orf101 is a late gene of Autographa californica nucleopolyhedrovirus (AcMNPV). It encodes a protein of 42 kDa which is a component of the nucleocapsid of budded virus (BV) and occlusion-derived virus (ODV). To reflect this viral localization, the product of orf101 was named BV/ODV-C42 (C42). C42 is predominantly detected within the infected-cell nucleus: at 24 h postinfection (p.i.), it is coincident with the virogenic stroma, but by 72 h p.i., the stroma is minimally labeled while C42 is more uniformly located throughout the nucleus. Yeast two-hybrid screens indicate that C42 is capable of directly interacting with the viral proteins p78/83 (1629K) and ODV-EC27 (orf144). These interactions were confirmed using blue native gels and Western blot analyses. At 28 h p.i., C42 and p78/83 are detected in two complexes: one at approximately 180 kDa and a high-molecular-mass complex (500 to 600 kDa) which also contains EC27.Occlusion-derived virus (ODV) of Autographa californica nucleopolyhedrovirus (AcMNPV) initiates primary infection through gut cells of the susceptible insect, where the columnar cells are the primary sites of infection (13, 31). Columnar cells, however, are in a differentiated state (7). Thus, AcMNPV must have the ability to progress the infected columnar cell from G 0 to G 1 and further progress the cell to a phase conducive to viral DNA replication (S phase). These events occur rapidly: in virus-challenged Trichoplusia ni larvae, midgut infection is detectable by 4 h postinoculation and systemic infection is detected by 12 h (31).Viral regulation of the host cell cycle could be accomplished through several mechanisms. One mechanism is the early transcription-translation of viral genes which interact with cellular proteins or protein complexes. Some evidence suggests that AcMNPV may be utilizing this mechanism. The ie-2 gene is sufficient to arrest transfected Sf9 cells in S phase: the arrested cells do not undergo mitosis, have abnormally large nuclei, and contain greater than 4N DNA content (19). Infected Sf9 cells, however, show only a transient increase of cells in S phase, and the cells quickly progress to G 2 /M phase, where they remain arrested throughout infection (4). A second viral strategy to regulate the host cell cycle is to present, as structural components of the virus, a protein(s) or protein complexes that interact with cellular proteins immediately upon infection. For AcMNPV, the structural protein ODV-EC27 (EC27) is a candidate for such a strategy: it has amino acid similarity with cellular cyclins, and it coprecipitates with cellular cyclin kinases (1, 4). Its introduction into the cell at the time of infection may allow it to interact immediately with cellular cyclin kinases or function as a cyclin homologue in a manner analogous to that of other viral cyclin homologues. In our continuing study of the function of AcMNPV structural proteins and their interactions with host cell proteins, we have identified a new structural protein of budded virus (BV) and ODV, BV/ODV-C42 (C42; or...

We describe a novel approach to genetic association analyses with proteins sub-divided into biologically relevant smaller sequence features (SFs), and their variant types (VTs). SFVT analyses are particularly informative for study of highly polymorphic proteins such as the human leukocyte antigen (HLA), given the nature of its genetic variation: the high level of polymorphism, the pattern of amino acid variability, and that most HLA variation occurs at functionally important sites, as well as its known role in organ transplant rejection, autoimmune disease development and response to infection. Further, combinations of variable amino acid sites shared by several HLA alleles (shared epitopes) are most likely better descriptors of the actual causative genetic variants. In a cohort of systemic sclerosis patients/controls, SFVT analysis shows that a combination of SFs implicating specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk.

The gastrointestinal tract is populated by a multitude of specialized immune cells endowed with receptors for classical (class Ia) and nonclassical (class Ib) MHC proteins. To identify class I products that engage these receptors and impact immunity/tolerance, we studied gut-transcribed class Ib loci and their polymorphism in inbred, outbred, and wild-derived mice. Intestinal tissues enriched in epithelial cells contained abundant transcripts of ubiquitously expressed and preferentially gut-restricted Q and T class I loci. The latter category included the “blastocyst Mhc” gene, H2-Bl, and its putative paralog, Tw5. Expression of H2-Bl was previously detected only at the maternal/fetal interface, where it was proposed to induce immune tolerance via interactions with CD94/NKG2A receptors. Analysis of coding region polymorphism performed here revealed two major alleles of H2-Bl with conserved residues at positions critical for class I protein folding and peptide binding. Both divergent alleles are maintained in outbred and wild mice under selection for fecundity and pathogen resistance. Surprisingly, we found that alternative splicing of H2-Bl mRNA in gut tissues is prevalent and allele-specific. It leads to strain-dependent expression of diverse repertoires of canonical and noncanonical transcripts that may give rise to distinct ligands for intestinal NK cell, T cell, and/or intraepithelial lymphocyte receptors.

The immune response HLA class II DRB1 gene provides the major genetic contribution to Juvenile Idiopathic Arthritis (JIA), with a hierarchy of predisposing through intermediate to protective effects. With JIA, and the many other HLA associated diseases, it is difficult to identify the combinations of biologically relevant amino acid (AA) residues directly involved in disease due to the high level of HLA polymorphism, the pattern of AA variability, including varying degrees of linkage disequilibrium (LD), and the fact that most HLA variation occurs at functionally important sites. In a subset of JIA patients with the clinical phenotype oligoarticularpersistent (OP), we have applied a recently developed novel approach to genetic association analyses with genes/proteins sub-divided into biologically relevant smaller sequence features (SFs), and their "alleles" which are called variant types (VTs). With SFVT analysis, association tests are performed on variation at biologically relevant SFs based on structural (e.g., beta-strand 1) and functional (e.g., peptide binding site) features of the protein. We have extended the SFVT analysis pipeline to additionally include pairwise comparisons of DRB1 alleles within serogroup classes, our extension of the Salamon Unique Combinations algorithm, and LD patterns of AA variability to evaluate the SFVT results; all of which contributed additional complementary information. With JIA-OP, we identified a set of single AA SFs, and SFs in which they occur, particularly pockets of the peptide binding site, that account for the major disease risk attributable † corresponding author: glenys@berkeley.edu. NIH Public Access Author ManuscriptPac Symp Biocomput. Author manuscript; available in PMC 2010 October 20. to HLA DRB1. These are (in numeric order): AAs 13 (pockets 4 and 6), 37 and 57 (both pocket 9), 67 (pocket 7), 74 (pocket 4), and 86 (pocket 1), and to a lesser extent 30 (pockets 6 and 7) and 71 (pockets 4, 5, and 7).

B cells isolated from the CSF of patients with multiple sclerosis (MS) have a unique accumulation of somatic hypermutation, within the B cell receptor, termed the antibody gene signature (AGS). The focus of this study was to investigate whether the AGS could also be detected in MS brain tissue. Genetic analysis of B cells isolated from post-mortem CNS tissue samples from four MS brains demonstrated that signature enriched B cells are present at the site of tissue injury as well as in the circulating CSF.