Factors influencing DNA expansion in the course of polymerase chain reaction

A Pilot Study to Investigate the Feasibility of a Multiple Locus Variable Number Tandem Repeat Analysis to Understand the Epidemiology of Dichelobacter nodosus in Ovine Footrot

Dichelobacter nodosus is the essential pathogen in ovine footrot, an important cause of lameness in sheep that reduces productivity and welfare. The aim of this study was to investigate the feasibility of using multiple locus variable number tandem repeat analysis (MLVA) developed to investigate isolates to understand the molecular epidemiology of Dichelobacter nodosus in ovine footrot by investigation of communities of strains. MLVA sensitivity was improved by optimizing PCR conditions to 100% specificity for D. nodosus. The improved MLVA scheme was used to investigate non-cultured DNA purified from swabs (swab DNA) and cultured DNA from isolates (isolate DNA) from 152 foot and 38 gingival swab samples from 10 sheep sampled on four occasions in a longitudinal study. Isolate DNA was obtained from 6/152 (3.9%) feet and 5/6 yielded complete MLVA profiles, three strains were detected. Two of the three isolate strains were also detected in isolate DNA from 2 gingival crevice cultures. Complete MLVA profiles were obtained from swab DNA from 39 (25.7%) feet. There were 22 D. nodosus community types that were comprised of 7 single strain and 15 multi-strain communities. Six community types were detected more than once and three of these were detected on the same four sheep and the same two feet over time. There were a minimum of 17 and a maximum of 25 strain types of D. nodosus in the study. The three isolate strain types were also the most frequently detected strain types in swab DNA. We conclude that the MLVA from swab DNA detects the same strains as culture, is much more sensitive and can be used to describe and differentiate communities and strains on sheep, feet and over time. It is therefore a sensitive molecular tool to study D. nodosus strains directly from DNA without culture.

High GC contents of primer 5'-end increases reaction efficiency in polymerase chain reaction

Many studies have suggested that regulation of the polymerase chain reaction (PCR) is influenced by several factors. However, the understanding of reaction efficiency factors is not sufficient. Here we propose that high GC contents of primer 5'-end increases reaction efficiency in PCR. Using 71 primers (45 pairs), we analyzed factors that affect reaction efficiency, and statistically tested the correlation between the amplification signals and several factors. As a result, there were significant correlations between the amplification signals and the GC contents in the first 1 approximately 3 bps of primer 5'-end.

Genome-wide copy number alterations detection in fresh frozen and matched FFPE samples using SNP 6.0 arrays

SNP arrays offer the opportunity to get a genome-wide view on copy number alterations and are increasingly used in oncology. DNA from formalin-fixed paraffin-embedded material (FFPE) is partially degraded which limits the application of those technologies for retrospective studies. We present the use of Affymetrix GeneChip SNP6.0 for identification of copy number alterations in fresh frozen (FF) and matched FFPE samples. Fifteen pairs of adenocarcinomas with both frozen and FFPE embedded material were analyzed. We present an optimization of the sample preparation and show the importance of correcting the measured intensities for fragment length and GC-content when using FFPE samples. The absence of GC content correction results in a chromosome specific "wave pattern" which may lead to the misclassification of genomic regions as being altered. The highest concordance between FFPE and matched FF were found in samples with the highest call rates. Nineteen of the 23 high level amplifications (83%) seen using FF samples were also detected in the corresponding FFPE material. For limiting the rate of "false positive" alterations, we have chosen a conservative False Discovery Rate (FDR). We observed better results using SNP probes than CNV probes for copy number analysis of FFPE material. This is the first report on the detection of copy number alterations in FFPE samples using Affymetrix GeneChip SNP6.0.

Simple sequence repeats in prokaryotic genomes

Simple sequence repeats (SSRs) in DNA sequences are composed of tandem iterations of short oligonucleotides and may have functional and/or structural properties that distinguish them from general DNA sequences. They are variable in length because of slip-strand mutations and may also affect local structure of the DNA molecule or the encoded proteins. Long SSRs (LSSRs) are common in eukaryotes but rare in most prokaryotes. In pathogens, SSRs can enhance antigenic variance of the pathogen population in a strategy that counteracts the host immune response. We analyze representations of SSRs in >300 prokaryotic genomes and report significant differences among different prokaryotes as well as among different types of SSRs. LSSRs composed of short oligonucleotides (1-4 bp length, designated LSSR(1-4)) are often found in host-adapted pathogens with reduced genomes that are not known to readily survive in a natural environment outside the host. In contrast, LSSRs composed of longer oligonucleotides (5-11 bp length, designated LSSR(5-11)) are found mostly in nonpathogens and opportunistic pathogens with large genomes. Comparisons among SSRs of different lengths suggest that LSSR(1-4) are likely maintained by selection. This is consistent with the established role of some LSSR(1-4) in enhancing antigenic variance. By contrast, abundance of LSSR(5-11) in some genomes may reflect the SSRs' general tendency to expand rather than their specific role in the organisms' physiology. Differences among genomes in terms of SSR representations and their possible interpretations are discussed.