<i>In silico</i> epitope prediction for ELISpot responders carrying HLA alleles currently unknown to restrict CRF01_AE epitopes.

<p>We found 27 CRF01_AE specific CTL responses induced in patients carrying HLA alleles previously unknown to restrict CRF01_AE epitopes. Prediction of the optimal epitope within the peptide and its restricting HLA allele was performed using the <i>in silico</i> epitope prediction model HLArestrictor. In total, 19 epitope-HLA combinations were detected with binder levels defined as SB (Strong Binder), WB (Weak Binder), or CB (Combined Binder). NA: Not available, and BL: Binder level.</p

Cytotoxicity assay with T cells Demonstration of a novel epitope-HLA association by ⁵¹Cr release assay.

<p>Specific lysis of Gag peptide p24_122–130 PPIPVGDIY (PY9) pulsed allogeneic target cells by effector CTLs from a HLA-B*40:01+ donor was assessed in a chromium release assay. The <i>Y</i> axis shows percentage specific lysis at an E∶T ratio of 20∶1 with the lysis (%) of unpulsed target cells subtracted. Effector cells were derived from patient 1509. HLA-B*40:01 matched cells pulsed with PY9 were also recognized by patient 326 (data not shown). HLA alleles shared by target cells and effector cells are shown; control indicates HLA-unmatched cells.</p

<i>C.botulinum</i> strains and sequences used in this study.

a<p>The subtypes and GenBank accession numbers for strains determined in this study are indicated in boldface.</p>b<p><i>boNT</i>/A producing and unexpressed <i>boNT</i>/B gene possessing.</p>c<p>Dual toxin producing strains; the major toxin type is indicated in uppercase letters and the minor type is indicated in lowercase letters.</p

Anti-HIV-1 neutralizing activity of 6 selected plasma samples against B-Env- and C-Env-recombinant viruses.

<p>Neutralizing activity of 6 plasma samples against 5 B-Env- and 6 C-Env-recombinant viruses was evaluated as described in the legend to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053920#pone-0053920-g001" target="_blank">Figure 1</a>. Data are presented as the means of at least three independent experiments. Plasma IDs and Env-recombinant viruses tested are denoted on the left side and above the panel, respectively. ID50 values 100–500 and 20–100 are highlighted in orange and yellow, respectively. No neutralization (ID50 values <20) of a recombinant virus is denoted by a gray background.</p

Anti-HIV-1 neutralizing activity of plasma derived from 33 rapid progressors against AE-Env-recombinant viruses.

<p>Neutralizing activity of plasma samples against 8 AE-Env-recombinant viruses was evaluated and reciprocal plasma dilution at which viral replication was suppressed by 50% (50% inhibitory dilution, ID50) was calculated, as described in Methods. Data are presented as the means of at least three independent experiments. Plasma IDs and AE-Env-recombinant viruses tested are denoted on the left side and above the panel, respectively. In addition, mean ID50 values and the percentages of virus/plasma combinations (% neutralization) in which viral neutralization was observed among the data sets in horizontal and vertical directions are shown on the right side and bottom of the panel, respectively. ID50 values >500, values 100–500, and values 20–100 are highlighted in red, orange and yellow, respectively. In addition, no neutralization (ID50 values <20) of a recombinant virus is denoted by a gray background.</p

Anti-HIV-1 neutralizing activity of plasma derived from 34 slow progressors against AE-Env-recombinant viruses.

<p>Neutralizing activity of plasma samples against 8 AE-Env-recombinant viruses was evaluated as described in the legend to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053920#pone-0053920-g001" target="_blank">Figure 1</a>. Data are presented as the means of at least three independent experiments. Plasma IDs and AE-Env-recombinant viruses tested are denoted on the left side and above the panel, respectively. In addition, mean ID50 values and the percentages of virus/plasma combinations (% neutralization) in which viral neutralization was observed among the data sets in horizontal and vertical directions are shown on the right side and bottom of the panel, respectively. ID50 values >500, values 100–500 and values 20–100 are highlighted in red, orange and yellow, respectively. No neutralization (ID50 values <20) of a recombinant virus is denoted by a gray background. Plasma samples that neutralized all recombinant viruses tested are highlighted in green.</p

Comparison of the neutralization breadth between plasma derived from rapid and slow progressors.

<p>The proportion of AE-Env-recombinant viruses in which replication was inhibited by a plasma sample was calculated and plotted. The levels of plasma-mediated neutralization against 60% and 80% of recombinant viruses tested are highlighted by horizontal blue and red grid lines, respectively. Plasma IDs are denoted below the panels.</p