AT A GLANCE
PhD in biochemistry from Cambridge University.
Postdoctoral fellowship at Stanford University. Research interests focus on applying flow cytometry and cell flow techniques to work in plant physiology.
Also enjoys playing the piano and the organ, traveling.
QHow did you get into the microarray field?
AWe started looking at microarrays in 1996 after reading a paper by Mark Schena in Science. Back then, it was almost impossible to buy microarraying equipment, so a postdoc in our lab adapted a Biomek 2000 lab automation workstation for making microarrays. The problem was the Biomek was rather slow, and with plant genome grants from the National Science Foundation, we were starting to print a large number of plant arrays to be distributed around the country. So we purchased a GeneMachines Omnigrid. It’s fine for our purposes, as it can print up to 100 slides at a time.
QWhat kinds of arrays do you make for these NSF projects?
AWe make microarrays from common plant species including Arabidopsis, rice, barley, and maize, as well as a special plant called the ice plant, which is adapted to drought. We are also doing a project looking at Arabidopsis p450 genes.
We have two NSF grants, the maize gene expression and plant stress program. For the plant stress program, we are using arrays to study which genes are altered in response to osmotic and salt stress. Ultimately we are trying to engineer plants to resist the stress.
QHow do other plant researchers obtain these arrays?
AWe have a website where they can order arrays and find out arraying protocols, http://latin.arizona.edu/~dgalbrai. They pay $75 per array per person.
QHow is the microarray facility set up within the university?
AWe turned a lab module of about 1,000 to 1,200 square feet into a genomics room. We have a flow cytometer, three robots, a colony picker, the gridder, a couple of scanners, and a few computers in there. We have hybridization stations, PCR machines, and a RT-PCR machine as well.
QWhat advice would you give to someone who is starting to get into the microarray field?
APeople have to realize when they are making arrays that preparation is 95 percent of making arrays. The actual printing of arrays is five percent. People can’t get their hybridizations to work and I ask, ‘did you follow the RNA preparation procedure?’ There are two problems: One, people don’t read the information provided. And two, they don’t follow it.
QWhat methods do you use to analyze microarray data?
AOne of our postdocs is developing a Linux cluster with my SQL database, and linking together a bunch of Pentiums and a bunch of server computers to store the data. They are doing the primary data extraction using BioDiscovery’s imaging software. We chose it because it was the only one available when we started.
QWhat is the biggest challenge you face in working with microarrays?
AThe biggest problem is in handling the data. Typically you find students and postdocs in front of a computer with a giant spreadsheet wondering what to do with it. If you have 5,000 genes and want to find out what’s significant, you need to find out the function of the genes. You need to find experts in those gene families.
Carefully designing the experiments before you do the microarray hybridizations is also important. Designing the experiments correctly means having good controls, and being aware of circadian rhythms. If you have plants, maybe the gene expression in plants is different just prior to watering. You have to be aware of that.
QIf you could make out a wish list for needed microarray technology advances or improvements over the next couple of years, what do you most want or need?
AThe technology needs to be improved in sensitivity and selectivity, and the data handling needs to be integrated so it can be more efficiently employed. Having microarrays which accurately report each gene expression level is going to be important. A lot of these genes are operating at low levels and increase in low levels.