Teaching the toolkit

Abstract

A major finding of comparative genomics and developmental genetics is that metazoans share certain conserved, embryonically deployed signaling pathways that instruct cells as to their ultimate fate. Because the DNA encoding these pathways predates the evolutionary split of most animal groups, it should in principle be possible to clone representatives of such signaling pathways from almost any species, demonstrating their sequence conservation. Here I describe an 8‐week laboratory series that tests this prediction by attempting to clone multiple members of a known signaling pathway from a species where the targets are unknown. Beginning with the molecular components of a signaling pathway and publicly available sequence information from related taxa, students designed partially degenerate PCR primers to amplify the corresponding mRNA sequences from a “new” organism, in this case a turtle ( Trachemys scripta ). Using a single round of degenerate PCR and standard DNA cloning techniques, we were able to retrieve 6 out of 16 species‐specific homologs on the first attempt (∼40% success rate). To conclude the project, the novel sequences were submitted back into the original public database. The molecular methods of the lab can be adapted to any combination of pathway and organism, demonstrating the conserved components of cellular signaling in any biological process, from gastrulation to aging. The linked labs offer intensive research–based training in bioinformatics and molecular biology, while empirically demonstrating the ubiquity of the metazoan cell‐signaling toolkit.