Supplementary material 1 Real-time quantitative PCR: Sequences of the primers and TaqMan probe for ADAMTS1, 4, 5, 8, 9 and 15 were designed using Primer Express software (Applied Biosystems, Foster City, CA): forward primer 5’-CCATCCCAAGAGTATCACATGTCT-3’, reverse primer 5’-CACTATGACACAGCAATTCTTTTCAC-3’ and TaqMan probe 5’-FAM-CCCACACAAGTCCTGTC-MGB-3 for ADAMTS1; forward primer 5’-TCACTGACTTCCTG...

A sensitive, labor-saving, and easily automatable nonradioactive procedure named APEX-FCS (amplified probe extension detected by fluorescence correlation spectroscopy) has been established to detect specific in vitro amplification of pathogen genomic sequences. As an example, Mycobacterium tuberculosis genomic DNA was subjected to PCR amplification with the Stoffel fragment of Thermus aquaticus...

A molecular maker for authenticating species origin of the stingless bee (Trigona collina) was developed. Initially, amplified fragment length polymorphism analysis was made of 11 stingless bee species using 64 primer combinations. A 316-bp band found only in T. collina was cloned and sequenced. A primer pair (CUTc1-F/R) was designed and tested for species-specificity in 15 stingless bee specie...

Recent data suggest that small differences in editing efficiency can have significant functional consequences. Here we present a fluorescent poisoned primer extension assay that is capable of distinguishing editing efficiency differences as low as 5%. For a poison-primer extension assay to be accurate, the extension product must stop at the intended base. Sometimes, however, it runs beyond. We ...

BACKGROUND Neonectria ditissima is one of the most important fungal pathogens of apple trees, where it causes fruit tree canker. Information about the amount and partitioning of genetic variation of this fungus could be helpful for improving orchard management strategies and for breeding apple cultivars with high levels of genetically determined resistance. In this study single-spore Neonectria...

A PCR primer sequence is called degenerate if some of its positions have several possible bases. The degeneracy of the primer is the number of unique sequence combinations it contains. We study the problem of designing a pair of primers with prescribed degeneracy that match a maximum number of given input sequences. Such problems occur when studying a family of genes that is known only in part,...

PCR is routinely used in detection of antibiotic resistance genes including different classes of tet and erm genes. It remains unknown how PCR conditions affect detection of resistance genes in terms of genetic diversity and prevalence. In this study, numbers of PCR cycles and MgCl2 concentrations were evaluated for their effect on the diversity and prevalence of the tet genes that encode ribos...

objectives: this study aimed to compare the microleakage beneath metallic brackets following two different methods of enamel preparation and light curing. materials and methods: a total of 120 bovine deciduous lower incisors were randomly divided into four groups of 30 teeth. the preparations were as follows: group i: acid etching + transbond xt primer + direct illumination, group ii: acid etch...

objectives: micromechanical retention of resin cements to alloys is an important factor affecting the longevity of metal base restorations. this study aimed to compare the bond strength and etching pattern of a newly introduced experimental etchant gel namely nano met etch with those of conventional surface treatment techniques for nickel-chrome (ni-cr) and high noble alloys.  materials and met...

The genetic diversity of Desulfovibrio species in environmental samples was determined by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified [NiFe] hydrogenase gene fragments. Five different PCR primers were designed after comparative analysis of [NiFe] hydrogenase gene sequences from three Desulfovibrio species. These primers were tested in different combinations on the genomic DN...