Priti Hegde

The African trypanosome genome

The haploid nuclear genome of the African trypanosome, Trypanosoma brucei, is about 35 Mb and varies in size among different trypanosome isolates by as much as 25%. The nuclear DNA of this diploid organism is distributed among three size classes of chromosomes: the megabase chromosomes of which there are at least 11 pairs ranging from 1 Mb to more than 6 Mb (numbered I-XI from smallest to largest); several intermediate chromosomes of 200-900 kb and uncertain ploidy; and about 100 linear minichromosomes of 50-150 kb. Size differences of as much as four-fold can occur, both between the two homologues of a megabase chromosome pair in a specific trypanosome isolate and among chromosome pairs in different isolates. The genomic DNA sequences determined to date indicated that about 50% of the genome is coding sequence. The chromosomal telomeres possess TTAGGG repeats and many, if not all, of the telomeres of the megabase and intermediate chromosomes are linked to expression sites for genes encoding variant surface glycoproteins (VSGs). The minichromosomes serve as repositories for VSG genes since some but not all of their telomeres are linked to unexpressed VSG genes. A gene discovery program, based on sequencing the ends of cloned genomic DNA fragments, has generated more than 20 Mb of discontinuous single-pass genomic sequence data during the past year, and the complete sequences of chromosomes I and II (about 1 Mb each) in T. brucei GUTat 10.1 are currently being determined. It is anticipated that the entire genomic sequence of this organism will be known in a few years. Analysis of a test microarray of 400 cDNAs and small random genomic DNA fragments probed with RNAs from two developmental stages of T. brucei demonstrates that the microarray technology can be used to identify batteries of genes differentially expressed during the various life cycle stages of this parasite.

Identification of genes involved in colon cancer metastasis using cDNA microarrays

50 population is required. To examine the ability of GMS to map genetic traits on a genome-wide scale, we performed selections for regions of IBD between multiple parent/segregant pairs of Saccharomyces cerevisiae to define candidate regions for loci of single and multigenic traits. DNA recovered from GMS of reciprocal parent/segregant pairs was amplified, differentially labelled with fluorescent probes and hybridised to microarrays containing all known yeast open reading frames. The degree of selection for regions of IBD was sufficient to allow determination of the parental genotype for approximately 85% of all open reading frames within the genome of each segregant based on a threshold ratio of 1.25. Our study results demonstrated that GMS was able to identify correct regions of the genome for all single gene traits examined. We were also able to identify two candidate regions for a multigenic trait predicted to result from the inheritance of two alleles.