Engineering Organisms for Renewable Energy

Jim Kelley (left) and Tony Lane (center) create mathematical models of organisms to better predict how they can be engineered to produce desirable products. Prof. Desmond Lun (right) oversees their project.

Jim Kelley (left) and Tony Lane (center) create mathematical models of organisms to better predict how they can be engineered to produce desirable products. Prof. Desmond Lun (right) oversees their project.

In the ongoing race to find new methods of sustainability, two Rutgers University–Camden students have pulled ahead of the pack.

Bacteria and other biological organisms can be genetically modified to produce larger amounts of fuel and similar products used for renewable energy. Using a software program they developed, computer science majors Jim Kelley and Tony Lane create mathematical models of organisms to better predict how they can be engineered to produce desirable products.

“We’re able to modify the organisms mathematically to see how they can produce the products we want, like biofuels,” says Kelley, a Gloucester City resident who received a bachelor’s degree in chemistry from Rutgers–Camden in 1991 and returned to the university in 2010 to pursue a degree in computer science. “By removing certain genes, we can determine how much more of a certain chemical the organism will produce, thus providing us with valuable renewable fuels.”

The software, which Kelley and Lane are calling MOST (Metabolic Optimization and Simulation Tool), is similar to other programs that can build mathematical models and perform similar analysis. The difference is simplicity. MOST employs spreadsheet style editing functions that are more user friendly than other software tools.

The research team has been working on the project under the guidance of Desmond Lun, an associate professor and chair of the Department of Computer Science at Rutgers–Camden.

“We want to use microorganisms as chemical factories, but doing that is pretty hard,” says Lun, whose past research has focused on how to alter the genetic makeup of E. coli bacteria to produce biofuel. “The core question is how you modify the organism. We can test these possibilities very quickly using a computer and this program can tell us what genes to knock out to get what we want.”

Kelley and Lane’s research article, “MOST: A Software Environment for Constraint-based Metabolic Modeling and Strain Design,” has been accepted for publication in an upcoming issue of Bioinformatics, a leading science and mathematics publication.

“I’m glad to have been able to work on this project that has an impact on the scientific community,” says Lane, a Riverside resident and graduate of Delran High School who wants to work in computer programming. “Working in collaboration with Dr. Lun and Jim is also a great and valuable experience for me.”

Kelley worked in an environmental testing lab after graduating from Rutgers–Camden in 1991, but became interested in computer science when his wife began taking classes in the subject.

“I feel like I found my niche,” says Kelley, who wants to pursue his doctoral degree in computer science when he graduates in the spring. “I began to realize that this is what I want to do and I’m grateful to have had the opportunity to come back to Rutgers and earn my degree in this field. Coming back to work on a project like this, and working with Tony and learning things from him, is one of the best things to ever happen to me.”

Kelley has been working on the software project for three years and Lane joined him this semester after transferring to Rutgers–Camden from Burlington County College.

“Computational modeling is important to genetic engineering and we already know a lot about the genetics of organisms. Programs like this one will help us manipulate them, creating a new way of producing energy,” Lun says.

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