Allele-specific expression and eQTL analysis in mouse adipose tissue.

BackgroundThe simplest definition of cis-eQTLs versus trans, refers to genetic variants that affect expression in an allele specific manner, with implications on underlying mechanism. Yet, due to technical limitations of expression microarrays, the vast majority of eQTL studies performed in the last decade used a genomic distance based definition as a surrogate for cis, therefore exploring local rather than cis-eQTLs.ResultsIn this study we use RNAseq to explore allele specific expression (ASE) in adipose tissue of male and female F1 mice, produced from reciprocal crosses of C57BL/6J and DBA/2J strains. Comparison of the identified cis-eQTLs, to local-eQTLs, that were obtained from adipose tissue expression in two previous population based studies in our laboratory, yields poor overlap between the two mapping approaches, while both local-eQTL studies show highly concordant results. Specifically, local-eQTL studies show ~60% overlap between themselves, while only 15-20% of local-eQTLs are identified as cis by ASE, and less than 50% of ASE genes are recovered in local-eQTL studies. Utilizing recently published ENCODE data, we also find that ASE genes show significant bias for SNPs prevalence in DNase I hypersensitive sites that is ASE direction specific.ConclusionsWe suggest a new approach to analysis of allele specific expression that is more sensitive and accurate than the commonly used fisher or chi-square statistics. Our analysis indicates that technical differences between the cis and local-eQTL approaches, such as differences in genomic background or sex specificity, account for relatively small fraction of the discrepancy. Therefore, we suggest that the differences between two eQTL mapping approaches may facilitate sorting of SNP-eQTL interactions into true cis and trans, and that a considerable portion of local-eQTL may actually represent trans interactions

Deeper Chandra Follow-up of Cygnus TeV Source Perpetuates Mystery

A 50 ksec Chandra observation of the unidentified TeV source in Cygnus reported by the HEGRA collaboration reveals no obvious diffuse X-ray counterpart. However, 240 Pointlike X-ray sources are detected within or nearby the extended TeV J2032+4130 source region, of which at least 36 are massive stars and 2 may be radio emitters. That the HEGRA source is a composite, having as counterpart the multiple point-like X-ray sources we observe, cannot be ruled out. Indeed, the distribution of point-like X-ray sources appears non-uniform and concentrated broadly within the extent of the TeV source region. We offer a hypothesis for the origin of the very high energy gamma-ray emission in Cyg OB2 based on the local acceleration of TeV range cosmic rays and the differential distribution of OB vs. less massive stars in this association.Comment: Substantially revised version; incorporates referee suggestions & expanded discussio

Genomic analysis of metabolic pathway gene expression in mice

BACKGROUND: A segregating population of (C57BL/6J × DBA/2J)F2 intercross mice was studied for obesity-related traits and for global gene expression in liver. Quantitative trait locus analyses were applied to the subcutaneous fat-mass trait and all gene-expression data. These data were then used to identify gene sets that are differentially perturbed in lean and obese mice. RESULTS: We integrated global gene-expression data with phenotypic and genetic segregation analyses to evaluate metabolic pathways associated with obesity. Using two approaches we identified 13 metabolic pathways whose genes are coordinately regulated in association with obesity. Four genomic regions on chromosomes 3, 6, 16, and 19 were found to control the coordinated expression of these pathways. Using criteria that included trait correlation, differential gene expression, and linkage to genomic regions, we identified novel genes potentially associated with the identified pathways. CONCLUSION: This study demonstrates that genetic and gene-expression data can be integrated to identify pathways associated with clinical traits and their underlying genetic determinants

Genetic and Genomic Analysis of a Fat Mass Trait with Complex Inheritance Reveals Marked Sex Specificity

The integration of expression profiling with linkage analysis has increasingly been used to identify genes underlying complex phenotypes. The effects of gender on the regulation of many physiological traits are well documented; however, “genetical genomic” analyses have not yet addressed the degree to which their conclusions are affected by sex. We constructed and densely genotyped a large F2 intercross derived from the inbred mouse strains C57BL/6J and C3H/HeJ on an apolipoprotein E null (ApoE(−/−)) background. This BXH.ApoE(−/−) population recapitulates several “metabolic syndrome” phenotypes. The cross consists of 334 animals of both sexes, allowing us to specifically test for the dependence of linkage on sex. We detected several thousand liver gene expression quantitative trait loci, a significant proportion of which are sex-biased. We used these analyses to dissect the genetics of gonadal fat mass, a complex trait with sex-specific regulation. We present evidence for a remarkably high degree of sex-dependence on both the cis and trans regulation of gene expression. We demonstrate how these analyses can be applied to the study of the genetics underlying gonadal fat mass, a complex trait showing significantly female-biased heritability. These data have implications on the potential effects of sex on the genetic regulation of other complex traits

High-throughput, fluorescent-aptamer-based measurements of steady-state transcription rates for the Mycobacterium tuberculosis RNA polymerase

The first step in gene expression is the transcription of DNA sequences into RNA. Regulation at the level of transcription leads to changes in steady-state concentrations of RNA transcripts, affecting the flux of downstream functions and ultimately cellular phenotypes. Changes in transcript levels are routinely followed in cellular contexts via genome-wide sequencing techniques. However, in vitro mechanistic studies of transcription have lagged with respect to throughput. Here, we describe the use of a real-time, fluorescent-aptamer-based method to quantitate steady-state transcription rates of the Mycobacterium tuberculosis RNA polymerase. We present clear controls to show that the assay specifically reports on promoter-dependent, full-length RNA transcription rates that are in good agreement with the kinetics determined by gel-resolved, α-32P NTP incorporation experiments. We illustrate how the time-dependent changes in fluorescence can be used to measure regulatory effects of nucleotide concentrations and identity, RNAP and DNA concentrations, transcription factors, and antibiotics. Our data showcase the ability to easily perform hundreds of parallel steady-state measurements across varying conditions with high precision and reproducibility to facilitate the study of the molecular mechanisms of bacterial transcription

The anxiolytic effects of cognitive behavior therapy for insomnia: preliminary results from a web-delivered protocol

Though the efficacy of cognitive behavior therapy for insomnia (CBTI) is well-established, the paucity of credentialed providers hinders widespread access. Further, the impact of alternatives such as web-delivered CBTI has not been adequately tested on common insomnia comorbidities such as anxiety. Therefore, we assessed the impact of an empirically validated web-delivered CBTI intervention on insomnia and comorbid anxiety symptoms. A sample of 22 adults (49.8±13.5 yo; 62.5% female) with DSM-5 based insomnia were randomized to either an active CBTI treatment group (n = 13) or an information-control (IC) group (n = 9). Participants in the CBTI group underwent a standard CBTI program delivered online by a 'virtual' therapist, whereas the IC group received weekly 'sleep tips' and general sleep hygiene education via electronic mail. All participants self-reported sleep parameters, including sleep onset latency (SOL), insomnia symptoms per the Insomnia Severity Index (ISI), and anxiety symptoms per the Beck Anxiety Inventory (BAI) at both baseline as well as follow- up assessment one week post-treatment. There were no significant differences between the CBTI and IC groups on baseline measures. The CBTI group showed significantly larger reductions in BAI scores (t = 2.6; p < .05; Cohen's d = .8) and ISI scores (t = 2.1; p < .05; Cohen's d = .9) at follow-up than did the IC group. Further, changes in SOL from baseline (62.3±44.0 minutes) to follow-up (22.3±14.4 minutes) in the CBTI group were also significantly greater (t = 2.3; p < .05; Cohen's d = .9) than in the IC group (baseline: 55.0±44.2 minutes; follow-up: 50.±60.2 minutes).This study offers preliminary evidence that a web-delivered CBTI protocol with minimal patient contact can improve comorbid anxiety symptoms among individuals with insomnia

Economic evaluation of a cluster randomized trial of interventions to improve health workers' practice in diagnosing and treating uncomplicated malaria in Cameroon.

BACKGROUND: Malaria rapid diagnostic tests (RDTs) are a valid alternative to malaria testing with microscopy and are recommended for the testing of febrile patients before prescribing an antimalarial. There is a need for interventions to support the uptake of RDTs by health workers. OBJECTIVE: To evaluate the cost-effectiveness of introducing RDTs with basic or enhanced training in health facilities in which microscopy was available, compared with current practice. METHODS: A three-arm cluster randomized trial was conducted in 46 facilities in central and northwest Cameroon. Basic training had a practical session on RDTs and lectures on malaria treatment guidelines. Enhanced training included small-group activities designed to change health workers' practice and reduce the consumption of antimalarials among test-negative patients. The primary outcome was the proportion of febrile patients correctly treated: febrile patients should be tested for malaria, artemisinin combination therapy should be prescribed for confirmed cases, and no antimalarial should be prescribed for patients who are test-negative. Individual patient data were obtained from facility records and an exit survey. Costs were estimated from a societal perspective using project reports and patient exit data. The analysis used bivariate multilevel modeling and adjusted for imbalance in baseline covariates. RESULTS: Incremental cost per febrile patient correctly treated was $8.40 for the basic arm and$3.71 for the enhanced arm. On scale-up, it was estimated that RDTs with enhanced training would save $0.75 per additional febrile patient correctly treated. CONCLUSIONS: Introducing RDTs with enhanced training was more cost-effective than RDTs with basic training when each was compared with current practice

Long-term Periodicities of Cataclysmic Variables with Synoptic Surveys

A systematic study on the long-term periodicities of known Galactic cataclysmic variables (CVs) was conducted. Among 1580 known CVs, 344 sources were matched and extracted from the Palomar Transient Factory (PTF) data repository. The PTF light curves were combined with the Catalina Real-Time Transient Survey (CRTS) light curves and analyzed. Ten targets were found to exhibit long-term periodic variability, which is not frequently observed in the CV systems. These long-term variations are possibly caused by various mechanisms, such as the precession of the accretion disk, hierarchical triple star system, magnetic field change of the companion star, and other possible mechanisms. We discuss the possible mechanisms in this study. If the long-term period is less than several tens of days, the disk precession period scenario is favored. However, the hierarchical triple star system or the variations in magnetic field strengths are most likely the predominant mechanisms for longer periods.Comment: 33 pages, 9 figures (manuscript form), Accepted for publication in PAS