Researchers at Purdue University have found a way to save time, money and a little frustration in searches for specific genes that shed light on the biological processes associated with all forms of life.
Andrew DeWoody, a professor of genetics, and postdoctoral associate Matthew C. Hale have provided evidence that a step called normalization is no longer necessary with recent advances in DNA sequencing technology. Instead, they used a theoretical approach called rarefaction for gene discovery, a process developed for ecological surveys to determine the abundance of a species in an ecosystem. Their results were published in the early online release of the journal BMC Genomics.
When searching for specific genes in a tissue sample, there may be thousands of genes that perform simple housekeeping functions, whereas others expressed in smaller numbers are charged with more complex and important functions. The difficulty is sorting through thousands of genes to find the ones that have unique functions.
"These housekeeping genes are highly expressed, often hundreds or thousands of times more than other genes," DeWoody said.
Through normalization, scientists heat up DNA to a point in which its two component strands split, or denature. As it is cooled, matching strands randomly find each other and reattach. Those that reunite quickly are typically the most numerous. By adding specific enzymes, many of the overabundant genes are decreased in number, while the few that reunite slowly are amplified until the genes are equal in number, making it easier to sort through them.
DeWoody and Hale believe normalization is not necessary given the vast amount of data that can be obtained through modern DNA sequencers.
"Normalization used to be required because commonly expressed genes would swamp the signal of rare genes," DeWoody said. "But normalization also discards valuable information about the relative levels of gene expression in a tissue sample."
Another key aspect of the paper is the novel use of analytical rarefaction in gene discovery.