What can Bioinformatics do for Parasitology Research?
Section snippets
Genome sequencing
Genome projects have been established for seven human parasites: Plasmodium falciparum, Leishmania, African and American Trypanosomes, Toxoplasma, Schistosomes and Filaria. All except Plasmodium and Toxoplasma have come under the umbrella of the World Health Organization's Strategic Committee on Parasite Genome Analysis. The malaria initiative is funded and executed by a consortium of institutions; funding agencies include the NIH, the Wellcome Trust, the Burroughs Wellcome Fund and the US
Dry lab cloning
Genomics is already revolutionizing gene cloning. Protein bands are excised from gels, short amino acid sequences are obtained using mass spectrometry and databases are searched for the corresponding cDNA. Full-length clones can often be assembled from existing random cDNAs, but once the entire genome is known, this approach will render wet lab cloning obsolete.
Intraspecies comparisons
While phenotype–genotype comparisons can be performed in many organisms by selective mating and genetic analysis, this is not possible in many parasites. The only informative genetic crosses so far performed among the commonly studied parasites of humans have been with P. falciparum[4], and this involved passage through mosquitoes and chimpanzees. The sequence information provided by the parasite genome projects will fill this gap and allow differences at the nucleotide level to be compared to
Interspecies comparisons
Comparisons between species have been useful in determining gene function and in identifying homologous genes and biochemical pathways6, 7. Significant success has already been achieved by searching for genes with similar sequences and surmising that similar sequence equates to similar function (frequently, but not invariably, true). Comparisons have also been made at the genome structural level, where syntenic regions in related species, known to house a gene of known function, have been used
Patterns of gene expression
Once the DNA sequence of an organism is known, all genes will be ultimately identifiable. Exon identification, from genomic sequences using computer programs, has already had practical applications, promising the elucidation of expression patterns of any gene11, 12, 13. This will provide a handle on the changes that parasites undergo when they pass from one life stage, or one host, to another, and will define biochemical pathways essential for survival of the organism in the host environment.
From sequence databases to parasite biology
The current emphasis on the generation of genomic structure and sequence information[14]will soon shift to the correlation between genomics and proteomics and the biological significance of this information. A first step has been the creation of protein databases necessary for modelling of molecular interactions. One such example is The Gene Interactions in the Fly DataBase (GIF-DB), which provides data on molecules involved in the pattern formation in Drosophila. In the yeast, the complete
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Cited by (4)
Genomics: From novel genes to new therapeutics in parasitology
2000, International Journal for ParasitologyCell biology of Leishmania
1999, Advances in ParasitologyBioinformatics Applications on Cryptosporidium Research: A Review
2022, Bangladesh Journal of Medical ScienceSelected works of Terry Speed
2012, Selected Works of Terry Speed