73 research outputs found
Investigating microRNA-Target Interaction-Supported Tissues in Human Cancer Tissues Based on miRNA and Target Gene Expression Profiling
<div><p></p><p>Recent studies have revealed that a small non-coding RNA, microRNA (miRNA) down-regulates its mRNA targets. This effect is regarded as an important role in various biological processes. Many studies have been devoted to predicting miRNA-target interactions. These studies indicate that the interactions may only be functional in some specific tissues, which depend on the characteristics of an miRNA. No systematic methods have been established in the literature to investigate the correlation between miRNA-target interactions and tissue specificity through microarray data. In this study, we propose a method to investigate miRNA-target interaction-supported tissues, which is based on experimentally validated miRNA-target interactions. The tissue specificity results by our method are in accordance with the experimental results in the literature.</p><p>Availability and Implementation</p><p>Our analysis results are available at <a href="http://tsmti.mbc.nctu.edu.tw/" target="_blank">http://tsmti.mbc.nctu.edu.tw/</a> and <a href="http://www.stat.nctu.edu.tw/hwang/tsmti.html" target="_blank">http://www.stat.nctu.edu.tw/hwang/tsmti.html</a>.</p></div
YjcC, a c-di-GMP Phosphodiesterase Protein, Regulates the Oxidative Stress Response and Virulence of <i>Klebsiella pneumoniae</i> CG43
<div><p>This study shows that the expression of <i>yjcC</i>, an in vivo expression (IVE) gene, and the stress response regulatory genes <i>soxR</i>, <i>soxS</i>, and <i>rpoS</i> are paraquat inducible in <i>Klebsiella pneumoniae</i> CG43. The deletion of <i>rpoS</i> or <i>soxRS</i> decreased <i>yjcC</i> expression, implying an RpoS- or SoxRS-dependent control. After paraquat or H<sub>2</sub>O<sub>2</sub> treatment, the deletion of <i>yjcC</i> reduced bacterial survival. These effects could be complemented by introducing the Δ<i>yjcC</i> mutant with the YjcC-expression plasmid pJR1. The recombinant protein containing only the YjcC-EAL domain exhibited phosphodiesterase (PDE) activity; overexpression of <i>yjcC</i> has lower levels of cyclic di-GMP. The <i>yjcC</i> deletion mutant also exhibited increased reactive oxygen species (ROS) formation, oxidation damage, and oxidative stress scavenging activity. In addition, the <i>yjcC</i> deletion reduced capsular polysaccharide production in the bacteria, but increased the LD50 in mice, biofilm formation, and type 3 fimbriae major pilin MrkA production. Finally, a comparative transcriptome analysis showed 34 upregulated and 29 downregulated genes with the increased production of YjcC. The activated gene products include glutaredoxin I, thioredoxin, heat shock proteins, chaperone, and MrkHI, and proteins for energy metabolism (transporters, cell surface structure, and transcriptional regulation). In conclusion, the results of this study suggest that YjcC positively regulates the oxidative stress response and mouse virulence but negatively affects the biofilm formation and type 3 fimbriae expression by altering the c-di-GMP levels after receiving oxidative stress signaling inputs.</p></div
The list of the selected MTI-supported tissues corresponding to 19 miRNAs with equal to or more than 10 targets among 743 experimentally validated MTIs.
<p>The list of the selected MTI-supported tissues corresponding to 19 miRNAs with equal to or more than 10 targets among 743 experimentally validated MTIs.</p
The heatmaps of hsa-miR-17 expression and regulated genes.
<p>a. The expression profiles of hsa-miR-17 and 24 targets across 19 extended tissues. The correlations between the expression profiles of hsa-miR-17 and target genes were annotated next to the gene symbols. Green represented low expression and red represented high expression in corresponding genes and tissues. b. Part of the expression profile of hsa-miR-17 and experimentally validated and predicted target genes. There are 20 negatively correlated target genes; 16 of these target genes are predicted to be hsa-miR-17 target genes. PTEN, MAPK9, MAP3K12 and BMPR2 are experimentally confirmed target genes.</p
Tissue selection pipeline for finding MTI-supported tissues of miR-17 based on experimentally validated MTIs.
<p>Experimentally validated MTIs sharing the same miRNA were selected from the miRTarBase database. The correlations of MTIs across a combination of tissues, which were selected by our method, are strongly negative.</p
The flowchart of the proposed algorithm for finding MTI-supported tissues.
<p>The flowchart of the proposed algorithm for finding MTI-supported tissues.</p
The correlation density plot and heatmap for experimentally validated MTIs (miRTarBase).
<p>a. Comparison of correlation densities for all 743 experimentally validated MTIs (solid line) and hsa-miR-17 with 24 targets across the top 6 MTI-supported tissues (dashed line). b. The expression profiles of hsa-miR-17 and 24 targets across the top 6 MTI-supported tissues. The correlations between the expression profile of hsa-miR-17 and the profiles of target genes were annotated next to the gene symbol. Green represented low expression and red represented high expression in corresponding genes and tissues.</p
Deletion of <i>yjcC</i> places bacteria in an oxidative stress state.
<p>(A) Cytoplasmic ROS content determination. (B) The oxidation determination of the cytoplasmic proteins and membrane lipids. The log-phased bacteria <i>K. pneumoniae</i> CG43S3[pRK415], Δ<i>yjcC</i>[pRK415] and Δ<i>yjcC</i>[pJR1] were exposed to 500 µM paraquat or 10 mM H<sub>2</sub>O<sub>2</sub> for 40 min and the intracellular peroxide levels and the carbonyl groups were determined. Bars represent standard deviations (n = 4). (C) The DPPH radical scavenging activity measurement. The upper panel shows that, correlating with the antioxidant activity, the color of DPPH gradually changes from purple to yellow. Ascorbic acid and Butylated hydroxytoluene (BHT) were used as positive control. The lower panel shows quantitative measurement of the DPPH scavenging activity of the log-phased bacteria <i>K. pneumoniae</i> CG43S3[pRK415], Δ<i>yjcC</i>[pRK415] and Δ<i>yjcC</i>[pJR1]. Bars represent standard deviations (n = 4). (D) SOD and (E) catalase activity determination as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066740#s4" target="_blank">Materials and Methods</a>. Left panels, in gel staining for the activity of Mn-SOD and Fe-SOD (D) and catalase HPI and HPIIs (E); Lanes 1, 2: CG43S3; 3, 4: Δ<i>yjcC</i>; 5, 6: Δ<i>yjcC</i>[pRK415-pJR1]; 7, 8: Δ<i>soxRS</i>; 9, 10: Δ<i>fur</i>; 11, 12: Δ<i>rpoS</i>. Lanes 1, 3, 5, 7, 9, and 11 are protein extracts of the bacteria with no stress treatment; 2, 4, 6, 8, and 10 are protein extracts of the bacteria with paraquat. Right panels, quantitative measurement of the total SOD (D) and catalase activity (E).</p
Additional file 1: of Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi
contains supplemental table 1, which summarize count of the reads of plant miRNAs found within each sample. (CSV 2 mb
- …