BioPipeline Creator-a user-friendly Java-based GUI for managing and customizing biological data pipelines.

Bioinformatics tools are essential for performing analyses in the omics sciences. Given the numerous experimental opportunities arising from advances in the field of omics and easier access to high-throughput sequencing platforms, these tools play a fundamental role in research projects. Despite the considerable progress made possible by the development of bioinformatics tools, some tools are tailored to specific analytical goals, leading to challenges for non-bioinformaticians who need to integrate the results of these specific tools into a customized pipeline.

ReNoteWeb - Web platform for the improvement of assembly result and annotation of prokaryotic genomes.

The reduction in the cost of DNA sequencing and the total time to perform this process has resulted in a significant increase in the deposit of biological information in public databases such as the NCBI (National Center for Biotechnology Information). The production of large volumes of data per run has culminated in the need to develop algorithms capable of handling data with this new feature and assisting in analyses such as the assembly and annotation of prokaryotic genomes. Over the years, several pipelines and computational tools have been developed to automate this task and consequently reduce the total time to know the genetic content of a given organism, especially non-model organisms, collaborating with the identification of possible targets with biotechnological applicability.

CODON-Software to manual curation of prokaryotic genomes.

Genome annotation conceptually consists of inferring and assigning biological information to gene products. Over the years, numerous pipelines and computational tools have been developed aiming to automate this task and assist researchers in gaining knowledge about target genes of study. However, even with these technological advances, manual annotation or manual curation is necessary, where the information attributed to the gene products is verified and enriched.

NGSReadsTreatment - A Cuckoo Filter-based Tool for Removing Duplicate Reads in NGS Data.

The Next-Generation Sequencing (NGS) platforms provide a major approach to obtaining millions of short reads from samples. NGS has been used in a wide range of analyses, such as for determining genome sequences, analyzing evolutionary processes, identifying gene expression and resolving metagenomic analyses. Usually, the quality of NGS data impacts the final study conclusions.

Evaluation of the effect of three constituent metals of monazita on the radiosensibility of human osteoblasts.

Thorium has gained notoriety in recent years, as a potential source of nuclear energy, substituting uranium in power plants. Monazite is an important source of thorium, as well of uranium and rare earths elements. Workers involved in the extraction and manipulation of this mineral are occupationally exposed to a range of metal mixtures containing thorium and to ionizing radiation.

Acute and chronic exercise modulates the expression of MOR opioid receptors in the hippocampal formation of rats.

Exercise stimulates the release of beta-endorphin and other endogenous opioid peptides that are believed to be responsible for changes in mood, perception of pain and also performance. Although the vast majority of literature data support the role of physical exercise in increasing beta-endorphin levels, indirect measures such as increased endorphin levels in peripheral blood do not reflect opioid levels in the central nervous system. The purpose of the present study was to verify whether acute and chronic exercise using both voluntary and forced exercise procedures could modify the expression of μ-opioid receptors (MOR) in rat hippocampal formation.

Effects of lanthanum on human lymphocytes viability and DNA strand break.

Lanthanum (La) is a rare-earth metal with applications in agriculture, industry, and medicine. Since lanthanides show a broad spectrum of applications there is an increased risk of contamination for humans. We examined the effects of lanthanum in Jurkat cells and human peripheral lymphocytes (HPL), and we found that it was cytotoxic and genotoxic on both cell lines.

210Po concentration in Perna perna mussels: looking for radiation effects.

Twenty ropes with 400 Perna perna mussels seeds (3 cm shell size) were set-up on floating structures at Cabo Frio Island, Arraial do Cabo, approximately 100 km northeast of Rio de Janeiro city. A rope was taken out on a monthly basis, and the shell sizes of 100 seeds were measured. The haemolymph of 10 male and 10 female individuals was taken, and the same individuals were separated for 210Po/210Pb determination.