Fairfield professor helps develop cutting-edge model to monitor cellular change
(Posted on November 19, 2010)
Discovery could lead to new technologies in cancer research
How scientists measure and understand the way biological systems function, could enhance methods and designs of technologies used in cancer and genetics research. Now, a group of researchers, including a Fairfield University mathematician, have developed an algebraic model of DNA "hybridization," a process central to most biotechnology devices that monitor changes in a cell's gene expression.
In an article published in Physical Review E, co-author Vera Cherepinsky, a math professor at Fairfield University, describes the application of a symbolic algebraic model to interpret microarray data measuring cellular activity. The mathematical tool can help researchers understand how biological systems function, and ultimately help in the fight against cancer. "Suppose you are a cancer researcher. You're interested in detecting how many copies of a certain cancer gene are being expressed. One way to do so is by performing hybridization experiments on microarray. Since many different tags (or probes) can be used to search for the same gene, part of the experiment design is deciding which ones to use. Our model can help you make that decision. If a particular gene over-expresses, that may give you a predictor for whether somebody has cancer, or even a measure of how serious it is," said Cherepinsky.
Cherepinsky says the primary focus of the study was to understand competitive hybridization, which is important in many biotechnologies, as hybridization is widely used. Probably the best known of these is microarray technology, which uses a two-step process to measure the abundance of RNA molecules. First RNA is converted into cDNA or "copy DNA," and then measured by hybridization. By creating mathematical models to analyze DNA-cDNA formation, Cherepinsky and researchers from New York University's Courant Institute added a new tool to the researchers' toolbox, which can help improve the biotechnology design for measuring cellular behavior, and eventually the detection of cancer-causing genes. "In other words, in situations when there are multiple options for which probes can be used, researchers could use our model to design better experiments," she added.
Cherepinsky and her fellow researchers focused on how a cell's most basic components are measured-its DNA and RNA. Specifically, they used a cell's gene expressions as a "tagging system" (probes) to monitor cell behavior at its most fundamental level. A biotechnology company, pursuing a specific practical application, posed the problem to the researchers. This advance in technology has many other uses as well, ranging from personalized medicine that can be modified to a person's DNA to cancer and genetics research.
Vol. 43, No. 122