Monday, August 20, 2018

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A new course at SDSU this semester teaches students viral discovery techniques. A new course at SDSU this semester teaches students viral discovery techniques.
 


New Course in Virus Hunting

Students can win a semester’s tuition with their presentation on viral discovery and metagenomics.
By Michael Price
 

“Viral discovery is critical for understanding how viruses evolved inside of us and in other ecosystems, and what they mean for human and ecosystem health.”

A few years ago, San Diego State University computer scientist Rob Edwards made headlines when he used a new computational technique to discover a previously unknown virus that lives in the guts of more than three-quarters of the world population. Beginning this semester, SDSU students will have that same chance in a new course that teaches viral discovery techniques.
 
And as a bonus, they will also compete to win a semester’s tuition financed by the professional services firm Deloitte Consulting.

In 2014, Edwards and colleagues devised computer software known as “cross assembly” that sorts through the DNA and RNA present in a sample, separates out the known microbes, and locates the genetic signatures of a virus. Using this, they discovered crAssphage, a type of virus known as a bacteriophage, which reproduces inside bacteria. It’s unclear what crAssphage does physiologically, but by analyzing samples from around the world, Edwards discovered that more than 75 percent of people have it.

Up to 48 undergraduate students enrolled in the newly created Biology 499: Microbial Metagenomics Discovery Challenge course will learn how to use the cross assembly program, then apply those skills by hunting for new viruses—as well as looking for the genetic hallmarks of antibiotic resistance—in real datasets of DNA. The independent study course doesn’t have any prerequisites, Edwards said, but a background in biological sciences or computer science would be helpful.

At the end of the semester, students will create a 3-5 minute video using the university’s Learning Glass technology to explain the tools they’ve learned, the importance of viral discovery and antibiotic resistance, and their discoveries. A committee of judges from SDSU will select the best presentation and that student will win a semester’s tuition.

The funding for this award comes from a gift to SDSU’s philanthropic auxiliary, The Campanile Foundation, by Deloitte Consulting, which is seeking to promote students entering the metagenomics workforce after graduation.

In addition to Deloitte, SDSU is partnering with the City University of New York (CUNY) in New York City and the National Center for Biotechnology Information (NCBI) to design and teach the course’s curriculum. Guest lecturers from CUNY and NCBI will help teach the course, and Edwards will visit CUNY as a guest lecturer. The partnership is an example of the type of academic-industry partnerships SDSU envisions taking place in the newly opened Engineering and Interdisciplinary Sciences Complex, which emphasizes interdisciplinary collaboration and connections to local, national and international industry partners.

“Viral discovery is critical for understanding how viruses evolved inside of us and in other ecosystems, and what they mean for human and ecosystem health,” Edwards said. “This course will help inspire a new generation of scientists to find the next crAssphage.”