Additional file 1: Table S1. of Genetic polymorphisms associated with the inflammatory response in bacterial meningitis

Allelic and genotypic frequencies of the SNPs in the studied population. Figure S1. Haplotype map showing the two TNF analyzed polymorphism and a D’ value of 0.11, suggesting that the TNF polymorphisms segregate independently (linkage equilibrium). Figure S2. Cytokine and chemokine concentration in relation to the genotype for SNP TNF -308G>A. (A): CSF samples of BM patients. (B): Plasma samples of controls. Figure S3. Cyto/chemokine concentration in CSF samples in relation to the combination of genotypes in BM patients. (A): APEX1 148Glu/_ plusIL8 -251 T/_ combination. (B): APEX1 148Glu/_ plus OGG1 326Cys/_ and PARP1 l762Ala/_ combination. (C): IL8 T/_ plus APEX1Glu/_ and AADATT/_combination. (D): APEX1 148 Glu/_ plus AADAT +401 T/_ combination. (E): APEX1 148Glu/_ and OGG1 326Cys/_ combination. (F): TNF −308 GG plusIL8 T/_ plus APEX1Glu/_ and AADATT/_ combination. Figure S4. Cyto/chemokine concentration in Plasma samples in relation to the combination of genotypes in controls. (A): APEX1 148Glu/_ plusIL8 -251 T/_ combination. (B): APEX1 148 Glu/_ plus AADAT +401 T/_ combination. (C): IL8 T/_ plus APEX1Glu/_ and AADATT/_ combination. It was not possible to compare all combinations in this biological sample due to the small amount of material. Figure S5. Cell count in CSF samples in relation to the combination of genotypes in BM patients: (A): APEX1 148Glu/_ plus OGG1 326Cys/_ and PARP1 l762Ala/_ combination. (B): IL8 T/_ plus APEX1 Glu/_ and AADATT/_ combination. (C): APEX1 148Glu/_ andOGG1 326Cys/_ combination. (D): TNF −308 GG plusIL8 T/_ plus APEX1Glu/_ and AADATT/_ combination. (DOCX 773 kb

Additional file 9: of Foreign peptide triggers boost in pneumococcal metabolism and growth

Table S8. Proteomic data for wild type and ΔORF 2 mutant without ORF 2 peptide. Table shows only significant changes in expression. A significant difference in expression was observed for 19 proteins of which 17 were more highly expressed in the wildtype and 2 were more highly expressed in the mutant. (PDF 46 kb

Additional file 1: of Foreign peptide triggers boost in pneumococcal metabolism and growth

Figure S1. Venn diagram of RNA-Seq analysis results showing number of genes with different levels of gene expression in untreated wildtype strain 110.58 vs mutant ΔORF 2 (purple), wild type with and without ORF 2 ligand peptide FPPQSV (blue) and mutant ΔORF 2 with and without peptide FPPQSV (green). The corresponding gene lists, including their expression values, can be found in Additional files 2: Table S1. Additional file 3: Table S2. Additional file 4: Table S3. Additional file 5: Table S4. Figure S2. Network of differentially regulated gene products. Nodes represent genes with significantly different expression in wild type and wild type treated with the peptide ligand (inferred from TIGR4 from STRING database). Edges represent evidence for protein-protein interactions. Proteins belonging to the KEGG pathway “purine metabolism” (FDR 3 × 10− 5) are coloured in blue, KEGG pathway “ribosomal proteins” (FDR 4 × 10− 34) in green, KEGG pathway “alanine, aspartate and glutamate” related genes in lilac, branched-chain amino acid transporter proteins [37] (FDR 4 × 10− 34) in yellow and pathogenesis related genes [38] in red. Other genes are shown in white. Figure S3. Correlation between RNA-Seq and proteome expression data. The Pearson correlation between RNA-Seq and proteomics data across all samples was 0.68. Figure S4. Growth of wildtype strain 110.58 and mutant ΔORF 2 in CDM with and without ORF2 ligand peptide FPPQSV at the concentrations indicated. Curves show the mean values for three independent experiments, error bars indicated SEM. (PDF 658 kb

Additional file 4: of Foreign peptide triggers boost in pneumococcal metabolism and growth

Table S3. RNA-Seq data for ΔORF 2 mutant with and without ORF 2 peptide. Table shows only significant changes in expression. A significant change in expression was observed for 249 genes of which 177 were upregulated by the ORF 2 peptide and 72 were downregulated by the peptide. (PDF 231 kb

Additional file 8: of Foreign peptide triggers boost in pneumococcal metabolism and growth

Table S7. Proteomic data for ΔORF 2 with and without ORF 2 peptide. Table shows only significant changes in expression. A significant change in expression was observed for 22 proteins of which 20 were upregulated by the ORF 2 peptide and 2 were downregulated by the peptide. (PDF 52 kb

Additional file 6: of Foreign peptide triggers boost in pneumococcal metabolism and growth

Table S5. Complete proteomic data. (PDF 3560 kb

Additional file 3: of Foreign peptide triggers boost in pneumococcal metabolism and growth

Table S2. RNA-Seq data for wild type with and without ORF 2 peptide. Table shows only significant changes in expression. A significant change in expression was observed for 210 genes of which 159 were upregulated by the ORF 2 peptide and 51 were downregulated by the peptide. (PDF 209 kb

Additional file 7: of Foreign peptide triggers boost in pneumococcal metabolism and growth

Table S6. Proteomic data for wild type with and without ORF 2 peptide. Table shows only significant changes in expression. A significant change in expression was observed for 12 proteins of which 11 were upregulated by the ORF 2 peptide (also shown in Table 2 in the main text) and 1 was downregulated by the peptide. (PDF 34 kb

Additional file 2: of Foreign peptide triggers boost in pneumococcal metabolism and growth

Table S1. Complete RNA-Seq data. (PDF 7151 kb

Additional file 1: Figure S1. of Multiple adaptive routes of Salmonella enterica Typhimurium to biocide and antibiotic exposure

MIC distributions to triclosan, chlorhexidine and benzalkonium chloride for 62 natural Salmonella isolates. The number of Salmonella isolates with reduced susceptibility to biocides analysed for gene expression are indicated above the arrows and MIC susceptibility values. Colors are according biocide distributions. (*) an isolate showed simultaneously reduced susceptibility to CHX and BKC. Other 6 isolates more susceptible for biocides were analysed for control (TRIS/CHXS/BKCS: 0.06-0.12/2-8/32-64 mg/L). Figure S2. XbaI digested-chromosomal DNA PFGE of several Salmonella mutants and its parental strain (5-35 s for 21 h). Figure S3. Growth curves of Salmonella mutants and the parental strain in plain LB at 37 °C with shaking. (DOCX 446 kb