High school students came to Tufts this summer to learn the intricacies of bioinformatics
In a typical biology experiment, especially those involving genomic sequencing, scientists might have to analyze up to 20 million pieces of data. They use sophisticated computational techniques to organize and decipher that complex biological data, which has given rise to the field known as bioinformatics.
This summer at Tufts, 18 students came from around the country—some from as close as Somerville, Medford and Boston, and others from as far away as Florida and Texas—to learn about bioinformatics firsthand, using advanced molecular biology and genetics techniques. They employed a state-of-the-art DNA sequencer, which determines the exact order of nucleotides, one of the building blocks in a DNA molecule.
While this is pretty advanced work for high school students, bioinformatics is now the foundation of biomedical research.
“In the post-genome era, you have to be able to incorporate a whole lot of information, and that requires computational skills that are now a necessary part of biology,” says Donna Slonim, an associate professor of computer science in the School of Engineering who helped create and teach the NIH-funded course, Bioinformatics Inquiry through Sequencing, or BIOSEQ.
High school is just the place to start introducing these concepts, which help get students excited about the possibilities of a career in science, says Slonim. “DNA has entered the popular imagination and permeated the culture, so students are already intrigued,” she says. But the equipment and specialized expertise required for teaching bioinformatics are beyond the reach of most high schools.
Seeing the need to introduce more sophisticated science to young students, Slonim and David Walt, a University Professor and the Robinson Professor of Chemistry in the School of Arts and Sciences, teamed up to win a five-year, $1.3 million NIH Science Education Partnership Award (SEPA). The grant will allow this summer’s course to be repeated over the next three years and will also fund related projects to support the teaching of bioinformatics and genetic sequencing in area high schools. SEPA awards create partnerships between researchers at institutions like Tufts and teachers and students at secondary schools in their surrounding communities.
“The tools available to collect genetic data are outstripping our ability to process these data into meaningful information,” says Walt. “There are tremendous opportunities available for students to contribute to this area. Our goal for the course was to get them interested in this important field by introducing them to some of the fundamental techniques while using real experimental data.”
While the current emphasis in bioinformatics is genetic sequencing—used for identifying everything from ancestry to markers for disease—it is far broader than that, Slonim says. It can, for example, include computations to analyze data about the West African Ebola epidemic being gathered by people on the ground; this information can track the spread of the disease and help prevent future epidemics, she says.
Watching Genetic Mutations
Tufts students were a key part of the teaching team. Two graduate and six undergraduate students taught the class and created future BIOSEQ experiments for the Tufts course.
This summer’s class projects were developed by undergraduates under the guidance of Candice Etson, a postdoctoral fellow in Walt’s lab who holds a doctorate in biophysics from Harvard. She taught the hands-on lab portions of the course.
She worked with recent graduate Tabitha Amondi, A14, to devise a way for the high school students to understand the rarity and effects of genetic mutations. They grew colonies of cells containing plasmids, or small DNA molecules that are separate from the chromosomal DNA, and then had students observe mutations within the colonies. These particular plasmids were chosen because mutations can appear distinct in color from the rest of the colonies. Students could observe mutations as white while non-mutated colonies remained blue.
In sequencing the DNA of the colonies, students discovered some mutations that could not be seen under a microscope.
“It taught them that genetic mutations don’t always have an observable, physical effect. It’s not always like X-Men,” Etson says. “A genetic mutation does not always produce a change in either the composition of a cell or in a living thing.”
Etson also partnered with Nathan Lingafelter, A14, to devise experiments in which the high schoolers learned about bacteria that live behind their ears and on the roofs of their mouths; they isolated small pieces of DNA from each site and determined what kind of microbes were present.
“In those cases, we had a sample that was a mixture of all kinds of DNA,” Etson says. “Looking at the DNA sequences of the molecules in the sample, you can put them into groups and categorize them by similarities. Then you can match the DNA to a particular bacterium.”
The ability to sequence and categorize DNA requires sophisticated algorithms and intricate programming. For that piece of the work, Phil Braunstein, a graduate student in computer science, taught the high school students about the computer science behind the programs they were using to sequence and sort DNA.
With bioinformatics, “there has been a whole paradigm shift in how we do biology,” he says. “That’s why I was so excited to teach high school students how these programs work. It really is the future of research.”
Gail Bambrick can be reached at gail.bambrick@tufts.edu.
