Validation of gene expression induced by CAV2 vector with qRT-PCR.

<p>A selection of genes was checked for CAV2-induced upregulation using qRT-PCR on cDNA from the CD103⁺ and CD11b⁺ -type DCs (4 different sheep were used in total, 3 per validated gene). Each gene detection was normalized with GAPDH expression and the relative gene expressions (log2(CTgene-CTGAPDH)) are reported. The gene names printed with regular font were selected as being up-regulated in the CD11b⁺ type DC microarrays (p < 0.05 ANOVA followed by Benjamini-Hochberg FDR and > 2 fold), the gene names printed in italic are not represented by any probe on the ovine microarray, the underlined gene names were close to be selected by the variance analysis in the CD11b⁺ -type DCs.</p

Top canonical pathways induced by CAV2 vector in CD103⁺ and CD11b⁺ -type DCs.

<p>Top canonical pathways induced by CAV2 vector in CD103⁺ and CD11b⁺ -type DCs.</p

Biological functions that are predicted to be activated by CAV2 vector in CD103⁺ and CD11b⁺ -type DCs.

*<p>the expression of the underlined molecules is down-modulated.</p

Transcriptional response to CAV2 vector in the CD103⁺ and CD11b⁺ -type DC subsets.

<p>(A)The mean fold induction of the selected genes up-regulated by Cav-null R⁰ are represented in graded yellow to red color (from 1 to >3) for both CD103⁺ and CD11b⁺ -type DCs from 4 sheep. The represented genes were selected from the significantly induced genes in the CD11b⁺ -type DC subset (222 genes, p<0.05, fold > 2) and they were ranked based on their fold induction in the CD11b⁺ -type DC subset. The significantly activated genes in the CD103⁺ subset (21 genes, p<0.05, fold > 2) are indicated by a star. (B) The mean fold reduction levels of the selected down-modulated genes by Cav-null R⁰ are represented in graded yellow to blue color (from 1 to <0.2) for both CD103⁺ and CD11b⁺ -type DCs from 4 sheep. The represented genes were selected from the significantly reduced genes in the CD11b⁺ -type DC subset (29 genes, p<0.05) and they were ranked based on their fold induction in the CD11b⁺ -type DC subset. No gene expression was significantly reduced in the CD103⁺ -type DC subset.</p

Antimicrobial gene network induced by CAV2 vector in CD11b⁺ -type DCs.

<p>An antimicrobial gene network centered on IFN was generated by the Ingenuity Pathways Analysis on the selected genes dys-regulated by CAV2 vector in CD11b⁺ -type DCs (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052513#pone.0052513.s003" target="_blank">Table S1</a>, p < 0.05 and fold > 2, or p < 0.05 and folds confirmed by qRT-PCR). Molecule types are represented by symbols: diamonds (enzymes), triangles (kinase), square (cytokine), double circle (complex), oval (transcription regulator), circle (others).</p

Additional file 3: of Expression of epigenetic machinery genes is sensitive to maternal obesity and weight loss in relation to fetal growth in mice

Description of the selection criteria of genes for the custom TLDA design and related bibliographic references

Additional file 2: of Expression of epigenetic machinery genes is sensitive to maternal obesity and weight loss in relation to fetal growth in mice

List of the gene symbol and name, and the design strand and TaqMan® Gene Expression Assay IDentification reference for the 96 genes studied on the Custom TLDA

Additional file 1: of Expression of epigenetic machinery genes is sensitive to maternal obesity and weight loss in relation to fetal growth in mice

Supplementary Figures S1 to S6. Food intake (FI) to body weight (BW) ratio in females during the preconceptional period. (a) P < 0.05 OB vs. CTRL, (b) P < 0.05 WL vs. CTRL, (c) P < 0.05 WL vs. OB. n = 18–20 CTRL, 23 OB, 17–19 WL. Figure S2. Fetal weight as a function of litter size in dams at E18.5. Both sexes were combined as there was no effect of sex on fetal weight. Figure S3. Placental weight as a function of litter size and sex at E18.5. Figure S4. Effect of maternal age on fetal parameters. (A) Relationship between maternal age and fetal weight. (B) Relationship between maternal age and fetal-weight-to-placental-weight ratio index (FPI). For statistical analysis, see text. Figure S5. Distribution of fetal weight in CTRL, OB, and WL dams at E18.5. CTRL dams are represented in black, WL dams in brown, and OB dams in blue. The red line represents the 10th percentile of CTRL population. Figure S6. Relationship between fetal and placental weight in female and male offspring at E18.5. For statistical analysis, see text and “Methods” section. M: males, F: females

Additional file 4: of Expression of epigenetic machinery genes is sensitive to maternal obesity and weight loss in relation to fetal growth in mice

Expression level and adjusted P values of 92 genes in the fetal liver, placental labyrinth, and junctional zone. We assessed the expression level of 60 epigenetic machinery genes and 32 genes implicated in metabolism or development in CTRL, OB, and WL females at E18.5 using TaqMan low-density arrays. Data are represented as mean expression levels ± St.Dev. *—differentially expressed genes. NA—non-amplified. Significant differences (P adj < 0.05) are indicated in red

Impact of PB1-F2 on expression profiles of several genes representative of the host response.

<p>Total RNA isolated from lungs of chickens infected with 1000PFU (A) and (B) (day 2 pi) were reverse-transcribed and used to quantify expression of several host response markers by qPCR: signal transducer and activator of transcription 1 (STAT1, Gene ID: 424044), beta-2-microglobulin (β2M, Gene ID: 414830), toll-like receptor 4 (TLR4, Gene ID: 417241), interferon (alpha, beta and omega) receptor 1 (IFNAR1, Gene ID: 395665), cytotoxic T-lymphocyte-associated protein 4 (CTLA-4, Gene ID: 424106), chemokine (C-C motif) ligand 5 (CCL5, Gene ID: 417465), toll-like receptor 7 (TLR7, Gene ID: 418638), heat shock 70 kDa protein 2 (HSPA2, Gene ID: 423504), interleukin 2 receptor gamma (IL2RG, Gene ID: 395199), toll-like receptor 6 (TLR6, Gene ID: 771173), and B-cell CLL/lymphoma 2-like 1 (BCL2L1, Gene ID: 373954). Gene expressions were normalized with the β-actin gene (Gene ID: 396526) expression level and presented as fold increase relative to mock-treated chickens. Data are means ± SEM obtained from the indicated number of chickens.</p