190 research outputs found

    ImmunomeBrowser analysis of B and T cell epitopes.

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    <p>R/T, number responded over number tested; RFscore, response frequency score; N-arm, N-terminal arm; NTD, N-terminal domain; CP, cytoplasmic, EC, extracellular; HBD, heparin binding domain; HRA/HRB, heptad repeats; DI, docking inhibition; Cys-noose, cysteine noose; bovine host*, natural infection in children/infants**, natural infection in adults***; bold indicates overlap.</p><p>ImmunomeBrowser analysis of B and T cell epitopes.</p

    Positional Bias of MHC Class I Restricted T-Cell Epitopes in Viral Antigens Is Likely due to a Bias in Conservation

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    <div><p>The immune system rapidly responds to intracellular infections by detecting MHC class I restricted T-cell epitopes presented on infected cells. It was originally thought that viral peptides are liberated during constitutive protein turnover, but this conflicts with the observation that viral epitopes are detected within minutes of their synthesis even when their source proteins exhibit half-lives of days. The DRiPs hypothesis proposes that epitopes derive from <b>D</b>efective <b>Ri</b>bosomal <b>P</b>roducts (DRiPs), rather than degradation of mature protein products. One potential source of DRiPs is premature translation termination. If this is a major source of DRiPs, this should be reflected in positional bias towards the N-terminus. By contrast, if downstream initiation is a major source of DRiPs, there should be positional bias towards the C-terminus. Here, we systematically assessed positional bias of epitopes in viral antigens, exploiting the large set of data available in the Immune Epitope Database and Analysis Resource. We show a statistically significant degree of positional skewing among epitopes; epitopes from both ends of antigens tend to be under-represented. Centric-skewing correlates with a bias towards class I binding peptides being over-represented in the middle, in parallel with a higher degree of evolutionary conservation.</p> </div

    Linear B cell epitopes associated with virus neutralization or <i>in vivo</i> protection.

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    <p>PT, passive transfer</p><p><sup>X</sup>, shows cross-protection; PC, polyclonal; VN, virus neutralization; Prot, <i>in vivo</i> challenge/survival; NI, natural infection</p><p>^ch101F is a mouse-human chimeric of 101F; <b>Motavizumab</b> is also a mouse-human chimera; all others are mouse; A2, HRSV A2 strain; Long, HRSV long strain</p><p>Linear B cell epitopes associated with virus neutralization or <i>in vivo</i> protection.</p

    Epitopes that induce IFNγ production from human CD8+ T cells.

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    <p>Role/Site abbreviations are included to indicate the role of the protein antigen in viral pathogenesis. VA: viral assembly; CP: cytoplasm; TM: transmembrane; EC: extracellular; HBD: heparin binding domain 184–198; RB: RNA binding; Inh IFN; inhibits IFN-mediated antiviral response; SS: signal sequence/N-terminus.</p><p>Epitopes that induce IFNγ production from human CD8+ T cells.</p

    Positional biases of predicted binders for 12 HLA supertypes.

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    <p>For each supertype, 9-mer peptide binding predictions were carried out and ratios of probability masses of predicted ‘binders’ and ‘non-binders’ were calculated. Peptide binding predictions were made for alleles belonging to each supertype, using SMM<sup>PMBEC</sup> method. All possible 9-mer peptides were generated from a set of viral proteins that contain at least one tested peptide from <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002884#pcbi-1002884-t001" target="_blank">Table 1</a>. Relationships between HLA molecules and supertypes are provided in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002884#pcbi.1002884-Sidney1" target="_blank">[11]</a>.</p

    List of validated tetramers (epitope/allele combinations).

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    <p>*Naturally eluted peptide; Prot, <i>in vivo</i> protection or survival; IFNγ, ELISPOT or ELISA; CTL, cytotoxicity assay; NR, None reported to date.</p><p>List of validated tetramers (epitope/allele combinations).</p

    Response by RSV protein.

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    <p>The total number of unique epitopes reported to date for each RSV protein are shown. Data are then further broken down into response type, antibody/B cell (black), T cell (grey) and MHC ligand (elution and binding combined; white). The percentages provided represent the portion of the total RSV-specific data.</p