Bringing General Genetics Students onto the Red Line: One Lab Period Lessons for New Genomics Students

A well-educated citizen is the foundation for democracy, yet most undergraduate students do not have undergraduate research experiences that allow them to absorb many of the key concepts which are necessary for a basic understanding of genomics.  The DNA Subway was developed to bridge this gap as it compiles sophisticated gene searching algorithms and cDNA and predicted protein databases with easily generated GBrowse output.  A one-lab (2.5 hour) exercise that guides students through the Red Line of the DNA Subway has been developed.  Students download an Arabidopsis BAC accession from NCBI and take it through the Red Line, noting repetitive DNA, different outputs of gene prediction programs and the alignment to known cDNAs and predicted proteins.  Students then download a BAC sequence from muskmelon, and are able to observe what occurs when cDNA and EST coverage is limited.  Finally, students work in groups to take a new Arabidopsis BAC through the DNA Subway and answer a list of synthetic questions.  This exercise has been taught by Masters-level Teaching Assistants to six lab sections (28 students each) for two years, and has received positive comments from both teaching assistants and students.  In collaboration with CSUPERB, two other modules that cover more advanced skills, annotation of splice sites and evolutionary relationships among genes, have also been developed.  All three modules are available at http://gep.wustl.edu/curriculum/course_materials_GEP_partners/csuperb_workshop.