Heatmap for 200 differentially expressed genes with the greatest fold differences from all pathogen challenges using hierarchical clustering analysis.

<p>Hierarchical clustering of gene expression profiles in all samples. Each row represents a gene and each column an animal. The extent of expression of each gene in each sample is indicated by a color code. The color key ranges from saturated red for log_<b>2</b> ratios less or equal to -5.0 to saturated yellow for log_<b>2</b> ratios greater than or equal to 10. Red indicates an increased gene expression in the challenged animals. Legend: bact_0, bact_1 and bact_2 are <i>M</i>. <i>bovis</i> challenged; bact_3, bact_4, bact_5 and bact_6 are <i>P</i>. <i>multocida</i> challenged; bact_7, bact_8, bact_9 and bact_10 are <i>M</i>. <i>haemolytica</i> challenged; virus_0, virus_1, virus_2 and virus_3 are BRSV challenged; virus_4, virus_5, virus_6 and virus_7 are BVDV challenged and virus_8, virus_9, virus_10 and virus_11 are IBR challenged.</p

Principal component analysis for gene-level features.

<p>Principal component analysis for gene-level features.</p

Dynamic range of FPKM values represented as log₁₀ transformed FPKM values for each gene calculated for each biological replicate.

<p>Legend: bact_0, bact_1 and bact_2 are <i>M</i>. <i>bovis</i> challenged; bact_3, bact_4, bact_5 and bact_6 are <i>P</i>. <i>multocida</i> challenged; bact_7, bact_8, bact_9 and bact_10 are <i>M</i>. <i>haemolytica</i> challenged; virus_0, virus_1, virus_2 and virus_3 are BRSV challenged; virus_4, virus_5, virus_6 and virus_7 are BVDV challenged and virus_8, virus_9, virus_10 and virus_11 are IBR challenged.</p

Histopathology of the lung from a <i>Mannheimnnia haemoytica</i> infected steer.

<p>Lobar pneumonia with irregular multilobular zones of coagulation necrosis and fibrinocelluar exudation bordered by dense bands of necrotic leukocytes (arrows).</p

Examples of gross pathology from bacterial infected steers:

<p>(A) <i>Mannheimnia haemolytica</i> lung showing consolidation (arrow) and (B) Lung from <i>Mannheimia haemolytica</i> infected steer demonstrating irregular dark red consolidated regions bordered by light grey inflammatory infiltrate with expanded interlobular septa. (C) <i>Pasteurella multocida</i> infected lung with minimal lesions consisting of scattered areas of consolidation (arrows), and (D) Lung from <i>Mycoplasma bovis</i> infected steer demonstrating a focal region (lower left) of consolidation associated with bronchitis with luminal exudate.</p

Numbers of Up- and Down-Regulated Differentially Expressed Genes and Isoforms for each Challenge Group in Contrast to Controls.

<p>Numbers of Up- and Down-Regulated Differentially Expressed Genes and Isoforms for each Challenge Group in Contrast to Controls.</p

Differentially Expressed Genes with the Largest Expression Variances by Challenge Group.

<p>Differentially Expressed Genes with the Largest Expression Variances by Challenge Group.</p

Histopathology of the ileum from a BVDV infected steer.

<p>(A) shows section of ileum with depletion of lymphocytes from Peyer’s patches (arrows), and (B) Immunohistochemistry showing positive staining for BVDV in ileum of infected steer (arrow showing brown color).</p

Histopathology of pharynx from IBR infected steer.

<p>(A) Focal ulcerative pharyngitis with epithelial necrosis (area indicated by length of the arrow), (B) Immunohistochemistry of lesions demonstrating positive cytoplasmic staining for IBR, indicated by arrows and red/brown color.</p

Histopathology of lung from BRSV infected steer.

<p>(A) Bronchiolitis with epithelial necrosis and numerous syncytia (arrows), (B) Immunohistochemistry stain showing positive stain for BRSV in bronchioles (brown color and arrow).</p