The Next Step

A Model for Humans click here to return to the feature article

ith the human genome sequenced, what do we have left to do? Lots.

"The field of functional genomics is the next step," says John Szot, director of the Penn State Microarray Facility. "We’ve decoded a dictionary and now we have to determine the arrangement of the words to make a story."

Micorarrays help you determine which genes are turned on or off when a cell is under stress ¾ any cell from yeast to plant to mammal. While you could previously compare a few genes, a microarray shows up to 7,000 genes on a slide only 18 millimeters on a side.

Here’s how it works: You send a DNA library — a collection of genes or gene fragments — to the facility. A robot built by Penn State Engineering Services, under the direction of Jerry Anderson, uses software by Szot to produce a microarray slide. The robot has an arm with quill-like pins that use capillary action to draw the DNA fragments up, like ink, and dab them onto the slide, forming dots. This process is repeated for as many slides as needed — the largest so far is a yeast project with 210 microarray slides of 6,200 spots each.

Next, you extract messenger-RNA — made only when a gene is working — from stressed (diseased) and unstressed (healthy) cells. You convert the messenger-RNA to single-stranded DNA and labeled it with a fluorescent dye, a different color for each cell line. For example, DNA from healthy cells might be green, while diseased cells are red. Then you mix the two samples together and pour them over the microarray slide. The DNA strand finds its match and sticks there.

A scanner captures the fluorescence emitted by each dye at each spot and a grid of red and green spots appears on the screen, showing which genes are active in each cell. Since brighter colors imply greater gene activity, you quantify the intensity, using another computer program, for each spot. This data shows which genes are turned on or off when a cell is under stress.

—Laura Driscoll Gatrone

John Szot, M.S., directs the Penn State Microarray Facility in the Life Sciences Consortium, 208 Wartik Lab, University Park, PA 16802; 814-865-4262; jcs33@psu.edu.