Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries-1

<p><b>Copyright information:</b></p><p>Taken from "Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries"</p><p>http://www.immunome-research.com/content/4/1/2</p><p>Immunome Research 2008;4():2-2.</p><p>Published online 25 Jan 2008</p><p>PMCID:PMC2248166.</p><p></p>g specificity factors (SF), as secondary anchor positions (green shading) were determined on the basis of standard deviation (SD), as described in the text

Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries-0

<p><b>Copyright information:</b></p><p>Taken from "Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries"</p><p>http://www.immunome-research.com/content/4/1/2</p><p>Immunome Research 2008;4():2-2.</p><p>Published online 25 Jan 2008</p><p>PMCID:PMC2248166.</p><p></p>tides. Binding assays were performed as described in the materials and methods for peptides previously [47] utilized to compare various publicly available prediction tools. Peptides were scored using the matrix as described in the text

Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries-3

<p><b>Copyright information:</b></p><p>Taken from "Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries"</p><p>http://www.immunome-research.com/content/4/1/2</p><p>Immunome Research 2008;4():2-2.</p><p>Published online 25 Jan 2008</p><p>PMCID:PMC2248166.</p><p></p>tides. Binding assays were performed as described in the materials and methods for peptides previously [47] utilized to compare various publicly available prediction tools. Peptides were scored using the matrix as described in the text

TCL Response to R-Enriched Peptides in Peripheral Blood

<div><p>(A) Proliferative response of peripheral TCL to the following: a mixture of ten peptides enriched in R, a mixture of ten peptides enriched in K, a mixture of ten peptides not enriched in any specific aa, and a mixture of randomized decapeptides. Negative control is medium without peptide mixture. Responses higher that the mean of the negative control plus 4 standard deviations have been considered positive. * Detailed information of mixtures used in IL-7 primary proliferation assay are available in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.0010041#ppat-0010041-st003" target="_blank">Table S3</a>.</p><p>(B) Comparison of the origin (naïve versus memory) of all TCLs with confirmed reactivity against R-enriched peptides.</p></div

TTV-DNA in Patient's Serum Samples

<div><p>(A) Detection of TTV-DNA by PCR amplification using two primer combinations with the respective nested primers. Six different serum samples from the same patient obtained at different time points were analyzed. The first two samples were obtained during relapse. Time points with simultaneous CSF are indicated. Plus symbol indicates presence of TTV DNA; minus symbol indicates absence.</p><p>(B) The sequences obtained by cloning and sequencing of all amplicons and the alignment with the closer related known TT viruses are shown. One isolate that was present in two different serum samples is shown in red.</p></div

Stimulatory Peptides from TTV and TLMV

<div><p>(A) Number and SIs of the stimulatory peptides from TTV and TLMV identified for TCCs MN19, MN27, and MN36.</p><p>(B) Number and SIs of the peptides co-recognized by different TCCs. Peptides have been tested in proliferation assays at 10 μg/ml and using PBMCs as antigen-presenting cells.</p></div

Rapid Scanning Structure–Activity Relationships in Combinatorial Data Sets: Identification of Activity Switches

We present a general approach to describe the structure–activity relationships (SAR) of combinatorial data sets with activity for two biological endpoints with emphasis on the rapid identification of substitutions that have a large impact on activity and selectivity. The approach uses dual-activity difference (DAD) maps that represent a visual and quantitative analysis of all pairwise comparisons of one, two, or more substitutions around a molecular template. Scanning the SAR of data sets using DAD maps allows the visual and quantitative identification of activity switches defined as specific substitutions that have an opposite effect on the activity of the compounds against two targets. The approach also rapidly identifies single- and double-target R-cliffs, i.e., compounds where a single or double substitution around the central scaffold dramatically modifies the activity for one or two targets, respectively. The approach introduced in this report can be applied to any analogue series with two biological activity endpoints. To illustrate the approach, we discuss the SAR of 106 pyrrolidine bis-diketopiperazines tested against two formylpeptide receptors obtained from positional scanning deconvolution methods of mixture-based libraries

Detected frequencies of TCR-Vβ families expressed on T cells from lines RM30.II and RM30.II.84.

<p>Detected frequencies of TCR-Vβ families expressed on T cells from lines RM30.II and RM30.II.84.</p

Antigen specific response in selected cultures from subject RM30.

<p>Cell lines were established from <i>T</i>. <i>cruzi</i> specific cultures, based on results from experiment depicted on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178380#pone.0178380.g003" target="_blank">Fig 3</a>. Cells were submitted to 2 PHA expansion cycles prior to specificity evaluation. Five thousand cells from each culture well were challenged with <i>T</i>. <i>cruzi</i> lysate, using 10⁴ autologous overnight-primed B-LCL per well as APC. SI was calculated for each well as the response against <i>T</i>. <i>cruzi</i> lysate divided by the cells baseline response (media only condition), cultures considered positive were those with an SI≥2 (dotted line). Bars show the mean values and standard deviation for three replicates of each measure.</p

Antigen specific response in cultures resulting from limiting dilution assay (LDA) of culture RM30.II.

<p><b>A</b>. Twenty-five thousand cells from each culture well were challenged with <i>T</i>. <i>cruzi</i> lysate, using 5×10⁴ autologous overnight-primed B-LCL per well as APC. Specificity against <i>T</i>. <i>cruzi</i> antigens was assessed for several potentially monoclonal lines by IFN-γ and GM-CSF secretion. N/A: Non applicable. <b>B</b>. Specific response was tested using lysates from different stages in the parasite’s life cycle (epimastigote and trypomastigote/amastigote) for T cell lines RM30.II.84 and .85.</p