Global Regulation on microRNA in Hepatitis B Virus-Associated Hepatocellular Carcinoma

Recent work has revealed the causative links between deregulation of microRNAs (miRNAs) and cancer development. In hepatocellular carcinoma (HCC), aberrant expression of miRNAs has been observed, but the molecular mechanisms that contribute to such changes remains to be elucidated. Here, we reported the analysis of miRNA expression in 94 pairs of tumor and adjacent nontumor tissues from HBV-associated HCC in Chinese patients. We found miRNAs were aberrantly expressed in HCC tissues. To investigate the cause of such deregulation, we detected changes in DNA copy number by measuring locus-specific hybridization intensity, and found changes in expression of several miRNAs are correlated with genomic amplification or deletion. For example, the genomic regions of miR-30d and miR-151 were amplified in ∼50% of HCC tumor tissues, and the expressions of these miRNAs are significantly correlated with DNA copy number. We also employed cDNA microarray data, and provide evidence that key regulators of the miRNA biosynthetic pathway, including DROSHA, DGCR8, AGO1, and AGO2, are frequently overexpressed in HCC. This study provides molecular clues that may contribute to the global changes of miRNA expression in HCC. Copyright © 2011, Mary Ann Liebert, Inc.published_or_final_versio

Thermochemistry of monazite-(La) and dissakisite-(La): implications for monazite and allanite stability in metapelites

Thermochemical properties have been either measured or estimated for synthetic monazite, LaPO4, and dissakisite, CaLaMgAl2(SiO4)3OH, the Mg-equivalent of allanite. A dissakisite formation enthalpy of −6,976.5±10.0kJmol−1 was derived from high-temperature drop-solution measurements in lead borate at 975K. A third-law entropy value of 104.9±1.6Jmol−1K−1 was retrieved from low-temperature heat capacity (C p) measured on synthetic LaPO4 with an adiabatic calorimeter in the 30-300K range. The C p values of lanthanum phases were measured in the 143-723K range by differential scanning calorimetry. In this study, La(OH)3 appeared as suitable for drop solution in lead borate and represents an attractive alternative to La2O3. Pseudo-sections were calculated with the THERIAK-DOMINO software using the thermochemical data retrieved here for a simplified metapelitic composition (La=∑REE+Y) and considering monazite and Fe-free epidotes along the dissakisite-clinozoïsite join, as the only REE-bearing minerals. Calculation shows a stability window for dissakisite-clinozoïsite epidotes (T between 250 and 550°C and P between 1 and 16kbar), included in a wide monazite field. The P-T extension of this stability window depends on the bulk-rock Ca-content. Assuming that synthetic LaPO4 and dissakisite-(La) are good analogues of natural monazite and allanite, these results are consistent with the REE-mineralogy sequence observed in metapelites, where (1) monazite is found to be stable below 250°C, (2) around 250-450°C, depending on the pressure, allanite forms at the expense of monazite and (3) towards amphibolite conditions, monazite reappears at the expense of allanit

Bit-Vector Model Counting using Statistical Estimation

Approximate model counting for bit-vector SMT formulas (generalizing \#SAT) has many applications such as probabilistic inference and quantitative information-flow security, but it is computationally difficult. Adding random parity constraints (XOR streamlining) and then checking satisfiability is an effective approximation technique, but it requires a prior hypothesis about the model count to produce useful results. We propose an approach inspired by statistical estimation to continually refine a probabilistic estimate of the model count for a formula, so that each XOR-streamlined query yields as much information as possible. We implement this approach, with an approximate probability model, as a wrapper around an off-the-shelf SMT solver or SAT solver. Experimental results show that the implementation is faster than the most similar previous approaches which used simpler refinement strategies. The technique also lets us model count formulas over floating-point constraints, which we demonstrate with an application to a vulnerability in differential privacy mechanisms

Expression of SMARCD1 interacts with age in association with asthma control on inhaled corticosteroid therapy.

BackgroundGlobal gene expression levels are known to be highly dependent upon gross demographic features including age, yet identification of age-related genomic indicators has yet to be comprehensively undertaken in a disease and treatment-specific context.MethodsWe used gene expression data from CD4+ lymphocytes in the Asthma BioRepository for Integrative Genomic Exploration (Asthma BRIDGE), an open-access collection of subjects participating in genetic studies of asthma with available gene expression data. Replication population participants were Puerto Rico islanders recruited as part of the ongoing Genes environments & Admixture in Latino Americans (GALA II), who provided nasal brushings for transcript sequencing. The main outcome measure was chronic asthma control as derived by questionnaires. Genomic associations were performed using regression of chronic asthma control score on gene expression with age in years as a covariate, including a multiplicative interaction term for gene expression times age.ResultsThe SMARCD1 gene (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1) interacted with age to influence chronic asthma control on inhaled corticosteroids, with a doubling of expression leading to an increase of 1.3 units of chronic asthma control per year (95% CI [0.86, 1.74], p = 6 × 10- 9), suggesting worsening asthma control with increasing age. This result replicated in GALA II (p = 3.8 × 10- 8). Cellular assays confirmed the role of SMARCD1 in glucocorticoid response in airway epithelial cells.ConclusionFocusing on age-dependent factors may help identify novel indicators of asthma medication response. Age appears to modulate the effect of SMARCD1 on asthma control with inhaled corticosteroids