Starting in 2019, Fort Lewis College has been one of several universities awarded funds through the Environmental Protection Agency’s People, Prosperity and Planet (P3) grant program.
This grant is provided to support student-led research towards developments in technology to combat issues of public health and environmental challenges, according to the EPA’s website.
Research was led by Yiyan Li, an associate professor of computer engineering, with the goal of identifying and analyzing waterborne bacteria in a sample, such as water from the Animas River or rural areas.
Researchers hope results from the study will help rural residents identify water contaminants sooner, Li said.
Students recreating by the Animas River, a collection site for water samples.
The first phase of this research was centered around developing an in-house polymerase chain reaction machine, or PCR machine, that allows scientists to amplify DNA from water and biological samples to detect any present pathogens, Li said.
Li spoke on some of the other collaboration opportunities this research has led to. “Because of the EPA grant, I was able to reach out to a professor at Navajo Tech University.”
“She said she used a traditional method to look at the quality of the water. Then she and her team found out the drinking water in the wells was contaminated,” Li said. “Eventually they tracked it down to a leak of the sewer pipe to the wells in the local community.”
With the understanding that access to water quality data is not something regularly updated for many rural communities, Li said with, “our rapid water monitoring technology, if we can have a functioning machine to give them, they can maybe do it every week or every month to avoid this kind of issue in the future. That will be a really significant contribution.”
In 2019, FLC’s team of researchers were able to build a PCR device for about $250. “The commercial ones probably cost somewhere around $30,000,” said Li.
Student researcher Don Ledvina spoke on his involvement with the project. “When I first started working under Li, I was a high school senior.”
As a student dual majoring in environmental biology and computer engineering, Ledvina said that his main goal is to combine these two fields for the development of technology to help the environment at large.
One of the ultimate objectives for the PCR device was for it to be fast and easily deployable, something that could be taken out into the field and used there, Ledvina said.
The device utilizes a laser beam that interacts with the water sample. DNA glows when passed under the laser, which is then quantified to record the strength and amount of DNA present, Ledvina said.
This data was collected through a process known as digital droplet PCR, or ddPCR.
“Through microfluidics, we created small droplets of water suspended in a surfactant, or an oil. That way, we have these small quantities of bacteria within each of these droplets. Then we'd run the PCR to amplify the DNA in these droplets, which would cause them to glow if they had the bacteria we were looking for in them,” Ledvina said.
Most of these tests were centered around identifying the presence of waterborne E. coli in water samples collected from the Animas River.
Ledvina spoke on this as a prevalent form of research that is also conducted annually as the final project for Biology 113.
Analysis conducted through the P3 grant research has determined levels of E. coli in water samples from the Durango area as being insufficient to pose a threat to public health, Li said.
Later in 2023, FLC was a recipient of the 19th annual P3 grant. At this time, students switched gears from PCR development and focused their efforts on conducting research with Raman spectroscopy paired with a deep learning AI model, Li said.
“Raman spectroscopy is basically this idea where you shoot a laser at a substance, and when it hits it, it'll give off a certain scattering of light,” Ledvina said. “This scattering effect is unique to every substance it hits.”
Using this process, the laser and spectrometer can be finely tuned to catch the scattered light to the point single bacterium cells can be identified. This gives the researcher a good understanding of what kind of bacteria is present, Ledvina said.
“The Raman system and the digital droplet PCR system were two separate things. Raman doesn’t have anything to do with droplets of water, it just focuses on bacteria.” Ledvina said
The research with Raman spectroscopy was paired with the programming of a deep learning AI model. Li said, “The reason that we need to use deep learning is because the Raman signal from bacteria or the bio samples is really small.” By training the model with thousands of bacteria samples, researchers ”don't have to read, resample and then recollect” data.
“That's a really time consuming part of it.” Li said.
The experiments in using Raman spectroscopy proved to be not worth further development for FLC’s purposes. The research team wants to use other researcher’s published systems on Raman to train their AI models, Li said.
FLC was not entirely reliant on the EPA to grow their labs and train students. Other federal and local grants were leveraged for these activities, Li said.
“We are engaged with a bigger grant collaborator in University of Colorado Boulder, because we have other research projects supported by the National Science Foundation.” Li said.
“They have a really strong optics lab, and one of the professors is really interested in Raman spectroscopy.”
On top of reducing costs and computation time, this research has assisted students with getting work outside of school. Almost 80% of students in computer engineering are getting full-time summer internships, Li said.
Jennifer Lowell, professor of biology and public health, expanded on the importance of technological advancement as it pertains to public safety.
“Right now, our more traditional methods in Microbiology and Molecular Biology can take anywhere from 24 hours to two days even to detect pathogenic microbes, because you have to grow them in the laboratory and then go through a series of tests to identify their species to see if they're actually problematic,” Lowell said.
Lowell said she sees an application with well water too.
“You wouldn't expect to have E. coli in well water, but if you do, there's a potential source of contamination getting into the well somehow from surface water,” Lowell said.
Testing wells for potential breaches, either from runoff or structural distress can help individuals put prevention measures in place, Lowell said
“Any application or technology that can be developed to speed up bacterial identification is a real boon to public health, because time is really of the essence,” Lowell said.