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Mark Eshoo, Director of the Buck Institute Genomics Core Facility

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AT A GLANCE PhD in Genetics from the University of California Davis. American Heart Association postdoctoral fellowship at Stanford University. Worked as a senior research scientist at the applied biotechnoloqy research group of Cognis-Henkel Chemicals, developing novel gene expression monitoring methods and working to improve biocatalytic processes. Interests: As a native “Marinite” living in Marin County, enjoys mountain biking.

QHow did you get into the microarray field?

AThroughout my career I have been working in the field of genetics and gene expression. While in industry I developed methods to quantitate gene expression using quantitative competitive reverse transcription PCR. Using this technology I was able to identify genes of interest based upon their transcriptional regulation. DNA microarrays are a high-throughput means to identify genes of interest based upon expression, and thus the use of microarray technology was a natural progression for my studies.

QWhat role do microarrays play in research at the Buck Institute?

ABuck Institute researchers are using microarrays to identify genes and patterns of gene expression involved with aging and diseases of aging such as cancer, Parkinson’s, Alzheimer’s, and Huntington’s. Our researchers work on a wide range of topics and models from mitochondrial biophysiology and oxidative radicals to the longevity and lifespan in the nematode, C. elegans.

QHow is the microarray facility set up within the institute?

AThe microarray facility is a component of our Gene Expression Resource Center, which provides all the resources and technologies needed for the performance of gene expression studies. In addition to stock microarrays, the center offers custom microarrays and quantitative reverse transcription PCR for the validation of gene expression changes identified by microarray analysis; as well as Laser Capture Microdissection (LCM) and linear amplification of RNA for gene expression studies using a small number of isolated cells.

QWhat types of microarrays do you use?

ACustom spotted cDNA and oligonucleotide microarrays.

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

AWe’ve had to develop and optimize every step of the microarray process,including methods for the high throughput PCR amplification of cDNA clones, the purification of the PCR products and their verification. We’ve also developed all the QA/QC protocols that we use for the production of microarrays. Microarray printing, RNA labeling, and linear amplification of RNA are other areas where we’ve invested a great deal of effort. This has been a focus and one of the greatest challenges for the Center.

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

AWe have a GeneMachines Omnigrid — it’s been a great instrument.

QWhat methods do you use to analyze microarray data?

AExcel, Spotfire, and GeneSpring.

QWhat is the biggest challenge you face in working with microarrays?

AOur greatest challenge has been data management.

QHow do you tackle these challenges?

AI started by establishing a bioinformatics research group. The group has been meeting and collaborating with database experts from both academia and industry. We are currently working to establish a web-accessible microarray database for the storage and retrieval of gene expression data. The gene annotations will be constantly updated and there will be custom annotations focused on the gene’s role in aging.

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?

AMy wish is to reduce the amount of RNA needed for a microarray experiment. With advances in this technology, the need for linear amplification will be reduced or eliminated, and true single-cell gene expression studies will be made possible.

 

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