Provenance in bioinformatics workflows

In this work, we used the PROV-DM model to manage data provenance in workflows of genome projects. This provenance model allows the storage of details of one workflow execution, e.g., raw and produced data and computational tools, their versions and parameters. Using this model, biologists can access details of one particular execution of a workflow, compare results produced by different executions, and plan new experiments more efficiently. In addition to this, a provenance simulator was created, which facilitates the inclusion of provenance data of one genome project workflow execution. Finally, we discuss one case study, which aims to identify genes involved in specific metabolic pathways of Bacillus cereus, as well as to compare this isolate with other phylogenetic related bacteria from the Bacillus group. B. cereus is an extremophilic bacteria, collectemd in warm water in the Midwestern Region of Brazil, its DNA samples having been sequenced with an NGS machine

Conhecimento, Responsabilidade, Visão e Futuro: bases programáticas da Lista F para o 3.º mandato do Conselho Geral da Universidade de Évora 2016-20

O presente documento inclui o programa de acção e os elementos de campanha da Lista F, candidata ao 3.º mandato do Conselho Geral da Universidade de Évora (2016-20)

Linfadenites tuberculóides em suínos abatidos no Estado de São Paulo, Brasil: aspectos macroscópicos histopatológicos e pesquisa de micobactérias

INTRODUÇÃO: Como a ocorrência de linfadenites tuberculóides nos suínos oferece riscos à saúde pública, sobretudo em indivíduos imunocomprometidos, foi estudada a distribuição das lesões tuberculóides e a presença de micobactérias em linfonodos, tecido hepático e muscular de suínos de abate, no Estado de São Paulo, SP (Brasil), no período de 1993-1994. MATERIAL E MÉTODO: Foram estudadas 60 carcaças de suínos abatidos, sendo que, trinta apresentavam lesões tuberculóides macroscópicas (grupo A) e trinta estavam livres de tais lesões (grupo B ou controle). Foram analisadas seis localizações: linfonodos (retrofaríngeos, jejunais e mediastínicos), tecido hepático e tecido muscular (masséter e diafragma). Os exames executados foram: histopatologia e o cultivo para micobactérias. RESULTADOS: No grupo A, 14 em 30 carcaças apresentaram granuloma na histopatologia e, em 14, houve o isolamento de representantes do Complexo MAC (Mycobacterium avium-intracellulare). No grupo B não foram observadas lesões na histopatologia, e de quatro carcaças houve o isolamento de micobactérias de rápido crescimento. As lesões macroscópicas foram encontradas predominantemente nos linfonodos mesentéricos. O Complexo MAC foi isolado apenas em linfonodos do grupo com lesão, não sendo isolado em tecido hepático e muscular. CONCLUSÃO: Não foi possível o estabelecimento de relação entre o tipo de micobactéria isolada e as características macroscópicas das lesões.INTRODUCTION: As the occurrence of tuberculosis lymphadenitis in swine constitutes a public health risk, especially in immunosuppressed individuals, the distribution of tuberculoid lesions and the presence of micobacteria in lymphonodes and hepatic and muscular tissue in swine for slaughter, in the State of S. Paulo, SP (Brazil), in the period from 1993 to 1994, were studied. MATERIAL E MÉTODO: Tuberculous lesions in 60 carcasses of swine, slaughtered at abattoirs during the period 1993-1994, were studied. When macroscopic lesions were observed, a representative sampling of lymphnodes, hepatic and muscular tissues (masseter and diaphragm) were examined using histophatological and micobacterial isolation techniques. RESULTS: The macroscopic lesions were found predominantly in mesenteric lymphnodes. The MAI Complex (M.avium-intracellulare) was isolated mainly in the carcass group that showed lesions and was not found in the control group. Microorganisms of the MAI Complex were not isolated from hepatic and muscular tissues. CONCLUSION: No clear relationship between the type of mycobacteria isolated and the macroscopic lesions observed during the carcass inspection was found

Validación del Nursing Activities Score en unidades de cuidados intensivos portuguesas

Objective: to describe the process of adaptation and validation of the Nursing Activities Score to the Portuguese context. Method: this was a pilot study of adaptation and validation of the Nursing Activities Score with a sample consisting of 67 patients hospitalized in the intensive care units of three Portuguese hospitals. The construct validity was assessed through factor analysis procedures and the internal consistency of the items was measured through the Cronbach’s alpha coeffi cient. Results: a mean workload value of 63.04% (SD = 14.25; Median = 61.30) was obtained. Psychometric data revealed a Cronbach’s alpha of 0.71 in the total scale, indicating an acceptable accuracy. Confi rmatory factor analysis suggested an appropriate adjustment between the model and the data (χ2 (199) = 214.5, p = 0.214; CFI = 0.95; RMSA = 0.035). Conclusion: in the present study, the Portuguese version of the Nursing Activities Score was found to be a valid instrument, enabling a safe assessment of the workload of nurses.Objetivo: descrever o processo de adaptação e validação do Nursing Activities Score para o contexto português. Método: trata-se de um estudo-piloto de adaptação e validação do Nursing Activities Score, com amostra de 67 doentes internados em unidades de cuidados intensivos de três hospitais portugueses. A validade de constructo avaliou-se mediante procedimentos de análise fatorial e a consistência interna dos itens através do coefi ciente Alpha de Cronbach. Resultados: obteve-se um valor médio da carga de trabalho de 63,04% (DP = 14,25; Mediana = 61,30). Os dados psicométricos revelaram um Alpha de Cronbach de 0,71, na escala total, indicando uma fi delidade aceitável. A análise fatorial confi rmatória sugeriu um ajustamento adequado entre o modelo e os dados (χ2(199) = 214,5, p = 0,214; CFI = 0,95; RMSA = 0,035). Conclusão: neste estudo, a versão portuguesa do Nursing Activities Score revelou-se um instrumento válido, permitindo avaliar a carga de trabalho dos enfermeiros com segurançaObjetivo: describir el proceso de adaptación y validación del Nursing Activities Score al contexto portugués. Método: estudio piloto de adaptación y validación del Nursing Activities Score, con muestra de 67 pacientes internados en unidades de cuidados intensivos de tres hospitales portugueses. La validez del constructo se evaluó mediante análisis factorial y por consistencia interna de los ítems evaluados a través del coefi ciente Alpha de Cronbach. Resultados: se obtuvo un valor medio de carga de trabajo de 63,04% (SD=14,25; Mediana=61,30). Los datos psicométricos expresaron un Alpha de Cronbach de 0,71 en la escala total, indicando fi delidad aceptable. El análisis factorial confi rmatorio sugirió un ajuste adecuado entre el modelo y os datos (χ2 (199)=214,5; p=0,214; CFI=0,95; RMSA=0,035). Conclusión: en este estudio, la versión portuguesa del Nursing Activities Score demostró ser un instrumento válido, permitiendo evaluar la carga de trabajo de los enfermeros con precisión

Correlations of mutations in katG, oxyR-ahpC and inhA genes and in vitro susceptibility in Mycobacterium tuberculosis clinical strains segregated by spoligotype families from tuberculosis prevalent countries in South America

Background Mutations associated with resistance to rifampin or streptomycin have been reported for W/Beijing and Latin American Mediterranean (LAM) strain families of Mycobacterium tuberculosis. A few studies with limited sample sizes have separately evaluated mutations in katG, ahpC and inhA genes that are associated with isoniazid (INH) resistance. Increasing prevalence of INH resistance, especially in high tuberculosis (TB) prevalent countries is worsening the burden of TB control programs, since similar transmission rates are noted for INH susceptible and resistant M. tuberculosis strains. Results We, therefore, conducted a comprehensive evaluation of INH resistant M. tuberculosis strains (n = 224) from three South American countries with high burden of drug resistant TB to characterize mutations in katG, ahpC and inhA gene loci and correlate with minimal inhibitory concentrations (MIC) levels and spoligotype strain family. Mutations in katG were observed in 181 (80.8%) of the isolates of which 178 (98.3%) was contributed by the katG S315T mutation. Additional mutations seen included oxyR-ahpC; inhA regulatory region and inhA structural gene. The S315T katG mutation was significantly more likely to be associated with MIC for INH ≥2 μg/mL. The S315T katG mutation was also more frequent in Haarlem family strains than LAM (n = 81) and T strain families. Conclusion Our data suggests that genetic screening for the S315T katG mutation may provide rapid information for anti-TB regimen selection, epidemiological monitoring of INH resistance and, possibly, to track transmission of INH resistant strains.Fil: Dalla Costa, Elis R. State Foundation for Production and Research in Health (FEPPS); Brasil.Fil: Ribeiro, Marta O. State Foundation for Production and Research in Health (FEPPS); Brasil.Fil: Silva, Márcia S. N. State Foundation for Production and Research in Health (FEPPS); Brasil.Fil: Arnold, Liane S. State Foundation for Production and Research in Health (FEPPS); Brasil.Fil: Rostirolla, Diana C. State Foundation for Production and Research in Health (FEPPS); Brasil.Fil: Cafrune, Patricia I. State Foundation for Production and Research in Health (FEPPS); Brasil.Fil: Espinoza, Roger C. Blufstein Clinic Laboratory; Perú.Fil: Palaci, Moises. Federal University of Espírito Santo; Brasil.Fil: Telles, Maria A. Adolfo Lutz Institute; Brasil.Fil: Ritacco, Viviana. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Servicio de Micobacterias; Argentina.Fil: Suffys, Philip N. Oswaldo Cruz Institute; Brasil.Fil: Lopes, Maria L. Evandro Chagas Institute; Brasil.Fil: Campelo, Creuza L. LACEN Ceará; BrasilFil: Miranda, Silvana S. Federal University of Minas Gerais; Brasil.Fil: Kremer, Kristin. National Institute for Public Healthand the Environment (RIVM). Mycobacteria Reference Unit (CIb-LIS); Países Bajos.Fil: Almeida da Silva, Pedro E. Federal Foundation of Rio Grande; Brasil.Fil: de Souza Fonseca, Leila. Federal University of Rio de Janeiro. Tuberculosis Academic Program; Brasil.Fil: Ho, John L. Cornell University; Estados Unidos.Fil: Kritski, Afrânio L. Federal University of Rio de Janeiro. Tuberculosis Academic Program; Brasil.Fil: Rossetti, María L. R. State Foundation for Production and Research in Health (FEPPS); Brasil

Roles of non-coding RNA in sugarcane-microbe interaction

Studies have highlighted the importance of non-coding RNA regulation in plant-microbe interaction. However, the roles of sugarcane microRNAs (miRNAs) in the regulation of disease responses have not been investigated. Firstly, we screened the sRNA transcriptome of sugarcane infected with Acidovorax avenae. Conserved and novel miRNAs were identified. Additionally, small interfering RNAs (siRNAs) were aligned to differentially expressed sequences from the sugarcane transcriptome. Interestingly, many siRNAs aligned to a transcript encoding a coppertransporter gene whose expression was induced in the presence of A. avenae, while the siRNAs were repressed in the presence of A. avenae. Moreover, a long intergenic non-coding RNA was identified as a potential target or decoy of miR408. To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR (qRT-PCR). Among these miRNAs, miR408—a copper- microRNA—was downregulated. The cleavage of a putative miR408 target, a laccase, was confirmed by a modified 50RACE (rapid amplification of cDNA ends) assay. MiR408 was also downregulated in samples infected with other pathogens, but it was upregulated in the presence of a beneficial diazotrophic bacteria. Our results suggest that regulation by miR408 is important in sugarcane sensing whether microorganisms are either pathogenic or beneficial, triggering specific miRNA-mediated regulatory mechanisms accordingly

Chloroplast genome assembly of Serjania erecta Raldk: comparative analysis reveals gene number variation and selection in protein-coding plastid genes of Sapindaceae

Serjania erecta Raldk is an essential genetic resource due to its anti-inflammatory, gastric protection, and anti-Alzheimer properties. However, the genetic and evolutionary aspects of the species remain poorly known. Here, we sequenced and assembled the complete chloroplast genome of S. erecta and used it in a comparative analysis within the Sapindaceae family. S. erecta has a chloroplast genome (cpDNA) of 159,297 bp, divided into a Large Single Copy region (LSC) of 84,556 bp and a Small Single Copy region (SSC) of 18,057 bp that are surrounded by two Inverted Repeat regions (IRa and IRb) of 28,342 bp. Among the 12 species used in the comparative analysis, S. erecta has the fewest long and microsatellite repeats. The genome structure of Sapindaceae species is relatively conserved; the number of genes varies from 128 to 132 genes, and this variation is associated with three main factors: (1) Expansion and retraction events in the size of the IRs, resulting in variations in the number of rpl22, rps19, and rps3 genes; (2) Pseudogenization of the rps2 gene; and (3) Loss or duplication of genes encoding tRNAs, associated with the duplication of trnH-GUG in X. sorbifolium and the absence of trnT-CGU in the Dodonaeoideae subfamily. We identified 10 and 11 mutational hotspots for Sapindaceae and Sapindoideae, respectively, and identified six highly diverse regions (tRNA-Lys — rps16, ndhC – tRNA-Val, petA – psbJ, ndhF, rpl32 – ccsA, and ycf1) are found in both groups, which show potential for the development of DNA barcode markers for molecular taxonomic identification of Serjania. We identified that the psaI gene evolves under neutrality in Sapindaceae, while all other chloroplast genes are under strong negative selection. However, local positive selection exists in the ndhF, rpoC2, ycf1, and ycf2 genes. The genes ndhF and ycf1 also present high nucleotide diversity and local positive selection, demonstrating significant potential as markers. Our findings include providing the first chloroplast genome of a member of the Paullinieae tribe. Furthermore, we identified patterns in variations in the number of genes and selection in genes possibly associated with the family’s evolutionary history