Review
doi: 10.1186/1479-7364-3-4-320.Human genomic diversity, viral genomics and proteomics, as exemplified by human papillomaviruses and H5N1 influenza viruses
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- PMID:19706363
- PMCID: PMC3525194
- DOI: 10.1186/1479-7364-3-4-320
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Review
Human genomic diversity, viral genomics and proteomics, as exemplified by human papillomaviruses and H5N1 influenza viruses
Meena K Sakharkar et al. Hum Genomics.2009 Jul.
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Abstract
The diversity of hosts, pathogens and host-pathogen relationships reflects the influence of selective pressures that fuel diversity through ongoing interactions with other rapidly evolving molecules in the environment. This paper discusses specific examples illustrating the phenomenon of diversity of hosts and pathogens, with special reference to human papillomaviruses and H5N1 influenza viruses. We also review the influence of diverse host-pathogen interactions that determine the pathophysiology of infections, and their responses to drugs or vaccines.
Figures
Examples of SNP genotypes and disease susceptibility. (a,b) The mutant G75D in RBP4 introduces a negative charge into the cavity, thereby interfering with retinol binding both electrostatically and sterically. The result is vitamin A deficiency, with a phenotype of night blindness. Panels a and b show the normal and mutant forms of RBP4 protein. (c,d) An example of a polymorphic variant that disrupts a critical disulphide bond is C260Y in HLA-H, culminating in hereditary haemochromatosis. Panels c and d show the normal and mutant forms of HLA-H protein.
Protein disorder probability based on the results of POODLE prediction. The table illustrates Tukey's multiple test for comparing low-risk and high-risk HPVs. One-way ANOVA reveals the differences in disorder scores for the HPV proteins.
Phylogenetic tree constructed for a total of 272 HA sequences of H5N1 virus strains. The HA sequences were downloaded from the NCBI Influenza Resource database.
(a) The 272 HA proteins of H5NI under investigation were optimally aligned both manually and using ClustalW and the frequency of polymorphisms for each residue was calculated. The amino acid number was plotted against the frequency of polymorphisms of the HA proteins. 312 residues exhibit at least one polymorphism, while three residues display seven polymorphisms.
(b) Mutation mapping on the HA protein structure. The frequency of polymorphism is depicted in colour.
MHC-peptide combinatorics is influenced by physical, chemical and genetic properties of the peptide and the corresponding MHC.
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