DEXP Values for S/MAR+ and S/MAR− TF Genes for Different Datasets

<p>The 5% confidence intervals for all values are shown.</p

DEXP Values for S/MAR− Genes and as a Function of the Position of the S/MAR within S/MAR+ Genes

<p>The 5% confidence intervals are shown.</p

Median Expression Values of S/MAR− and S/MAR+ Genes in Different Organs, Root Tissues, and Flower Tissues

<p>MPSS data recorded in five different organs are shown (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 1) (A); for Affymetrix-based measurements (B–D), median values for five root tissues (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 2) (B), ten organs (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 4) (C), and five flower tissues (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 6) (D) are given. For MPSS-based experiments (A), tpm are indicated; for experiments based on the Affymetrix platform (B–D), Affymetrix expression values are plotted. The 5% confidence intervals calculated using bootstrap set for all values are shown.</p

Proteomic screen in the simple metazoan identifies 14-3-3 binding proteins implicated in cellular metabolism, cytoskeletal organisation and Casignalling-4

<p><b>Copyright information:</b></p><p>Taken from "Proteomic screen in the simple metazoan identifies 14-3-3 binding proteins implicated in cellular metabolism, cytoskeletal organisation and Casignalling"</p><p>http://www.biomedcentral.com/1471-2121/8/31</p><p>BMC Cell Biology 2007;8():31-31.</p><p>Published online 25 Jul 2007</p><p>PMCID:PMC1964759.</p><p></p>tags from at NCBI. Helices 1-9 are indicated. Conserved amino acids that have been shown in the crystal structure to constitute the binding groove for target proteins are indicated with asterisks (basic face of the groove) and circles (hydrophobic surface) above the sequence (information from [24]). Alignments were made with the program GeneJockeyII (under MacOS9

Proteomic screen in the simple metazoan identifies 14-3-3 binding proteins implicated in cellular metabolism, cytoskeletal organisation and Casignalling-1

<p><b>Copyright information:</b></p><p>Taken from "Proteomic screen in the simple metazoan identifies 14-3-3 binding proteins implicated in cellular metabolism, cytoskeletal organisation and Casignalling"</p><p>http://www.biomedcentral.com/1471-2121/8/31</p><p>BMC Cell Biology 2007;8():31-31.</p><p>Published online 25 Jul 2007</p><p>PMCID:PMC1964759.</p><p></p

Proteomic screen in the simple metazoan identifies 14-3-3 binding proteins implicated in cellular metabolism, cytoskeletal organisation and Casignalling-3

<p><b>Copyright information:</b></p><p>Taken from "Proteomic screen in the simple metazoan identifies 14-3-3 binding proteins implicated in cellular metabolism, cytoskeletal organisation and Casignalling"</p><p>http://www.biomedcentral.com/1471-2121/8/31</p><p>BMC Cell Biology 2007;8():31-31.</p><p>Published online 25 Jul 2007</p><p>PMCID:PMC1964759.</p><p></p>nexin1 (lanes 1-6). Inputs of 14-3-3 HyA (lane 1) and 14-3-3 HyB (lane 4) represent 12.5% of the total 14-3-3 proteins used in each assay. Eluted 14-3-3 HyA (lanes 2 and 3) and 14-3-3 HyB (lanes 5 and 6) are shown after pulldown with GST-fusion-proteins. Western blots were probed with anti-Xpress antibody, which recognises the His-tag of the bacterially expressed 14-3-3 proteins. In (B) Western blots with samples from (A) were probed with anti-GST antibody to show that equal amounts of GST-fusion-protein were eluted in all assays. Asterisks indicate full-length GST-fusion proteins. Smaller fragments represent degradation products

WT and A30A′ replicons show similar rates of replication in BHK cells electroporated with KUNRep-WT or KUNRep-A30A transcribed RNAs.

<p>(<b>A</b>) Schematic depiction of the translational path of non-PRF and PRF Flavivirus polyprotein. Numbers represent amino acid positions from WNV_KUN genome (Accession number AY274504). The underlined sequence represents the start of the NS2A coding region and the box indicates the amino acids encoded by the frameshifted region in NS2A gene. Arrow indicates cleavage between NS1 and NS2A proteins. (<b>B</b>) Schematic representation of plasmid DNA encoding WNV_KUN replicon KUN-rep. SP6- SP6 RNA polymerase promoter, C20aa – WNV_KUN coding sequence encompassing fist 20aa of C gene, PAC- puromycin resistance gene F2A – foot and mouth virus 2A autoprotease, LacZ – β-galactosidase gene, E22 – WNV_KUN coding sequence representing last 22 aa of E gene, NS1-NS5 proteins – WNV_KUN sequence coding for entire non-structural region, HDVr – hepatitis delta virus ribozyme, pA- polyA signal. (<b>C</b>) WNV_KUN nucleotide and amino acid sequence in the frameshift region encoded in the WT and A30A′ mutant replicons. The underlined sequence indicates the slippery heptanucleotide frameshift motif and in bold are the two silent nucleotide changes disrupting downstream pseudoknot interactions, introduced in KUNRep-A30A′ replicon. Numbers represent nucleotide positions in WNV_KUN genomic RNA. (<b>D</b>) <i>In vitro</i> transcribed KUNRep-WT and KUNRep-A30A′ RNAs (left panel) was electroporated into BHK cells and expression levels were measured by β-gal staining (48, 72, 96 hpe) (middle panel) and by Northern hybridization (72 hpe) with WNV 3′UTR-specific, ³²P-labelled DNA probe (right panel).</p

PRF/NS1′-deficient WNV_KUN mutants show reduced replication and dissemination in <i>Culex annulirostris</i> mosquitoes.

<p>(<b>A</b>) Infection (bodies), dissemination (legs and wings) and transmission (saliva) rates in mosquitoes exposed to either WT virus or mutant viruses by feeding on virus infected blood meals containing approximately 10⁷TCID₅₀/mL of virus or intrathoracic inoculation with 220 nL of a 10⁶ TCID₅₀/mL virus stock. A two-tailed Fisher's exact test was used to determine significant difference between infection, dissemination and transmission rates between each of the mutant viruses and the WT virus (*<i>P</i><0.05) and between the mutant viruses (^†P<0.05). (<b>B</b>) and (<b>C</b>) Mean ± 95% CI (confidence interval) virus titers in bodies and saliva expectorates from mosquitoes exposed to the mutant or WT-viruses by oral feeding (B) or intrathoracic inoculation (C). Twelve days post exposure, mosquitoes were processed by removing the legs and wings, and collecting the saliva using a forced salivation technique. Homogenized and filtered mosquito components (bodies, legs and wings, and saliva expectorates) were inoculated onto confluent monolayers of C6/36 cells in a 96 well microtiter plate, and infection detected by a cell culture enzyme immunoassay (CC-EIA). Viral titers of the bodies and saliva expectorates was determined by inoculation of ten-fold dilutions of the filtered homogenates in C6/36 cells with virus detected using the CC-EIA. A one-way ANOVA was employed to determine significant differences in mean viral titers within the mosquito bodies and saliva expectorates (****P<0.0001; ***P<0.001; **P<0.005; *P<0.05; only statistically significant differences are shown).</p

Ion Torrent sequencing analysis of variants in WT and A30A′ mutant WNV_KUN virus populations.

<p>Ion Torrent sequencing analysis of variants in WT and A30A′ mutant WNV_KUN virus populations.</p

Infection of WT and IRF3^−/−7^−/− MEFs with PRF-deficient WNV_KUN viruses induces differential expression of several genes.

<p>Low passage primary WT and IRF3^−/−7^−/− MEFs were infected at MOI of 1 with WNV_KUN WT, WNV_KUN A30A′, or WNV_KUN A30P viruses and 48 hpi total RNA was extracted and used for analysis of global gene expression by microarrays. (<b>A</b>) Virus titres in the infected cell culture supernatants were assayed by plaque assay at 0 and 48 hpi. (<b>B</b>) Heat map showing top differentially expressed genes ranked by log fold change between different experimental conditions.</p