16S sam files

Alignments of 16S high-throughput sequencing reads to reference sequences

COI sam files

Alignments of COI high-throughput sequencing reads to reference sequences

MOESM1 of Host-specific differences in the response of cultured macrophages to Campylobacter jejuni capsule and O-methyl phosphoramidate mutants

Additional file 1. Campylobacter jejuni capsule and MeOPN mutants elicit an enhanced cytokine responses in mBMDCs. The mBMDCs were differentiated from vials of frozen C57BL/6 mouse bone marrow following the protocol of Rose et al. [31] in the presence of GM-CSF (final concentration of 20 ng/mL; Peptro Tech) for 7 days. Live or fixed C. jejuni 11168H (WT), Δcj1417 (MeOPN) and Δcj1439 (capsule) mutants were incubated with mBMDCs at MOI 50 for 3 h. Salmonella LPS was used as a positive control, while PBS in the medium was used as a negative control. Graphs show representative results of two independent experiments. Error bars are the standard deviation of two independent experiments. Asterisks indicate a statistically significant difference of mRNA levels of inflammatory-related cytokines compared to C. jejuni WT (*P < 0.05; **P < 0.01)

Analysis of host response to bacterial infection using error model based gene expression microarray experiments-0

<p><b>Copyright information:</b></p><p>Taken from "Analysis of host response to bacterial infection using error model based gene expression microarray experiments"</p><p>Nucleic Acids Research 2005;33(7):2352-2353.</p><p>Published online 22 Apr 2005</p><p>PMCID:PMC1084327.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p

Numbers and ages of GF and colonised pigs in each experiment.

<p>Four experiments were performed with between five and seven pigs in each. Pigs were euthanised and samples taken either at 0 (1 experiment), 5 (1 experiment) or 21 (2 experiments) days of age.</p

Colonisation expands mucosal CD4⁺ T cells by 21 days of age.

<p>(A) CD4 staining in jejunal mucosa from a GF pig and (B) a colonised pig at 21 days of age. Sections were stained with antibodies to CD4 (green) and capillary endothelium (MIL11; in blue). In both (A) and (B), (i) shows the two-colour image; (ii) shows the original greyscale image for the blue channel (endothelium); (iii) shows the original greyscale image for the green channel (CD4). Scale bar represents 10 µm. (C) Area of CD4+ T cell staining in jejunal sections from piglets at birth (open diamonds) and GF piglets (open squares) and colonised piglets (black squares) at 5 and 21 days of age (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033707#pone-0033707-t001" target="_blank">Table 1</a> for numbers of piglets in each experiment). *p<0.05.</p

Colonisation expands IgM and IgA-producing mucosal plasma cells.

<p>(A) IgA staining in jejunal mucosa from a GF pig and (B) a colonised pig at 21 days of age. Sections were stained with antibodies to IgA (red) and capillary endothelium (MIL11; in blue). In both (A) and (B), (i) shows the two-colour image; (ii) shows the original greyscale image for the red channel (IgA); (iii) shows the original greyscale image for the blue channel (endothelium). Scale bar represents 10 µm. (C) IgM staining in jejunal mucosa from a GF pig and (D) a colonised pig at 21 days of age. Sections were stained with antibodies to IgM (red). Scale bar represents 10 µm. (E) Area of IgM and (F) IgA staining in jejunal sections from piglets at birth (open diamonds) and GF piglets (open squares) and colonised piglets (black squares) at 5 and 21days of age (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033707#pone-0033707-t001" target="_blank">Table 1</a> for numbers of piglets in each experiment). * p<0.01.</p

Additional file 1: Table S1. of Systemic inflammation is an independent predictive marker of clinical outcomes in mucosal squamous cell carcinoma of the head and neck in oropharyngeal and non-oropharyngeal patients

Patient demographic differences between p16 tested and non-tested oropharyngeal patients. (XLSX 11 kb

Repertoire is not altered on expansion of mucosal CD4 T-cells.

<p>(A) Representative spectratype electropherograms of <i>TRβV</i>29 for a germ-free pig, and a colonised pig from the same litter of piglets. In general, samples from the spleen demonstrate a more Gaussian electropherogram distribution than intestinal samples. RFU: relative fluorescence units, x axis: CDR3 length (base pair size). (B) Hierarchical cluster analysis of CDR3 lengths from 20 <i>TRβV</i> groups and 1 subgroup from the proximal jejunum, distal jejunum and spleen from pigs at 21 days of age.</p

Colonisation selectively increases SIRPα⁺ APC subsets within the first five days of life.

<p>Intestinal APC (MHCII⁺) subsets were defined by their expression of SIRPα, CD11R1 and CD16. (A–D) show SIRPα⁺ subsets (E–G) show SIRPα⁻ subsets from piglets at birth (n = 5; light grey bars) and GF piglets (white bars) and colonised piglets (dark grey bars) at 5 (n = 3 GF and n = 3 colonised) and 21 (n = 4 GF and n = 6 colonised) days of age (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033707#pone-0033707-t001" target="_blank">Table 1</a> for numbers of piglets in each experiment). Error bars represent standard errors of the mean. After a Bonferroni correction was applied for multiple tests (ANOVA), a p-value of <0.003 was considered to be significant.*p<0.003. The MHCII⁺ SIRPα⁻ CD11R1⁻CD16⁻ subset is not shown as this represents endothelial MHCII, which was unaffected by colonisation or age.</p