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Supercomputing Simulations in Multiyear Study of Corn to Address Food Insecurity Reveal Surprising Molecular Results

Published February 23, 2024

 Credit: Freepik

By Kimberly Mann Bruch, Rajan Tavathia and Cynthia Dillon, SDSC Communications

UC President Postdoctoral Fellow Edwin Solares used high-performance computing resources at the San Diego Supercomputer Center (SDSC) at UC San Diego and UC Irvine to complete a project as part of his mission to help address the growing concern of food insecurity.

According to the U.S. Department of Agriculture, Economic Research Service, food security means “access by all people at all times to enough food for an active, healthy life.” Food insecurity as defined by Feeding America refers to “when people don’t have enough to eat and don’t know where their next meal will come from.” In the U.S. that is a problem for more than 44 million adults and children each year.

The study of genomic features in maize resulted in the discovery of a tiny ribonucleic acid (RNA), as explained in a paper published in the journal Genome Research.

“In this long-term study, we first used the Comet supercomputer to run tens of millions of simulations – looking at how ribonucleic acid (RNA) works within individual maize genes,” said Solares, a lecturer and researcher with the UC San Diego Computer Science and Engineering Department. “We ran our sims primarily on SDSC’s Comet and then switched to a cluster I built at UC Irvine, where I was working at the time.”

Solares said that the team’s simulations of RNA "folding" of various genes, junk DNA, randomized DNA and other genomic features led to a surprising discovery.

“Previous work in this arena focused on ancient viral infections called ‘sireviruses,’ where DNA from the virus was inserted into the genome, was duplicated across the whole genome, and showed that the RNA produced from these ancient viral domains, degrades and creates a specific size RNA due to formation of what we call ‘secondary structure (folding in on itself),’ and regulates and even sometimes shuts down that machinery, effectively silencing it,” Solares explained. “In our study, we saw the same presence of these small RNA that most likely came from sireviruses, but also other ancient viral infections and other repetitive areas – the most interesting finding was the presence of tiny RNA from genes!”

Solares said that this discovery was not expected and the origins of this mechanism – the degradation and cutting into these size fragments – are still unknown, as is the function. He said that now his focus is on examining these small RNA to see if they are from genes or from ancient viral and repetitive domains.

“Was it co-opted into genes or was it co-opted into repeats and ancient viral infections?” Solares asked. “We aren’t quite sure, but we will next use SDSC’s Expanse to better understand this phenomenon and look forward to continuing our work with the center.”

This work was published in the Genome Research journal and funding for the time on Comet and Expanse at SDSC is made possible by the National Science Foundation ACCESS (allocation no. MCB180035).