Additional file 1: of Genetic diversity of BoLA-DRB3 in South American Zebu cattle populations

Information and genotyping data used in this study. (XLSX 173 kb

MOESM1 of Single nucleotide polymorphisms in the bovine MHC region of Japanese Black cattle are associated with bovine leukemia virus proviral load

Additional file 1: Table S1. Genes around rs110616206 SNP (Tab "CNTN3") and rs29026690 and rs17872126 SNPs (Tab "BTA23")

MOESM2 of Single nucleotide polymorphisms in the bovine MHC region of Japanese Black cattle are associated with bovine leukemia virus proviral load

Additional file 2: Figure S1. Regional Manhattan plot showing the association of 33,006 SNPs (BovineSNP BeadChip) with BLV proviral load in 359 Japanese Black cattle. Regional plot of the locus on chromosome 22 that harbors SNPs associated with BLV proviral load. The imputed SNPs are indicated by arrows. The horizontal blue lines represent the Bonferroni-corrected thresholds for genome-wide significance (−log10(p) = 5.82). The indicated positions are based on the bovine genome (assembled in UMD3.1)

Validation of differentially expressed genes at the protein level.

<p>Human monocyte-derived macrophages (MDMs) were infected with Ad-Vpr or Ad-Zs, or mock-infected as a control. At 48 h post-infection, the cells were washed, lysed, and subjected to Western blot analyses with the indicated antibodies. A β-actin antibody was used as a loading control.</p

Differential expression profiling of cellular genes after infection with Ad-Vpr in human monocyte-derived macrophages (MDMs).

<p>Heat map of hierarchical gene clustering showing all genes that were either up- or down-regulated (>2-fold change) upon Ad-Vpr infection in MDMs from both donors. The color represents the normalized expression of genes in MDMs infected with Ad-Vpr or Ad-Zs (see color key). Gene up-regulation is denoted in red and gene down-regulation is denoted in blue.</p

Schematic diagram of the Ad-Vpr and Ad-Zs vectors and analysis of their functional expression.

<p>(A) Recombinant adenovirus vectors expressing either FLAG-Vpr and ZsGreen1 or ZsGreen1 were generated using the Adeno-X™ expression system, as described in Materials and Methods. The transgene cassettes that replace the deleted E1 region contain a cytomegalovirus (CMV) promoter driving the expression of FLAG-Vpr and ZsGreen1 or ZsGreen1 protein, followed by an SV40 polyadenylation signal. The solid triangles indicate the regions deleted in the recombinant adenovirus (rAd) backbone. ITR: Inverted terminal repeats. (B) HeLa cells were infected with Ad-Vpr or Ad-Zs at MOI 50. At 48 h post-infection, cells were fixed and stained with propidium iodide for the analysis of DNA content. ZsGreen1-positive cells were analyzed by flow cytometry using Cell Quest for acquisition and ModFit LT. Arrowheads indicate peaks representing cells in the G1 and G2+M phases. The G2+M: G1 ratio is indicated in the upper right of each graph.</p

Expression analyses of HIV-1 Vpr protein in human monocyte-derived macrophages (MDMs).

<p>(A) Peripheral blood mononuclear cells (PBMCs) were isolated from two healthy donors through leukophoresis, cultured <i>in vitro</i>, and differentiated into MDMs as described in Materials and Methods. At day 7, the MDMs were infected with either Ad-Vpr or Ad-Zs, or were left untreated as mock-infected controls (left). At 48 h post-infection, the cells from Donor 1 were visualized by fluorescence (FL) and bright field phase contrast (BF) microscopy. (B) The cells from the two donors (upper panel, Donor 1; lower panel, Donor 2) were lysed and subjected to Western blot analyses using Vpr, ZsGreen1, and β-actin antibodies.</p

Primers used for real-time PCR.

<p>Primers used for real-time PCR.</p

Differentially expressed genes (fold change >2.0) associated with immune response (GO: 0006955) upon Ad-Vpr infection in Donor 1 and Donor 2.

<p>Differentially expressed genes (fold change >2.0) associated with immune response (GO: 0006955) upon Ad-Vpr infection in Donor 1 and Donor 2.</p

Gene ontology of differentially expressed genes after infection of human monocyte-derived macrophages (MDMs) with Ad-Vpr.

<p>(A) Venn diagram representing the number of differentially expressed cellular genes (>2-fold change in both donors) after infection of human MDMs with Ad-Vpr. (B) The top ten genes ontology classified by corrected p-value, and (C) heat map of hierarchical gene clustering of the 66 differentially regulated in both donors. Gene up-regulation is denoted in red and gene down-regulation is denoted in blue.</p