De novo transcriptome assembly for a non-model species, the blood-sucking bug Triatoma brasiliensis, a vector of Chagas disease

High throughput sequencing (HTS) provides new research opportunities for work on non-model organisms, such as differential expression studies between populations exposed to different environmental conditions. However, such transcriptomic studies first require the production of a reference assembly. The choice of sampling procedure, sequencing strategy and assembly workflow is crucial. To develop a reliable reference transcriptome for Triatoma brasiliensis, the major Chagas disease vector in Northeastern Brazil, different de novo assembly protocols were generated using various datasets and software. Both 454 and Illumina sequencing technologies were applied on RNA extracted from antennae and mouthparts from single or pooled individuals. The 454 library yielded 278 Mb. Fifteen Illumina libraries were constructed and yielded nearly 360 million RNA-seq single reads and 46 million RNA-seq paired-end reads for nearly 45 Gb. For the 454 reads, we used three assemblers, Newbler, CAP3 and/or MIRA and for the Illumina reads, the Trinity assembler. Ten assembly workflows were compared using these programs separately or in combination. To compare the assemblies obtained, quantitative and qualitative criteria were used, including contig length, N50, contig number and the percentage of chimeric contigs. Completeness of the assemblies was estimated using the CEGMA pipeline. The best assembly (57,657 contigs, completeness of 80 %, < 1 % chimeric contigs) was a hybrid assembly leading to recommend the use of (1) a single individual with large representation of biological tissues, (2) merging both long reads and short paired-end Illumina reads, (3) several assemblers in order to combine the specific advantages of each.

Metagenomic assembly and draft genome sequence of an Uncharacterized prevotella sp. from Nelore rumen

Prevotella is one of the most abundant genera in bovine rumen, although no genome has yet been assembled by a metagenomics approach applied to Brazilian Nelore. We report the draft genome sequence of Prevotella sp., comprising 2,971,040 bp, obtained using the Illumina sequencing platform. This genome includes 127 contigs and presents a low 48% GC.

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.

Coordinated dispersal and pre-isthmian assembly of the Central American ichthyofauna

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A importância da atenção farmacêutica após a verificação da qualidade microbiológica de medicamentos contendo paracetamol encontrados em algumas residências de Américo Brasiliense - SP

It is known that a high microbial count can compromise the stability of medicines, thus reducing their therapeutic efficacy. This work tried to demonstrate that the microbial contamination can be directly related to the inadequate handling of the medicines stored in homes, making it possible to draw strategies to reduce the possible risks of medical therapy offering correct information and advising. The objective of this work was to evaluate the quality of the medicines containing paracetamol found in the residences of Américo Brasiliense-SP, using the microbial analysis of non-sterile method described in the Brazilian Pharmacopoeia (1988). The medicine samples (30 samples) were obtained directly from the interviewed local residents, who had received new medicine bottles of the same product. An analysis of viable microorganisms (bacteria and fungus) was carried out to identify pathogens found in the collected samples. Although 90% of the analyzed samples have shown some microbial contamination, the results indicated the absence of pathogenic microorganisms, and the total count of viable microorganisms was below the maximum value for non-sterile (104 UFC/g or mL). It was also verified that the local residents stored the medicines in appropriate places, according to the orientations received when they bought the medicines in pharmacies and drugstores, showing the importance of information for the correct use and conservation of pharmaceuticals.

Design gráfico ergonômico: método para verificação de níveis de usabilidade de fontes tipográficas para texto em suportes impressos e digitais

Pós-graduação em Design - FAAC

Avaliação da ação da melatonina em células-tronco tumorais mamárias RE-positivas tratadas com disruptores estrogênicos: verificação da via do receptor de estrógeno mediada pelo gene OCT 4

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Verificação de pilares metálicos compostos constituídos por perfis formados a frio por meio de programa computacional

In this work, we discuss the procedures adopted for the design of built-up columns (laced and battened columns). Built-up columns are widely used in steel construction generally when the compression forces are relatively low and the column buckling lengths are large. They are commonly used in industrial buildings, for example, as posts for cladding, or as columns supporting a crane girder. Unlike columns with full section, in the case of built-up columns, it is necessary to evaluate the shear stiffness. In fact, the shear strength leads to a significant reduction of the critical load. In the context of this work, the components of the columns (chords, diagonals, posts, etc.) are formed by cold-formed members. In order to systematize and rationalize the verification of the built-up columns, this work aim to develop a computer program based on the standards NBR 14762, NBR 6355 and Eurocode 3, basically the considerations of the part EN 1993-1-1