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Howard Grey

Publications and source records attributed to Howard Grey.

7 recordsLinked to original sources
PubMed2006

Curation of complex, context-dependent immunological data.

BACKGROUND: The Immune Epitope Database and Analysis Resource (IEDB) is dedicated to capturing, housing and analyzing complex immune epitope related data http://www.immuneepitope.org. DESCRIPTION: To identify and extract relevant data from the scientific literature in an efficient and accurate manner, novel processes were developed for manual and semi-automated annotation. CONCLUSION: Formalized curation strategies enable the processing of a large volume of context-dependent data, which are now available to the scientific community in an accessible and transparent format. The experiences described herein are applicable to other databases housing complex biological data and requiring a high level of curation expertise.

Allergy and Immunology↗
PubMed2006

A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus.

The value of predictive algorithms for identifying CD8+ T (T(CD8+))-cell epitopes has not been adequately tested experimentally. Here we demonstrate that conventional bioinformatic methods predict the vast majority of T(CD8+)-cell epitopes derived from vaccinia virus WR strain (VACV-WR) in the H-2(b) mouse model. This approach reveals the breadth of T-cell responses to vaccinia, a widely studied murine viral infection model, and may provide a tool for developing comprehensive antigenic maps of any complex pathogen.

Algorithms↗
PubMed2005

HLA-A*0201, HLA-A*1101, and HLA-B*0702 transgenic mice recognize numerous poxvirus determinants from a wide variety of viral gene products.

In virus models explored in detail in mice, CTL typically focus on a few immunodominant determinants. In this study we use a multipronged approach to understand the diversity of CTL responses to vaccinia virus, a prototypic poxvirus with a genome approximately 20-fold larger than that of the model RNA viruses typically studied in mice. Based on predictive computational algorithms for peptide binding to HLA supertypes, we synthesized a panel of 2889 peptides to begin to create an immunomic map of human CTL responses to poxviruses. Using this panel in conjunction with CTLs from vaccinia virus-infected HLA transgenic mice, we identified 14 HLA-A*0201-, 4 HLA-A*1101-, and 3 HLA-B*0702-restricted CD8(+) T cell determinants distributed over 20 distinct proteins. These peptides were capable of binding one or multiple A2, A3, and B7 supertype molecules with affinities typical of viral determinants. Surprisingly, many of the viral proteins recognized are predicted to be late gene products, in addition to the early intermediate gene products expected. Nearly all of the determinants identified have identical counterparts encoded by modified vaccinia virus Ankara as well as variola virus, the agent of smallpox. These findings have implications for the design of new smallpox vaccines and the understanding of immune responses to large DNA viruses in general.

Animals↗
PubMed2002

Interactions between double positive thymocytes and high affinity ligands presented by cortical epithelial cells generate double negative thymocytes with T cell regulatory activity.

Previous studies on thymocyte differentiation by using reaggregate cultures (RC) of double positive T cell receptor (TCR) transgenic thymocytes and the thymic epithelial cell line ANV indicated that low concentrations of high affinity ligands for the TCR were efficient inducers of thymocyte maturation to CD4 single positive (SP) functional cells. In this study, it is demonstrated that, when high concentrations of high affinity ligands are used in this RC system, double positive (DP) cells down-modulate expression of both coreceptors and that, as a result, large numbers of double negative (DN) cells are generated. These DN cells proliferated modestly in response to stimulation by antigen, and this response was considerably augmented by the addition of IL-2 to the cultures. Notably, these antigen-stimulated DN cells produced large amounts of IL-10. When the DN cells generated in RC were cocultured with naive TCR transgenic T cells in the presence of antigen, they suppressed the proliferative response of the naive T cells. Thus, high affinity ligands, when presented to DP thymocytes by cortical thymic epithelial cells in reaggregate cultures, rather than causing deletion of the immature thymocytes, induce their differentiation into immunoregulatory DN cells, suggesting a distinct mechanism by which self tolerance may be maintained.

Animals↗
PubMed2002

How H13 histocompatibility peptides differing by a single methyl group and lacking conventional MHC binding anchor motifs determine self-nonself discrimination.

The mouse H13 minor histocompatibility (H) Ag, originally detected as a barrier to allograft transplants, is remarkable in that rejection is a consequence of an extremely subtle interchange, P4(Val/Ile), in a nonamer H2-D(b)-bound peptide. Moreover, H13 peptides lack the canonical P5(Asn) central anchor residue normally considered important for forming a peptide/MHC complex. To understand how these noncanonical peptide pMHC complexes form physiologically active TCR ligands, crystal structures of allelic H13 pD(b) complexes and a P5(Asn) anchored pD(b) analog were solved to high resolution. The structures show that the basis of TCRs to distinguish self from nonself H13 peptides is their ability to distinguish a single solvent-exposed methyl group. In addition, the structures demonstrate that there is no need for H13 peptides to derive any stabilization from interactions within the central C pocket to generate fully functional pMHC complexes. These results provide a structural explanation for a classical non-MHC-encoded H Ag, and they call into question the requirement for contact between anchor residues and the major MHC binding pockets in vaccine design.

Amino Acid Motifs↗
PubMed2002

Strong induction of tyrosine phosphorylation, intracellular calcium, nuclear transcription factors and interferongamma, but weak induction of IL-2 in naïve T cells stimulated by bacterial superantigen.

The outcome of T cell receptor (TCR) engagement is controlled by the differential recruitment of a variety of pathways, depending on the nature of the TCR ligand. Studies on superantigens (SAGs) were among the first describing such differential signaling; however, reported results are inconsistent. We took a quantitative approach to reinvestigate this question. Using nai;ve T cells from TCR transgenic mice, we found that compared to the antigenic peptide from pigeon cytochrome c, the SAG staphylococcal enterotoxin A very efficiently (100-2000-fold more sensitive on a weight basis) induced tyrosine kinase activity, intracellular calcium increase, and interferon (IFN)gamma production. Up-regulation of CD25 and CD69 and proliferation were less efficiently induced (20-30-fold more sensitive), and interleukin (IL)-2 production was induced least efficiently (only 2-fold more sensitive). This differential activation profile that varies with the activation event analyzed is discussed with respect to the propensity for SAG to induce anergy.

Animals↗
PubMed2002

Multicenter study of the LCx HIV RNA quantitative assay--a new competitive reverse transcriptase-PCR which targets pol genomic region of HIV-1 for the measurement of type B, non-type B and group O HIV-1 RNA.

Performance characteristics of the Abbott LCx HIV RNA Quantitative Assay (LCx HIV) were established in a multicenter study comparing it with the manual (Amplicor v1.5) and automated (Cobas) ultra-sensitive Roche Amplicor HIV-1 Monitor v1.5, the Bayer Quantiplex HIV RNA 3.0 (bDNA v3.0), and the Organon NucliSens HIV QT 2.0 (NucliSens). Within-run precision of LCx HIV assessed in clinical specimens was SD log10 0.210 at approximately 50 copies/ml, and log10 0.133 at approximately 400 copies/ml. Total precision in a reconstituted type B HIV-1 RNA panel was SD log10 0.380 at 100 copies/ml, and SD log10 0.180 at 1000 copies/ml. Type B HIV-1 RNA sensitivity (1 ml input) assessed at a 50%, 75% and 95% detection rate ranged from 29 to 41, 54 to 75 and 94 to 176 copies/ml, respectively. Overall specificity in HIV seronegative individuals was 99.78%. Linear regression indicated close assay correlations and agreements for measurement of type B HIV-1 RNA. Pearson's correlations and (Log10LCx=aLog10x + b) linear regressions were 0.91 (y=0.892 Log10Amplicor + 0.595), 0.93 (y=0.827 Log10Cobas + 0.969), 0.93 (y=0.951 Log10bDNA + 0.550), and 0.79 (y=0.834 Log10NucliSens + 0.911). LCx HIV was least affected by the genetic variability of HIV-1. LCx HIV detected 99% of non-type B HIV-1 group M samples (subtypes A-G), Amplicor v1.5 detected 96%, and bDNA v3.0 detected 99%. The assays detected 10/11, 1/11 and 8/11, respectively of the HIV-1 group O samples. LCx HIV vs. Amplicor/bDNA Spearman's rank correlations for quantification of non-type B HIV-1 RNA were 0.76/0.84 (A), 0.93/0.93 (C), 0.73/0.99 (D), 0.86/0.98 (E), and 0.40/0.83 (group O). LCx HIV assays consistently detect and quantify type B, non-type B and group O HIV-1 RNA.

Acquired Immunodeficiency Syndrome↗