The fingerprint pattern in the gel was analyzed using a computer software package, Bionumeric (Applied Maths, Belgium). After background subtraction and gel normalization, the fingerprint patterns were typed according to banding similarity and dissimilarity, using the Dice similarity coefficient and unweighted-pair group method employing average linkage (UPGMA) clustering, as recommended by the manufacturer. The results were graphically represented as dendrograms.
Bionumeric
Manufactured by bioMérieux
Sourced in Belgium
Bionumeric is a data management and analysis software developed by bioMérieux. It is designed to streamline the management and interpretation of microbiological data generated in laboratory settings.
Automatically generated - may contain errors
6 protocols using bionumeric
1
Gel Fingerprint Analysis with Bionumerics
2
Fingerprint Pattern Analysis Using Bionumeric
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The fingerprint pattern in the gel was analyzed using a computer software package, Bionumeric (Applied Maths, Belgium, version 3.1). After background subtraction and gel normalization, the fingerprint patterns were typed according to banding similarity and dissimilarity, using the Dice similarity coefficient and unweighted-pair group method employing average linkage (UPGMA) clustering, as recommended by the manufacturer. The results were graphically represented as dendrograms.
3
Pulsed-Field Gel Electrophoresis for Salmonella Typing
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Whole agarose-embedded genomic DNA from the Salmonella isolates was prepared. PFGE was carried out using a contour-clamped homogeneous electrical field-DRII apparatus (Bio-Rad), according to procedures described elsewhere [25 (link)]. Genomic DNA of the test strains was digested by XbaI restriction enzyme (Gibco-BRL, Gaithersburg, MD), and Salmonella Enterica serovar Braenderup was digested using XbaI, with fragments employed as molecular size markers. Restriction fragments were separated in 1% pulsed-field-certified agarose in 0.5X TBE (Tris-borate-ethylenediaminetetraacetic acid) buffer. Post-electrophoresis gel-treatment included gel stained and de-stained. The DNA was visualized using a UV-transilluminator, and images were digitized via a one-dimensional gel documentation system (Bio-Rad). The fingerprint pattern in the gel was analyzed using a computer software package, Bionumeric (Applied Maths, Belgium). The fingerprint patterns were subjected to typing based on banding similarity and dissimilarity, using the dice similarity coefficient and unweighted pair group method employing average linkage (UPGMA) clustering, as recommended by the manufacturer. The results were graphically represented as a dendrogram.
4
Gel Fingerprint Pattern Analysis
5
PFGE Analysis of Vibrio cholerae
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PFGE was performed using the PulseNet recommended procedure. [13 ] The plugs containing agarose embedded V. cholerae DNA were digested with 50 Units/µl of NotI (Takara). For digestion of Salmonella Braenderup H9812 the molecular size marker, XbaI (15 Units/µl) was used and the DNA fragments were separated electrophoretically under the contour-clamped homogeneous electric field (CHEF) on a CHEF DRIII system (Bio-Rad) on 1% PFGE grade agarose gel in 0.5xTBE (44.5 mM Tris/HCl, 44.5 mM boric acid, 1.0 mM EDTA, pH 8.0) at 14°C. Following electrophoresis, the gels were stained for 30 min in Elix MilliQ water (Millipore, Bangalore, India) containing 1.0 µg ethidium bromide, destained in Elix MilliQ water for 15 min and photographed under UV light using the Gel Doc 2000 gel documentation system (Bio-Rad). DNA fingerprint patterns were analyzed using a computer software package, Bionumeric (Applied Maths, Belgium). Fingerprint patterns were typed on the basis of banding similarity using Dice similarity coefficient and unweighted-pair group method using average linkages (UPGMA) clustering methods.
6
Fingerprint Pattern Analysis using Bionumeric
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The fingerprint pattern in each gel was analyzed using a computer software package, Bionumeric (Applied Maths, Belgium). After background subtraction and gel normalization, the fingerprint patterns were typed according to banding similarity and dissimilarity, using the Dice similarity coefficient and unweighted-pair group method employing average linkage (UPGMA) clustering, as recommended by the manufacturer. The results were graphically represented as dendrograms.
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