Comparative modeling of proteins: a method for engaging students' interest in bioinformatics tools.

The huge increase in data being produced in the genomic era has produced a need to incorporate computers into the research process. Sequence generation, its subsequent storage, interpretation, and analysis are now entirely computer-dependent tasks. Universities from all over the world have been challenged to seek a way of encouraging students to incorporate computational and bioinformatics skills since undergraduation in order to understand biological processes. The aim of this article is to report the experience of awakening students' interest in bioinformatics tools during a course focused on comparative modeling of proteins. The authors start by giving a full description of the course environmental context and students' backgrounds. Then they detail each class and present a general overview of the protein modeling protocol. The positive and negative aspects of the course are also reported, and some of the results generated in class and in projects outside the classroom are discussed. In the last section of the article, general perspectives about the course from students' point of view are given. This work can serve as a guide for professors who teach subjects for which bioinformatics tools are useful and for universities that plan to incorporate bioinformatics into the curriculum.

Evidence of substantial recombination among Trypanosoma cruzi II strains from Minas Gerais.

Due to the scarcity of evidence of sexuality in Trypanosoma cruzi, the causative agent of Chagas disease, it has been general accepted that the parasite reproduction is essentially clonal with infrequent genetic recombination. This assumption is mainly supported by indirect evidence, such as Hardy-Weinberg imbalances, linkage disequilibrium and a strong correlation between independent sets of genetic markers of T. cruzi populations. However, because the analyzed populations are usually isolated from different geographic regions, the possibility of population substructuring as generating these genetic marker imbalances cannot be eliminated. To investigate this possibility, we firstly compared the allele frequencies and haplotype networks using seven different polymorphic loci (two from mitochondrial and five from different nuclear chromosomes) in two groups of TcII strains: one including isolates obtained from different regions in Latin America and the other including isolates obtained only from patients of the Minas Gerais State in Brazil. Our hypothesis was that if the population structure is essentially clonal, Hardy-Weinberg disequilibrium and a sharp association between the clusters generated by analyzing independent markers should be observed in both strain groups, independent of the geographic origin of the samples. The results demonstrated that the number of microsatellite loci in linkage disequilibrium decreased from 4 to 1 when only strains from Minas Gerais were analyzed. Moreover, we did not observed any correlation between the clusters when analyzing the nuclear and mitochondrial loci, suggesting independent inheritance of these markers among the Minas Gerais strains. Besides, using a second subset of five physically linked microsatellite loci and the Minas Gerais strains, we could also demonstrate evidence of homologous recombination roughly proportional to the relative distance among them. Taken together, our results do not support a clonal population structure for T. cruzi, particularly in TcII, which coexists in the same geographical area, suggesting that genetic exchanges among these strains may occur more frequently than initially expected.