Comparison of copy numbers of short tandem repeat loci in multiple skin biopsies taken at the same time, from different lesions, from individual patients in Malawi.

<p>Histopathological classifications in column 3.</p

PE/PPE proteins selected for this study.

<p><b>a.</b> C, PE/PPEs encoded by complete <i>esx</i> gene cluster; P, PE/PPE encoded by partial <i>esx</i> cluster; I, PE/PPE encoded by isolated <i>pe/ppe</i> pair (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040890#pone.0040890.s001" target="_blank">Figure S1</a>).</p><p><b>b.</b> Single peptide for Rv3018A/PE27A mixed with PE13 set.</p><p><b>c.</b> Pool does not include all possible overlapping peptides, some were excluded due to 100% identity.</p

Comparison of copy numbers of short tandem repeat loci from multiple biopsies taken at a single timepoint from different anatomical locations, from individual patients in Malawi.

<p>Histopathological classifications in column 3.</p

Distribution of copy numbers of seven different short tandem repeat loci in the 43 Malawi biopsies.

<p>Numbers in the table give the number of biopsies with each particular number of copies of each of seven tandem repeat loci. The “reference” strain was derived from a patient in USA; the “sequence” strain was derived from a South Indian patient (Cole et al, 2001).</p

Comparison of copy numbers of short tandem repeat loci in biopsies from patients in multicase families in India.

<p>All members of each family group lived in the same household residence except for individuals marked ^*, who lived in separate residences nearby, and individual marked ^** who lived in another household, in another village. Abbreviations: <i>rrxn = </i>reversal reaction (type 1 reaction); <i>rel = </i>relapse; <i>enl = </i>erythema nodosum leprosum (type 2 reaction).</p

Whole blood IFN-Υ responses to individual and pooled PE/PPE peptides.

<p>Peptide pools eliciting positive responses were further analysed by assessing the contribution of each constituent peptide at 3, 5 or 9 weeks post-infection<b>.</b> Representative data are shown for peptides corresponding to (A) One pool derived from PE8, and (B) One pool derived from PPE15. The solid lines represent the temporal response to a peptide pool, while individual symbols correspond to individual peptides. (C) and (D) BLASTP homology searches were performed with peptides which elicited positive responses, and closest matches are shown in a CLUSTALW alignment.</p

IFN-γ responses of short-term T cell lines to potentially cross-reactive PPE peptides.

<p>Short-term T cell lines were raised by primary stimulation of bovine PBMC with individual PE or PPE peptides in the presence of IL-2. Following initial expansion with (A) PE31.10, (B) PPE18.14 or (C) PPE60.14, cells were re-stimulated with selected peptides, predicted to be immunologically cross-reactive. IFN-γ production was then measured using the ELISA-based Bovigam assay. The amino acid sequence of the initial stimulation peptide is shown in alignment with restimulation peptides, with amino acid substitutions indicated. Responses are shown as ΔOD₄₅₀ values, and the dashed line indicates the positivity cut-off value of 0.1.</p

Comparison of copy numbers of short tandem repeat loci from multiple biopsies taken from the same anatomical location at different times, from individual patients in Malawi.

<p>The initial biopsies of patients 4 and 5 are included in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0000214#pntd-0000214-t003" target="_blank">Tables 3</a> and <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0000214#pntd-0000214-t004" target="_blank">4</a>, respectively.</p>*<p>The biopsy from patient 8 in 1990 was considered by the histopathologist to show “normal epidermis”.</p

Expression of ncRv12659 during infection.

<p>Mycobacterial RNA extracted from tissues of mice infected with PhiRv2-positive <i>M. tuberculosis</i> H37Rv or PhiRv2-negative <i>M. tuberculosis</i> N0072 was compared to RNA from exponential and starved cultures of the same strains. The levels of ncRv12659 was measured by qRT-PCR using amplicons specific for the 5′ or 3′ regions of ncRv12659 and normalised to the level of 16S rRNA. ncRv12659 was induced during infection, though to a lower extent than during <i>in vitro</i> starvation; the 5′ portion of the sRNA accumulated to levels much higher than the 3′ end. The low level of 3′ amplicon detected in <i>in vitro</i> cultures of N0072 was not seen <i>in vivo</i>. Data represent mean and standard deviation of three biological replicates.</p

Bovine and human responses to selected PE/PPE peptide pools.

<p><b>a.</b> Individual cattle samples were scored as positive if ΔOD₄₅₀ values were ≥0.1, and human samples were scored as positive if ≥20 SFC were counted per 10⁶ PBMC.</p