Transposable Elements, Gene Discovery, and DNA Barcoding (Yellow and Blue Lines)

DNA sequence analysis can be a daunting task due to multiple file formats, many programs, and a myriad of steps. DNA Subway was developed for students and scientists to simplify the process. The Yellow Line of the DNA Subway is used to characterize the TE landscape of an organism’s genome and identify recently active elements using either nucleotide or protein sequences. We will walk through the process of identifying a TE family in the genome of an organism. Within this family of elements we will identify the potentially active elements. The Yellow Line can also be used to characterize gene families. This powerful feature uses a protein query to find and predict gene structure. Comparing host gene trees with TE can be used to demonstrate positive selection on vital host genes versus the relaxed selection on TEs.

DNA barcoding is a methodology for student groups to explore species relationships and learn current molecular techniques. In spring 2013 and 2014 students from three local community colleges met on a Saturday at the Neil A. Campbell Science Learning Laboratory at UCR to amplify gene of plants or animals. Back at their respective campuses the students analyzed DNA sequences using the Blue Line. They collaborated remotely with UCR staff using an online notebook. The students met for a second Saturday on the UCR campus for a poster session. In addition to the scientific research experience the students received an introduction to the benefits continuing for a bachelors degree in science.