methanogens population appear only with higher level of roughage. These findings are important for reducing methane without any impact on rumen performance.     

Comparative transcript profiling of a peach and its nectarine mutant at harvest reveals differences in gene expression related to storability

Gene expression at harvest was compared for two stone fruit cultivars, a peach and its near-isogenic nectarine mutant, using two microarray platforms, μPEACH1.0 and ChillPeach. Together, both platforms covered over 6,000 genes out of which 417 were differentially expressed between the fruits of the two cultivars at a p value of 0.05. A total of 47 genes in nectarine and 60 genes in peach were at least twofold higher relative to each other. Nectarine had much better storage characteristics than peach and could be stored for over 5 weeks at 5 °C without storage disorders. In an attempt to determine whether gene expression at harvest could give an indication of storage potential, the expression analysis of the two cultivars was compared to that of two genotypes with different sensitivities to chilling injury. Principal component analysis of gene expression results across four fruit types differing in chilling sensitivity resulted in 41 genes whose expression levels separated the fruits according to sensitivity to storage disorders, suggesting that the genes have a role in cold response adaptation.     

An integrated diabetic index using heart rate variability signal features for diagnosis of diabetes

Electrocardiogram (ECG) signals are difficult to interpret, and clinicians must undertake a long training process to learn to diagnose diabetes from subtle abnormalities in these signals. To facilitate these diagnoses, we have developed a technique based on the heart rate variability signal obtained from ECG signals. This technique uses digital signal processing methods and, therefore, automates the detection of diabetes from ECG signals. In this paper, we describe the signal processing techniques that extract features from heart rate (HR) signals and present an analysis procedure that uses these features to diagnose diabetes. Through statistical analysis, we have identified the correlation dimension, Poincaré geometry properties (SD2), and recurrence plot properties (REC, DET, L _mean) as useful features. These features differentiate the HR data of diabetic patients from those of patients who do not have the illness, and have been validated by using the AdaBoost classifier with the perceptron weak learner (yielding a classification accuracy of 86%). We then developed a novel diabetic integrated index (DII) that is a combination of these nonlinear features. The DII indicates whether a particular HR signal was taken from a person with diabetes. This index aids the automatic detection of diabetes, thereby allowing a more objective assessment and freeing medical professionals for other tasks.     

Socioeconomic status and incidence of sudden cardiac arrest

Background:

Low socioeconomic status is associated with poor cardiovascular health. We evaluated the association between socioeconomic status and the incidence of sudden cardiac arrest, a condition that accounts for a substantial proportion of cardiovascular-related deaths, in seven large North American urban populations.

Methods:

Using a population-based registry, we collected data on out-of-hospital sudden cardiac arrests occurring at home or at a residential institution from Apr. 1, 2006, to Mar. 31, 2007. We limited the analysis to cardiac arrests in seven metropolitan areas in the United States (Dallas, Texas; Pittsburgh, Pennsylvania; Portland, Oregon; and Seattle–King County, Washington) and Canada (Ottawa and Toronto, Ontario; and Vancouver, British Columbia). Each incident was linked to a census tract; tracts were classified into quartiles of median household income.

Results:

A total of 9235 sudden cardiac arrests were included in the analysis. For all sites combined, the incidence of sudden cardiac arrestin the lowest socioeconomic quartile was nearly double that in the highest quartile (incidence rate ratio [IRR] 1.9, 95% confidence interval [CI] 1.8–2.0). This disparity was greater among people less than 65 years old (IRR 2.7, 95% CI 2.5–3.0) than among those 65 or older (IRR 1.3, 95% CI 1.2–1.4). After adjustment for study site and for population age structure of each census tract, the disparity across socioeconomic quartiles for all ages combined was greater in the United States (IRR 2.0, 95% CI 1.9–2.2) than in Canada (IRR 1.8, 95% CI 1.6–2.0) (p < 0.001 for interaction).

Interpretation:

The incidence of sudden cardiac arrest at home or at a residential institution was higher in poorer neighbourhoods of the US and Canadian sites studied, although the association was attenuated in Canada. The disparity across socioeconomic quartiles was greatest among people younger than 65. The association between socioeconomic status and incidence of sudden cardiac arrest merits consideration in the development of strategies to improve survival from sudden cardiac arrest, and possibly to identify opportunities for prevention.An estimated 250 000–300 000 sudden cardiac arrests occur each year in the United States,¹ accounting for up to 63% of cardiac-related deaths annually.² Despite advances in resuscitation, more than 95% of people who experience sudden cardiac arrest die,³ and up to 50% of sudden cardiac arrests occur in people who do not have a history of coronary artery disease.⁴Socioeconomic status has been shown to predict many health outcomes, including all-cause mortality,⁵ prevalence of risk factors for cardiovascular disease⁶ and incidence of cardiovascular disease.^7–9 Despite this substantial literature, we found only three studies that examined the potential association between socioeconomic status and sudden cardiac arrest. Although the studies were small and conducted in single communities, each showed that the incidence of sudden cardiac arrest was significantly higher in lower socioeconomic areas.^10–12 The Oregon Sudden Unexplained Death Study (Ore-SUDS) reported a 30%–80% higher incidence of sudden cardiac arrest in poorer neighbourhoods. A stronger association was observed among people less than 65 years old, a group for whom basic health care funding is not guaranteed in the United States.¹¹Low socioeconomic status may be linked to an increased risk of sudden cardiac arrest by a variety of mechanisms related to individual risk factors or health-promoting behaviours or neighbourhood characteristics. Individuals of lower socioeconomic status have been found to have a greater burden of risk factors for cardiovascular disease,¹³ poorer control of established cardiovascular risk factors¹⁴ and longer delays in seeking hospital care for acute myocardial infarction.¹⁵ Numerous studies have also shown that disparities in health outcomes are apparent across the spectrum of socioeconomic status.¹⁶A better understanding of community-level patterns in the distribution of sudden cardiac arrest may identify opportunities for improving survival, such as effective targeting of community training for cardiopulmonary resuscitation and placement of automated external defibrillators in lower-income communities. We tested the hypothesis that disparities in the incidence of sudden cardiac arrest by level of socioeconomic status would be evident in a variety of urban communities in the United States and Canada, and that this association would be most prominent among people less than 65 years old residing in US communities.     

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.     

Plant folk medicines among the nicobarese of Katchal Island,India

This paper deals with the plant folk medicines among Nicobarese aboriginals of Katchal Island, in the Nicobar group, India. The tribals, living in complete geographical isolation, have been using folk medicines from time immemorial. Data on 65 plant species were gathered from experienced old men and women. Therapeutic applications and manner of using are initially documented and described as plant remedies in folkloric tradition and popular domestic medicine. No chemical principles are identified; no putative herbal remedies are pharmaceutically and medically evaluated. A brief account of the geography of the islands, climate, ethnology, and methodology of the present work is given. Vernacular name(s) of the plants in the Nicobarese language are incorporated for the first time in literature.     

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 a helix conformation in SSM. This conformational transition was amplified at 37 degrees 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 alpha helix in SSM. This process is associated with potentiation and prolongation of VIP-induced vasodilation in the in situ peripheral microcirculation.