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Biomedical subjects

Austin L Hughes

Publications and source records attributed to Austin L Hughes.

At least 19 recordsLinked to original sources
PubMed2007

A gene family of putative immune recognition molecules in the hydroid Hydractinia.

Animal taxa display a wide array of immune-type receptors that differ in their specificities, diversity, and mode of evolution. These molecules ensure effective recognition of potential pathogens for subsequent neutralization and clearance. We have characterized a family of putative immune recognition molecules in the colonial hydroid Hydractinia symbiolongicarpus. A complementary DNA fragment with high similarity to the sea urchin L: -rhamnose-binding lectin was isolated and used to screen 9.5 genome equivalents of a H. symbiolongicarpus bacterial artificial chromosome library. One of the resulting 19 positive clones was sequenced and revealed the presence of a 5,111-bp gene organized in 13 exons and 12 introns. The gene was predicted to encode a 726-amino acid secreted modular protein composed of a signal peptide, an anonymous serine-rich domain, eight thrombospondin type 1 repeats, and a L: -rhamnose-binding lectin domain. The molecule was thus termed Rhamnospondin (Rsp). Southern hybridization and sequence analyses indicated the presence of a second Rsp gene. The cDNA from both Rsp genes was sequenced in 18 individuals, revealing high levels of genetic polymorphism. Nucleotide substitutions were distributed throughout the molecule and showed a significantly higher number of synonymous substitutions per synonymous sites than its nonsynonymous counterparts. Whole-mount in situ hybridization and semi-quantitative reverse transcription polymerase chain reaction of microorganism-challenged colonies indicated that Rsp molecules were specifically and constitutively expressed in the hypostome of gastrozooids' mouth. Thus, the combination of (1) comparative analysis on domain composition and function, (2) polymorphism, and (3) expression patterns, suggest that Rsp genes encode a family of putative immune recognition receptors, which may act by binding microorganisms invading the colony through the polyp's mouth.

Amino Acid Sequence↗
PubMed2006

Evolution of cytotoxic T-lymphocyte epitopes in hepatitis B virus.

In hepatitis B virus (HBV), while mutations that escape from cytotoxic T-lymphocyte (CTL) recognition have been described it has been difficult to determine how natural selection by host CTL has influenced long-term evolution of HBV. We used statistical analysis of published HBV genomic sequences to examine the role of natural selection in evolution of CTL epitopes. Based on a phylogenetic analysis, we identified 25 pairs of closely related genomes isolated from different HBV genotypes and examined pattern of nucleotide substitution in genomic regions encoding well-characterized CTL epitopes. On average, both epitope and non-epitope regions are subject to purifying selection acting at non-synonymous sites. However, certain CTL epitopes showed a pattern of nucleotide substitution suggesting repeated positive selection across the population. The results support the hypothesis that CTL-driven selection has been an important factor in long-term evolution of HBV.

Antigens, Viral↗
PubMed2006

Evolutionary relationships of vertebrate NACHT domain-containing proteins.

Phylogenetic analyses of conserved [neuronal apoptosis inhibitory protein (NAIP), MHC class II transcription activator (CIITA), incompatibility locus protein from Podospora anserina (HET-E), and telomerase-associated protein (TP1)] (NACHT) domains were used to reconstruct the evolutionary history of vertebrate NACHT-containing proteins. The results supported the hypothesis that NOD3 is basal to the other NACHT-containing proteins found in tetrapods. The latter formed two strongly supported clusters or subfamilies, here designated NALP and nucleotide-binding oligomerization domain (NOD). The presence of apparent bony fish orthologs of NOD3 and CIITA supported the hypothesis that the origin of these molecules predates the origin of tetrapods, and the presence of avian sequences in both NALP and NOD clusters supported the origin of these subfamilies before the bird-mammal divergence. However, the extensive diversification of the NALP subfamily seen in mammals evidently occurred within the mammalian lineage. Both NALP and NOD subfamilies include members with differential expression in the antigen-presenting cells of the immune system, and the phylogenetic analyses supported the hypothesis that this expression pattern has evolved independently more than once in each of these subfamilies.

Adaptor Proteins, Signal Transducing↗
PubMed2006

Nucleotide usage, synonymous substitution pattern, and past recombination in genomes of Streptococcus pyogenes.

We examined (1) five variables summarizing nucleotide usage at synonymous sites; (2) pairwise patterns of nucleotide substitution among five genomes of Streptococcus pyogenes in order to examine the extent to which these variables are associated with past recombination events. Predicted prophage genes of MGAS10394 were characterized by an average pattern of nucleotide usage at synonymous sites that was distinct from that seen at most other genes. Ribosomal protein genes also showed a distinctive pattern, but one that differed from prophage genes in several key respects. The six most anomalous genes with respect to synonymous substitution in pairwise comparisons among the genomes included four prophage genes; these six genes were characterized by unusually high values of d(S), suggesting that these genes had different evolutionary histories from those of the other shared genes in the genome. This hypothesis was supported by phylogenetic analyses, which revealed phylogenies inconsistent with that of the majority of genes. Eighty-nine genes outside prophage regions were found to resemble prophage genes with respect to nucleotide content and the pattern of synonymous substitution, suggesting that these genes may have been involved in horizontal gene transfers. Although prophage genes do show distinctive patterns of nucleotide composition, the results indicated that those patterns were not in themselves sufficient to distinguish all known prophage genes from other genes. On the other hand, nucleotide content, when suitably measured, can form one of a set of biological indicators that can be used to identify candidate genes for horizontal gene transfer.

Amino Acid Substitution↗
PubMed2006

Variable intensity of purifying selection on cytotoxic T-lymphocyte epitopes in hepatitis C virus.

In an analysis of the patterns of nucleotide diversity in 26 datasets providing population-level data on different genomic regions of different hepatitis C virus (HCV) subtypes, known cytotoxic T-lymphocyte (CTL) epitope regions in most cases showed evidence of the occurrence of purifying selection. Two main factors were found to be associated with the strength of purifying selection: (1) purifying selection was stronger in CTL epitopes in non-envelope proteins than in envelope proteins and (2) purifying selection was stronger when the epitope was "matched", i.e., when the described or "canonical" epitope sequence was present unaltered in at least one sequence in the dataset. Of all polymorphic sites, non-synonymous sites in matched CTL epitopes in non-envelope proteins had the lowest gene diversities, implying that these variants are subject to ongoing purifying selection. This in turn suggests that the population frequency of such variants may of be the result of a balance between opposing forces: on the one hand, positive selection favoring escape mutants in hosts that express the presenting MHC molecule and, on the other hand, purifying selection acting, in the absence of the presenting MHC molecule, to reduce the frequency of slightly deleterious variants.

Epitopes, T-Lymphocyte↗
PubMed2006

Homologous recombination and the pattern of nucleotide substitution in Ehrlichia ruminantium.

Patterns of nucleotide substitution at orthologous loci were examined between three genomes of Ehrlichia ruminantium, the causative agent of heartwater disease of ruminants. The most recent common ancestor of two genomes (Erwe and Erwo) belonging to the Welgevonden strain was estimated to have occurred 26,500-57,000 years ago, while the most recent common ancestor of these two genomes and the Erga genome (Gardel strain) was estimated to have occurred 2.1-4.7 million years ago. The search for genes showing extremely high values of the number of synonymous substitutions per site was used to identify genes involved in past homologous recombination. The most striking case involved the map1 gene, encoding major antigenic protein-1; evidence for homologous recombination is consistent with previous phylogenetic analysis of map1 alleles. At this and certain other loci, homologous recombination may have contributed to the evolution of host-pathogen interactions. In addition, comparison of the patterns of synonymous and nonsynonymous substitution provided evidence for positive selection favoring a high level of amino acid change between the Welgevonden and Gardel strains at a locus of unknown function (designated Erum4340 in the Erwo genome).

Computational Biology↗
PubMed2006

Sharing of transcription factors after gene duplication in the yeast Saccharomyces cerevisiae.

In a set of 190 duplicate gene pairs in yeast Saccharomyces cerevisiae, the sharing of transcription factors tended to decrease with increased divergence in coding sequence, at both synonymous and nonsynonymous sites. Our results showed a significantly higher sharing of transcription factors by duplicated gene pairs falling within duplicated genomic blocks than in other duplicated gene pairs; and genes in duplicated blocks also showed significantly greater conservation at the coding sequence level. In spite of the overall trends, there were certain gene pairs, both in duplicated blocks and in other genomic regions, which were highly divergent in coding sequence and yet had identical patterns of transcription factor binding. These results suggest that functional differentiation of genes after duplication is a multi-dimensional process, with different duplicate pairs differentiating in different ways.

Base Sequence↗
PubMed2006

Likelihood-ratio tests for positive selection of human and mouse duplicate genes reveal nonconservative and anomalous properties of widely used methods.

Two commonly used methods based on likelihood-ratio tests (LRTs) for detecting positive Darwinian selection at the molecular level were applied to a data set of 604 gene families containing two members in the human genome and two members in the mouse genome. These methods detected positive selection in a very high proportion of families; in over 50% of families, there was significant evidence of positive selection by one or both methods. However, less than a third of families showing evidence for positive selection by at least one of the methods showed evidence of positive selection by both methods. The outcome of these tests was predicted better by sequence length, G+C content at third-codon positions, and the level of synonymous substitution than by the level of nonsynonymous substitution or the ratio of nonsynonymous to synonymous substitution. These results suggested that LRT-based tests for positive selection may be sensitive to certain factors that make it difficult to reconstruct the true pattern of nucleotide substitution.

Animals↗
PubMed2006

Nucleotide substitution at the highly polymorphic K1 locus of human herpesvirus 8 (Kaposi's sarcoma-associated herpesvirus).

The K1 locus is a highly polymorphic locus in the genome of human herpesvirus 8, the causative agent of Kaposi's sarcoma. Analysis of the pattern of nucleotide substitution among alleles at this locus supported the hypothesis that natural selection has acted to enhance amino acid diversity in the two hypervariable regions (VR1 and VR2) of the extracellular portion of the K1 protein. A phylogenetic analysis of 125 complete K1 sequences revealed two major clades, designated A/C and B. There was strong evidence against recombination between VR1 and VR2 among alleles belonging to different clades, and little support for frequent recombination within clades. The pattern of diversification of VR1 and VR2 within clades was similar to that between clades, but the immunoreceptor tyrosine-based activation motif (ITAM)-like sequence in the cytoplasmic region of K1 showed strong divergence between clades despite conservation within clades. The latter finding suggests that, while being subject to similar selection favoring diversity in the extracellular region, the two major clades of K1 alleles may be adapted for different types of interaction with host intracellular signal transduction mechanisms.

Amino Acid Substitution↗
PubMed2006

Rapid evolution of the trophoblast kunitz domain proteins (TKDPs)-a multigene family in ruminant ungulates.

The trophoblast Kunitz domain proteins (TKDPs) are products of the outer cells (trophoblasts) of the placenta of cattle, sheep, and related species. Most are expressed abundantly for only a few days during the time at which the ruminant conceptus is first establishing intimate contacts with the uterine lining. The TKDPs are secretory proteins that possess a carboxyl-terminal peptidase inhibitory domain related to the Kunitz family of serine peptidase inhibitors. On the amino-terminal end are one or more highly unusual regions that are unique to the TKDP genes and have no apparent similarity to any other known sequences. The TKDPs are a rather divergent family that exhibits a good deal of variation among the members. To better understand the reason for such variation, the rates of synonymous (dS) and nonsynonymous (dN), as well as radical (pNR) and conservative (pNC), substitutions were assessed. Phylogenetic trees revealed that the Kunitz domains represented three related groups, whereas the amino-terminal domains formed four groupings. Pairwise comparisons between Kunitz and amino-terminal domain groups demonstrated that dN was consistently greater than dS. In addition, nonsynonymous substitutions in the Kunitz domains tended to be radical (changing charge or polarity), while those in the amino-terminal domains exhibited neither a preponderance of conservative nor radical substitution rates. In summary, the rapid evolution of the TKDPs, coupled with their restricted temporal expression during development, likely reflects the establishment of protein-protein interactions that have evolved to serve the unusual synepitheliochorial placenta of ruminant ungulates.

Amino Acid Sequence↗
PubMed2006

Across-tissue expression and evolution of genes controlled by the Aire transcription factor.

Aire (autoimmune regulatory protein) enhances expression of certain genes in thymic medullary epithelial cells (MECs). Using publicly available data, we examined expression patterns, across 82 distinct tissue types, of genes previously identified as Aire-activated, Aire-repressed, and Aire-independent. Consistent with the hypothesis that the effect of Aire in MECs is to increase expression of tissue-specific genes, Aire-activated genes had a low overall level of expression but a large range between the lowest and the highest levels of expression in different tissues. By contrast, Aire-repressed genes tended to have a high overall level of expression and less marked differences between the highest and the lowest levels of expression. Nonetheless, the expression scores of Aire-repressed genes showed broader ranges of values than those of Aire-independent genes. Phylogenetic analyses of members of two gene families that included two Aire-activated genes illustrated two contrasting patterns of the relationship of Aire-activated genes within the same family. The two Aire-activated members of the major urinary protein family arose through a recent gene duplication (after the rat-mouse divergence), whereas the most recent common ancestor of the two Aire-activated members of cytochrome p450 family 2 duplicated prior to the radiation of the eutherian orders. In the latter family, the Aire-activated Cyp2a4 gene and the Aire-independent Cyp2a5 gene arose through a recent duplication, after the rat-mouse divergence. Thus the set of Aire-activated genes is subject to change over evolutionary time and includes genes of recent origin.

Animals↗
PubMed2006

Pattern of gene duplication in the Cotesia congregata Bracovirus.

Polydnaviruses (PDVs) are a family of double-stranded DNA viruses genetically linked to their wasp hosts. These viruses utilize the transcriptional machinery of the wasp cells to manufacture viral particles which contain circular segments of DNA. The female wasp, hosting the polydnavirus, lays its eggs along with the viral particles inside a caterpillar. Because no replication of the virus occurs while inside the caterpillar, fixed genetic changes occur solely inside the female wasp, as an integrated portion of its genome. Therefore, evolution of the polydnavirus is expected to parallel that of the wasp. Phylogenetic analysis of the polydnavirus genome showed a pattern of gene duplication consistent with the "birth-and-death" process frequently observed in eukaryotic genomes. Phylogenies provided no unequivocal evidence of horizontal gene transfer between the wasp host and the polydnavirus, but in some cases there were suggestions of such gene transfer.

Animals↗
PubMed2006

Contrasting patterns of transcript abundance in tumour tissue and cancer cell lines.

Comparison of data on transcript abundance in ovarian, prostate and colon tumours with the corresponding cancer cell lines was used to assess the similarities of expression profiles. Although transcript abundances in tumours and cell lines were positively correlated, there were substantial differences with respect to the overall expression pattern. Compared with tumours, cancer cell lines showed more variable patterns of transcript abundance among tissue types. In the ovary and colon, cancer cell lines showed greater overall transcript abundance than normal tissue; this increase was much more marked in the case of the colon. However, in the prostate, cancer cell lines showed overall reduced transcript abundance when compared with normal tissue. Principal component analyses, applied separately to each tissue type, showed that approximately 80% of the variance was explained by overall expression level differences, which were maintained across normal tissue, tumour tissue and cancer cell lines. The remaining variance ( approximately 20%) could be attributed to contrasts in expression pattern among normal tissue, tumour tissue and cancer cell lines. In each dataset and in a combined dataset of transcripts shared among the three datasets, principal components revealed both contrasts in expression pattern between tumour tissue and cancer cell lines, and common features in the expression pattern of cancer cell lines that were distinct from those of tumour tissue and were shared across the different tissue types. These results imply that data on gene expression in cancer cell lines should be used with caution in inferring gene expression of in vivo tumours.

Biomarkers, Tumor↗
PubMed2005

Consistent across-tissue signatures of differential gene expression in Crohn's disease.

An approach based on analysis of variance was applied to raw expression data on 44,760 transcripts in order to identify those with significant differential expression across ileum and colon in Crohn's disease (CD) and ulcerative colitis (UC). The design treated tissue as a block effect, thereby removing this effect statistically and increasing the power to test for effects of disease states (control, CD, and UC). A significant F-statistic for the disease effect was not correlated with the ratios CD/control or UC/control, evidently because many transcripts with high-expression ratios to the control showed inconsistent patterns across tissues. Of 1,053 transcripts showing a significant effect of disease state at the 1% level by the bootstrap test, 508 showed significant difference at the 1% level in a post hoc test for difference between the mean scores for CD and control. These included a number of genes relevant to the mechanism of pathogenesis of CD and a number of genes mapping to genomic regions that have previously shown linkage to CD in association studies.

Analysis of Variance↗
PubMed2005

Gene duplication and the properties of biological networks.

Patterns of network connection of members of multigene families were examined for two biological networks: a genetic network from the yeast Saccharomyces cerevisiae and a protein-protein interaction network from Caenorhabditis elegans. In both networks, genes belonging to gene families represented by a single member in the genome ("singletons") were disproportionately represented among the nodes having large numbers of connections. Of 68 single-member yeast families with 25 or more network connections, 28 (44.4%) were located in duplicated genomic segments believed to have originated from an ancient polyploidization event; thus, each of these 28 loci was thus presumably duplicated along with the genomic segment to which it belongs, but one of the two duplicates has subsequently been deleted. Nodes connected to major "hubs" with a large number of connections, tended to be relatively sparsely interconnected among themselves. Furthermore, duplicated genes, even those arising from recent duplication, rarely shared many network connections, suggesting that network connections are remarkably labile over evolutionary time. These factors serve to explain well-known general properties of biological networks, including their scale-free and modular nature.

Animals↗
PubMed2005

Within-host evolution of CD8+-TL epitopes encoded by overlapping and non-overlapping reading frames of simian immunodeficiency virus.

In order to understand the impact of overlapping reading frames on natural selection by host CD8+ T lymphocytes (CD8(+)-TL), we analyzed the pattern of nucleotide substitution in simian immunodeficiency virus (SIV) genomes sampled from populations at time of death in 35 rhesus monkeys. Both the mean number of nonsynonymous nucleotide substitutions per nonsynonymous site (d(N)) and the mean number of synonymous nucleotide substitutions per synonymous site (d(S)) were elevated in overlap regions in comparison to non-overlap regions. Mean d(N) exceeded mean d(S) in CD8(+)-TL epitopes restricted by the host's class I major histocompatibility complex molecules. This pattern, which is indicative of positive Darwinian selection favoring amino acid changes in these epitopes, was seen in both overlap and non-overlap regions; but mean d(N) was particularly elevated in restricted CD8(+)-TL epitopes encoded in overlap regions. Amino acid changes from the inoculum were defined as parallel if the same amino acid change occurred at the same site independently in two or more monkeys, and a surprisingly high proportion (71.9%) of observed amino acid changes throughout the SIV genome occurred in parallel in different monkeys. The proportion of parallel changes in restricted epitopes encoded by overlapping reading frames was still higher (80%), supporting the hypothesis that the interaction of positive selection and overlapping reading frames enhances the probability of convergent or parallel amino acid change.

Animals↗
PubMed2005

High level of functional polymorphism indicates a unique role of natural selection at human immune system loci.

Several studies have shown that immune system proteins have on average a higher rate of amino acid evolution between different species of mammals than do most other proteins. To test whether immune-system-expressed loci show a correspondingly elevated rate of within-species nonsynonymous (amino acid altering) polymorphism, we examined gene diversity (heterozygosity) at 4,911 single nucleotide polymorphism (SNP) sites at 481 protein-coding loci. At loci with nonimmune functions, gene diversity at nonsynonymous SNP sites was typically lower than that at silent SNP sites (those not altering the amino acid sequence) in the same gene, a pattern that is an evidence of purifying selection acting to eliminate slightly deleterious variants. However, this pattern was not seen at nonsynonymous SNPs causing conservative amino acid replacements in immune system proteins, indicating that the latter are subject to a reduced level of functional constraint. Similarly, immune system genes showed higher gene diversities in their 5' noncoding regions than did other proteins. These results identified certain immune system loci that are likely to be subject to balancing selection that acts to maintain polymorphism in either coding or regulatory regions.

Chromosomes, Human↗