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

Phosphorylation of eIF2α on Threonine 169 is not required for Trypanosoma brucei cell cycle arrest during differentiation.

The trypanosome life cycle consists of a series of developmental forms each adapted to an environment in the relevant insect and/or mammalian host. The differentiation process from the mammalian bloodstream form to the insect-midgut procyclic form in Trypanosoma brucei occurs in two steps in vivo. First proliferating 'slender' bloodstream forms differentiate to non-dividing 'stumpy' forms arrested in G1. Second, in response to environmental cues, stumpy bloodstream forms re-enter the cell cycle and start to proliferate as procyclic forms after a lag during which both cell morphology and gene expression are modified. Nearly all arrested cells have lower rates of protein synthesis when compared to the proliferating equivalent. In eukaryotes, one mechanism used to regulate the overall rate of protein synthesis involves phosphorylation of the alpha subunit of initiation factor eIF2 (eIF2α). The effect of eIF2α phosphorylation is to prevent the action of eIF2B, the guanine nucleotide exchange factor that activates eIF2 for the next rounds of initiation. To investigate the role of the phosphorylation of eIF2α in the life cycle of T. brucei, a cell line was made with a single eIF2α gene that contained the phosphorylation site, threonine 169, mutated to alanine. These cells were capable of differentiating from proliferating bloodstream form cells into arrested stumpy forms in mice and into procyclic forms in vitro and in tsetse flies. These results indicate that translation attenuation mediated by the phosphorylation of eIF2α on threonine 169 is not necessary for the cell cycle arrest associated with these differentiation processes.This work was supported by Fapesp grants 09/52047-5 and 11/51973-3 to B.A.C. and S. S., respectively, and CNPq grants 309860/2011-3 and 478903/2012-0 to B.A.C. and 477143/2011-3 and 445655/2014-3 to S.S.. C.C.A. was supported by a Fapesp doctoral fellowship (2007/59753-7) and a CAPES-PSDE fellowship. Work in Cambridge and Bristol was supported by Wellcome Trust Project, Grants 085956 and 088099 respectively.This is the final version of the article. It first appeared from Elsevier via https://doi.org/10.1016/j.molbiopara.2016.03.00

Improving the room-temperature ferromagnetism in ZnO and low-doped ZnO:Ag films using GLAD sputtering

ZnO and doped ZnO films with non-ferromagnetic metal have been widely used as biosensor elements. In these studies, the electrochemical measurements are explored, though the electrical impedance of the system. In this sense, the ferromagnetic properties of the material can be used for multifunctionalization of the sensor element using external magnetic fields during the measurements. Within this context, we investigate the room-temperature ferromagnetism in pure ZnO and Ag-doped ZnO films presenting zigzag-like columnar geometry. Specifically, we focus on the films’ structural and quasi-static magnetic properties and disclose that they evolve with the doping of low-Ag concentrations and the columnar geometry employed during the deposition. The magnetic characterization reveals ferromagnetic behavior at room temperature for all studied samples, including the pure ZnO one. By considering computational simulations, we address the origin of ferromagnetism in ZnO and Ag-doped ZnO and interpret our results in terms of the Zn vacancy dynamics, its substitution by an Ag atom in the site, and the influence of the columnar geometry on the magnetic properties of the films. Our findings bring to light an exciting way to induce/explore the room-temperature ferromagnetism of a non-ferromagnetic metal-doped semiconductor as a promising candidate for biosensor applications.This works was partially supported by the Brazilian agencies CNPq and CAPES. Furthermore, this work was also supported by the Portuguese Foundation for Science and Technology (FCT) in the framework of the Strategic Funding UID/FIS/04650/2019 and project PTDC/BTMMAT/28237/2017. A. Ferreira thanks FCT for the contract under the Stimulus of Scientific Employment (CTTI-31/18–CF (2) junior researcher contract). RMT thanks the Center for Computational Engineering & Sciences (CCES) at Unicamp for financial support through the FAPESP/CEPID Grant 2013/08293-7. LDM would also like to thank the support of the High-Performance Computing Center at UFRN (NPAD/UFRN). The work reported in this paper was supported by On-Surf Mobilizar Competencias Tecnologicas em Engenharia de Superficies, Project POCI-01-0247-FEDER-024521

Contaminantes bacterianos y perfil de susceptibilidad del semen porcino en centros de recogida em Brasil

Objectivo: Evaluar el perfil microbiológico de siete centros de recogida de semen porcino (CRSP) en el sur de Brasil, así como evaluar la susceptibilidad antimicrobiana a la mayoría de los microorganismos encontrados en los CRSP. Material y métodos: El análisis bacteriológico se realizó en muestras del sistema de purificación de agua, diluyentes de semen, semen crudo y almacenado, bancos de laboratorio y otras superficies de trabajo. Resultados: El crecimiento de una población bacteriana mixta se observó en muestras de agua de todas las CRSP excepto una. Aproximadamente el 85% de la CRSP tenía contaminación significativa en sus superficies de trabajo con al menos un contaminante bacteriano. Un total de 86% de muestras de semen crudo fueron contaminadas con una o más bacterias diferentes, mientras que el 100% de CRSP proporcionaron muestras contaminadas. La susceptibilidad bacteriana a agentes antimicrobianos varió en más del 80% para gentamicina, neomicina y ceftiofur a 40% o menos para penicilina y lincomicina. Conclusiones: La identificación de los puntos críticos proporciona el apoyo necesario para idear mejores estrategias para minimizar la contaminación en CRSP. Además, la evaluación del nivel de resistencia a los antimicrobianos ofrece información precisa para formular protocolos antibacterianos más eficientes que tengan en cuenta el uso racional de los antibióticos

Findings on ranking evaluation functions for feature weighting in image retrieval

Background: There are substantial benefits to be gained from ranking optimization in several information retrieval and recommendation systems. However, the analysis of ranking evaluation functions (REFs), which play a major role in many ranking optimization models, needs to be further investigated. An analysis of previous studies that investigated REFs was performed, and evidence was found which indicated that the choice of a proper REF is context sensitive. \ud Methods: In this study, we analyze a broad set of REFs for feature weighting aimed at increasing the image retrieval effectiveness. The REFs analyzed sums ten and includes the most successful and representative REFs from the literature. The REFs were embedded into a genetic algorithm (GA)-based relevance feedback (RF) model, called WLSP-C±, aimed at improving image retrieval results through the use of learning weights for image descriptors and image regions. \ud Results: Analyses of precision-recall curves in five real-world image data sets showed that one non-parameterized REF named F5, not analyzed in previous studies, overcame recommended ones, which require parameter adjustment. We also provided a computational analysis of the GA-based RF model investigated, and it was shown that it is linear in regard to the image data set cardinality. \ud Conclusions: We conclude that REF F5 should be investigated in other contexts and problem scenarios centered on ranking optimization, as rankingCNPqCAPESFAPES

Synthesis of natural ether lipids and 1-O-hexadecylglycero-arylboronates via an epoxide-ring opening approach: Potential antifouling additives to marine paint coatings

In this paper a new and efficient procedure for the synthesis of natural 1-O- alkyl glyceryl ethers such as chimyl (1), batyl (2) and selachyl (3) is described. Alkyl glycidyl ethers (4-6) were synthetized using solvents free reactions. A stereospecific ring-opening reaction of epoxides (4-6) with phenylboronic acid in dry dioxane, giving rise to cyclic arylboronates in high yields (90-98%). Seven new 1-O-hexadecylglycero-arylboronates (7-f) and chimyl alcohol (1) were evaluated in laboratory antifouling assays