28 research outputs found
<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 <sup>51</sup>Cr release assay.
<p>Specific lysis of Gag peptide p24<sub>122–130</sub> 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
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 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
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
<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
Summary of <i>boNT</i>/B amino acid substitution between strain Maehongson 2010(MH 2010) and 111 in each domain (light chain and H<sub>N</sub>) or subdomain (H<sub>CN</sub> and H<sub>CC</sub> in H<sub>C</sub>). Hyphens indicate residues identical to those in strain 111.
Multiplex PCR of <i>ha33</i> and <i>p47genes</i> for confirmation of <i>boNT/</i>A and <i>boNT</i>/B typing Isolate from Saraburi 2010 strain showed positive <i>ha</i>33 and <i>p47</i> amplicon (534 bp and 344 bp, lane7), <i>ha</i> 33 of <i>boNT</i>/A1 amplicon (534 bp, lane 1), <i>p47</i> of <i>boNT</i>/A2 amplicon (344 bp, lane 2).
Percentage of identity and similarity of <i>boNT</i>/B gene and nontoxic component genes compared with strain Maehongson 2010 and Okra (subtype B1) and strain Maehongson 2010 and 111 (subtype B2).
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