MapRepeat: an approach for effective assembly of repetitive regions in prokaryotic genomes

The newest technologies for DNA sequencing have led to the determination of the primary structure of the genomes of organisms, mainly prokaryotes, with high efficiency and at lower costs. However, the presence of regions with repetitive sequences, in addition to the short reads produced by the Next-Generation Sequencing (NGS) platforms, created a lot of difficulty in reconstructing the original genome in silico. Thus, even today, genome assembly continues to be one of the major challenges in bioinformatics specifically when repetitive sequences are considered. In this paper, we present an approach to assemble repetitive regions in prokaryotic genomes. Our methodology enables (i) the identification of these regions through visual tools, (ii) the characterization of sequences on the extremities of gaps and (iii) the extraction of consensus sequences based on mapping of raw data to a reference genome. We also present a case study on the assembly of regions that encode ribosomal RNAs (rRNA) in the genome of Corynebacterium ulceransFRC11, in order to show the efficiency of the strategies presented here. The proposed methods and tools will help in finishing genome assemblies, besides reducing the running time and associated costs. Availability All scripts are available at http://github.com/dcbmariano/maprepea

Mineral and volatile composition of agua-mel from Portugal

Agua-mel (honey-water) is a typical honey-based product produced by the Portuguese beekeepers, particularly in southern Portugal. Agua-mel was characterized by mineral content and volatiles contents. Mineral content evaluation was performed based on a random sampling of 14 samples from a total of 16 samples provided by local producers. Mineral content showed that potassium predominated in agua-mel samples (1270-4105 mg/kg). The concentration of aluminium in one sample was tenfold higher (5.8 mg/kg) than in the remaining samples (0.3-0.6 mg/kg). Agua-mel volatiles were isolated by hydrodistillation and analysed by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS) from a subset of eight samples. Cluster analysis showed two poorly correlated clusters (S (corr) < 0.3). Cluster I only sample was dominated by trans-beta-ocimene (19 %), gamma-terpinene (15 %) and 2-furfural (9 %). Cluster II that included the remaining seven samples showed two moderately correlated subclusters (S (corr) < 0.5). The six samples with high correlation from subcluster IIa were dominated by 2-furfural (18-41 %) and benzene acetaldehyde (12-39 %). n-Nonadecane (14 %), n-heneicosane and 2-furfural (both 13 %) were the main components of subcluster IIb sample. Although the presence of some volatile compounds can help in the correlation between agua-mel and honey botanical source, the final product varies largely according to the preparation process even for the same producer, in different years. Agua-mel detailed characterization may assist in bringing added value to this typical Portuguese honey-based product

Effect of the carbon nanotube surface characteristics on the conductivity and dielectric constant of carbon nanotube/poly(vinylidene fluoride) composites

Commercial multi-walled carbon nanotubes (CNT) were functionalized by oxidation with HNO3, to introduce oxygen-containing surface groups, and by thermal treatments at different temperatures for their selective removal. The obtained samples were characterized by adsorption of N2 at -196°C, temperature-programmed desorption and determination of pH at the point of zero charge. CNT/poly(vinylidene fluoride) composites were prepared using the above CNT samples, with different filler fractions up to 1 wt%. It was found that oxidation reduced composite conductivity for a given concentration, shifted the percolation threshold to higher concentrations, and had no significant effect in the dielectric response

Effect of high-pressure torsion on microstructure, mechanical properties and corrosion resistance of cast pure Mg

© 2018, The Author(s). High-pressure torsion (HPT) processing was applied to cast pure magnesium, and the effects of the deformation on the microstructure, hardness, tensile properties and corrosion resistance were evaluated. The microstructures of the processed samples were examined by electron backscatter diffraction, and the mechanical properties were determined by Vickers hardness and tensile testing. The corrosion resistance was studied using electrochemical impedance spectroscopy in a 3.5% NaCl solution. The results show that HPT processing effectively refines the grain size of Mg from millimeters in the cast structure to a few micrometers after processing and also creates a basal texture on the surface. It was found that one or five turns of HPT produced no significant difference in the grain size of the processed Mg and the hardness was a maximum after one turn due to recovery in some grains. Measurements showed that the yield strength of the cast Mg increased by about seven times whereas the corrosion resistance was not significantly affected by the HPT processing

New approaches to measuring anthelminthic drug efficacy: parasitological responses of childhood schistosome infections to treatment with praziquantel

By 2020, the global health community aims to control and eliminate human helminthiases, including schistosomiasis in selected African countries, principally by preventive chemotherapy (PCT) through mass drug administration (MDA) of anthelminthics. Quantitative monitoring of anthelminthic responses is crucial for promptly detecting changes in efficacy, potentially indicative of emerging drug resistance. Statistical models offer a powerful means to delineate and compare efficacy among individuals, among groups of individuals and among populations.; We illustrate a variety of statistical frameworks that offer different levels of inference by analysing data from nine previous studies on egg counts collected from African children before and after administration of praziquantel.; We quantify responses to praziquantel as egg reduction rates (ERRs), using different frameworks to estimate ERRs among population strata, as average responses, and within strata, as individual responses. We compare our model-based average ERRs to corresponding model-free estimates, using as reference the World Health Organization (WHO) 90 % threshold of optimal efficacy. We estimate distributions of individual responses and summarize the variation among these responses as the fraction of ERRs falling below the WHO threshold.; Generic models for evaluating responses to anthelminthics deepen our understanding of variation among populations, sub-populations and individuals. We discuss the future application of statistical modelling approaches for monitoring and evaluation of PCT programmes targeting human helminthiases in the context of the WHO 2020 control and elimination goals