Gel Scramble: An E-Tool for Teaching Molecular Neuroscience.

In this completely digital teaching module, students interpret the results of two separate procedures: a restriction endonuclease digestion, and a polymerase chain reaction (PCR). The first consists of matching restriction endonuclease digest protocols with images obtained from stained agarose gels. Students are given the sequence of six plasmid cDNAs, characteristics of the plasmid vector, and the endonuclease digest protocols, which specify the enzyme(s) used. Students calculate the expected lengths of digestion products using this information and free tools available on the web. Students learn how to read gels and then match their predicted fragment lengths to the digital images obtained from the gel electrophoresis of the cDNA digest. In the PCR experiment, students are given six cDNA sequences and six sets of primers. By querying NCBI BLAST, students can match the PCR fragments to the lengths of the predicted in silico PCR products. The ruse posed to students is that the gels were inadvertently mislabeled during processing. Although students know the experimental details, they do not know which gel goes with a given restriction endonuclease digest or PCR-they must deduce the answers. Because the gel images are from actual students' experiments, the data sometimes result from mishandling/mislabeling or faulty protocol execution. The most challenging part of the exercise is to explain these errors. This latter aspect requires students to use critical thinking skills to explain aberrant outcomes. This entire exercise is available in a digital format and downloadable for free at http://mdcune.psych.ucla.edu/modules/gel.