Using Web-based Tools in the Biology Lab Course Bioinformatics

By Rev. John Braverman, S.J., Assistant Professor, Department of Biology

Undergraduate research has become a major part of science education in the natural sciences. The Summer Scholars Program at SJU is a fine example of a research opportunity for undergrads. Yet, how can even more students experience this type of learning and formation? Is there a way to conduct authentic science more routinely? Recently, my colleagues posted a blog entry on these pages offering such an opportunity through the Biology lab course, Phage Safari. This coordinated, funded program deals with the genetic material of simple, yet diverse viruses found by students in soil samples. I wish now to share with readers a similar but different undergraduate research experience also offered through a Biology course.

My course this semester includes student research on the DNA sequences just obtained from certain types of fruit flies. This data, genomic sequences, are so new, so fresh, that no one knows what’s in it. The students are diving in, laboriously identifying stretches of DNA which are genes — a basic functional unit of heredity.

The course is Bioinformatics (BIO 420), and the research is made possible by the Genomics Education Partnership, centered at Washington University in St. Louis, MO. I have been grateful to receive their data and the web-based tools for the analysis. The main tool is called a genome browser. Sort of like a map, the browser contains and shows visually the DNA sequence, as well as preliminary analysis thereof. The students look at this analysis and see what the computer says about the DNA. However, several competing evidence tracks are shown, often contradicting one another. The computer cannot definitively sort through multiple lines of evidence to identify the genes — but a student can do so with a reasonable amount of training.

Screen capture displaying DNA sequence of D. melanogaster.

This figure illustrates information students use to annotate genes. They must study multiple lines of evidence (“tracks”) presented visually on a genome browser and judge which one(s) to accept. The process is time-consuming, yet rewarding! Perhaps you can notice the actual DNA sequence and possible translations into amino acids. This image is from a portion of the Drosophila biarmapes genome presented in the Gander Genome Browser of the Genome Education Partnership.

In the course of the semester, the students make models of genes right down to the coordinates, for a stretch of DNA assigned to them. What makes it all worthwhile is the joy of seeing all “passes” on the software called the Gene Model Checker. I find it rewarding to witness those moments. Much of this work is done on PCs in Science Center Room 209, but many of the students get set up on their own laptops so they have a personalized portable bioinformatics work station.

Most students share their results in oral presentations to their classmates at the end of the semester. Those of you coming to the Sigma Xi Research Symposium can see the results of three students who are presenting their findings in a poster there. Indeed, they will have gone the full journey of conducting research and presenting it to other scientists.  Meanwhile, all the students have the chance to be co-authors on the papers published using the genomic data, via the Genomics Education Partnership. Beyond merely documenting gene locations (annotation), these papers answer scientific questions about categories of chromosomal segments and their evolution.

For me, I assess student learning to find out if the research experience in a course really compares to that in a summer research experience. Yes, that was borne out in the past and we just submitted a second paper to a major journal documenting this result in more detail. (I am learning a lot about assessment protocols!)

In short, the work of training students to think scientifically and to imagine the intricacy of a very complex genome such as the fly’s has really been a fascinating and valuable experience for me as an educator.