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J R Schafer

Publications and source records attributed to J R Schafer.

4 recordsLinked to original sources
PubMed2004

Activation by malaria antigens renders mononuclear cells susceptible to HIV infection and re-activates replication of endogenous HIV in cells from HIV-infected adults.

We have tested the hypothesis that activation of T cells by exposure to malaria antigens facilitates both de novo HIV infection and viral reactivation and replication. PBMC from malaria-naive HIV-uninfected European donors could be productively infected with HIV following in vitro stimulation with a lysate of Plasmodium falciparum schizonts and PBMC from malaria-naive and malaria-exposed (semi-immune) HIV-positive adults were induced to produce higher levels of virus after stimulation with the same malaria extract. These findings suggest that effective malaria control measures might con-tribute to reducing the spread of HIV and extending the life span of HIV-infected individuals living in malaria endemic areas.

Adult↗
PubMed1998

Prediction of well-conserved HIV-1 ligands using a matrix-based algorithm, EpiMatrix.

This preliminary study was undertaken to identify new human leucocyte antigens (HLA) ligands from human immunodeficiency virus type 1 (HIV-1) which are highly conserved across HIV-1 clades and which may serve to induce cross-reactive cytotoxic T lymphocytes (CTLs). EpiMatrix was used to predict putative ligands from HIV-1 for HLA-A2 and HLA-B27. Twenty-six peptides that were both likely to bind and also highly conserved across HIV-1 strains in the Los Alamos HIV sequence database were selected for binding assays using the T2 stabilization assay. Two peptides that were also highly likely to bind (for A2 and B27, as determined by EpiMatrix) and well conserved across HIV-1 strains, and had previously been described to bind in the published literature, were also selected to serve as positive controls for the assays. Ten new major histocompatibility complex (MHC) ligands were identified among the 26 study peptides. The control peptides bound, as expected. These data confirm that EpiMatrix can be used to screen HIV-1 protein sequences for highly conserved regions that are likely to bind to MHC and may prove to be highly conserved HIV-1 CTL epitopes.

Algorithms↗
PubMed1997

An interactive Web site providing major histocompatibility ligand predictions: application to HIV research.

EpiMatrix/HIV, a tool that is currently available on the World Wide Web, enables researchers to screen HIV proteins for potential MHC ligands. We have performed a comparison of EpiMatrix predictions to 158 published allotype-specific HLA-associated peptides (MHC ligands) derived from 133 proteins. The top 10 ranked EpiMatrix predictions for each of the 158 HLA allotype-protein pairs were selected for comparison with these published ligands. EpiMatrix correctly identified 134 of 158 published ligands (85%). The algorithm is now available for use by the HIV research community at the URL http:/(/)www.EpiMatrix.com/HIV.

Computer Communication Networks↗