Project description:Objective - The TRIB1 locus has been linked to hepatic triglyceride metabolism in mice and to plasma triglycerides and coronary artery disease (CAD) in humans. The lipid associated SNPs identified by genome-wide association studies (GWAS) are located ~ 30 kb downstream from TRIB1 suggesting complex regulatory effects on genes or pathways relevant to hepatic triglyceride metabolism. The goal of this study was to investigate the functional relationship between common SNPs at the TRIB1 locus and plasma lipid traits. Methods & Results - Characterization of the risk locus reveals that it encompasses a gene, TRIB1 associated locus (TRIBAL) comprised of a well conserved promoter region and an alternatively spliced transcript. Bioinformatic analysis and re-sequencing identified a single nucleotide polymorphism (SNP), rs2001844, within the promoter region that associates with increased plasma triglycerides, reduced HDL-C and CAD risk. Furthermore, we show that rs2001844 is an expression trait locus (eQTL) for TRIB1 expression in blood and alters TRIBAL promoter activity in a reporter assay model. The TRIBAL transcript has features typical of long noncoding RNAs (lncRNA), including poor sequence conservation. Modulation of TRIBAL expression had limited impact on either TRIB1 or lipid regulatory genes mRNA levels in human hepatocyte models. In contrast, TRIB1 knockdown markedly increased TRIBAL expression in HepG2 cells and primary human hepatocytes. Conclusions - These studies demonstrate an interplay between a novel locus,TRIBAL, and TRIB1. TRIBAL is located in the GWAS identified risk locus, responds to altered expression of TRIB1, harbors a risk SNP that is an eQTL for TRIB1 expression and associates with plasma triglyceride concentrations. HepG2 hepatoma cells were stably infected with TRIBAL1 or no insert carrying lentiviruses
Project description:Shigella is an intracellular bacterial pathogen known to activate numerous innate immunity and inflammatory signaling pathways. Many of these pathways are also involved in mTOR signaling. We used HEK293T cell cultures and sought to understand how Shigella infection and rapamycin treatment affect the transcriptome and in particular whether there were commonly affected pathways in the two experimental conditions. 8 samples were used - 2 control that were uninfected/untreated -- 1 sample lost due to RNA degradation, 3 infected with Shigella for 4 hours, and 3 treated with Rapamycin (50 ug/mL) for 4 hours. All samples were from independent experiments. We used the program AltAnalyze to perform pairwise comparisons between Uninfected with Infected, and Uninfected with Rapamycin using default parameters.
Project description:Adult mammalian cardiomyocytes (CM) are differentiated post-mitotic cells that lack significant proliferative potential through their inability to reactivate the cell cycle postnatally. In the week after birth, the mammalian heart goes through distinct stages of cell cycle progression and differentiation that govern the development of the mature adult CM phenotype. By establishing the fundamental framework of the molecular signals governing these early events after birth, a potential treatment strategy that restores the heart’s ability to proliferate, and in theory, undergo ‘repair’ after injury could be developed. At 0 days (d), 1d, 3d, 5d, 7d, 10d, and 15d after birth, hearts from C57BL/6J wild-type mice were excised and processed for total RNA isolation. Samples were analyzed by genome-wide messenger RNA (mRNA) microarray profiling. All experiments were performed on age- and sex-matched mice, with equal ratio of male to female mice.
Project description:Expression profiling of stem cell lines derived from the early embryo representing the trophoblast, primitive endoderm, early epiblast (inner cell mass E3.5) and late post-implantation epiblast (E5.5). Cells were grown without feeders and harvested. Comparisons were made to provide evidence of unique gene expression between the cell lines. Specifically, pre-implantation (ICM, epiblast and primitive endoderm, and trophoblast), as well as pre-implantation and post-implantation epiblasts.
Project description:Proteomics analysis was used to determine the relative abundance of proteins in HeLa rtTA-HIV-ΔMls cells treated with a HIV-1 RNA processing inhibitor (5342191 or 9147791) or DMSO +/- Dox.
Project description:Genome-wide transcriptome analyses of transgenic mice, that express Cre recombinase flanked by mutated estrogen receptors (MerCreMer; mcm), and carry loxP-flanked sequences of p53 and Mdm2 was performed in the presence and absence of Tamoxifen.<br>The molecular mechanisms underlying heart failure remain poorly understood. As such, identifying the factors which effectively maintain cardiac tissue homeostasis is of great scientific and clinical importances. The tumor suppressor Trp53 (p53) inhibits cell growth after acute stress by regulating gene transcription. The mammalian genome contains hundreds of p53 binding sites. However, whether p53 participates in the regulation of cardiac tissue homeostasis under normal conditions is not known. To examine the physiologic consequences of p53 and Mdm2 ablation in adult cardiomyocytes in vivo, cardiac morphology and function were assessed in conditional mutant mice.
Project description:The regenerative capacity of the mammalian heart is lost quickly after birth when cardiomyocytes stop dividing and undergo cell cycle arrest. Thus, the adult mammalian heart lacks the ability to heal itself to any appreciable amount after ischemic injury such as myocardial infarction. Heart growth begins during fetal life with the first phase of DNA synthesis that is exclusively associated with cardiomyocyte proliferation. This process proceeds until 12 hours after birth and is defined as 0 days in our submitted samples. Cardiomyocytes division is undetectable at neonatal day 1. To analyze the molecular mechanisms responsible for cessation of cardiomyocyte proliferation, we performed genome-wide miRNA microarray profiling by comparing postnatal days 0 vs 1d.This revealed a profile of 8 significantly downregulated miRNAs in the proliferative DKO hearts (versus vehicle-injected control), that were enriched for mRNA targets involved in cell cycle regulation. In vitro studies have demonstrated that knockdown of these 8 miRNAs in neonatal rat cardiomyocytes can increase the occurrence of cytokinetic events. Ultimately, we aim to inject antagomirs targeting these miRNAs into mice post-myocardial infarction to determine the effect of these miRNAs on heart function and cardiomyocyte proliferation in vivo.
Project description:Methylation profiling of CpG Island Methylation of genomic DNA samples extracted from placentae of Intra-Uterine Growth Restricted newborns and gestational age matched controls. These data can be used for methylation comparisons between these two types of samples. The results of such comparisons can be used to generate hypotheses on the involvement of DNA methylation variation in placenta development and fetal growth. Two-condition Methyl DNA Immunoprecipitation (MeDIP) experiment, IUGR vs. Control placenta samples. Biological replicates: 8 control, 8 IUGR cases.
Project description:Analysis of the cardiac transcriptome by heart-specific acute genetic ablation of Huwe1 in adult male mice employing a tamoxifen-inducible Cre-loxP system.
Project description:Behaviour is derived from complex molecular interactions within the brain, in response to specific environmental stimuli. In some rare cases, the direct causes of behaviour have been attributed to the interactions of a single or small group of gene transcripts and proteins. We conducted two experiments with the hope of defining some of the molecular interactors for four separate behaviours: sugar feeding, locomotor activity in a novel field, and acoustic startle reflex, and prepulse inhibition of the acoustic startle reflex, which have been linked to prefrontal cortex dopaminergic function or as predictors of sensorimotor gating in diseases such as schizophrenia. Rats with high and low response phenotypes were selected to determine the differences between these two extremes of behaviour. From our analyses, transcripts of Homer1, a neuronal scaffolding protein which interacts with group1 metabotropic glutamate receptors, were found to be significantly correlated with array data in both experiments, and with behaviour data across three separate tests in the second experiment, indicating that this gene's transcripts and probably downstream protein interactions have a significant correlation with behaviour phenotype in the inbred Lewis rat. Future areas of pursuit for this data should involve modification of the expression of Homer1 in an isolated fashion to determine a pharmacological threshold for differences in behaviour. Experiment Overall Design: Nine rats with varying behavioural phenotypes were analyzed. Three behavioural tests: SF, locomotion, and ASR.