ABSTRACT
BACKGROUND: Mutations in the KRAS gene have been identified in approximately 50% of colorectal cancers (CRCs). KRAS mutations are well established biomarkers in anti–epidermal growth factor receptor therapy. Therefore, assessment of KRAS mutations is needed in CRC patients to ensure appropriate treatment. METHODS: We compared the analytical performance of the cobas test to Sanger sequencing in 264 CRC cases. In addition, discordant specimens were evaluated by 454 pyrosequencing. RESULTS: KRAS mutations for codons 12/13 were detected in 43.2% of cases (114/264) by Sanger sequencing. Of 257 evaluable specimens for comparison, KRAS mutations were detected in 112 cases (43.6%) by Sanger sequencing and 118 cases (45.9%) by the cobas test. Concordance between the cobas test and Sanger sequencing for each lot was 93.8% positive percent agreement (PPA) and 91.0% negative percent agreement (NPA) for codons 12/13. Results from the cobas test and Sanger sequencing were discordant for 20 cases (7.8%). Twenty discrepant cases were subsequently subjected to 454 pyrosequencing. After comprehensive analysis of the results from combined Sanger sequencing–454 pyrosequencing and the cobas test, PPA was 97.5% and NPA was 100%. CONCLUSIONS: The cobas test is an accurate and sensitive test for detecting KRAS-activating mutations and has analytical power equivalent to Sanger sequencing. Prescreening using the cobas test with subsequent application of Sanger sequencing is the best strategy for routine detection of KRAS mutations in CRC.
Subject(s)
Humans , Biomarkers , Codon , Colorectal NeoplasmsABSTRACT
Bacteria, actinomycetes and fungi are the three major groups of soil microbes. Soil microbes play a critical role in ecological and biodegradation processes in petroleum-contaminated soils. Based on the actual situation, this study took the oil polluted soil around the abandoned oil well in Shehong County, Suining City, Sichuan Province as the test soil. First, we determined the physiochemical properties of the tested soil; then we analyzed the changes of physiochemical properties and the three major microbes in petroleum contaminated soils. The number of the three major microbes in contaminated soils was relatively fewer than uncontaminated samples, and the water content of the soil was in positive correlation with the number of microbes. Also we assessed the soil bacteria community diversity and changes therein in petroleum-contaminated soils using 454 pyrosequencing of 16S rRNA genes. No less than 23 982 valid reads and 6 123 operational taxonomic units (OTUs) were obtained from all 4 studied samples. OTU richness was relatively higher in contaminated soils than uncontaminated samples. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Proteobacteria were the dominant phyla among all the soil samples. However, the prokaryotes community abundance of phyla was significantly different in the four samples. The most abundant OTUs associated with petroleum-contaminated soil sample were the sequences related to Acidobacteria, Actinobacteria and Proteobacteria, whereas the most abundance sequences with uncontaminated sample were those related to Actinobacteria, Bacteroidetes and Proteobacteria.
ABSTRACT
Diariamente los seres humanos están en interacción con objetos de uso continuo, como el papel moneda, sin el conocimiento de que estos almacenan microorganismos y de que nos exponemos al contacto con potenciales patógenos. La composición de la comunidad bacteriana en un billete colombiano fue determinada mediante el secuenciamiento profundo de librerías de amplicones 16S. Se encontraron 233 géneros bacterianos; 12 de estos géneros corresponden a especies con potencial patogénico. El género más abundante fue Propionibacterium, seguido de Streptococcus, Staphylococcus Pseudomonas . Este es el primer reporte de la diversidad bacteriana que puede ser alojada en este objeto de alta circulación en Colombia. Pocos estudios en el mundo han mostrado este nivel de detalle de la microbiota en billetes de circulación y ofrece un panorama mucho más amplio de la exposición diaria a microorganismos al utilizar papel moneda en las condiciones en las que se utiliza en Colombia.
Commonly used objects such as currency paper can be colonised by bacteria and can serve as carriers of microbes. This colonisation might expose us to unnoticed pathogenic bacteria. In this study, the researchers obtained a detailed panorama of the microbes that can be carried on currency notes in Colombia by using 454 next-generation deep sequencing of 16S amplicón libraries. A total of 233 bacterial genera were detected and classified, 12 of which are potential human pathogens. The most abundant genera were Propionibacterium, Streptococcus, Staphylococcus and Pseudomonas. To date, this is the first in-depth analysis of the microbiota carried by circulating banknotes in our continent and it offers insights into daily exposure to microbes when using banknotes in Colombia.
Subject(s)
Humans , Male , Female , Paper , Bacteria , Microbiota , Propionibacterium , Streptococcus , Environmental Health , Colombia , NoxaeABSTRACT
Paeonia suffruticosa also named Moutan that cultivated in five geographic regions during different growth stages were chosen in this study. Biolog and 454 pyrosequencing technology were used to detect the whole microbial activity and fungal diversity for exploring the relationship between the geo-authentic features of the medicinal plant and the rhizosphere microorganism. The results suggest that the value of average well color development (AWCD) from the rhizosphere soil of P. suffruticosa in the five regions at the fo ur growth stage have an increasing tendency. 9 703 operational taxonomic unit (OTU) were obtained from 272 463 high quality sequences according to the similarity of 97% by the pyrosequencing. Fungi in five phyla, twenty-two classes, seventy orders, one hundred and thirty-nine families and two hundred and sixty-six genera were detected in the five regions excluding twelve percent to fifty-eight percent unidentified fungi. They were divided into four branches, i.e. Blastocladiales, Chytridiomycota, Dikarya and Glomeromycetes. Twenty-four genera such as Leptosphaeria were found in the five regions while six genera such as Curvularia were only detected in the geo-authentic regions. The dominant genera were Guehomyces, Exophiala and Fusarium in geo-authentic regions, whereas genus Leptosphaeria, Cryptococcus, Exophiala, Fusarium and Ceratobasidium in non-authentic regions. The results from principal co-ordinates analysis (PCoA) showed that the fungi formations were similar in Tongling and Nanling region at four different growth stages, and the same in Heze at the leaf bud and fruiting stage. According to heatmap analysis, Tongling and Nanling region showed a close similarity in fungal community structures on phylogenetic analysis, while Bozhou, Heze and Luoyang showed the same. In brief, the whole microbial activity was higher in geo-authentic regions than the non-authentic. Fungi in rhizosphere soil of the medicinal peony presented diversity and region specificity. We found not only the abundant new species in the five regions, but also the phylogenetic similarity in the geo-authentic regions.