ABSTRACT
Background noise in metagenomic studies is often of high importance and its removal requires extensive post-analytic, bioinformatics filtering. This is relevant as significant signals may be lost due to a low signal-to-noise ratio. The presence of plasmid residues, that are frequently present in reagents as contaminants, has not been investigated so far, but may pose a substantial bias. Here we show that plasmid sequences from different sources are omnipresent in molecular biology reagents. Using a metagenomic approach, we identified the presence of the (pol) of equine infectious anemia virus in human samples and traced it back to the expression plasmid used for generation of a commercial reverse transcriptase. We found fragments of multiple other expression plasmids in human samples as well as commercial polymerase preparations. Plasmid contamination sources included production chain of molecular biology reagents as well as contamination of reagents from environment or human handling of samples and reagents. Retrospective analyses of published metagenomic studies revealed an inaccurate signal-to-noise differentiation. Hence, the plasmid sequences that seem to be omnipresent in molecular biology reagents may misguide conclusions derived from genomic/metagenomics datasets and thus also clinical interpretations. Critical appraisal of metagenomic data sets for the possibility of plasmid background noise is required to identify reliable and significant signals.
Subject(s)
DNA Contamination , DNA, Viral/analysis , Genes, pol/genetics , Indicators and Reagents/analysis , Metagenomics , Plasmids/analysis , Computational Biology , DNA, Viral/genetics , Diagnostic Errors/prevention & control , High-Throughput Nucleotide Sequencing , Humans , Infectious Anemia Virus, Equine/genetics , Plasmids/genetics , Retrospective Studies , Sequence Analysis, DNA/methodsABSTRACT
We report on the nucleotide sequences of geminiviruses of the genus Bemogovirus infecting Sida micrantha Schr., a common weed in Brazil. For decades, the mosaic frequently associated with Sida plants was considered to be caused by a Brazilian strain of Abutilon mosaic virus (AbMV). By infection studies and sequence comparisons, we demonstrate that it is associated with a complex of at least two begomoviruses as different from AbMV as most South American geminiviruses. Two molecules of DNA A (A1, A2) and three of DNA B (B1, B2, B3) were cloned and sequenced. According to the high homology in their common regions, DNA A1 and DNA B3, as well as DNA A2 and DNA B2, are cognate components of two begomoviruses, which were infectious in Nicotiana benthamiana plants. No trans-replication was found for any other A/B combination. The intergenic region of DNA B2 appears to be the product of the recombination between DNA B1 and DNA A2. These results show that a coinfection of begomoviruses can persist over decades, producing a reservoir of partially recombined but distinct geminiviruses.
Subject(s)
Geminiviridae/classification , Malvaceae/virology , Mosaic Viruses/classification , Plant Diseases/virology , Base Sequence , Brazil , Cloning, Molecular , DNA, Viral/genetics , Geminiviridae/genetics , Molecular Sequence Data , Phylogeny , Sequence Alignment , Species SpecificityABSTRACT
This is an evaluation of the negative impact and the way in which the Niño phenomenon was handled during 1997-1998 in the community Andina de Naciones (Bolivia,Colombia,Ecuador,Perú y Venezuela). This report was prepared by Corporacion Andina de Fomento (CAF). A summary of the economic impact of the event is given
Subject(s)
34613 , Impact of Disasters , 32465 , Damage Assessment , Economics , Damage Assessment in the Economic SectorABSTRACT
Se señalan los efectos de los desastres naturales sobre el desarrollo y las condiciones de vida en la Región de América Latina y el Caribe. Sobre la base de los análisis cuantitativos realizados para evaluar los daños causados por los principales desastres que se han producido en esta región en los últimos 16 años, el autor justifica la adopción de medidas de prevención, planificación y preparación para disminuir sus efectos
Subject(s)
Natural Disasters , Latin America , Caribbean Region , Damage Assessment , Socioeconomic Factors , Economic DevelopmentABSTRACT
This paper identifies the effects of natural disasters on economic development and living conditions in the Latin American and Caribbean region. On the basis of quantitative analyses and undertaken to asses the damage caused by the main natural disasters which have occurred in the region during the past 16 years, the author justifies the undertaking of preventive, planning and preparedness measures to reduce the impact of disasters(AU)
