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.

Cissus quadrangularis Linn exerts dose-dependent biphasic effects: osteogenic and anti-proliferative, through modulating ROS, cell cycle and Runx2 gene expression in primary rat osteoblasts

Objectives: This report highlights phytoconstituents present in Cissus quadrangularis (CQ) extract and examines biphasic (proliferative and anti-proliferative) effects of its extract on bone cell proliferation, differentiation, mineralization, ROS generation, cell cycle progression and Runx2 gene expression in primary rat osteoblasts. Materials and methods: Phytoconstituents were identified using gas chromatography-mass spectroscopy (GC-MS). Osteoblasts were exposed to different concentrations (10-100g/ml) of CQ extract and cell proliferation and cell differentiation were investigated at different periods of time. Subsequently, intracellular ROS intensity, apoptosis and matrix mineralization of osteoblasts were evaluated. We performed flow cytometry for DNA content and real-time PCR for Runx2 gene expression analysis.Results: CQ extract's approximately 40 bioactive compounds of fatty acids, hydrocarbons, vitamins and steroidal derivatives were identified. Osteoblasts exposed to varying concentrations of extract exhibited biphasic variation in cell proliferation and differentiation as a function of dose and time. Moreover, lower concentrations (10-50g/ml) of extract slightly reduced ROS intensity, although they enhanced matrix mineralization, DNA content in S phase of the cell cycle, and levels of Runx2 expression. However, higher concentrations (75-100g/ml) considerably induced the ROS intensity and nuclear condensation in osteoblasts, while it reduced mineralization level, proportion of cells in S phase and Runx2 level of the osteogenic gene.Conclusions: These findings suggest that CQ extract revealed concentration-dependent biphasic effects, which would contribute notably to future assessment of pre-clinical efficacy and safety studies.

Effect of temperature on salt-salt aqueous biphasic systems: manifestations of upper critical solution temperature

Water-miscible ionic liquids (ILs) may be salted out using kosmotropic salts such as potassium phosphate (K3PO4) to form salt-salt aqueous biphasic systems (ABS). The effect of temperature on these systems has been studied using phase diagrams and it is observed that the degree of binodal shift decreases (requiring lower IL and kosmotropic salt concentrations) with the increase of temperature following the trend [C(4)mim]Cl > [C(4)py]Cl > [C(4)mmim] Cl > [N-4444]Cl. This trend can be correlated with the decreasing hydrogen bonding abilities of each salt. The phase behavior was also interpreted on the basis of critical solution temperature behavior of pure aqueous ionic liquid solutions. Additionally, the distribution of alcohols in these systems was studied as a function of temperature and it was found that the distribution ratios did not change with changes in temperature. The Gibbs energy of transfer of a methylene group in these systems and correlation to tie-line length was also determined. It was concluded that while the miscibility of alcohols increases in the ILs with increasing temperature, phase divergence in the aqueous biphasic system decreases, and thus these competing forces tend to cancel each other out for small polar molecules. A comparison is provided for the response to temperature in the currently studied salt-salt systems and analogous ABS formed by the addition of hydrophilic polymers to kosmotropic salts (polymer-salt) or other polymers (polymer-polymer).

Reator anaeróbio compartimentado para o tratamento de águas residuárias de suinocultura

Water and soil pollution caused by the waste from the swine production causes severe environmental impacts in producing areas. An efficient alternative to reduce these impacts can be the use of high-rate anaerobic reactors. In this work, it was evaluated the effect of the swine wastewater with total suspended solids concentrations around 6.000 mg.L-1 in the anaerobic baffled reactor with three compartments. The volume of the first compartment was 210 L and of the second and third ones of 160 L. The anaerobic baffled reactor was submitted at hydraulic detention times of 56, 28 and 18 hours and to organic load rates of 5.0 to 10.1 g total COD (L.d)(-1). The highest total COD removals, of 42 to 68%, and volumetric methane productions, of 0.261 to 0.454 L CH4 (L reactor d)(-1), occurred in the second compartment.

Mechanochemical synthesis of CaTiO3 from CaCO3 - TiO2 mixture

The synthesis of calcium titanate, CaTiO3, was performed by mechanical activation and thermal treatment. Milling for up to 360 minutes in a planetary ball mill mechanically activated an equimolar mixture of CaCO 3 and TiO2 powders. A small amount of mechanically activated mixtures was pressed into briquettes and calcined at 850°C for two hours. The effect of mechanical activation on the solid-state reaction was studied using X-ray powder diffraction and differential thermal analysis. The change of morphology and size of powder particles due to milling, were determined by SEM, while BET analysis was used to determine the specific surface area of the powder. The sintering process was followed by a dilatometer during thermal treatment up to 1300°C. The main conclusion of the analysis of conducted investigations is that CaTiO3 ceramics can be obtained from an activated mixture at a much lower temperature than reported in the literature owing to acceleration of the chemical reaction and sintering.

Association of apolipoprotein B and adiponectin receptor 1 genes with carcass, bone integrity and performance traits in a paternal broiler line

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Comparative morpho-physiology of the metapleural glands of two Atta leaf-cutting ant queens nesting in clayish and organic soils

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

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.

Aspectos clínicos influentes no planejamento das próteses sobre implantes tipo overdenture e protocolo

The aim of his study was to review the current scientific literature in order to discuss the surgical, prosthetics and psychological/psychosocial aspects during the treatment planning of edentulous patients, when a total fixed prosthesis or overdenture is indicated. To identify studies to take part in this review, a search was conducted for the following databases: PubMed, Dentistry and Oral Sciences Source, Journals@Ovid, SpringerLink, Wiley Online Library, Nature (NPG), Oxford Journals. It was used as descriptors: total fixed prostheses and overdentures. Inclusion criteria were: clinical articles, clinical case reports, case series, literature reviews and systematic reviews that addressed the study and comparison of total fixed prostheses and overdentures for a surgical- prosthetic planning. Exclusion criteria were: laboratory and in vitro studies and those whose first language was not English or Portuguese. Of a total of 454 articles, after an analysis according to inclusion and exclusion criteria, 76 articles were selected. During an implantsupported prosthesis rehabilitation with dental in edentulous patients, the use of alternative procedures appear to be effective when compared to more invasive surgical techniques, and thus, the amount of dental implants possible to install associated with prosthetic issues such as lip support, smile line, quantity and quality of mucosa, phonetics, etc., will allow an appropriate treatment planning to each clinical case

Características epidemiológicas da frequência cardíaca de repouso: relação com a prática de atividade física estratificada por sexo e controlada por fatores de confusão

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Dimensões da qualidade em serviços: um estudo no setor de B2C brasileiro

With the focus on quality of services, this work uses a methodology based on questionnaires for evaluating companies and consumers, with the objective of studying the dimensions of quality within the segment of Brazilian e-commerce. The research conducted a study to identify the situation of companies regarding the dimensions of quality and, among costumers, a survey was done to determine their requirements with regard to these dimensions and to identify those dimensions considered as winning factors when making the orders. The results demonstrate that customers consider reliability to be the most important order winner, followed by safety and communications. The study of these enterprises demonstrates that their quality of service is good, however there is a need for improvements in the business processes related to the dimensions of service quality.

Metabolomic evaluation of interactions in rhizosphere between Senna spectabilis and associated microorganisms

Pós-graduação em Química - IQ

Análise de parentesco e variabilidade genética de pacu (Piaractus mesopotamicus) por meio de marcadores SNPs: subsídios para o melhoramento genético

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

Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica

The Antarctic is a pristine environment that contributes to the maintenance of the global climate equilibrium. The harsh conditions of this habitat are fundamental to selecting those organisms able to survive in such an extreme habitat and able to support the relatively simple ecosystems. The DNA of the microbial community associated with the rhizospheres of Deschampsia antarctica Desv (Poaceae) and Colobanthus quitensis (Kunth) BartI (Caryophyllaceae), the only two native vascular plants that are found in Antarctic ecosystems, was evaluated using a 16S rRNA multiplex 454 pyrosequencing approach. This analysis revealed similar patterns of bacterial diversity between the two plant species from different locations, arguing against the hypothesis that there would be differences between the rhizosphere communities of different plants. Furthermore, the phylum distribution presented a peculiar pattern, with a bacterial community structure different from those reported of many other soils. Firmicutes was the most abundant phylum in almost all the analyzed samples, and there were high levels of anaerobic representatives. Also, some phyla that are dominant in most temperate and tropical soils, such as Acidobacteria, were rarely found in the analyzed samples. Analyzing all the sample libraries together, the predominant genera found were Bifidobacterium (phylum Actinobacteria), Arcobacter (phylum Proteobacteria) and Faecalibacterium (phylum Firmicutes). To the best of our knowledge, this is the first major bacterial sequencing effort of this kind of soil, and it revealed more than expected diversity within these rhizospheres of both maritime Antarctica vascular plants in Admiralty Bay, King George Island, which is part of the South Shetlands archipelago. The ISME Journal (2010) 4, 989-1001; doi:10.1038/ismej.2010.35; published online 1 April 2010