Functional annotation clusters in the up-regulated genes (analyzed with the DAVID 6.7 BETA bioinformatics resource).

<p>Functional annotation clusters in the up-regulated genes (analyzed with the DAVID 6.7 BETA bioinformatics resource).</p

Activities of detoxification enzymes of resistant and susceptible lines.

<p>Activities of detoxification enzymes of resistant and susceptible lines.</p

Mapping of the lethality and resistance loci on the right arm of the second chromosome in the resistant line MiT[<i>w⁻</i>]3R2.

<p>The resistance locus was mapped relative to P element insertions to a region between 8 Mb and 8.5 Mb (black arrows on the second scale, distance between insertion and resistance region is indicated with dotted horizontal lines). The location of the three highly expressed P450 genes (Cyp6a2, Cyp6g1 and Cyp4p2) in the resistant MiT[<i>w⁻</i>]3R2 line is indicated. Below is a comparison of single nucleotide polymorphism (SNP) density (per 1 Kb) between resistant line MiT[<i>w⁻</i>]3R2 and susceptible line iso31. At the bottom, Bloomington deletions overlapping lethality locus (filled box) and flanking the lethality locus (open boxes) (lethality maps to the region between 8.5 Mb and 9.9 Mb, close to the place of recombination).</p

Functional annotation clusters in the down-regulated genes (analyzed with the DAVID 6.7 BETA bioinformatics resource).

<p>Functional annotation clusters in the down-regulated genes (analyzed with the DAVID 6.7 BETA bioinformatics resource).</p

Next-Generation Sequencing Analysis Reveals Differential Expression Profiles of MiRNA-mRNA Target Pairs in KSHV-Infected Cells

<div><p>Kaposi’s sarcoma associated herpesvirus (KSHV) causes several tumors, including primary effusion lymphoma (PEL) and Kaposi’s sarcoma (KS). Cellular and viral microRNAs (miRNAs) have been shown to play important roles in regulating gene expression. A better knowledge of the miRNA-mediated pathways affected by KSHV infection is therefore important for understanding viral infection and tumor pathogenesis. In this study, we used deep sequencing to analyze miRNA and cellular mRNA expression in a cell line with latent KSHV infection (SLKK) as compared to the uninfected SLK line. This approach revealed 153 differentially expressed human miRNAs, eight of which were independently confirmed by qRT-PCR. KSHV infection led to the dysregulation of ~15% of the human miRNA pool and most of these cellular miRNAs were down-regulated, including nearly all members of the 14q32 miRNA cluster, a genomic locus linked to cancer and that is deleted in a number of PEL cell lines. Furthermore, we identified 48 miRNAs that were associated with a total of 1,117 predicted or experimentally validated target mRNAs; of these mRNAs, a majority (73%) were inversely correlated to expression changes of their respective miRNAs, suggesting miRNA-mediated silencing mechanisms were involved in a number of these alterations. Several dysregulated miRNA-mRNA pairs may facilitate KSHV infection or tumor formation, such as up-regulated miR-708-5p, associated with a decrease in pro-apoptotic caspase-2 and leukemia inhibitory factor LIF, or down-regulated miR-409-5p, associated with an increase in the p53-inhibitor MDM2. Transfection of miRNA mimics provided further evidence that changes in miRNAs are driving some observed mRNA changes. Using filtered datasets, we also identified several canonical pathways that were significantly enriched in differentially expressed miRNA-mRNA pairs, such as the epithelial-to-mesenchymal transition and the interleukin-8 signaling pathways. Overall, our data provide a more detailed understanding of KSHV latency and guide further studies of the biological significance of these changes.</p></div

LC50s for Imidacloprid and DDT of susceptible and resistant flies.

*<p>RR (resistance ratio) – LC50 value of the MiT[<i>w⁻</i>]3R2 line/LC50 value of the iso31 line.</p

Crossing scheme of the genome-wide insertional mutagenesis system.

<p>TREP 2.30 – promoter delivery, minimal promoter under tTA control, <i>w⁺</i> marker <i>CyO</i> [MiT 2.4] – <i>Minos</i> transposase source, CyO marker <i>Sco</i> – Sco marker BOEtTA – tTA source, <i>egfp</i> marker.</p

miRNA-mRNA pairs found inversely correlated and validated in the literature.

<p>This table shows the association between miRNAs and mRNAs that were significantly dysregulated in SLKK cells compared to SLK cells. Only the miRNA-mRNA pairs experimentally validated in the literature are shown here. The majority of the targets were identified through IPA-integrated TarBase v5.0 and others independently.</p><p>miRNA-mRNA pairs found inversely correlated and validated in the literature.</p

Gene functional groups in the up-regulated genes (analyzed with the DAVID 6.7 BETA bioinformatics resource).

*<p>Kappa score – The Kappa value quantitatively measures the degree to which genes share similar annotation terms (the higher the Kappa, the stronger the functional similarity).</p

Expression of miRNAs and mRNAs in the analyzed libraries.

<p>A. Volcano plot of differentially expressed human mature miRNAs in KSHV-infected versus uninfected cells. Vertical red lines indicate the threshold for a relative expression fold change (FC) of 2 or -2 fold compared to uninfected controls. The horizontal red line represents the threshold of a 0.05 P-value. Thus, the blue points lying in the top right and top left sectors are significantly up-regulated and down-regulated, respectively, in KSHV-positive versus KSHV-negative cells (<i>P</i> <0.05, FC ≥2 or ≤-2). Selected miRNAs that have been validated by qRT-PCR are labeled. B. Volcano plot of differentially expressed mRNAs in KSHV-infected versus uninfected cells. The plot is depicted as in Fig 2A, with vertical and horizontal red lines similarly representing the thresholds of a fold-change of 2 or -2 fold, and of a false-discovery rate (FDR) of 0.05 respectively. C. Top 15 repressed and induced miRNAs in KSHV-positive vs. uninfected SLK cells with <i>P</i> <0.05 and medium to high miRNA expression (threshold of a mean miR count of 10 or more across all replicates).</p