TreeMap visualization obtained by REVIGO analysis (see Materials and Methods for details) of the summary of GO Biological process deemed by DIA to be overall inhibited during full lactation (from 15 to 120 d) compared to −30 d.

<p>Similar colors denote semantic similarity and dimension of the area is proportional to the overall direction of the impact, as calculated by the DIA. Not all the terms are reported due to space constraints (see Additional <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033268#pone.0033268.s014" target="_blank">file S4</a> for details).</p

Summary figure of the most relevant biological functions in bovine mammary gland during the lactation cycle as revealed by the Dynamic Impact Approach (DIA) analysis of KEGG pathways and Gene Ontology terms (see Additional file S1 for details).

<p>Shown at the center are the curve of lactation, yield of main milk constituents (protein, lactose, and fat) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033268#pone.0033268-Bionaz1" target="_blank">[7]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033268#pone.0033268-Bionaz2" target="_blank">[8]</a>, and estimates of fatty acid import and <i>de novo</i> synthesis <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033268#pone.0033268-Bionaz2" target="_blank">[8]</a>. Red titles are the most relevant metabolism as revealed by the KEGG pathway and Gene Ontology analysis. Other color titles denote main functions impacted during lactation. The large increase at the transcriptomic level of caseins or other milk proteins are not shown. The X-axis depicts the day relative to parturition and the Y-axis the direction of the impact as calculated by DIA. Legend: AA = amino acid; Arg = arginine; Ca = calcium; Chol = cholesterol; Cl = chloride; Cu = copper; Cys = cysteine; ER = endoplasmic reticulum; FA = fatty acids; GnRH = Gonadotropin-releasing hormone pathway; Gly = glycine; GPI = Glycophosphatidylinositol; His = histidine; Ile = isoleucine; LCFA = long-chain fatty acids; Leu = leucine; Met = methionine; mTOR = mTOR = mammalian target of rapamycin signaling pathway; Na = sodium; NH4 = ammonium; Notch = Notch signaling pathway; P = phosphate; PPAR = peroxisome proliferator-activated receptor signaling pathway; S = sulfate; Ser = serine; TAG = triacylglycerol; Thr = threonine; Val = valine; VEGF = vascular endothelial growth factor signaling pathway.</p

Pathway Score Heat Map for Cell Communication Related Pathways.

<p>This heat map shows the repressed state of activity for the Tight Junction (TJ) and Trefoil Factors (TF) pathway in comparison to the Gap Junction, Integrin-mediated Cell Adhesion and Cell Adhesion Molecules pathways. Note that the TJ and TF pathways have a complex activation pattern. The TJ is tri-phasic in that it is highly repressed in the early stage, becomes moderately activated at 60 and 120 min p.i, and then becomes repressed at 240 min p.i. The TF pathway is bi-phasic in that it is highly repressed in the early stage but becomes moderately activated at 120 and 240 min p.i. The darker red gradients indicate higher Bayesian activation scores (more up-regulated gene expression within the pathway) while the darker green gradients indicate more repressed pathway activity (more down-regulated gene expression).</p

Interleukin Gene Score Heat Map by Time Point Post Inoculation.

<p>The heat map shows a number of both up-regulated and down-regulated genes (15–240 minutes post-inoculation). The heat map shows that much of the up-regulation is short-lived for many of these genes and reversed expression direction or minimally expressed in later time points. Red indicates an activated state while green indicates repression and grey is no expression change from control.</p

Heatmap of Significantly Perturbed Pathways Scores in Bovine Peyer's Patch Infected with <i>B. melitensis</i>.

<p>Thirty-seven pathways were identified as significantly perturbed (97.5% confidence) from the early stage of infection (15–60 m.p.i.). The darker red gradients indicate higher Bayesian activation scores (more up-regulated gene expression within the pathway) while the darker green gradients indicate more repressed pathway activity (more down-regulated gene expression).</p

Genes Significantly Expressed in the TLRS Pathway (<i>z</i>-score |2.24|).

<p>The table lists significantly perturbed (activated or repressed) genes at any time among the 5 different time points (0.25 h through 4 h p.i.).</p

Graphic Representation of Bovine Genes Differentially Expressed throughout the Experiment.

<p>(DE  =  differentially expressed). Solid bars represent genes up-regulated; open bars represent genes down-regulated.</p

Significantly Altered Genes (Bayesian <i>z</i>-score |2.24|) in the Extra-Cellular Membrane (ECM) pathway.

<p>The table lists significantly perturbed (activated or repressed) genes at any time among the 5 different time points (0.25 h through 4 h p.i.).</p

Kinetics of Peyer's Patch Infection with <i>B. melitensis</i> 16 M.

<p>Jejunal-ileal loops were intraluminally inoculated in 3 ml containing 1×109 CFU of <i>B. melitensis</i> 16 M/ml. Tissue (Peyer's patch) samples of 0.1 g of mucosal tissue were extracted at 0.25, 0.5, 1, 2, 4, 8 and 12 h from every infected loop, intensively washed 3 times in PBS, macerated and diluted in 1 ml of distilled water. To evaluate the kinetics of the infection, macerated samples were serially diluted and cultured on Farrell's medium. Numbers of CFU recovered from bovine Peyer's patches are the average of 4 calves. Bars represent standard deviation.</p

Graphic Representation of Number of Pathways and GO Terms Differentially Expressed at each time point from 15 min to 4 h p.i.

<p>Squares  =  GO Biological processes; Squares with X  =  GO Molecular functions; Triangle  =  Cellular components; Diamond  =  Pathways.</p