Cloud Computing Steps Up Undergraduate Research

Rhiann Swancutt (left) and Jenna Nieveen (right) had to start from scratch to learn cloud computing. (Image by Tessa Durham Brooks/Doane University)

By Shelley Littin

Jenna Nieveen and Rhiann Swancutt, senior honors students studying biology at Doane University, are “not technological people,” Nieveen said, “at all.”

The undergraduates thus were somewhat alarmed when Tessa Durham Brooks, their honors theses advisor and an associate professor of biology at Doane, asked them to complete their projects using CyVerse’s cloud-computing platform Atmosphere.

Nieveen studies small nucleolar RNA molecules, called snoRNAs, that guide the chemical modifications of other RNA molecules (RNA, or ribonucleic acid, is found in all living cells and carries instructions for protein synthesis, among other purposes).

Nieveen was interested in a specific snoRNA called snoR30, which could be involved in controlling how roots grow in response to gravity in Arabidopsis (a member of the mustard family that is commonly used for research) seedlings.

Arabidopsis root growth

Brooks’ previous experiments had indicated that different sizes of seedlings affected the way roots grew: large seeds produced uniform root tip angles, while small seeds produced roots with much more variation. Brooks also found that snoR30 was downregulated, or not highly expressed, in the large seeds, but the same snoRNA was expressed in small seeds.

Nieveen wanted to find out if snoR30 was responsible for root variation. She examined small seeds with snoR30 unexpressed to determine if they then grew root tip angles similar to the large seeds.

She planted seeds with mutated, unexpressed snoR30, let them grow, and then imaged the roots after gravity had stimulated root growth (shown at right). “That’s where CyVerse came into play,” Nieveen explained. “Once we collected the pictures we transferred them into Atmosphere to calculate root tip angle based on the images.”

Brooks introduced Nieveen to the suite of CyVerse computational tools, but she had to learn to use them by herself. “I had never used a virtual machine before,” Nieveen said. “But somehow, I did it. Atmosphere was pretty self-explanatory with a little guidance. It was easy enough for somebody with no computer skills to figure out.”

Nieveen was delighted to be able to do the computational component of her honors project by herself, and “once I got it the first time, it was easy,” she said.

She found that the small seeds with mutated, unexpressed snoR30 did become more uniform, but still not as much as the large seeds. She concluded that snoR30 is important in determining how roots grow in response to gravity, but is likely not the only genetic factor that plays a role.

Rhiann Swancutt and Jenna Nieveen

Meanwhile Swancutt focused on determining whether a gene called ppr–1 plays a role in glutamate biochemical pathways that affect root growth in Arabidopsis. She compared ppr–1 to a mutated gene, glr3.3, which is known to affect glutamate pathways, and the corresponding unmutated, wild type gene.

Swancutt grew samples of Arabidopsis that had either glr3.3, the wild type gene, or ppr–1 expressed. Like Nieveen, she used an automated software to collect hundreds of infrared images of the plants’ root growth. She also used CyVerse’s Atmosphere platform to measure the plants’ root tip angles and help her understand the data after processing.

Swancutt determined that root growth of the plants with ppr–1 were significantly different from the plants with the wild type gene, indicating that ppr–1 is a likely component affecting the glutamate biochemical pathways controlling root growth.

Glutamate receptors in Arabidopsis are remarkably similar to the same receptors in the mammalian central nervous system, which allows biologists to compare the two systems, Swancutt explained: “we have these similar mechanisms despite the fact the organisms are completely different.”

The biological connection between Arabidopsis and humans is what Swancutt finds most intriguing. It shows the bridge point between animals, specifically mammals, and plants,” she said. Swancutt hopes to work as a lab technician after graduating, and later attend graduate school.

Nieveen, who plans to study occupational therapy as a graduate student, believes her experience with computational sciences may help her future career. “In the health system there are always new technological advances. Figuring out the computational part of my project on my own gave me confidence that I can adapt to whatever technological systems may get thrown at me in the medical field.”