Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs

Controlling for background demographic effects is important for accurately identifying loci that have recently undergone positive selection. To date, the effects of demography have not yet been explicitly considered when identifying loci under selection during dog domestication. To investigate positive selection on the dog lineage early in the domestication, we examined patterns of polymorphism in six canid genomes that were previously used to infer a demographic model of dog domestication. Using an inferred demographic model, we computed false discovery rates (FDR) and identified 349 outlier regions consistent with positive selection at a low FDR. The signals in the top 100 regions were frequently centered on candidate genes related to brain function and behavior, including LHFPL3, CADM2, GRIK3, SH3GL2, MBP, PDE7B, NTAN1, and GLRA1. These regions contained significant enrichments in behavioral ontology categories. The 3^rd top hit, CCRN4L, plays a major role in lipid metabolism, that is supported by additional metabolism related candidates revealed in our scan, including SCP2D1 and PDXC1. Comparing our method to an empirical outlier approach that does not directly account for demography, we found only modest overlaps between the two methods, with 60% of empirical outliers having no overlap with our demography-based outlier detection approach. Demography-aware approaches have lower-rates of false discovery. Our top candidates for selection, in addition to expanding the set of neurobehavioral candidate genes, include genes related to lipid metabolism, suggesting a dietary target of selection that was important during the period when proto-dogs hunted and fed alongside hunter-gatherers.     

The role of HMGB1 in liver inflammation in obese rats

ABSTRACT

Obesity is a chronic disease that is characterized by increased body fat owing to imbalance between consumed and expended energy. Inflammation generally is accompanied by accumulation of excess lipid in adipose tissue and liver. High mobility group box-1 (HMGB1) participates in the pathogenesis of inflammatory diseases. We investigated the relation of the number of HMGB1 positive cells to body mass index (BMI), liver inflammation and the number of Kupffer cells. We divided 18 female Wistar albino rats into two groups: group 1, untreated control fed normal commercial rat diet and group 2, obese rats fed a special diet containing 40% fat. The plasma concentrations of cholesterol, glucose, superoxide dismutase enzyme (SOD) and catalase activities were measured for all animals. The numbers of hepatocytes, Kupffer cells and HMGB1 positive cells were counted using stereological methods. The mean numbers of Kupffer cells and HMGB1 positive cells were higher for group 2 than for group 1. The concentrations of plasma cholesterol and glucose levels also were higher in group 2. Plasma levels of SOD and catalase were significantly lower in group 2 compared to group 1. The number of HMGB1 cells was related directly to BMI and inflammation. The role of HMGB1 was demonstrated for the liver of the obese group. We demonstrated the relations among HMGB1, BMI, obesity and inflammation.     

Robustness of Massively Parallel Sequencing Platforms

The improvements in high throughput sequencing technologies (HTS) made clinical sequencing projects such as ClinSeq and Genomics England feasible. Although there are significant improvements in accuracy and reproducibility of HTS based analyses, the usability of these types of data for diagnostic and prognostic applications necessitates a near perfect data generation. To assess the usability of a widely used HTS platform for accurate and reproducible clinical applications in terms of robustness, we generated whole genome shotgun (WGS) sequence data from the genomes of two human individuals in two different genome sequencing centers. After analyzing the data to characterize SNPs and indels using the same tools (BWA, SAMtools, and GATK), we observed significant number of discrepancies in the call sets. As expected, the most of the disagreements between the call sets were found within genomic regions containing common repeats and segmental duplications, albeit only a small fraction of the discordant variants were within the exons and other functionally relevant regions such as promoters. We conclude that although HTS platforms are sufficiently powerful for providing data for first-pass clinical tests, the variant predictions still need to be confirmed using orthogonal methods before using in clinical applications.     

Response of Selenium Status Indicators to Supplementation of Healthy North American Men with High-Selenium Yeast

The essential nutrient selenium is required in microgram amounts [recommended dietary allowance (RDA) = 55 μg/day, 699 nmol/day] and has a narrow margin of safety (upper tolerable intake limit = 400 μg/day, 5 μmol/day). We conducted a randomized placebo-controlled study of high-selenium yeast, the form used in most supplements (300 μg/day, 3.8 μmol/day), administered to 42 free-living healthy men for 48 weeks. Dietary intakes of selenium, macronutrients, and micronutrients were not different between groups and did not change during the study. Supplementation more than doubled urinary selenium excretion from 69 to 160 μg/day (876 to 2,032 nmol/day). Urinary excretion was correlated with recent selenium intake estimated from 3-day diet records: urinary selenium excretion = 42 μg/day (533 nmol/day) + 0.132 × dietary selenium intake, p < 0.001. Dietary selenium intake was not significantly correlated with the other indicators of selenium status, presumably because urinary selenium excretion reflected recent intake, and tissue selenium was homeostatically controlled. After 48 weeks of supplementation, plasma selenium was increased 60% from 142 to 228 μg/l (1.8 to 2.9 μmol/l), and erythrocyte selenium was approximately doubled from 261 to 524 μg/l (3.3 to 6.6 μmol/l). Selenium concentrations increased more modestly in hair (56%) and platelets (42%). Platelets were the only blood component in which glutathione peroxidase activity was significantly related to selenium content. Selenium levels decreased rapidly after the end of supplementation, and there were no significant differences in selenium status indicators between groups by week 96. The absorption, distribution, and excretion of selenium from high-Se yeast were similar to selenium in foods.     

Role of ammonia secretion and pH modulation on pathogenicity of Colletotrichum coccodes on tomato fruit

Colletotrichum coccodes was found to alkalinize the decaying tissue of tomato fruit via accumulation and secretion of ammonia. Alkalinization dynamics caused by ammonia secretion from growing hyphae was examined microscopically using the pH-sensitive fluorescent dye 2',7'-bis(carboxyethyl)-5(6)-carboxyfluorescein. Values of pH of 7.9 observed in the host tissue close to the hyphal tips declined to pH 6.0 at 10 mm away from the hyphal tip, which was a value that was still higher than that detected in the healthy tissue, pH 4.2. Ammonia accumulation at the infection site depended on the initial environmental pH. Treatments with low (4.0) pH buffer at the infection site resulted in high levels of ammonia secretion and increased virulence of C. coccodes compared with similar treatments with buffer at pH 7.0. Significantly, mutants of C. coccodes defective in nitrogen utilization, nit-, and areA- were impaired in ammonia secretion and showed reduced decay development. The reduced infection rate of nit- mutants could be complemented by adding glutamine at the infection site. Thus, ammonia accumulation is a critical factor contributing to C. coccodes pathogenicity on tomato fruit. The results show that the initial acidic pH of the fruit is conducive to ammonia secretion and the subsequent alkalinization of the infection site, and facilitates fungal virulence and the transformation from the quiescent-biotrophic to active-necrotrophic state.     

Production of Extracellular Alkaline α‐Amylase by Solid State Fermentation with a Newly Isolated Bacillus sp.

Abstract

Production of alkaline α‐amylase employing our laboratory isolate, Bacillus sp., under solid state fermentation, was optimized. The effect of wheat bran and lentil husk was examined. Lentil husk exhibited the highest enzyme production. The appropriate incubation time, inoculum size, moisture level, and buffer solution level were determined. Maximum yields of 216,000 and 172,800 U/g were achieved by employing lentil husk and wheat bran as substrates in 0.1 M carbonate/bicarbonate buffer at pH 10.0 with 30% initial moisture level at 24 h. Inoculum size and buffer solution level were found to be 20% and 1:0.5 for two solid substrates.     

A public genome-scale lentiviral expression library of human ORFs

Functional characterization of the human genome requires tools for systematically modulating gene expression in both loss-of-function and gain-of-function experiments. We describe the production of a sequence-confirmed, clonal collection of over 16,100 human open-reading frames (ORFs) encoded in a versatile Gateway vector system. Using this ORFeome resource, we created a genome-scale expression collection in a lentiviral vector, thereby enabling both targeted experiments and high-throughput screens in diverse cell types.     

Differentiation between vergence and saccadic functional activity within the human frontal eye fields and midbrain revealed through fMRI

Purpose

Eye movement research has traditionally studied solely saccade and/or vergence eye movements by isolating these systems within a laboratory setting. While the neural correlates of saccadic eye movements are established, few studies have quantified the functional activity of vergence eye movements using fMRI. This study mapped the neural substrates of vergence eye movements and compared them to saccades to elucidate the spatial commonality and differentiation between these systems.

Methodology

The stimulus was presented in a block design where the ‘off’ stimulus was a sustained fixation and the ‘on’ stimulus was random vergence or saccadic eye movements. Data were collected with a 3T scanner. A general linear model (GLM) was used in conjunction with cluster size to determine significantly active regions. A paired t-test of the GLM beta weight coefficients was computed between the saccade and vergence functional activities to test the hypothesis that vergence and saccadic stimulation would have spatial differentiation in addition to shared neural substrates.

Results

Segregated functional activation was observed within the frontal eye fields where a portion of the functional activity from the vergence task was located anterior to the saccadic functional activity (z>2.3; p<0.03). An area within the midbrain was significantly correlated with the experimental design for the vergence but not the saccade data set. Similar functional activation was observed within the following regions of interest: the supplementary eye field, dorsolateral prefrontal cortex, ventral lateral prefrontal cortex, lateral intraparietal area, cuneus, precuneus, anterior and posterior cingulates, and cerebellar vermis. The functional activity from these regions was not different between the vergence and saccade data sets assessed by analyzing the beta weights of the paired t-test (p>0.2).

Conclusion

Functional MRI can elucidate the differences between the vergence and saccade neural substrates within the frontal eye fields and midbrain.