Publications

Patr-AL is an expressed, non-polymorphic MHC class I gene carried by ?50% of chimpanzee MHC haplotypes. Comparing Patr-AL+ and Patr-AL? haplotypes showed Patr-AL defines a unique 125-kb genomic block flanked by blocks containing classical Patr-A and pseudogene Patr-H. Orthologous to Patr-AL are polymorphic orangutan Popy-A and the 5? part of human pseudogene HLA-Y, carried by ?10% of HLA haplotypes. Thus, the AL gene alternatively evolved in these closely related species to become classical, nonclassical, and nonfunctional. Although differing by 30 aa substitutions in the peptide-binding ?1 and ?2 domains, Patr-AL and HLA-A*0201 bind overlapping repertoires of peptides; the overlap being comparable with that between the A*0201 and A*0207 subtypes differing by one substitution. Patr-AL thus has the A02 supertypic peptide-binding specificity. Patr-AL and HLA-A*0201 have similar three-dimensional structures, binding peptides in similar conformation. Although comparable in size and shape, the B and F specificity pockets of Patr-AL and HLA-A*0201 differ in both their constituent residues and contacts with peptide anchors. Uniquely shared by Patr-AL, HLA-A*0201, and other members of the A02 supertype are the absence of serine at position 9 in the B pocket and the presence of tyrosine at position 116 in the F pocket. Distinguishing Patr-AL from HLA-A*02 is an unusually electropositive upper face on the ?2 helix. Stimulating PBMCs from Patr-AL? chimpanzees with B cells expressing Patr-AL produced potent alloreactive CD8 T cells with specificity for Patr-AL and no cross-reactivity toward other MHC class I molecules, including HLA-A*02. In contrast, PBMCs from Patr-AL+ chimpanzees are tolerant of Patr-AL.

Salmonella enterica serovar Typhimurium is a Gram-negative bacterium that has a significant impact on both human and animal health. It is one of the most common food-borne pathogens responsible for a self-limiting gastroenteritis in humans and a similar disease in pigs, cattle and chickens. In contrast, intravenous challenge with S. Typhimurium provides a valuable model for systemic infection, often causing a typhoid-like infection, with bacterial replication resulting in the destruction of the spleen and liver of infected animals. Resistance to systemic salmonellosis in chickens is partly genetically determined, with bacterial numbers at systemic sites in resistant lines being up to 1000-fold fewer than in susceptible lines. Identification of genes contributing to disease resistance will enable genetic selection of resistant lines that will reduce Salmonella levels in poultry flocks. We previously identified a novel resistance locus on Chromosome 5, designated SAL1. Through the availability of high-density SNP panels in the chicken, combined with advanced back-crossing of the resistant and susceptible lines, we sought to refine the SAL1 locus and identify potential positional candidate genes. Using a 6th generation backcross mapping population, we have confirmed and refined the SAL1 locus as lying between 54.0 and 54.8 Mb on the long arm of Chromosome 5 (F = 8.72, P = 0.00475). This region spans 14 genes, including two very striking functional candidates; CD27-binding protein (Siva) and the RAC-alpha serine/threonine protein kinase homolog, AKT1 (protein kinase B, PKB).

Semliki Forest virus (SFV) provides an experimental model of acute virus encephalitis and virus-induced demyelinating disease. Two marker viruses expressing fluorescent proteins as part of the replicase or the structural open reading frame were used to evaluate virus replication in cells of the adult mouse brain. Both marker viruses established a high-titer infection in the adult mouse brain. As determined by location, morphology, and immunostaining with neural cell type-specific phenotypic markers, both viruses infected neurons and oligodendrocytes but not astrocytes. Determination of eGFP expression from either the replicase or the structural open-reading frame coupled with immunostaining for either the virus structural protein or the virus nonstructural protein-3 readily distinguished cells at early and late stages of infection. Neurons but not oligodendrocytes rapidly down-regulated virus replication. Rapid down-regulation of virus replication was also observed in mature but not immature primary cultures of rat hippocampal neurons. This study demonstrates for the first time that in vivo central nervous system (CNS) cells differ in their ability to suppress alphavirus replication.

The current chicken genome build contains only a single colony-stimulating factor (CSF) gene, granulocyte/macrophage (GM)-CSF (CSF2). However, genes encoding receptors for two other CSFs, G-CSF (CSF3) and M-CSF (CSF1), are present in the genome. Another apparently chicken-specific CSF, myelomonocytic growth factor (MGF), shares substantial sequence homology with mammalian CSF3 but is absent from the genome. The putative region of the chicken genome that should contain the CSF3 ortholog, while not currently mapped to a specific chromosome, exhibits considerable conserved synteny with loci containing this gene in several other species. In silico analysis of the predicted CSF3 location revealed a large region homologous with the MGF promoter, upstream of a large sequence gap. In view of the many structural and functional features common to both MGF and huCSF3, we predicted that MGF is in fact CSF3 and its gene would be located within the sequence gap. To validate this hypothesis, a primer walking strategy was used to bridge the genomic sequence gap. Full-length sequencing of the entire region and thorough, detailed analysis of the coding region confirmed that the MGF gene lay within this sequence gap, and therefore that it should be renamed CSF3.