Increasing cases of human infections with the high pathogenic avian influenza virus H5N1 have raised great concern on potential human flu pandemics caused by H5N1. The two viral surface glycoproteins, the hemagglutini...Increasing cases of human infections with the high pathogenic avian influenza virus H5N1 have raised great concern on potential human flu pandemics caused by H5N1. The two viral surface glycoproteins, the hemagglutinin (HA) and the neuraminidase (NA) proteins, are major antigens o H5N1. Introducing new mutations on these two pro teins is the major strategy used by H5N1 to expand host range and to avoid the recognition of host im mune systems. We analyzed the two surface proteins of H5N1 from Asian human patients and identified many new mutation sites, including a few that were unique to certain lethal strains. We also analyzed the distribution of mutations on different epitopes of the two surface proteins. A receptor-binding site tha might involve in the determination of host specificity of H5N1 was also found. Results reported here pro vided information for better understanding of the evolution trend of H5N1 genome in human.展开更多
This note reports simulation study on the rate of decay in linkage disequilibrium (LD) in mixed populations over multiple discrete generations and explores the usefulness of the LD analysis in high-resolution gene map...This note reports simulation study on the rate of decay in linkage disequilibrium (LD) in mixed populations over multiple discrete generations and explores the usefulness of the LD analysis in high-resolution gene mapping. The results indicate that the smaller the recombination fraction and the fewer generations since admixture event, the higher power of the approach in gene mapping. The expected estimate of recombination fraction would give an estimate that is slightly biased upwards, if relevant genes are in tight linkage. The estimated recombination fraction is usually larger than the true value within 2-5 generations. From generations 10-20, the mean estimates are in good agreement with the true value. The method presented here enables estimation of means and corresponding confidence intervals of the recombination fraction at any number of generations.展开更多
The rates and patterns of InDel (insertions and deletions) and substitution in rodent (mouse and rat) have been studied. The result reveals that deletions occur more frequently than insertions, and single nucleotide i...The rates and patterns of InDel (insertions and deletions) and substitution in rodent (mouse and rat) have been studied. The result reveals that deletions occur more frequently than insertions, and single nucleotide insertion and deletion are the most frequent in both mouse and rat. The frequencies of both deletions and insertions decrease rapidly with increasing InDels length, and the size distributions of both insertions and deletions can be described well by power-law. There are more AT→GC than GC→ AT substitutions in the introns of rat. However, there are more GC→AT than AT→GC substitutions in the introns in mouse. The deletion bias found in introns in mouse and rat supports the prediction that in- tron insertions are more deleterious than deletions because of reduced transcription and splicing effi- ciency. The patterns of substitution suggest that both composition and GC content are not equilibrium in the introns in rodents.展开更多
文摘Increasing cases of human infections with the high pathogenic avian influenza virus H5N1 have raised great concern on potential human flu pandemics caused by H5N1. The two viral surface glycoproteins, the hemagglutinin (HA) and the neuraminidase (NA) proteins, are major antigens o H5N1. Introducing new mutations on these two pro teins is the major strategy used by H5N1 to expand host range and to avoid the recognition of host im mune systems. We analyzed the two surface proteins of H5N1 from Asian human patients and identified many new mutation sites, including a few that were unique to certain lethal strains. We also analyzed the distribution of mutations on different epitopes of the two surface proteins. A receptor-binding site tha might involve in the determination of host specificity of H5N1 was also found. Results reported here pro vided information for better understanding of the evolution trend of H5N1 genome in human.
基金supported by the National Natural Science Foundation of China (Grant No. 30600384)Outstanding Younger Scholar Foundation of Northwest A & F University
文摘This note reports simulation study on the rate of decay in linkage disequilibrium (LD) in mixed populations over multiple discrete generations and explores the usefulness of the LD analysis in high-resolution gene mapping. The results indicate that the smaller the recombination fraction and the fewer generations since admixture event, the higher power of the approach in gene mapping. The expected estimate of recombination fraction would give an estimate that is slightly biased upwards, if relevant genes are in tight linkage. The estimated recombination fraction is usually larger than the true value within 2-5 generations. From generations 10-20, the mean estimates are in good agreement with the true value. The method presented here enables estimation of means and corresponding confidence intervals of the recombination fraction at any number of generations.
文摘The rates and patterns of InDel (insertions and deletions) and substitution in rodent (mouse and rat) have been studied. The result reveals that deletions occur more frequently than insertions, and single nucleotide insertion and deletion are the most frequent in both mouse and rat. The frequencies of both deletions and insertions decrease rapidly with increasing InDels length, and the size distributions of both insertions and deletions can be described well by power-law. There are more AT→GC than GC→ AT substitutions in the introns of rat. However, there are more GC→AT than AT→GC substitutions in the introns in mouse. The deletion bias found in introns in mouse and rat supports the prediction that in- tron insertions are more deleterious than deletions because of reduced transcription and splicing effi- ciency. The patterns of substitution suggest that both composition and GC content are not equilibrium in the introns in rodents.
