Choice of Separation Matrix

Gels of 12% hydrolyzed potato starch have been the mainstay of isozyme analysis for decades, Advantages are cost and throughput. A single starch gel can yield 3-4 horizontal slices (possibly more), each of which can be stained for a different enzyme. Depending on the size of the filter-paper wicks used for sample loading and the width of the gel, 20-50 or more samples can be loaded per gel. Thus, more than 200 data points (50 individuals times four enzymes) can be obtained per gel once the system is optimized, and an average of 80 or more is common. This high sample capacity is excellent for population genetics analyses that require large sample sizes for meaningful conclusions. Starch gels can be photographed easily for a permanent record.

A newer approach is to use precast cellulose-acetate plates obtained from commercial suppliers. This technique has been used for many years in medical diagnostics but has only been applied to isozyme analysis in general since the mid 1980s (Hebert and Beaton 1993). Advantages of cellulose acetate are that the pre-cast gels can be purchased ahead of time and stored dry until needed, so there is no time, effort, or skill involved in pouring the gels; specially designed gel boxes and sample applicators can be purchased so a laboratory can be set up quickly; and the complete analysis can be run in an hour from start to finish, so many runs can be completed in the same day. Very small volumes are needed so extremely small amounts of tissue can be analyzed. The stained gels can be photographed or the gels themselves dried and saved for a permanent record.

Isozymes also can be separated on many other types of solid matrix and approach, such as polyacrylamide gels or using isoelectric focusing. Polyacrylamide in particular is often used in an attempt to gain increased resolution. Although these systems often do reveal additional bands, the banding patterns can be difficult to interpret genetically. Furthermore, throughput and ease of use are lower, and costs often are higher compared to starch and cellulose acetate.

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