Additional file 1: Figure S1. of Nanoparticle exposure reactivates latent herpesvirus and restores a signature of acute infection

Average Size and size distribution of the used NP. Figure S2. Measurement of cell viability. Figure S3. Exposure to NP reactivates lytic virus in persistently infected cells in vitro in a dose dependent manner. Figure S4. Exposure to NP reactivates lytic virus in persistently infected cells independently of the particle aspect ratio. Figure S5. Short-time exposure of latently infected mice to NP differentially regulates gene expression in whole lung tissue cells independently of the particle aspect ratio. Figure S6. Confirmation of gene expression data by real-time quantitative PCR for selected genes. Figure S7. Exposure of latently infected mice to CNP leads to an increase in glycerophospholipids. Figure S8. Exposure of latently infected mice to DWCNT leads to an increase in glycerophospholipids. Figure S9. Exposure of persistently infected cells to TiO2 NP or DEP has differential effects on virus reactivation in vitro. Table S1. Gene expression values of selected genes (PDF 1767 kb

Shows the two highest scoring networks in IPA derived from the analysis of dysregulated genes in placentas of obese women <i>vs</i>. normal weight women.

<p>(<b>A)</b> Genes involved in embryonic development, organismal development and cancer. (<b>B)</b> Dysregulated genes involved in cellular movement, haematological system development and function, and immune cell trafficking. The intensity of the node colour indicates the degree of up- (red) or down- (green) regulation of gene expression. A white node represents a gene that is not part of our dataset, but is incorporated into the network through relationships with other genes. Nodes are displayed using various shapes that represent the functional class of the gene product, and a biological relationship between two nodes is represented as a line. Detailed information about the figure symbols can be found at <a href="http://www.ingenuity.com" target="_blank">www.ingenuity.com</a>.</p

List of dysregulated genes in term placentas from obese women <i>vs</i>. normal weight women.

<p>The genes identified in previous transcriptome studies in human placentas in health and disease are indicated.</p

The Circos plot represents significantly enriched pathways associated with regulated genes in the placentae of obese women <i>vs</i>. normal weight women, detected using the Ingenuity Pathway Analysis library of canonical pathways.

<p>Outside the circle dysregulated genes and IPA pathways together with biological process are indicated. All genes are down-regulated (highlighted in green), except for HLA-DRB1 and CCL2 genes that are up-regulated (highlighted in red).</p

Microarray validation by real-time PCR.

<p>The expression levels of genes <i>AREG</i>, <i>CCL2</i>, <i>FSTL3</i>, <i>IGFBP1</i> and <i>MMP12</i> from our gene array analysis in comparison with real-time PCR gene expression levels are presented. QRT-PCR data are shown as dCp values (Cp_targetgene-Cp_{referencegene}), where higher dCp values represent lower expression and therefore, graphs are represented with reversed Y-axis. Mann-Whitney <i>U</i>-test *p <0.05, n = 5 samples/group.</p

Clinical characteristics of the participating women in the study and their perinatal outcomes.

<p>Clinical characteristics of the participating women in the study and their perinatal outcomes.</p

Histological sections of <i>LacZ</i> stained <i>Ifitm1^tm1IEG/wt</i> mouse embryo at E12.5.

<p>Lines in the bleached whole embryo (left panel) indicate planes of histological sections in panels <b>A</b> and <b>B</b> on the right. (<b>A</b>) <i>LacZ</i> expression was found in cells of the floor plate (fp) of the neural tube. (<b>B</b>) Gene expressions in cells of the genital ridge (gr) is weak and strong in the tubuli of the metanephros (tu). Scale bars indicate 100 µm.</p

Schematic view of the <i>Ifitm1</i> targeting strategy by homologous recombination in mouse ES cells.

<p>(<b>A</b>) Shows the scheme of the linearized targeting vector used for electroporation in mouse ES cells. The coding sequence of the <i>lacZ</i> reporter gene (lacZ) was inserted in frame into the first codon of the <i>Ifitm1</i> gene. The three <i>Ifitm1</i> exons are indicated as I, II, and III. The <i>lacZ</i> gene is followed by a poly-adenylation signal (bGHpA) and a neomycin/kanamycin selection cassette (neo/kan) that was flanked by <i>loxP</i> sites (L) for subsequent deletion of the cassette. The backbone of the vector (vb) included the coding sequence for the diphtheria toxin fragment A (DTA) to support the selection of clones carrying the homologous recombination of the targeting vector. The location of the probe used for Southern blotting (sp) and PvuII restriction sites (P) are also indicated. The PvuII restriction sites that are relevant for the diagnostic restriction fragments in Southern blots in combination with DNA probe sp are marked with an underline (<u>P</u>). (<b>B</b>) Shows a scheme of the wildtype <i>Ifitm1</i> locus on mouse chromosome 7. The three <i>Ifitm1</i> exons (I, II, and III) are indicated as boxes. Black shading in the boxes indicates the coding sequence of <i>Ifitm1</i>. The genomic region that was amplified by PCR to genotype the <i>Ifitm1^wt</i> allele is indicated (wt-PCR). (<b>C</b>) Shows the <i>Ifitm1</i> locus following homologous recombination in mouse ES cells. As result of recombination, the complete <i>Ifitm1</i> coding sequence is replaced by the <i>lacZ</i> reporter gene and the selection cassette (lacZ-bGHpA-Lneo/kanL). The genomic region that is covered by the homologous sequence of the targeting vector (tv) is designated. The genomic region that was amplified by PCR to genotype the targeted <i>Ifitm</i> locus in the electroporated ES cells following G418 selection is indicated (ES-PCR). (<b>D</b>) Shows a scheme of the <i>Ifitm1^tm1IEG</i> loss-of-function allele that was generated by expression of the <i>Cre</i> recombinase and subsequent deletion of the neo/kan selection cassette from the targeted <i>Ifitm1</i> allele shown in (<b>C</b>). As result of this excision, a single <i>loxP</i> site (L) is left behind as indicated. The genomic region that was amplified by PCR to genotype the targeted <i>Ifitm^tm1IEG</i> loss-of-function allele in mice obtained from matings between chimeric mice and <i>Cre</i> expressing mice is indicated (flox-ko-PCR). The size bar (bottom left) indicates 1 kb length.</p

Histological sections of <i>LacZ</i> stained mouse <i>Ifitm1^tm1IEG/wt</i> embryo at E14.5. Lines

<p>in the bleached whole embryo (panel at the op left) indicate planes of histological sections (<b>A</b> to <b>M</b>). (<b>A</b>) <i>LacZ</i> expression was found in sympathetic ganglia (sg), (<b>B</b>) the eyelids (e), (<b>C</b>) the epithelium of the oropharynx (o), (<b>D</b>) the olfactory epithelium (oe), (<b>E</b>) primordia of the teeth (pt), (<b>F</b>) the thymus (th), (<b>G</b>) the serous glands associated with the nasal septum, (<b>H</b>) primordia of hair follicles (h), (<b>I</b>) in cells of the floor plate (fp) of the neural tube, (<b>J</b>) mesenchymal cells at the inner side of the limbs (l), (<b>K</b> and <b>K’</b>) cells of the outer wall of the intestine (i), (<b>L</b>) cells of the ovary (ov), and (<b>M</b>) in cells of the hindgut (hg). Scale bars indicate 100 µm.</p

Histological sections of <i>LacZ</i> stained <i>Ifitm1^tm1IEG/wt</i> mouse embryo at E13.5.

<p>Lines in the bleached whole embryo (panel at the top left) indicate planes of histological sections (<b>A</b> to <b>E</b>). (<b>A</b>) <i>LacZ</i> expression was found in the epithelium of the cerebral aqueduct (eca), (<b>B</b> and <b>B’</b>) the sympathetic ganglion (sg), (<b>C</b>) in the papillae of the tongue (p) and the epithelium of the oropharynx (o), (<b>D</b>) the olfactory epithelium (oe), (<b>E</b>) the thymus (th), (<b>F</b>) primordia of the teeth (pt), (<b>G</b>) cells of the floor plate (fp) of the neural tube, (<b>H</b>) the genital ridge (gr) and the (<b>I</b>) metanephros (m). Scale bars indicate 100 µm.</p