1d gel documentation system

The whole agarose-embedded genomic DNA for V. cholerae was prepared. PFGE was carried out with a contour-clamped homogeneous electrical field (CHEF-DR II) apparatus (Bio-Rad), according to procedures described elsewhere (Cooper et al., 2006 (link)). Genomic DNAs of the test strains were digested by the NotI restriction enzyme (Gibco-BRL), and Salmonella enterica serovar Braenderup was digested by XbaI, with the fragments being used as molecular size markers. The restriction fragments were separated in 1% pulsed-field-certified agarose in 0.5X TBE (Tris/borate-EDTA) buffer. In the post electrophoresis gel treatment step, the gel was stained and de-stained. The DNA was visualized using a UV trans illuminator, and images were digitized by a 1D gel documentation system (Bio-Rad). The fingerprint pattern in the gel was analyzed using the Bionumeric software (Version 3.1). Dendrogram was constructed on the basis of banding similarity and dissimilarity using the Dice similarity coefficient and unweighted-pair group method (UPGMA) as recommended by the manufacturer.

The whole agarose-embedded genomic DNA for V. cholerae was prepared. PFGE was carried out with a contour-clamped homogeneous electrical field (CHEF-DR II) apparatus (Bio-Rad), according to procedures described elsewhere (37 (link)). Genomic DNAs of the test strains were digested by the NotI restriction enzyme (Gibco-BRL), and Salmonella enterica serovar Braenderup was digested by XbaI, with the fragments being used as molecular size markers. The restriction fragments were separated in 1% pulsed-field-certified agarose in 0.5X TBE (Tris/borate-EDTA) buffer. In the post electrophoresis gel treatment step, the gel was stained and de-stained. The DNA was visualized using a UV trans illuminator, and images were digitized by a 1D gel documentation system (Bio-Rad). The fingerprint pattern in the gel was analyzed using the Bionumeric software (Version 3.1). A dendrogram was constructed on the basis of banding similarity and dissimilarity using the Dice similarity coefficient and unweighted-pair group method (UPGMA) as recommended by the manufacturer.