ABSTRACT
The use of serological tests is valuable to diagnose Zika virus (ZIKV) infection and carry out epidemiological surveillance. However, ZIKV serological tests may result in false positives due to cross-reactivity between antibodies against other Flavivirus, especially dengue virus that worldwide disseminated. We used three online tools to predict amino acid sequences of B-cell epitopes. We selected and synthetized two epitopes that showed appropriate features in the molecular dynamic simulation and demonstrated to be suitable for serological assays.
Subject(s)
Dengue Virus , Dengue , Zika Virus Infection , Zika Virus , Antibodies, Viral , Cross Reactions , Epitopes, B-Lymphocyte , Humans , Serologic TestsABSTRACT
Endophytes improve the host performance in areas of high plant endemicity. Paullinia cupana is an Amazonia plant species of economic and social importance due to the high caffeine concentration in its seeds. An interesting strategy to identify endophytic microorganisms with potential biotechnological application is to understand the factors that influence the endophytic community to rationalize the host management programs. We used the next-generation sequencing for bacterial 16S rRNA gene to examine how the P. cupana organ, genotype, and geographic location influenced its endophytic bacterial community. We obtained 1520 operational taxonomic units (OTUs) distributed in 19 phyla, 32 classes, 79 orders, 114 families and 174 genera. The P. cupana roots and leaves were specifically colonized by the bacterial genera Acidothermus and Porphyromonas, respectively, with high relative frequency. The plant organ type influenced the endophytic community's richness, diversity, OTUs composition, relative abundance of phyla and genera, and genera interaction network. However, the host plant genotype and geographic location influenced the composition and interaction among genera in the network analysis. Prevotella is a super-generalist genus in the interaction network of endophytic bacteria of P. cupana. This study revealed endophytic bacterial groups of importance to P. cupana and stressed that the host plant organ modulates the structure and interactions within this community. Our results indicated that the microbial community adapted to colonize P. cupana by adjusting to its composition and interaction network. The isolation of abundant and super-generalist bacterial genera shall help to examine their functionality to the composition and fitness of the endophytic community of P. cupana.
Subject(s)
Bacteria/classification , Bacteria/isolation & purification , Ecology , Endophytes/classification , Endophytes/isolation & purification , Paullinia/microbiology , Bacteria/genetics , Brazil , DNA, Bacterial/isolation & purification , Endophytes/genetics , Genotype , High-Throughput Nucleotide Sequencing , Microbial Interactions , Microbiota/genetics , Phylogeny , Plant Leaves/microbiology , Plant Roots/microbiology , RNA, Ribosomal, 16S/genetics , Seeds/microbiologyABSTRACT
BACKGROUND: Copy number variations (CNVs) have been shown to account for substantial portions of observed genomic variation and have been associated with qualitative and quantitative traits and the onset of disease in a number of species. Information from high-resolution studies to detect, characterize and estimate population-specific variant frequencies will facilitate the incorporation of CNVs in genomic studies to identify genes affecting traits of importance. RESULTS: Genome-wide CNVs were detected in high-density single nucleotide polymorphism (SNP) genotyping data from 1,717 Nelore (Bos indicus) cattle, and in NGS data from eight key ancestral bulls. A total of 68,007 and 12,786 distinct CNVs were observed, respectively. Cross-comparisons of results obtained for the eight resequenced animals revealed that 92 % of the CNVs were observed in both datasets, while 62 % of all detected CNVs were observed to overlap with previously validated cattle copy number variant regions (CNVRs). Observed CNVs were used for obtaining breed-specific CNV frequencies and identification of CNVRs, which were subsequently used for gene annotation. A total of 688 of the detected CNVRs were observed to overlap with 286 non-redundant QTLs associated with important production traits in cattle. All of 34 CNVs previously reported to be associated with milk production traits in Holsteins were also observed in Nelore cattle. Comparisons of estimated frequencies of these CNVs in the two breeds revealed 14, 13, 6 and 14 regions in high (>20 %), low (<20 %) and divergent (NEL > HOL, NEL < HOL) frequencies, respectively. CONCLUSIONS: Obtained results significantly enriched the bovine CNV map and enabled the identification of variants that are potentially associated with traits under selection in Nelore cattle, particularly in genome regions harboring QTLs affecting production traits.
Subject(s)
DNA Copy Number Variations , Genome , Genomics , Quantitative Trait Loci , Quantitative Trait, Heritable , Animals , Cattle , Chromosome Mapping , Computational Biology/methods , Genome-Wide Association Study , Genomics/methods , High-Throughput Nucleotide Sequencing , Molecular Sequence Annotation , Polymorphism, Single Nucleotide , Reproducibility of ResultsABSTRACT
The aim of this research was to assess water quality in a stretch of the Paraguay River within the Brazilian Pantanal by means of a micronucleus assay with fish, and by water and sediment physicochemical analysis. Significant increases (p >0.05) in the frequency of micronuclei (MN) and micronucleated cells (MNC) occurred in erythrocytes of Pimelodus maculatus and Leporinus friderici at two river sites in the town of Caceres relative to an upstream reference site. The results demonstrate that the Paraguay River water near Caceres has been receiving genotoxic effluents, which may be associated with the presence of chromium, sulfides, oil and grease, and/or other chemicals.