Stained Light Show

From microscopic mosaics of color created when genetic material is sandwiched in a “gene chip,” researchers are unveiling the secrets of cells.

One of the most striking and far-reaching new techniques in genomics and proteinomics is the use of gene chips. Made of silicon, these chips contain many thousands of microscopic chemical detectors – imagine a tiny chess board of more than 64,000 squares. Each detector is “sticky” for a certain bit of genetic coding, a particular message in the four-letter chemical alphabet. If DNA containing that message is present, it adheres to the detector, producing a color change on the corresponding square. A few companies now make such chips and the supporting equipment necessary to use them.
USC has a gene chip system in operation at Childrens Hospital Los Angeles and is acquiring more. With this technology, biochemist Joseph Hacia can study differences between normal and cancerous cells by staining one gene chip blue, another gene chip yellow, then superimposing them. Most of this chip sandwich will appear green due to the overlap of the two colors, but even one or two differences will stand out sharply.
Such comparisons are only the beginning, however, because the world of genes isn’t a static one. Some genes work around the clock; others take breaks. A complex process of gene signaling might involve different genes turning each other on and off continuously. To decode the signal, researchers must build up huge stores of gene chip evidence and use modern computational analytical tools to study the data in the hopes of finding patterns in the pulsating flashes of activity seen on gene chips. Mathematician Simon Tavaré and his graduate students are hard at work on the computational challenges of analyzing gene expression, and USC electrical engineer Richard Leahy is developing software to let scientists watch and understand this intracellular light show.

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