For PFGE analysis

Trapitz P. and Bunemann H. 1992. Preparation of high molecular weight DNA from Drosophila adults for PFGE analysis. Trends Genet. 8 371-372. 

LC-MS intact protein expression profiles assigned the correct serovar type for all 36 isolates, as determined by the study key based on PFGE and WGS of the outbreak samples. Mass and abundance profiles generated from triplicate analysis of each strain were used for PCA analysis. Each of the 36 isolates clustered into one of four distinct clusters corresponding to each of the four serovars. Although LC-MS may not provide the strain-level specificity of WGS, LC-MS should offer the same level of specificity as any marker-based method but without the need for preselection of markers. This offers flexibility given that different combinations of markers will be required depending on the serovar in question. 

A recently acquired DNA sequencer gave us the opportunity to use another modem technique for bacterial identification, multiple-locus variable number tandem repeat analysis (MLVA). MLVA is a higher-resolution technique and permits better differentiation of F. tularensis strains that had an identical PFGE pattern. 

Once the HMW DNA is separated via PFGE, standard methods for DNA transfer to a membrane (Protocol 29.4) and Southern hybridization analysis are used to visualize specific HMW fragments. 

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