Analysis of memory T lymphocyte activity following stimulation with overlapping HLA-A*2402, A*0101 and Cw*0402 restricted CMV pp65 peptides

The continuous efforts aimed at the identification of new immune epitopes across the MHC system has led to the discovery that more than one peptide may be restricted to the same HLA antigen and function as an immune determinant for that association. The aim of this study was to compare the ability of two overlapping peptides, the nonamer (9-mer) cytomegalovirus (CMV) pp65(341–349 )(QYDPVAALF) and the decamer (10-mer) CMV pp65(341–350 )(QYDPVAALFF), and the esadecamer (16-mer) peptide containing both the 9-mer and 10-mer sequences, CMV pp65(340–355 )(RQYDPVAALFFFDIDL), to stimulate and maintain over time a T cell immune reactivation by HLA-A*2402, A*0101, and Cw*0402 cells from CMV-seropositive subjects. The 9-mer, 10-mer, and 16-mer peptides effectively stimulated CTLs from HLA-A*2402, HLA-A*0101, and HLA-Cw*0402 CMV seropositive donors. This data confirms that both the 9-mer and the 10-mer peptides are promiscuous and are not restricted to a single HLA antigen. CMV pp65(341–349 )and CMV pp65(341–350 )have the ability to produce CMV-specific CTLs in subjects with several different HLA types, presenting a practical advantage over other peptides that are restricted only to a single HLA antigen, and thus being optimal for CMV adoptive immune therapy. Moreover, since the 16-mer peptide encompasses both the 9-mer and 10-mer peptides, it may be better than either of these peptides for CMV adoptive immune therapy

The Role of the QCD Vacuum in the Heavy-Quark Bound State Dynamics

The effective field theory approach allows a rigorous disentangling of high and low energy effects in the heavy quarkonium dynamics. Focusing in particular on the spectrum, we describe the nature of the non-perturbative effects and discuss our present knowledge of them.Comment: Invited talk presented at the Fifth Workshop on Quantum Chromodynamics, Villefranche-sur-Mer, France, 3-7 January 2000; 9 pages, sprocl.st

Nuclease resistant methylphosphonate-DNA/LNA chimeric oligonucleotides

Synthesis of chimeric 9-mer oligonucleotides containing methylphosphonate-linkages and locked nucleic acid (LNA) monomers, their binding affinity towards complementary DNA and RNA, and their 3′-exonucleolytic stability are described. The obtained methylphosphonate-DNA/LNA chimeric oligonucleotides display similarly high RNA affinity and RNA selectivity as a corresponding 9-mer DNA/LNA chimeric oligonucleotide, but much higher resistance towards 3′-exonucleolytic degradation

Non-perturbative gluodynamics of high energy heavy-ion collisions

The dynamics of low-x partons in the transverse plane of a high-energy nuclear collision is classical, and therefore admits a fully non--perturbative numerical treatment. We report results of a recent study estimating the initial energy density in the central region of a collision. Preliminary estimates of the number of gluons per unit rapidity, and the initial transverse momentum distribution of gluons, are also provided.Comment: Latex,9 pages, 4 figures, invited talk at 5th workshop on QCD (QCD2000), Villefrance-sur-Mer, Jan.3rd-7th, 2000; minor typo correcte

Conservation Analysis of Dengue Virus T-cell Epitope-Based Vaccine Candidates Using Peptide Block Entropy

Broad coverage of the pathogen population is particularly important when designing CD8+ T-cell epitope vaccines against viral pathogens. Traditional approaches are based on combinations of highly conserved T-cell epitopes. Peptide block entropy analysis is a novel approach for assembling sets of broadly covering antigens. Since T-cell epitopes are recognized as peptides rather than individual residues, this method is based on calculating the information content of blocks of peptides from a multiple sequence alignment of homologous proteins rather than using the information content of individual residues. The block entropy analysis provides broad coverage of variant antigens. We applied the block entropy analysis method to the proteomes of the four serotypes of dengue virus (DENV) and found 1,551 blocks of 9-mer peptides, which cover 99% of available sequences with five or fewer unique peptides. In contrast, the benchmark study by Khan et al. (2008) resulted in 165 conserved 9-mer peptides. Many of the conserved blocks are located consecutively in the proteins. Connecting these blocks resulted in 78 conserved regions. Of the 1551 blocks of 9-mer peptides 110 comprised predicted HLA binder sets. In total, 457 subunit peptides that encompass the diversity of all sequenced DENV strains of which 333 are T-cell epitope candidates

Quadruple 9-mer-based protein binding microarray with DsRed fusion protein

<p>Abstract</p> <p>Background</p> <p>The interaction between a transcription factor and DNA motif (<it>cis</it>-acting element) is an important regulatory step in gene regulation. Comprehensive genome-wide methods have been developed to characterize protein-DNA interactions. Recently, the universal protein binding microarray (PBM) was introduced to determine if a DNA motif interacts with proteins in a genome-wide manner.</p> <p>Results</p> <p>We facilitated the PBM technology using a DsRed fluorescent protein and a concatenated sequence of oligonucleotides. The PBM was designed in such a way that target probes were synthesized as quadruples of all possible 9-mer combinations, permitting unequivocal interpretation of the <it>cis</it>-acting elements. The complimentary DNA strands of the features were synthesized with a primer and DNA polymerase on microarray slides. Proteins were labeled via N-terminal fusion with DsRed fluorescent protein, which circumvents the need for a multi-step incubation. The PBM presented herein confirmed the well-known DNA binding sequences of Cbf1 and CBF1/DREB1B, and it was also applied to elucidate the unidentified <it>cis</it>-acting element of the OsNAC6 rice transcription factor.</p> <p>Conclusion</p> <p>Our method demonstrated PBM can be conveniently performed by adopting: (1) quadruple 9-mers may increase protein-DNA binding interactions in the microarray, and (2) a one-step incubation shortens the wash and hybridization steps. This technology will facilitate greater understanding of genome-wide interactions between proteins and DNA.</p