Navegando por Palavras-chave "Shannon entropy"

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    Homology, paralogy and function of DGF-1, a highly dispersed Trypanosoma cruzi specific gene family and its implications for information entropy of its encoded proteins
    (Elsevier B.V., 2009-05-01) Kawashita, Silvia Y. [UNIFESP]; Silva, Claudio V. da [UNIFESP]; Mortara, Renato A. [UNIFESP]; Burleigh, Barbara A.; Briones, Marcelo R. S. [UNIFESP]; Universidade Federal de São Paulo (UNIFESP); Harvard Univ; Universidade Federal de Uberlândia (UFU)
    Surface adhesion proteins are essential for Trypanosoma cruzi invasion of mammalian cells. Here we show that Dispersed Gene Family-1 (DGF-1) members, previously identified as nuclear repeated sequences present in several chromosomes and comprising the third largest T cruzi specific gene family, have conserved adhesin motifs including four segments with significant similarity to human beta 7 integrin. How cytometry and biotinylation assays with anti-DGF-1 antibodies indicated that, as expected, DGF-1 members are expressed on the trypomastigote surface. the DGF-1 genealogy, inferred using T cruzi Genome Project data and network phylogeny algorithms, suggests that this gene family is separated in at least three groups with differential distribution of functional domains. To identify which members of this gene family are expressed we used a combined approach of RT-PCR and codon usage profiles, showing that expressed members have a very biased codon usage favoring CC, whereas non-expressed members have a homogeneous distribution. Shannon information entropy was used to measure sequence variability and revealed four major high entropy segments in the extracellular domain of DGF-1 overlapping with important putative functional modules of the predicted proteins. Testing for natural selection, however, indicated that these high entropy segments were not under positive selection, which contradicts the notion that positive selection is the cause of high variability in specific domains of a protein relative to other less variable regions in the same molecule. We conjectured that members of the DGF-1 family might be associated with the ability of T cruzi to bind extracellular matrix proteins, such as fibronectin and laminin, and speculated on mechanisms that would be generating the localized diversity in these molecules in the absence of selection. (C) 2009 Elsevier B.V. All rights reserved.
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    Phylogenetic evidence based on Trypanosoma cruzi nuclear gene sequences and information entropy suggest that inter-strain intragenic recombination is a basic mechanism underlying the allele diversity of hybrid strains
    (Elsevier B.V., 2012-07-01) Ferreira, Renata Carmona [UNIFESP]; Briones, Marcelo Ribeiro da Silva [UNIFESP]; Universidade Federal de São Paulo (UNIFESP)
    The diversity of Trypanosoma cruzi is categorized into six discrete typing units (DTUs) T. cruzi I to VI. Several studies indicate that T. cruzi I and II are ancestors of T. cruzi which are considered products of independent hybridization events. the individual haplotypes or alleles of these hybrids cluster in three groups, either closer to T. cruzi I or T. cruzi II or forming a midpoint clade between T. cruzi I and II in network phylogenies. To understand the origins of these different sets of haplotypes and test the hypothesis of a direct correlation between high entropy and positive selection, we analyzed four nuclear protein coding genes. We show that hybrid strains contain haplotypes that are mosaics probably originated by intragenic recombination. Accordingly, in phylogenies, the hybrid haplotypes are closer to one or both parentals (T. cruzi I and II) depending on the proportion of parental sequences composing the mosaics. in addition, Shannon entropy, used to measure sequence diversity, is highly correlated with positive selection in the four genes here analyzed. Our data on recombination patterns also support the hypothesis of two hybridization events in the hybrid structures of T. cruzi Data presented and discussed here are consistent with a scenario where TcI and TcII are phylogenetically divergent forming a hybrid zone in between (T. cruzi III-VI). We predict that because of the quasi-random nature of T. cruzi I and II hybridization more DTUs, with different haplotype combinations, will be discovered in the hybrid zone. (C) 2012 Elsevier B.V. All rights reserved.