DNA microarrays are widely used in public health research. For example, they are used to monitor virulence/antimicrobial resistance genes in recreational waters and to genotype bacterial and viral genomes in outbreak management. Noisy data, complex bioinformatics requirements, and a need to confirm findings using independent techniques such as quantitative PCR are all factors that have negatively impacted the use of this technology. About ten years ago, we recognized these problems and embarked on a journey to understand the physicochemistry of DNA microarray technology in order to improve upon them. In 2012, we successfully devised a fundamentally new way to design microarray experiments, where each gene sensor – a DNA oligonucleotide probe – is individually calibrated (PlosOne, 9: e91295). Calibrated microarrays permit direct measurement of relative or absolute gene expression as well as gene copy number in a biological sample. The new design distinguishes itself from others because the microarray calibration is straightforward, and it alleviates the need for normalization procedures and reference standards. Calibrated microarrays are now “truly analytical instruments”, similar to pH meters. In this talk, I will discuss the quagmires, twists and turns encountered in our journey and highlight how we serendipitously discovered a solution that makes DNA microarrays now yield accurate, reliable, and repeatable results that are currently not attainable with next generation sequencing technology.
Speaker Biography - Peter Noble, Ph.D.
Peter Noble, Ph.D.
Professor, Doctoral Program in Microbiology, Alabama State University Montgomery
Dr. Noble is an environmental microbiologist who inadvertently got pulled into DNA microarray research because no accurate and reliable methods existed to conduct research on microbial community dynamics. His prior research involved studying the natural microbial communities in the Gulf of Mexico, Chesapeake Bay, and North Inlet surface waters. He has worked on the biostability of groundwater from Irvine Ranch Water District that was treated for organic carbon removal. For nine years, he served as faculty in the Department of Civil and Environmental Engineering at University of Washington (UW) and he is currently affiliated with the Department of Periodontology (UW). His current research interests include: characterizing biofilms associated with organic/inorganic air diffusers in wastewater treatment plants; the role of microorganisms in titanium corrosion in patients with peri-implantitis; the feasibility of transplanting health-associated oral microbiome for treatment of patients with periodontitis; and determination of the elapsed-time-since death (i.e., post-mortem interval) by using the human thanatomicrobiome (i.e., thanato-, Greek definition: death microbiome). NIH and NSF currently fund his research program.
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