Comparing de novo and reference-based transcriptome assembly strategies by applying them to the blood-sucking bug Rhodnius prolixus

High Throughput Sequencing capabilities have made the process of assembling a transcriptome easier, whether or not there is a reference genome. But the quality of a transcriptome assembly must be good enough to capture the most comprehensive catalog of transcripts and their variations, and to carry out further experiments on transcriptomics. There is currently no consensus on which of the many sequencing technologies and assembly tools are the most effective. Many non-model organisms lack a reference genome to guide the transcriptome assembly. One question, therefore, is whether or not a reference-based genome assembly gives better results than de novo assembly. The blood-sucking insect Rhodnius prolixus-a vector for Chagas disease-has a reference genome. It is therefore a good model on which to compare reference-based and de novo transcriptome assemblies. In this study, we compared de novo and reference-based genome assembly strategies using three datasets (454, Illumina, 454 combined with Illumina) and various assembly software. We developed criteria to compare the resulting assemblies: the size distribution and number of transcripts, the proportion of potentially chimeric transcripts, how complete the assembly was (completeness evaluated both through CEGMA software and R. prolixus proteome fraction retrieved). Moreover, we looked for the presence of two chemosensory gene families (Odorant-Binding Proteins and Chemosensory Proteins) to validate the assembly quality. The reference-based assemblies after genome annotation were clearly better than those generated using de novo strategies alone. Reference-based strategies revealed new transcripts, including new isoforms unpredicted by automatic genome annotation. However, a combination of both de novo and reference-based strategies gave the best result, and allowed us to assemble fragmented transcripts.

Molecular identification of food sources in triatomines in the Brazilian northeast: roles of goats and rodents in Chagas disease epidemiology

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

The basement membrane and the sex establishment in the juvenile hermaphroditism during gonadal differentiation of the Gymnocorymbus ternetzi (Teleostei: Characiformes: Characidae)

Although there are several studies on morphogenesis in Teleostei, until now there is no research describing the role of the basement membrane in the establishment of the germinal epithelium during gonadal differentiation in Characiformes. In attempt to study these events that result in the formation of ovarian and testicular structures, gonads of Gymnocorymbus ternetzi were prepared for light microscopy. During gonadal development in G. ternetzi, all individuals first developed ovarian tissue. The undifferentiated gonad was formed by somatic cells (SC) and primordial germ cells (PGCs). After successive mitosis, the PGCs became oogonia, which entered into meiosis originating oocytes. An interstitial tissue developed. In half of the individuals, presumptive female, prefollicle cells synthesized a basement membrane around oocyte forming a follicle. Along the ventral region of the ovary, the tissue invaginated to form the ovigerous lamellae, bordered by the germinal epithelium. Stroma developed and the follicle complexes were formed. The gonadal aromatase was detected in interstitial cells in the early steps of the gonadal differentiation in both sexes. In another half of the individuals, presumptive male, there was no synthesis of basement membrane. The interstitium was invaded by numerous granulocytes. Pre-Leydig cells proliferated. Apoptotic oocytes were observed and afterward degenerated. Spermatogonia appeared near the degenerating oocytes and associated to SCs, forming testicular tubules. Germinal epithelium developed and the basement membrane was synthesized. Concomitantly, there was decrease of the gonadal aromatase and increase in the 3β-HSD enzyme expression. Thus, the testis was organized on an ovary previously developed, constituting an indirect gonochoristic differentiation.

Um microfone às formigas: crimes, narrativas e História

Some remarks on how Cultural History has been used in Mathematics Education are the main focus of this paper. It tries to discuss, basically, three works (In Cold Blood, by Truman Capote; O crime do restaurante chinês, by Boris Fausto; and Os protagonistas anônimos da História, de Ronaldo Vainfas) in order to present some perspectivas about narratives and textual elaboration in the field of Historiography.

A support system that delineates location-choice sets for firms seeking office space

Factors influencing the location decisions of offices include traffic, accessibility, employment conditions, economic prospects and land-use policies. Hence tools for supporting real-estate managers and urban planners in such multidimensional decisions may be useful. Accordingly, the objective of this study is to develop a GIS-based tool to support firms who seek office accommodation within a given regional or national study area. The tool relies on a matching approach, in which a firm's characteristics (demand) on the one hand, and environmental conditions and available office spaces (supply) on the other, are analyzed separately in a first step, after which a match is sought. That is, a suitability score is obtained for every firm and for every available office space by applying some value judgments (satisfaction, utility etc.). The latter are powered by a focus on location aspects and expert knowledge about the location decisions of firms/organizations with respect to office accommodation as acquired from a group of real-estate advisers; it is stored in decision tables, and they constitute the core of the model. Apart from the delineation of choice sets for any firm seeking a location, the tool supports two additional types of queries. Firstly, it supports the more generic problem of optimally allocating firms to a set of vacant locations. Secondly, the tool allows users to find firms which meet the characteristics of any given location. Moreover, as a GIS-based tool, its results can be visualized using GIS features which, in turn, facilitate several types of analyses.