iBMQ: a R/Bioconductor package for integrated Bayesian modeling of eQTL data.

MOTIVATION: Recently, mapping studies of expression quantitative loci (eQTL) (where gene expression levels are viewed as quantitative traits) have provided insight into the biology of gene regulation. Bayesian methods provide natural modeling frameworks for analyzing eQTL studies, where information shared across markers and/or genes can increase the power to detect eQTLs. Bayesian approaches tend to be computationally demanding and require specialized software. As a result, most eQTL studies use univariate methods treating each gene independently, leading to suboptimal results. RESULTS: We present a powerful, computationally optimized and free open-source R package, iBMQ. Our package implements a joint hierarchical Bayesian model where all genes and SNPs are modeled concurrently. Model parameters are estimated using a Markov chain Monte Carlo algorithm. The free and widely used openMP parallel library speeds up computation. Using a mouse cardiac dataset, we show that iBMQ improves the detection of large trans-eQTL hotspots compared with other state-of-the-art packages for eQTL analysis. AVAILABILITY: The R-package iBMQ is available from the Bioconductor Web site at http://bioconductor.org and runs on Linux, Windows and MAC OS X. It is distributed under the Artistic Licence-2.0 terms. CONTACT: christian.deschepper@ircm.qc.ca or rgottard@fhcrc.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

An integrated hierarchical Bayesian model for multivariate eQTL mapping.

Recently, expression quantitative loci (eQTL) mapping studies, where expression levels of thousands of genes are viewed as quantitative traits, have been used to provide greater insight into the biology of gene regulation. Originally, eQTLs were detected by applying standard QTL detection tools (using a "one gene at-a-time" approach), but this method ignores many possible interactions between genes. Several other methods have proposed to overcome these limitations, but each of them has some specific disadvantages. In this paper, we present an integrated hierarchical Bayesian model that jointly models all genes and SNPs to detect eQTLs. We propose a model (named iBMQ) that is specifically designed to handle a large number G of gene expressions, a large number S of regressors (genetic markers) and a small number n of individuals in what we call a ``large G, large S, small n'' paradigm. This method incorporates genotypic and gene expression data into a single model while 1) specifically coping with the high dimensionality of eQTL data (large number of genes), 2) borrowing strength from all gene expression data for the mapping procedures, and 3) controlling the number of false positives to a desirable level. To validate our model, we have performed simulation studies and showed that it outperforms other popular methods for eQTL detection, including QTLBIM, R-QTL, remMap and M-SPLS. Finally, we used our model to analyze a real expression dataset obtained in a panel of mice BXD Recombinant Inbred (RI) strains. Analysis of these data with iBMQ revealed the presence of multiple hotspots showing significant enrichment in genes belonging to one or more annotation categories.

The Collaborative Cross, a community resource for the genetic analysis of complex traits.

The goal of the Complex Trait Consortium is to promote the development of resources that can be used to understand, treat and ultimately prevent pervasive human diseases. Existing and proposed mouse resources that are optimized to study the actions of isolated genetic loci on a fixed background are less effective for studying intact polygenic networks and interactions among genes, environments, pathogens and other factors. The Collaborative Cross will provide a common reference panel specifically designed for the integrative analysis of complex systems and will change the way we approach human health and disease.

Importance of randomization in microarray experimental designs with Illumina platforms.

Measurements of gene expression from microarray experiments are highly dependent on experimental design. Systematic noise can be introduced into the data at numerous steps. On Illumina BeadChips, multiple samples are assayed in an ordered series of arrays. Two experiments were performed using the same samples but different hybridization designs. An experiment confounding genotype with BeadChip and treatment with array position was compared to another experiment in which these factors were randomized to BeadChip and array position. An ordinal effect of array position on intensity values was observed in both experiments. We demonstrate that there is increased rate of false-positive results in the confounded design and that attempts to correct for confounded effects by statistical modeling reduce power of detection for true differential expression. Simple analysis models without post hoc corrections provide the best results possible for a given experimental design. Normalization improved differential expression testing in both experiments but randomization was the most important factor for establishing accurate results. We conclude that lack of randomization cannot be corrected by normalization or by analytical methods. Proper randomization is essential for successful microarray experiments.

Alterations in mitochondrial function as a harbinger of cardiomyopathy: lessons from the dystrophic heart.

While compelling evidence supports the central role of mitochondrial dysfunction in the pathogenesis of heart failure, there is comparatively less information available on mitochondrial alterations that occur prior to failure. Building on our recent work with the dystrophin-deficient mdx mouse heart, this review focuses on how early changes in mitochondrial functional phenotype occur prior to overt cardiomyopathy and may be a determinant for the development of adverse cardiac remodelling leading to failure. These include alterations in energy substrate utilization and signalling of cell death through increased permeability of mitochondrial membranes, which may result from abnormal calcium handling, and production of reactive oxygen species. Furthermore, we will discuss evidence supporting the notion that these alterations in the dystrophin-deficient heart may represent an early "subclinical" signature of a defective nitric oxide/cGMP signalling pathway, as well as the potential benefit of mitochondria-targeted therapies. While the mdx mouse is an animal model of Duchenne muscular dystrophy (DMD), changes in the structural integrity of dystrophin, the mutated cytoskeletal protein responsible for DMD, have also recently been implicated as a common mechanism for contractile dysfunction in heart failure. In fact, altogether our findings support a critical role for dystrophin in maintaining optimal coupling between metabolism and contraction in the heart.

Medial temporal lobe functioning and structure in the spontaneously hypertensive rat: comparison with Wistar-Kyoto normotensive and Wistar-Kyoto hypertensive strains.

The spontaneously hypertensive rat (SHR) is used as an animal model of attention deficit hyperactivity disorder (ADHD). It displays deficits in frontostriatal functioning, but it is unclear if medial temporal lobe functioning and structure are affected. We used behavioral tasks that evaluate functioning of the amygdala and hippocampus to compare male SHR to male rats from two inbred comparator strains, the normotensive Wistar-Kyoto (WKY) and the hypertensive Wistar-Kyoto (WKHT) rat (n = 8/strain). The three strains showed similar levels of amygdala-related stimulus-reward learning during conditioned cue preference testing. In the ambiguous T-maze task, which dissociates between spatial and habit learning, significantly more WKHT than SHR or WKY used a response (indicative of habit learning) versus a place (indicative of spatial learning) strategy during an early probe test on day 8. During a later probe test on day 24, WKY progressed significantly from using a place strategy to a response strategy. Throughout all probe tests, a place strategy was used predominately by SHR and a response strategy by WKHT. Thus, SHR exhibited deficits in dorsal striatum-related habit learning, whereas WKHT exhibited deficits in hippocampus-related spatial learning. Following behavioral testing, fluid attenuated inversion recovery (FLAIR) magnetic resonance imaging scans were conducted in subgroups of rats from each strain (n = 4/strain). FLAIR imaging detected bilateral hippocampal hyperintensities in three of four WKHT and unilateral hippocampal atrophy in one of four SHR. The association between response strategy use during the initial probe test to forage for food in the ambiguous T-maze task and bilateral hippocampal abnormalities was significant. Collectively, while medial temporal lobe functioning appears to be normal in SHR exhibiting an ADHD-like phenotype, WKHT rats display both hippocampal functioning deficits and signs of bilateral hippocampal cell loss. The latter characteristics might be used to develop a new animal model of age- or disease-related decline in hippocampal functioning.

Early predictors of cardiac decompensation in experimental volume overload.

In humans, volume overload (VOL) increases the risk of sudden cardiac death, but there is also important inter-individual variability, presumably because of differences in genetic backgrounds. Although VOL has rapid effects on myocardial properties, it is not known to which extent the severity of these early responses correlate with the effect of sustained VOL on mortality. In order to test this question, we induced VOL in male rats from two genetically distinct strains [i.e., Sprague-Dawley (SD) and Wistar Kyoto-derived Hyperactive (WKHA) rats] by creating a surgical aorto-caval fistula (ACF). Only 36% of SD rats remained alive after 39 weeks of ACF, in contrast to 82% of the operated WKHA rats. We also monitored myocardial hemodynamic function, mitochondrial properties, left ventricular (LV) morphology and LV wall diastolic properties at different times ranging from 2 to 12 weeks after either ACF or sham surgery. ACF had a rapid impact on the LV walls of both rat strains, but the only variables that were affected to a greater extent in the mortality-prone SD strain were normalized LV weight, LV cavity area, and myocardial wall stiffness. In contrast, there were only marginal strain-related differences in the way ACF affected hemodynamic and mitochondrial functions. Thus, while early morphologic responses of LV walls to ACF (along with their downstream consequences on myocardial diastolic wall stress) correlated well with strain-dependent differences in late mortality, other functional changes showed no predictive effects. Close monitoring of early changes in cardiac geometry (as well as new methods to analyze myocardial diastolic strain) might, therefore, be helpful to further improve risk stratification in humans with volume overload cardiopathies.

Regulatory effects of the Uty/Ddx3y locus on neighboring chromosome Y genes and autosomal mRNA transcripts in adult mouse non-reproductive cells.

In addition to sperm-related genes, the male-specific chromosome Y (chrY) contains a class of ubiquitously expressed and evolutionary conserved dosage-sensitive regulator genes that include the neighboring Uty, Ddx3y and (in mice) Eif2s3y genes. However, no study to date has investigated the functional impact of targeted mutations of any of these genes within adult non-reproductive somatic cells. We thus compared adult male mice carrying a gene trap within their Uty gene (UtyGT) to their wild-type (WT) isogenic controls, and performed deep sequencing of RNA and genome-wide profiling of chromatin features in extracts from either cardiac tissue, cardiomyocyte-specific nuclei or purified cardiomyocytes. The apparent impact of UtyGT on gene transcription concentrated mostly on chrY genes surrounding the locus of insertion, i.e. Uty, Ddx3y, long non-coding RNAs (lncRNAs) contained within their introns and Eif2s3y, in addition to possible effects on the autosomal Malat1 lncRNA. Notwithstanding, UtyGT also caused coordinate changes in the abundance of hundreds of mRNA transcripts related to coherent cell functions, including RNA processing and translation. The results altogether indicated that tightly co-regulated chrY genes had nonetheless more widespread effects on the autosomal transcriptome in adult somatic cells, most likely due to mechanisms other than just transcriptional regulation of corresponding protein-coding genes.

Increased expression and intramitochondrial translocation of cyclophilin-D associates with increased vulnerability of the permeability transition pore to stress-induced opening during compensated ventricular hypertrophy.

Opening of the permeability transition pore (PTP) of mitochondria is a critical permeation event that compromises cell viability and may constitute a factor that participates to the loss of cardiomyocytes in compromised hearts. Mitochondria from hearts with volume overload-induced compensated hypertrophy are more vulnerable to opening of the PTP opening in response to a Ca2+ stress. Several of the factors known to affect PTP opening, including respiratory function, membrane potential, the rate of mitochondrial Ca2+ uptake and endogenous levels of Ca2+ in the mitochondrial matrix, were not altered by volume overload. In contrast, there was an 80% increase in the abundance of the PTP regulating protein cyclophilin-D and a 3.7 fold enhancement of Cyp-D binding to membrane, which all predispose to PTP opening. Mitochondria from volume overloaded animals also displayed elevated rates of production of reactive oxygen species, which may be causally related to both the intramitochondrial translocation of cyclophilin-D and PTP opening, since incubation of cardiac mitochondria with terbutylhydroperoxyde in vitro increased to binding of cyclophilin-D to mitochondrial membranes in a dose-related fashion, except when cyclosporin A (a ligand of cyclophilin D with a known ability to delay PTP opening) was present prior to the addition of terbutylhydroperoxyde. Taken together, these results constitute the first evidence obtained in a pathophysiologic situation that increased abundance of cyclophilin-D within mitochondrial membranes may increase mitochondrial vulnerability to stress, and thus possibly initiate a vicious cycle of cellular dysfunction that may ultimately lead to activation of cell death.

Chromosome Y variants from different inbred mouse strains are linked to differences in the morphologic and molecular responses of cardiac cells to postpubertal testosterone.

BACKGROUND: We have reported previously that when chromosome Y (chrY) from the mouse strain C57BL/6J (ChrYC57) was substituted for that of A/J mice (ChrYA), cardiomyocytes from the resulting "chromosome substitution" C57BL/6J-chrYA strain were smaller than that of their C57BL/6J counterparts. In reverse, when chrYA from A/J mice was substituted for that of chrYC57, cardiomyocytes from the resulting A/J-chrYC57 strain were larger than in their A/J counterparts. We further used these strains to test whether: 1) the origin of chrY could also be linked to differences in the profile of gene expression in the hearts of adult male mice, and 2) post-pubertal testosterone could play a role in the differential morphologic and/or molecular effects of chrYC57 and chrYA. RESULTS: The increased size of cardiomyocytes from adult male C57BL/6J mice compared to C57BL/6J-chrYA resulted from the absence of hypertrophic effects of post-pubertal testosterone on cells from the latter strain. However, gene profiling revealed that the latter effect could not be explained on the basis of an insensitivity of cells from C57BL/6J-chrYA to androgens, since even more cardiac genes were affected by post-pubertal testosterone in C57BL/6J-chrYA hearts than in C57BL/6J. By testing for interaction between the effects of surgery and strain, we identified 249 "interaction genes" whose expression was affected by post-pubertal testosterone differentially according to the genetic origin of chrY. These interaction genes were found to be enriched within a limited number of signaling pathways, including: 1) p53 signaling, which comprises the interacting genes Ccnd1, Pten and Cdkn1a that are also potential co-regulators of the androgen receptors, and 2) circadian rhythm, which comprises Arntl/Bmal1, which may in turn regulate cell growth via the control of Cdkn1a. CONCLUSION: Although post-pubertal testosterone increased the size of cardiomyocytes from male C56BL/6J mice but not that from their C57BL/6J-chrYA counterparts, it affected gene expression in the hearts from both strains. However, several cardiac genes responded to post-pubertal testosterone in a strict strain-selective manner, which provides possible mechanisms explaining how chrY may, in part via interference with androgen regulatory events, be linked to morphologic differences of cardiac cells of adult male mice.

Cyclic GMP signaling in cardiomyocytes modulates fatty acid trafficking and prevents triglyceride accumulation.

While the balance between carbohydrates and fatty acids for energy production appears to be crucial for cardiac homeostasis, much remains to be learned about the molecular mechanisms underlying this relationship. Given the reported benefits of cGMP signaling on the myocardium, we investigated the impact of its chronic activation on cardiac energy metabolism using mice overexpressing a constitutively active cytoplasmic guanylate cyclase (GC(+/0)) in cardiomyocytes. Ex vivo working GC(+/0) heart perfusions with (13)C-labeled substrates revealed an altered pattern of exogenous substrate fuel selection compared to controls, namely a 38+/-9% lower contribution of exogenous fatty acids to acetyl-CoA formation, while that of carbohydrates remains unchanged despite a two-fold increase in glycolysis. The lower contribution of exogenous fatty acids to energy production is not associated with changes in energy demand or supply (contractile function, oxygen consumption, tissue acetyl-CoA or CoA levels, citric acid cycle flux rate) or in the regulation of beta-oxidation (acetyl-CoA carboxylase activity, tissue malonyl-CoA levels). However, GC(+/0) hearts show a two-fold increase in the incorporation of exogenous oleate into triglycerides. Furthermore, the following molecular data are consistent with a concomitant increase in triglyceride hydrolysis: (i) increased abundance of hormone sensitive lipase (HSL) protein (24+/-11%) and mRNA (22+/-4%) as well as (ii) several phosphorylation events related to HSL inhibitory (AMPK) and activation (ERK 1/2) sites, which should contribute to enhance its activity. These changes in exogenous fatty acid trafficking in GC(+/0) hearts appear to be functionally relevant, as demonstrated by their resistance to fasting-induced triglyceride accumulation. While the documented metabolic profile of GC(+/0) mouse hearts is partly reminiscent of hypertrophied hearts, the observed changes in lipid trafficking have not been previously documented, and may be part of the molecular mechanism underlying the benefits of cGMP signaling on the myocardium.

Cardiac mass and cardiomyocyte size are governed by different genetic loci on either autosomes or chromosome Y in recombinant inbred mice.

Left ventricular hypertrophy is one of the main risk factors for cardiovascular mortality and morbidity. It has been proposed that hypertrophic stimuli act in great part by increasing the size of cardiomyocytes, and that the latter characteristic is a necessary condition to differentiate left ventricular hypertrophy from other benign forms of cardiac enlargement. To test whether the same genetic loci control the size of cardiomyocytes and left ventricular mass, we performed whole genome linkage analyses in a panel of 24 recombinant inbred AXB/BXA mouse strains. Whereas one major locus was linked to left ventricular mass in both males and females, loci linked to the size of cardiomyocytes were clearly distinct and showed sex-specific linkage. Moreover, the parental origin of chromosome Y had strong effects on the size of cardiomyocytes in male mice but did not affect left ventricular mass. In addition to showing that genetic loci that increase the size of cardiomyocytes are not necessarily linked to increased left ventricular mass, our findings have important consequences in evaluating cardiac phenotypes when performing genetic manipulations in mice, and in determining the cause of sex-specific differences when using models derived from C57BL/6J mice.

Fibroblast apoptosis precedes cardiomyocyte mass reduction during left ventricular remodeling in hypertensive rats treated with amlodipine.

BACKGROUND: A transient induction of apoptosis accompanies the normalization of left ventricular mass index in spontaneously hypertensive rats (SHR) treated with dihydropyridine calcium-channel blockers. However, the cell type undergoing apoptosis in this model and the temporal correlation with onset cardiac remodeling remain undefined. METHODS AND RESULTS: SHR were treated either with vehicle or amlodipine (20 mg/kg per day) for 4, 7, 10, 14 or 28 days. Amlodipine stably reduced systolic blood pressure by day 2 (-26 +/- 2%) and stably reduced the left ventricular concentration of atrial natriuretic peptide (ANP) mRNA by approximately 50% as early as day 4, suggesting the early reduction of cardiomyocyte stress. Left ventricular mass index was significantly reduced by day 7 (-4.6 +/- 1.5%), in coordination with reduced DNA content (-23 +/- 2%) and non-cardiomyocyte number (-17 +/- 4%). However, the cardiomyocyte cross-sectional area was reduced only starting from day 14. Caspase-3 cleavage was significantly increased at day 7 only. Ultimately, amlodipine for 28 days induced a slight increase in capillary density without affecting total cardiomyocyte number, while reducing the total number of non-cardiomyocytes down to levels seen in untreated normotensive Wistar-Kyoto rats. Bax to Bcl-2 protein ratios were increased from day 7 to day 28. In situ double labeling by the terminal deoxynucleotidyl transferase biotin-dUTP nick end labeling (TUNEL) method (apoptosis) combined with rhodamine-labeled lectin binding (endothelial cell marker) revealed a significant increase (> 3-fold) in TUNEL-positive, lectin-negative non-cardiomyocytes in the interstitium between days 7 and 14. CONCLUSIONS: Left ventricular remodeling induced by amlodipine in SHR involves selective deletion of excess fibroblasts via apoptosis prior to cardiomyocyte mass reduction, but after attenuation of ANP gene expression.

High-Resolution Maps of Mouse Reference Populations.

Genetic reference panels are widely used to map complex, quantitative traits in model organisms. We have generated new high-resolution genetic maps of 259 mouse inbred strains from recombinant inbred strain panels (C57BL/6J × DBA/2J, ILS/IbgTejJ × ISS/IbgTejJ, and C57BL/6J × A/J) and chromosome substitution strain panels (C57BL/6J-Chr#, C57BL/6J-Chr#, and C57BL/6J-Chr#). We genotyped all samples using the Affymetrix Mouse Diversity Array with an average intermarker spacing of 4.3 kb. The new genetic maps provide increased precision in the localization of recombination breakpoints compared to the previous maps. Although the strains were presumed to be fully inbred, we found residual heterozygosity in 40% of individual mice from five of the six panels. We also identified de novo deletions and duplications, in homozygous or heterozygous state, ranging in size from 21 kb to 8.4 Mb. Almost two-thirds (46 out of 76) of these deletions overlap exons of protein coding genes and may have phenotypic consequences. Twenty-nine putative gene conversions were identified in the chromosome substitution strains. We find that gene conversions are more likely to occur in regions where the homologous chromosomes are more similar. The raw genotyping data and genetic maps of these strain panels are available at http://churchill-lab.jax.org/website/MDA.

Comparisons of chromosome Y-substituted mouse strains reveal that the male-specific chromosome modulates the effects of androgens on cardiac functions.

BACKGROUND: The C57BL/6J.YA/J mouse strain is a chromosome-substituted line where the original male-specific portion of chromosome Y (MSY) from C57BL/6J mice was substituted for that from A/J mice. In hearts from male C57BL/6J.YA/J and C57BL/6J mice, orchidectomy (ORX) affected in a strictly strain-specific fashion the expression a subset of genes showing enrichment for functional categories, including that of circadian rhythms and cardiac contractility. We further tested whether: (1) there were strain-specific differences in cardiac circadian rhythms; (2) strain-dependent differences in the effects of ORX on contractility genes translated into differences in cardiac functions; and (3) differential contractility responses occurred preferentially at times when circadian rhythms also showed strain-specific differences. METHODS: In hearts from the two above strains, we (1) profiled the expression levels of 15 circadian genes at 4-h intervals across a 24 h period; (2) tested the effects of either ORX or androgen replacement on expression of cardiac contractility genes, and that of ORX on myocardial functional reserve; and (3) verified whether the effects of MSY variants on cardiac contractility-related responses showed synchronicity with differences in circadian rhythms. RESULTS: Among the 15 tested circadian genes, a subset of them were affected by strain (and thus the genetic origin of MSY), which interacted with the amplitude of their peak of maximal expression at 2:00 PM. At that same time-point, ORX decreased (and androgen supplementation increased) the expression of three contractility-related genes, and decreased myocardial relaxation reserve in C57BL/6J.YA/J, but not in C57BL/6J mice. These effects were not detected at 10:00 AM, i.e., at another time-point when circadian genes showed no strain-specific differences. CONCLUSIONS: The results indicate that in mice, androgens have activational effects on cardiac circadian rhythms, contractile gene expression, and myocardial functional reserve. All effects occurred preferentially at the same time of the day, but varied as a function of the genetic origin of MSY. Androgens may therefore be necessary but not sufficient to impart male-specific characteristics to some particular cardiac functions, with genetic material from MSY being one other necessary factor to fully define their range of actions.

Cardiac morphology and function reference values derived from a large subset of healthy young Caucasian adults by magnetic resonance imaging.

AIMS: Assessment of cardiac anatomy and function by cardiovascular magnetic resonance (CMR) is accurate and reproducible and is commonly performed to clarify borderline results obtained by other techniques. Normal reference values are lacking in a large sample of young healthy adults. As CMR is increasingly solicited to discriminate normality from equivocal disease in this population, we sought to determine reliable reference values. METHODS AND RESULTS: A sample of 434 Caucasian adults aged 26 ± 4 years (45% male) without cardiovascular disease or risk factors (including obesity and smoking) underwent CMR. Blood pressure, electrocardiogram, and plasma markers (lipid profile, fasting glucose, troponin, and Nt-pro-BNP) were within normal limits and typical of a low-cardiometabolic-risk profile. End-diastolic (ED), end-systolic (ES), and stroke volumes were greater in men for left and right atria and ventricles. Left ventricular (LV) mass was higher in men. ED wall thickness of all segments was greater in men, whereas ES wall thickening (segmental function) was similar in both genders. After normalization to body surface area, all gender differences remained. Left and right ventricular volumes were lower, and left atrial volumes were higher in older individuals. In contrast, LV mass was not associated with age. CONCLUSION: This is the first large database of reference ranges for ventricular and atrial functions, volumes, and mass in young Caucasian men and women devoid of cardiovascular disease and risk factors. These data will contribute to improving the accuracy of CMR interpretation for clinical and research applications.

Association of a Network of Interferon-Stimulated Genes with a Locus Encoding a Negative Regulator of Non-conventional IKK Kinases and IFNB1.

Functional genomic analysis of gene expression in mice allowed us to identify a quantitative trait locus (QTL) linked in trans to the expression of 190 gene transcripts and in cis to the expression of only two genes, one of which was Ypel5. Most of the trans-expression QTL genes were interferon-stimulated genes (ISGs), and their expression in mouse macrophage cell lines was stimulated in an IFNB1-dependent manner by Ypel5 silencing. In human HEK293T cells, YPEL5 silencing enhanced the induction of IFNB1 by pattern recognition receptors and phosphorylation of TBK1/IKBKE kinases, whereas co-immunoprecipitation experiments revealed that YPEL5 interacted physically with IKBKE. We thus found that the Ypel5 gene (contained in a locus linked to a network of ISGs in mice) is a negative regulator of IFNB1 production and innate immune responses that interacts functionally and physically with TBK1/IKBKE kinases.

Beneficial effects of long-term use of the antioxidant probucol in heart failure in the rat.

BACKGROUND: Congestive heart failure (CHF) is a disease that is characterized by progressive left ventricular (LV) dysfunction and dilatation. Oxidative stress is thought to contribute to the progression of CHF, and antioxidants have been shown to have beneficial effects when started early after myocardial infarction (MI). In this study, we tested whether the powerful antioxidant probucol would attenuate progression of CHF once it was established after MI in the rat. METHODS AND RESULTS: Ligation of a coronary artery was used to create an MI in rats (n=266). Survivors were then randomized 20 days after MI to either probucol 61 mg. kg(-1). d(-1) or vehicle and followed up for a total of 100 days after MI. Studies of cardiac hemodynamics, LV remodeling, cardiac apoptosis and morphology, systemic neurohumoral activation, oxidative stress, and renal function were then evaluated. Probucol improved LV function (LV maximum rate of pressure rise from 3103 to 4250 mm Hg/s, P<0.05, and LV end-diastolic pressure decrease from 28 to 24 mm Hg, P<0.05), reduced pulmonary weights, prevented right ventricular systolic hypertension, and preserved renal function compared with vehicle. Probucol also prevented LV dilatation, prevented wall thinning (1.70 versus 1.42 mm, P<0.05), reduced cardiac fibrosis and cardiac apoptosis, attenuated increased myocardial cell cross-sectional area, and increased scar thickness. CONCLUSIONS: In chronic CHF, probucol exerts multiple beneficial morphological effects that result in better LV remodeling and function, reduced neurohumoral activation, and preserved renal function.

Identification and validation of Loci and candidate genes linked to cardiac hypertrophy.

Left ventricular hypertrophy (LVH) is a complex quantitative trait that has a strong prognostic value for cardiovascular mortality and morbidity. Cardiac mass is determined in part by the influence of genetic loci that are known as quantitative trait loci (QTLs), the localization of which can be performed experimentally in genetic animal crosses. The present chapter outlines standard procedures for the selection of appropriate animal strains, for assessment of mode of inheritance, for characterizing the cardiac phenotype, for performing whole-genome scans, and for conducting linkage analyses. Identification of QTLs may lead to the identification of candidate genes whose roles can be further investigated in either transgenic, knockout, or pharmacologically manipulated animal models.

Comparisons of behavioral and neurochemical characteristics between WKY, WKHA, and Wistar rat strains.

WKHA rats constitute a recombinant inbred rat strain derived by phenotypic selection of the progeny of hybrid F2 crosses between SHR and WKY rats. WKHA are normotensive and show some features of hyperactivity and of hyper-reactivity to stress, but their utility as model of attention deficit/hyperactivity disorder (ADHD) has not yet been settled. To address these questions, we performed behavioral and neurochemical evaluations of WKHA, and compared them to both WKY and Wistar (WIS) rats. In locomotor activity tests, the respective scores for each strain were WKY