E-Mail Technology Used to Analyze DNA Data

E-mail is quickly becoming the bane of our existence. There’s no doubt, however, that e-mail has improved world-wide communications. Now, the technology used to track e-mails is being used to track DNA microanalysis data.

Using the check-sum protocol, it’s possible to monitor more closely time-series data from DNA microarrays of genes turning on and off. Generally, when biological pathways such as cell division or immune system responses are being studied, there is some loss of information between sequential “snapshots” of the microarray.

The procedure behind the use of the check-sum protocol in DNA microanalysis:

1. As genes turn “on” and “off,” the information is coded as binary 0’s and 1’s, similar to the way computers transmit e-mails.
2. E-mail binary code flip to the opposite value during transmission and a gene’s activation between microarray samples can be coded similarly.
3. A “check sum” protocol adds up all the 0’s and 1’s in a message/DNA microarray data-gathering snapshot.
4. A comparison of the the total check sum of 0’s and 1’s from one snapshot and the following one can detect whether a gene was activated between snapshots. For example, if a set of DNA microanalysis data points have a lower “check sum” result than the previous set, the technology alerts scientists to the fact that they have missed a gene’s activation.

Studying the complex machinery of biological systems is daunting. But polymaths like Ziv Bar-Joseph, assistant professor of computer science and biological sciences at Carnegie Mellon University in Pittsburgh, and other experts at The Hebrew University in Jerusalem, are able to gather ideas across disciplines to come up with innovative solutions.

Red Herring, December 8, 2005