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Rossato D.O.,Federal University of Rio Grande do Sul | Ludwig A.,Instituto Carlos Chagas ICC | Depra M.,Federal University of Rio Grande do Sul | Loreto E.L.S.,Federal University of Rio Grande do Sul | And 3 more authors.
Genome Biology and Evolution | Year: 2014

The hAT superfamily comprises a large and diverse array of DNA transposons found in all supergroups of eukaryotes. Here we characterized the Drosophila buzzatii BuT2 element and found that it harbors a five-exon gene encoding a 643-aa putatively functional transposase. Aphylogeny built with 85hAT transposases yielded, in addition to the two major groups already described, Ac and Buster, a thirdone comprising 20 sequences that includes BuT2, Tip100, hAT-4-BM, and RP-hAT1. This third group is here named Tip. In addition, we studied the phylogenetic distribution and evolution of BuT2 by in silico searches and molecular approaches. Our data revealed BuT2 was, most often, vertically transmitted during the evolution of genus Drosophila being lost independently in several species. Nevertheless, we propose the occurrence of three horizontal transfer events to explain its distribution and conservation amongspecies. Another aspect of BuT2 evolution and life cycle is the presence of short related sequences, which contain similar 50 and 30 regions, including the terminal inverted repeats. These sequences that can be considered asminiature inverted repeat transposable elements probably originated by internal deletion of complete copies and show evidences of recent mobilization. © The Author(s) 2014. Source


Wagner G.,Instituto Oswaldo Cruz IOC | Wagner G.,Campus Universitario | Wagner G.,University of West Santa Catarina | Jardim R.,Instituto Oswaldo Cruz IOC | And 13 more authors.
BMC Research Notes | Year: 2014

Background: The STINGRAY system has been conceived to ease the tasks of integrating, analyzing, annotating and presenting genomic and expression data from Sanger and Next Generation Sequencing (NGS) platforms. Findings. STINGRAY includes: (a) a complete and integrated workflow (more than 20 bioinformatics tools) ranging from functional annotation to phylogeny; (b) a MySQL database schema, suitable for data integration and user access control; and (c) a user-friendly graphical web-based interface that makes the system intuitive, facilitating the tasks of data analysis and annotation. Conclusion: STINGRAY showed to be an easy to use and complete system for analyzing sequencing data. While both Sanger and NGS platforms are supported, the system could be faster using Sanger data, since the large NGS datasets could potentially slow down the MySQL database usage. STINGRAY is available at http://stingray.biowebdb.org and the open source code at. © 2014 Wagner et al.; licensee BioMed Central Ltd. Source


Reignault L.C.,Federal University of Rio de Janeiro | Barrias E.S.,Brazilian National Institute of Technology | Soares Medeiros L.C.,Instituto Carlos Chagas ICC | De Souza W.,Federal University of Rio de Janeiro | And 2 more authors.
Parasitology Research | Year: 2014

Trypanosoma cruzi has a complex life cycle where the infective forms for the vertebrate host are trypomastigotes and amastigotes. Both forms invade and lyse their parasitophorous vacuole (PV) membrane, entering into the cytoplasm of its host cells. Galectin-3 (Gal-3) is a protein abundantly distributed in macrophages and epithelial cells. Previous studies demonstrated that Gal-3 binds to a 45KDa mucin of trypomastigotes surface, enhancing its adhesion to the extracellular matrix and even its entry into cells. Gal-3 has another novel cytoplasmic function recently described: a vacuole lyses marker in intracellular bacteria. Considering (1) the importance of Gal-3 during T. cruzi early infection and (2) the importance of T. cruzi PV lyses for parasite differentiation and replication, this study intended to explore a possible recruitment of structures containing Gal-3 (G3CSs) to T. cruzi PVs. Microscopy analyses showed these G3CSs around PVs after 30 and 90 min of amastigotes and trypomastigotes infection, respectively. This recruitment was specific for T. cruzi PVs since we did not observe the same distribution at macrophages vacuoles containing fluorescent microspheres (FM). Concomitantly, this study intended to analyze the participation of actin cytoskeleton in T. cruzi PV maturation. We observed that actin filaments form a "belt-like" structure around trypomastigotes and amastigotes PVs, also labeled for Gal-3. At the time proposed for PV lysis, we observed an actin disassembling while LAMP-1 was recruited to PVs membrane. However, this pattern was maintained in macrophages derived from Gal-3 knockout mice, revealing that the actin belt structure forms independently from Gal-3. Taken together, these data suggest that G3CSs are recruited to vicinity of T. cruzi PV and that actin filaments localize and remain around T. cruzi PVs until the time of its lysis. © 2014 Springer-Verlag. Source


Serpeloni M.,Federal University of Parana | Serpeloni M.,Instituto Carlos Chagas ICC | Moraes C.B.,Institute Pasteur Korea | MunizJoa J.R.C.,University of Oxford | And 12 more authors.
PLoS ONE | Year: 2011

In eukaryotic cells, different RNA species are exported from the nucleus via specialized pathways. The mRNA export machinery is highly integrated with mRNA processing, and includes a different set of nuclear transport adaptors as well as other mRNA binding proteins, RNA helicases, and NPC-associated proteins. The protozoan parasite Trypanosoma cruzi is the causative agent of Chagas disease, a widespread and neglected human disease which is endemic to Latin America. Gene expression in Trypanosoma has unique characteristics, such as constitutive polycistronic transcription of protein-encoding genes and mRNA processing by trans-splicing. In general, post-transcriptional events are the major points for regulation of gene expression in these parasites. However, the export pathway of mRNA from the nucleus is poorly understood. The present study investigated the function of TcSub2, which is a highly conserved protein ortholog to Sub2/ UAP56, a component of the Transcription/Export (TREX) multiprotein complex connecting transcription with mRNA export in yeast/human. Similar to its orthologs, TcSub2 is a nuclear protein, localized in dispersed foci all over the nuclei -except the fibrillar center of nucleolus- and at the interface between dense and non-dense chromatin areas, proposing the association of TcSub2 with transcription/processing sites. These findings were analyzed further by BrUTP incorporation assays and confirmed that TcSub2 is physically associated with active RNA polymerase II (RNA pol II), but not RNA polymerase I (RNA pol I) or Spliced Leader (SL) transcription, demonstrating participation particularly in nuclear mRNA metabolism in T. cruzi. The double knockout of the TcSub2 gene is lethal in T. cruzi, suggesting it has an essential function. Alternatively, RNA interference assays were performed in Trypanosoma brucei. It allowed demonstrating that besides being an essential protein, its knockdown causes mRNA accumulation in the nucleus and decrease of translation levels, reinforcing that Trypanosoma-Sub2 (Tryp-Sub2) is a component of mRNA transcription/export pathway in trypanosomes. © 2011 Serpeloni et al. Source


Depra M.,Federal University of Rio Grande do Sul | Ludwig A.,Federal University of Rio Grande do Sul | Ludwig A.,Instituto Carlos Chagas ICC | Ludwig A.,Pontifical Catholic University of Parana | And 3 more authors.
Mobile DNA | Year: 2012

Background: Miniature inverted-repeat transposable elements (MITEs) are short, nonautonomous DNA elements flanked by subterminal or terminal inverted repeats (TIRs) with no coding capacity. MITEs were originally recognized as important components of plant genomes, where they can attain extremely high copy numbers, and are also found in several animal genomes, including mosquitoes, fish and humans. So far, few MITEs have been described in Drosophila. Results: Herein we describe the distribution and evolution of Mar, a MITE family of hAT transposons, in Drosophilidae species. In silico searches and PCR screening showed that Mar distribution is restricted to the willistoni subgroup of the Drosophila species, and a phylogenetic analysis of Mar indicates that this element may have originated prior to the diversification of these species. Most of the Mar copies in D. willistoni present conserved target site duplications and TIRs, indicating recent mobilization of these sequences. We also identified relic copies of potentially full-length Mar transposon in D. tropicalis and D. willistoni. The phylogenetic relationship among transposases from the putative full-length Mar and other hAT superfamily elements revealed that Mar is placed into the recently determined Buster group of hAT transposons. Conclusion: On the basis of the obtained data, we can suggest that the origin of these Mar MITEs occurred before the subgroup willistoni speciation, which started about 5.7 Mya. The Mar relic transposase existence indicates that these MITEs originated by internal deletions and suggests that the full-length transposon was recently functional in D. willistoni, promoting Mar MITEs mobilization. © 2012 Deprá et al.; licensee BioMed Central Ltd. Source

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