Family-based analysis using a dense single-nucleotide polymorphism-based map defines genetic variation at PSORS1, the major psoriasis-susceptibility locus

Psoriasis is a common skin disorder of multifactorial origin. Genomewide scans for disease susceptibility have repeatedly demonstrated the existence of a major locus, PSORS1 (psoriasis susceptibility 1), contained within the major histocompatibility complex (MHC), on chromosome 6p21. Subsequent refinement studies have highlighted linkage disequilibrium (LD) with psoriasis, along a 150-kb segment that includes at least three candidate genes (encoding human leukocyte antigen-C [HLA-C], alpha-helix-coiled-coil-rod homologue, and corneodesmosin), each of which has been shown to harbor disease-associated alleles. However, the boundaries of the minimal PSORS1 region remain poorly defined. Moreover, interpretations of allelic association with psoriasis are compounded by limited insight of LD conservation within MHC class I interval. To address these issues, we have pursued a high-resolution genetic characterization of the PSORS1 locus. We resequenced genomic segments along a 220-kb region at chromosome 6p21 and identified a total of 119 high-frequency SNPs. Using 59 SNPs (18 coding and 41 noncoding SNPs) whose position was representative of the overall marker distribution, we genotyped a data set of 171 independently ascertained parent-affected offspring trios. Family-based association analysis of this cohort highlighted two SNPs (n.7 and n.9) respectively lying 7 and 4 kb proximal to HLA-C. These markers generated highly significant evidence of disease association (P<10-9), several orders of magnitude greater than the observed significance displayed by any other SNP that has previously been associated with disease susceptibility. This observation was replicated in a Gujarati Indian case/control data set. Haplotype-based analysis detected overtransmission of a cluster of chromosomes, which probably originated by ancestral mutation of a common disease-bearing haplotype. The only markers exclusive to the overtransmitted chromosomes are SNPs n.7 and n.9, which define a 10-kb PSORS1 core risk haplotype. These data demonstrate the power of SNP haplotype-based association analyses and provide high-resolution dissection of genetic variation across the PSORS1 interval, the major susceptibility locus for psoriasis.     

Isolation of an intertypic poliovirus capsid recombinant from a child with vaccine-associated paralytic poliomyelitis

The isolation of a capsid intertypic poliovirus recombinant from a child with vaccine-associated paralytic poliomyelitis is described. Virus 31043 had a Sabin-derived type 3-type 2-type 1 recombinant genome with a 5'-end crossover point within the capsid coding region. The result was a poliovirus chimera containing the entire coding sequence for antigenic site 3a derived from the Sabin type 2 strain. The recombinant virus showed altered antigenic properties but did not acquire type 2 antigenic characteristics. The significance of the presence in nature of such poliovirus chimeras and the consequences for the current efforts to detect potentially dangerous vaccine-derived poliovirus strains are discussed in the context of the global polio eradication initiative.     

The role of dendritic cell subsets in selection between tolerance and immunity

Dendritic cells (DC) are considered nature's adjuvants. They are potent stimulators of naive T cells and key inducers of primary immune responses. In recent times it has become clear that they can also play a central role in the development of T cell tolerance. Further complicating our understanding of DC function is the realization that DC can no longer be viewed as a homogeneous cell type. Rather, they exist as a complex mixture of strikingly different cell populations. The mechanisms that drive the conflicting immunological outcomes of tolerance and immunity have been the subject of intense scrutiny in recent years, most recently in terms of how the various DC subsets are involved in these events. Here we review recent experiments that provide insights into how DC subsets control the outcome of T cell activation and in so doing select between immunity and tolerance induction.     

Studying the functional genomics of stress responses in loblolly pine with the Expresso microarray experiment management system

Conception, design, and implementation of cDNA microarray experiments present a variety of bioinformatics challenges for biologists and computational scientists. The multiple stages of data acquisition and analysis have motivated the design of Expresso, a system for microarray experiment management. Salient aspects of Expresso include support for clone replication and randomized placement; automatic gridding, extraction of expression data from each spot, and quality monitoring; flexible methods of combining data from individual spots into information about clones and functional categories; and the use of inductive logic programming for higher-level data analysis and mining. The development of Expresso is occurring in parallel with several generations of microarray experiments aimed at elucidating genomic responses to drought stress in loblolly pine seedlings. The current experimental design incorporates 384 pine cDNAs replicated and randomly placed in two specific microarray layouts. We describe the design of Expresso as well as results of analysis with Expresso that suggest the importance of molecular chaperones and membrane transport proteins in mechanisms conferring successful adaptation to long-term drought stress.     

Analysis of three separate probes suggests the absence of endocytosis in Neurospora crassa hyphae

Reports of the existence of endocytosis in filamentous fungi have been conflicting and inconclusive. For this reason, we have tested three independent markers in Neurospora crassa: the electron opaque marker lanthanum (La) and the fluorescent probes Lucifer yellow (LY) and FM4-64. Both La and LY were endocytosed by Saccharomyces cerevisiae cells, which were used as positive controls for endocytosis, but the probes did not accumulate in N. crassa hyphae. Only FM4-64 became internalized into N. crassa hyphae, but it induced abnormal changes in membrane systems and its internalization could be explained by mechanisms other than endocytosis. Together, our results suggest that endocytosis does not occur in N. crassa hyphae and question whether the styryl dyes do in fact reliably report normal endocytosis in filamentous fungi.     

Predicting the distribution,conservation, and functions of SNAREs and related proteins in fungi

Hyphal tip growth, the hallmark of the fungi, requires highly polarized and localized exocytosis, but how this requirement is met is unknown. Members of conserved protein families called SNAREs and Rabs mediate vesicle trafficking and fusion at virtually every step of the intracellular pathway in all examined eukaryotes. We have searched the available nearly complete fungal genomes, established the presence or absence of members of the SNARE and Rab families in these genomes, and predicted their evolutionary relationships to one another. Comparisons with the extensively studied Saccharomyces cerevisiae indicate that, in general, most of the members of these families (including those involved in mediating exocytosis) are conserved. The presence of exceptional SNAREs and Rabs in some fungi that are not conserved in S. cerevisiae may be indicative of specialized steps that occur in these fungi. The implications of these findings for current tip growth models are discussed.     

Development of a bioartificial nerve graft. I. Design based on a reaction-diffusion model

A simple reaction-diffusion model has been developed to describe the mass transport of nutrients and nerve growth factor within a bioartificial nerve graft (BNG). The BNG consists of a porous polymer conduit that is preseeded with Schwann cells in its lumen. The Schwann cells produce growth factors to stimulate nerve regeneration within the lumen of the conduit. The model can predict the wall thickness, porosity, and Schwann cell seeding density needed to maximize the axon extension rate while ensuring that sufficient nutrients, especially oxygen, are made available to the neurons until the formation of the neovasculature. The model predicts a sixteen-fold increase in the levels of nerve growth factor by dropping the porosity from 95 to 55% but only at the expense of reducing the oxygen concentration. At higher porosities, increasing the wall thickness and increasing the Schwann cell seeding density both have the same effect of increasing the concentration of nerve growth factor within the lumen of the conduit. This model provides a simple tool for evaluating various conduit designs before continuing with experimental studies in vivo.     

Formation of ovarian follicles during fetal development in sheep

The origin of follicle (i.e., pregranulosa) cells that become the somatic component of primordial follicles is obscure. In addition, information regarding the structural changes that accompany the concomitant regression of ovigerous cords and the appearance of primordial follicles is lacking. In the present study, ovine ovaries collected at frequent time intervals between Day 38 and Day 100 of fetal life were examined by light and electron microscopy. To gain new information regarding the origin of follicular cells, incorporation of 5-bromo-2'-deoxyuridine was used to identify proliferating cells at selected stages of development. Based on the location and identity of proliferating cells, apoptotic cells, and sequential changes in histoarchitecture, we hypothesize 1) that most (i.e., >95%) of the granulosal cells in newly formed primordial follicles originate from the ovarian surface epithelium; 2) that the sequential events leading to follicle formation take place entirely within ovigerous cords, with the first follicles forming at the interface of the cortex and medulla; and 3) that the loss (i.e., >75%) of germ cells, but not of somatic cells, within the ovigerous cords is a means by which each surviving oocyte gains additional pregranulosal cells before follicle formation. Conceptual models detailing the chronology of developmental events involved in the formation of primordial follicles in sheep are discussed.     

Heparin-binding epidermal growth factor and its receptor ErbB4 mediate implantation of the human blastocyst

The mechanisms that mediate implantation of the human embryo remain poorly understood and represent a fundamental problem in reproductive biology. Candidate molecules that mediate and facilitate implantation have been identified in animal studies, and include heparin binding epidermal growth factor. Here we demonstrate a potential function for the transmembrane form of heparin-binding epidermal growth factor in mediating blastocyst attachment to the endometrium, in two different novel in vitro models for human implantation. Furthermore, we demonstrate specific localisation of the heparin-binding epidermal growth factor receptor ErbB4, on the surface of the trophectoderm in peri-implantation human blastocysts. Our data lead the way for further dissection of the molecular mechanisms of implantation of the human embryo, and have implications for infertility, in vitro fertilization and contraception.     

Temporal change in genetic structure and effective population size in steelhead trout (Oncorhynchus mykiss)

There is a wealth of published molecular population genetic studies, however, most do not include historic samples and thus implicitly assume temporal genetic stability. We tested for changes in genetic diversity and structure in three populations of steelhead trout (Oncorhynchus mykiss) from a northern British Columbia watershed using seven microsatellite loci over 40 years. We found little change in genetic diversity (mean allele numbers and observed and expected heterozygosity), despite large variation in the estimated numbers of steelhead returning to the watershed over the same time period. However, the temporal stability in genetic diversity is not reflected in population structure, which appears to be high among populations, yet significantly variable over time. The neighbour-joining tree showed that, overall, two of the populations (Zymoetz and Kispiox) clustered separately from the third (Babine); a finding which was not consistent with their geographical separation. The clustering pattern was also not temporally consistent. We used the temporal method to estimate the effective number of breeders (Nb ) for the three populations; our values (Nb = 17-102) were low for the large and presumed vigorous populations of steelhead trout sampled. The low Nb values were also not consistent with the generally high genetic diversity estimates, suggesting the possibility of intermittent gene flow among the three populations. The use of temporal analyses in population genetic samples should be a priority; first, to verify observed patterns in contemporary data, and second, to build a dataset of temporal analyses to allow generalizations to be made concerning temporal genetic stability and effective population size in natural populations.