43), Fn1 (10.19), Ccl2 (9.99), Cd81 (9.07), Il1b (8.65), Trf (8.55), Slc28a2 (8.24), Cd14 (8.10), Cdh17

(7.15), and Sdc4 (6.52); and the top ten click here down-regulated ones were Hspa1a (-17.44), Hspa1b (-13.90), Hspb1 (-7.76), Hsph1 (-6.70), Tac1 (-6.16), Prkcb (-5.68), Atf3 (-4.91), Dnajb1 (-4.88), Fos (-4.54), and Ptprc (-3.92). Values in the parentheses are fold changes. Effect of Pneumocystis infection on alveolar macrophage gene expression (Pc vs. D) Comparison of the expression profiles between Dex-Pc and Dex groups (Pc vs. D) revealed 116 genes up-regulated and 140 genes down-regulated by Pneumocystis infection (Additional file 1, Tables S3 and S4) also with the filter of FDR ≤ 0.1 and FC ≥ 1.5. The top ten up-regulated genes were Cxcl10 (12.33), Spp1 (11.78), S100A9 (11.55), Rsad2 (7.62), S100A8 (6.52), Nos2 (6.35), RT1-Bb (5.42), Lcn2 (5.36), RT1-Db1 (5.35), and Srgn (5.34); and the top ten down-regulated ones were Lgals1 (-4.24), Psat1 (-3.10), Tbc1d23 (-3.00), Gsta1 (-2.63),

Car5b (-2.47), Xrcc5 (-2.35), Pdlim1 (-2.33), Alcam (-2.29), Cidea (-2.27), and Pkib (-2.25). Genes affected by dexamethasone but reversed by Pneumocystis infection Since both dexamethasone and P. carinii infection have effects on gene expression in AMs, genes that were affected differently were examined. Thirty-two genes that were up regulated by dexamethasone treatment were reversely down regulated by Pneumocystis infection (Table 3). Another 32 genes that were up-regulated by dexamethasone were further up-regulated by Pneumocystis infection (Table 4). Nine genes that were down regulated by dexamethasone were found to be up regulated by Pneumocystis infection (Table 5), and twenty-one genes Raf inhibitor that were down-regulated by dexamethasone were further down-regulated by Pneumocystis infection (Table 6). Table 3 Rat AM genes up-regulated by dexamethasone but down-regulated by Pneumocystis

infection Gene D vs. N Pc vs. D Cdh17 7.15 -1.61 Gsta2 4.77 -2.63 Fxyd2 3.79 -1.97 Hsd11b1 3.19 -1.60 Diablo 2.72 -1.74 Mmp12 2.50 -1.70 Ccng1 2.36 -1.63 Btd 2.28 -1.85 Gaa 2.27 Ribose-5-phosphate isomerase -1.60 Agt 2.25 -1.51 Hacl1 2.22 -2.13 Prkacb 2.03 -1.56 Pcsk1 2.01 -1.80 Tfpi 1.98 -1.65 Atp6v1d 1.96 -1.65 Hsd17b12 1.89 -1.61 Vldlr 1.82 -2.17 Hspa9 1.72 -1.72 Aco1 1.71 -1.85 Atp6v1a 1.69 -1.58 Tceb1 1.62 -1.62 Bloc1s2 1.61 -1.63 Tbc1d23 1.60 -3.00 Aifm1 1.57 -1.57 Gpd2 1.57 -1.54 Ufsp2 1.57 -1.51 Gnptg 1.56 -1.95 Sqstm1 1.56 -1.79 Hook1 1.55 -1.64 Plod1 1.52 -1.65 PVR 1.51 -1.68 Fah 1.50 -1.80 Values shown are fold changes. D vs. N: expression affected by dexathamethasone (D) treatment compared to the normal control (N); Pc vs. D: expression affected by Pneumocystis (Pc) infection compared to the Dex (D) control. Table 4 Rat AM genes up-regulated by dexamethasone and further up-regulated by Pneumocystis infection Gene D vs.