Biomedical subjects

Melissa Da Silva

Publications and source records attributed to Melissa Da Silva.

4 recordsLinked to original sources

PubMed2006

Predicted function of the vaccinia virus G5R protein.

MOTIVATION: Of the approximately 200 proteins that have been identified for the vaccinia virus (VACV) genome, many are currently listed as having an unknown function, and seven of these are also found in all other poxvirus genomes that have been sequenced. The G5R protein of VACV is included in this list, and to date, very little is known about this essential and highly conserved protein. Conventional similarity searches of protein databases do not identify significantly similar proteins, and experimental approaches have been unsuccessful at determining protein function. RESULTS: Using HHsearch, a hidden Markov model (HMM) comparison search tool, the G5R protein was found to be similar to both human and archaeal flap endonucleases (FEN-1) with 96% probability. The G5R protein structure was subsequently successfully modeled using the Robetta protein structure prediction server with an archaeal FEN-1 as the template. The G5R model was then compared to the human FEN-1 crystal structure and was found to be structurally similar to human FEN-1 in both active site residues and DNA substrate binding regions.

Amino Acid Sequence↗

PubMed2005

Host-derived pathogenicity islands in poxviruses.

BACKGROUND: Poxviruses are important both as pathogens and as vaccine vectors. Poxvirus genomes (150-350 kb) consist of a single linear dsDNA molecule; the two polynucleotide strands are joined by short hairpin loops. The genomes encode highly conserved proteins required for DNA replication and mRNA transcription as well as a variable set of virulence factors; transcription takes place within the cytoplasm of the host cell. We are interested in evolution of poxvirus genomes and especially how these viruses acquire host-derived genes that are believed to function as virulence factors. RESULTS: Using a variety of bioinformatics tools, we have identified regions in poxvirus genomes that have unusual nucleotide composition (higher or lower than average A+T content) compared to the genome as a whole; such regions may be several kilobases in length and contain a number of genes. Regions with unusual nucleotide composition may represent genes that have been recently acquired from the host genome. The study of these genomic regions with unusual nucleotide content will help elucidate evolutionary processes in poxviruses. CONCLUSION: We have found that dotplots of complete poxvirus genomes can be used to locate regions on the genome that differ significantly in A+T content to the genome as a whole. The genes in these regions may have been acquired relatively recently from the host genome or from another AT-rich poxvirus.

Amino Acid Sequence↗

PubMed2005

Using purine skews to predict genes in AT-rich poxviruses.

BACKGROUND: Clusters or runs of purines on the mRNA synonymous strand have been found in many different organisms including orthopoxviruses. The purine bias that is exhibited by these clusters can be observed using a purine skew and in the case of poxviruses, these skews can be used to help determine the coding strand of a particular segment of the genome. Combined with previous findings that minor ORFs have lower than average aspartate and glutamate composition and higher than average serine composition, purine content can be used to predict the likelihood of a poxvirus ORF being a "real gene". RESULTS: Using purine skews and a "quality" measure designed to incorporate previous findings about minor ORFs, we have found that in our training case (vaccinia virus strain Copenhagen), 59 of 65 minor (small and unlikely to be a real genes) ORFs were correctly classified as being minor. Of the 201 major (large and likely to be real genes) vaccinia ORFs, 192 were correctly classified as being major. Performing a similar analysis with the entomopoxvirus amsacta moorei (AMEV), it was found that 4 major ORFs were incorrectly classified as minor and 9 minor ORFs were incorrectly classified as major. The purine abundance observed for major ORFs in vaccinia virus was found to stem primarily from the first codon position with both the second and third codon positions containing roughly equal amounts of purines and pyrimidines. CONCLUSION: Purine skews and a "quality" measure can be used to predict functional ORFs and purine skews in particular can be used to determine which of two overlapping ORFs is most likely to be the real gene if neither of the two ORFs has orthologs in other poxviruses.

Aspartic Acid↗

PubMed2005

New bioinformatics tools for viral genome analyses at Viral Bioinformatics--Canada.

Viruses are much smaller than prokaryotes and eukaryotes, and it is now practical to sequence closely related members of virus families, strains, or even different isolates recovered during the course of an outbreak. However, comparative analysis of viral genomes requires the development of novel bioinformatics tools that allow us to align, edit, compare and interact with these genomes at all levels, from whole genome, to gene family, to single nucleotide polymorphisms. Comparative viral genomics can lead to the identification of the core characteristics that define a virus family, as well as the unique properties of viral species or isolates that contribute to variations in pathogenesis. This paper describes a number of tools, mainly developed for Viral Bioinformatics--Canada, that can be used for annotation and comparative genomic analysis of poxviruses. Nonetheless, these tools are also broadly applicable to other virus families.

Base Sequence↗