Background.  Escherichia coli is a highly clonal pathogen. Extraintestinal isolates belong to a limited number of genetically related groups, which often exhibit characteristic antimicrobial resistance profiles. Methods.  We developed a rapid clonotyping method for extraintestinal E coli based on detection of the presence or absence of 7 single nucleotide polymorphisms (SNPs) within 2 genes (fu...

Flavescence dorée (FD) is the most threatening grapevine yellows (GY) disease in Europe. Despite strict control measures, alarming signs of spread viticultural areas continue to be detected. FD attributed infection by phytoplasma strains an incidentally cited species, ‘Candidatus Phytoplasma vitis’. In 2017, a GY field survey was carried out traditional viticulture Tuscany, central Italy. (FDp)...

Since 2004, variable-number tandem-repeat (VNTR) typing of Mycobacterium tuberculosis complex isolates has been applied on a structural basis in The Netherlands to study the epidemiology of tuberculosis (TB). Although this technique is faster and technically less demanding than the previously used restriction fragment length polymorphism (RFLP) typing, reproducibility remains a concern. In the ...

Uncovering DNA sequence variations that correlate with phenotypic changes, e.g., diseases, is the aim of sequence variation studies. Common types sequence variations are Single nucleotide polymorphism (SNP, pronounced snip).SNPs are the third-generation molecular marker. SNP represents a DNA sequence variant of a single base pair with the minor allele occurring in more than 1% of a given popula...

Much attention is being given to the identification of common disease genes through whole-genome linkage disequilibrium (LD) screens with single nucleotide polymorphisms (SNPs). Simulation studies have suggested that useful LD is unlikely to extend beyond 3 kb, and that > 500 000 SNPs may be needed for comprehensive coverage of the genome. The TCR α/δ locus on chromosome 14q contains many V, J ...

objective(s): the development of reliable and ecofriendly process for the synthesis of nano-metals is an important aspect in the field of nanotechnology. nano-metals are a special group of materials with broad area of applications. materials and methods: in this study, extracellular synthesis of silver nanoparticles (snps) performed by use of the gram positive soil streptomycetes. streptomycete...

We used the LOKI software to generate multipoint identity-by-descent matrices for a microsatellite map (with 31 markers) and two single-nucleotide polymorphism (SNP) maps to examine information content across chromosome 7 in the Collaborative Study on the Genetics of Alcoholism dataset. Despite the lower information provided by a single SNP, SNP maps overall had higher and more uniform informat...

BACKGROUND A large isoniazid-resistant tuberculosis outbreak centred on London, United Kingdom, has been ongoing since 1995. The aim of this study was to investigate the power and value of whole genome sequencing (WGS) to resolve the transmission network compared to current molecular strain typing approaches, including analysis of intra-host diversity within a specimen, across body sites, and o...

Genotyping in DNA pools reduces the cost and the time required to complete large genotyping projects. The aim of the present study was to evaluate pooling as part of a strategy for fine mapping in regions of significant linkage. Thirty-nine single nucleotide polymorphisms (SNPs) were analyzed in two genomic DNA pools of 384 individuals each and results compared with data after typing all indivi...

To make large-scale association studies a reality, automated high-throughput methods for genotyping with single-nucleotide polymorphisms (SNPs) are needed. We describe PCR conditions that permit the use of the TaqMan or 5' nuclease allelic discrimination assay for typing large numbers of individuals with any SNP and computational methods that allow genotypes to be assigned automatically. To dem...