Participants to USDA- Sponsored Workshop see Microarray Facility at ISU
On Wednesday, the 29th of August, the workshop participants visited the Department of Agronomy at Iowa State University. Visitors were shown their microarray facilities which allow molecular biologists to study the composite gene function of a complex trait such as flowering, fruit ripening, vascular development etc., or their function in response to an environmental stress such as drought, gravity pull, heat or cold shock. Those genes that are activated or inactivated in the genome of the organism as a result of a stress can be identified in a microarray experiment. cDNA fragments of the material of interest are arranged in the form of tiny square grids in a glass slide by a computer-aided robot.
Visitors were informed that microarray machines cost about a quarter of a million dollars each*. Equipped with computer aided automation (robot), these machines use high throughput methods for not only depositing 20,000 different cDNA samples on a glass slide but also isolating plasmid DNA from 500 recombinant clones in one day and send them for sequencing. (It costs about $3 per base pair.) DNA samples are deposited by steel needles on a glass slide. Needles which cost $ 200 each, have a built-in a very thin slit. They collect DNA samples by capillary action and deposit them simultaneously on poly-l-lysine coated slides The needles then change alignment by about 0.5 mm and deposit another set of samples, next to the earlier slots of eight. The process goes on until all 20,000 cDNA samples are printed on one slide.
The slide can then be hybridized with different cDNA's, labelled with different fluorescent probes. Once the machine is set up, the microarray work can be carried out routinely by trained technicians. Since the expression of a complex character is the result of the interaction of a large number of genes which light up in the microarray, analysis and interpretation of data is the most difficult part of a microarray experiment. The University has 50 Ph.D. students specializing in bioinformatics to do the above difficult task.
