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Paul Debbie, CGEP Manager, Cornell s Boyce Thompson Institute

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AT A GLANCE: MBA, University of Denver, 1999.

Graduate work in biology at the University of Paris with Miroslav Radman, studying on MutS-based mutation detection.

Enjoys golfing: “After a day of golf everything that can go wrong with microarrays doesn''t look so bad,” Debbie says.

QHow did you get into the microarray field?

AMy background has been in SNP detection. Along with a few other scientists I worked with in grad school, I developed an enzyme-based method that we used as a basis for a company we launched in Ft. Collins, Colo. After we sold the company to a firm in France, I went to business school and got an MBA. Circumstance landed me at Cornell, and when the Boyce Thompson Institute for Plant Research needed someone to manage the Center for Gene Expression Profiling I jumped at the chance.

QWhat role do microarrays play in research at the Boyce Thompson Institute (BTI)?

AMicroarrays are used here to study plant pathogen interactions, fruit development, as well as chloroplast gene expression. We also work with other labs here at Cornell making custom arrays for organisms not easily commercially available in an array format.

QHow is the microarray facility set up within the institute?

AWe are a core facility as well as a lab that works specifically on all aspects of the array process for some projects. We are supported in part by a National Science Foundation MRI grant (equipment purchase) and we get direct support from BTI.

QWhat types of microarrays do you use and in what combination?

AWe exclusively use spotted arrays, mostly cDNA, some spotted oligo. We use these for several reasons, including cost and flexibility. We can make arrays that are not easy to buy at reasonable prices. Also, nobody sells tomato or Pseudomonas syringae (a bacteria that serves as a natural plant pesticide) arrays.

QHow are you spotting down tomato DNA and how are researchers using these arrays? What other unique types of arrays do you have at BTI?

AThese tomato arrays will be cDNA arrays. We are using them for plant pathogen interaction, fruit and flower development, etc. We have made Pseudomonas syringae arrays, chloroplast gene arrays, Chlamydomonas sp. (green alga) arrays, and others.

QHave you developed any special protocols for optimization of array performance?

AWe have developed a number of protocols, including a PCR purification protocol; amine and aldehyde slide processing protocols; an amino-allyl labeling protocol; and a cDNA subtraction protocol using Clontech’s PCR-Select kit. These protocols are all available to the public on our web site. http://bti.cornell.edu/CGEP/CGEP.html.

QWhat kind of arrayer do you use to make your own arrays?

AWe have two, a BioRobotics MicroGrid Pro 16-pin spilt pin arrayer, and a GMS/Affymetrix 417 pin-ring arrayer.

QWhat methods do you use to analyze microarray data?

AWe use Imagene 4.0 from Biodiscovery for image analysis and GeneSight II from the same company for data analysis.

QWhat is the biggest challenge you face in working with microarrays and how do you tackle this challenge?

AIt is often related to RNA quality and quantity for labeling, so we are careful with RNA! And we work with companies like [array detection kit maker] Genisphere to try and find labeling protocols that will give us highly reproducible results.

QWhat advice would you give to a colleague who is setting up and running a core microarray facility?

ADon''t wait for tomorrow’s big promised technology in arraying. Jump in and get to work. I see too many academic labs waiting to see what will work best here or there before starting themselves. If you do that you are left in the dust. You just have to learn to adapt with the technology.

QIf you could make out a wish list for microarray technology advances or improvements over the next couple of years, what do you most want or need?

AI would like to have a highly effective way of labeling prokaryotic RNA, along with better analysis software that doesn''t cost an arm and a leg!

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