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Next-Generation Gene Sequencing Technology
The University of Texas at Austin has acquired new technology targeted at better deciphering the genetic basis of complex disease systems. The SOLiD System from Applied Biosystems, generates massively parallel genomic profiles of various eukaryotic organisms. This technology, also know as “next-generation sequencing” is fast becoming the industry standard in DNA sequencing.
Supported by the Institute for Cellular and Molecular Biology, the Texas Institute for Drug and Diagnostic Development and the Center for Systems and Synthetic Biology, the SOLiD System is available to the entire life sciences community at UT Austin.
Waggoner Center members Dr. Vishwanath Iyer and Dr. R. Dayne Mayfield will use the new technology in various alcohol-related studies.
Our understanding of cellular function and complex diseases increased dramatically with genome-wide expression studies using cDNA microarrays to examine large numbers of known RNA transcripts simultaneously. Numerous laboratories have performed gene expression studies utilizing microarrays to identify transcripts that change as a result of drug abuse. However, these hybridization-based studies are limited by the reliance upon known genome sequence, potential cross-hybridization, and a limited dynamic range of signal intensities.
Next-generation sequencing technology will likely revolutionize whole transcriptome profiling. It allows detection of all known and novel RNAs present in biological samples without bias toward known transcripts. Thus, the expression of all coding and non-coding RNAs, alternative splicing events, and expressed single nucleotide polymorphisms (SNPs) can all be identified in a single experiment. The technology allows unparalleled accuracy and intricacy in the detection of transcriptome differences.
The Iyer lab is using the technology to identify the target sites of transcriptional regulatory proteins across the genome at high resolution, and to examine dynamic chromatin remodeling across the genome. The new technology makes it possible to observe differences in the behavior of the two nearly identical copies of each chromosome in a cell, which was not possible with earlier approaches.
Dr. Mayfield will profile transcriptional regulation in human brain regions that are known substrates of reward circuitry involved in the development of alcohol and nicotine dependence. Understanding gene expression changes resulting from alcohol and nicotine abuse (and the resulting phenotypes) will accelerate treatment and prevention strategies.
Of Note
Chancellor Holden Thorp and Graduate School Dean Steve Matson of The University of North Carolina at Chapel Hill invited Dr. R. Adron Harris to speak at UNC Chapel Hill’s 2009 doctoral hooding ceremony, held May 9, 2009. In choosing a speaker, a selection committee considered graduates of UNC’s doctoral program with distinguished subsequent careers. Dr. Harris was recommended based on his numerous research accomplishments and commitments to higher education. That evening Dr. Harris attended a dinner as an honored guest along with UNC’s general Commencement speaker, The Most Reverend Desmond M. Tutu, Anglican Archbishop Emeritus of Cape Town, winner of the Nobel Peace Prize and renowned South African anti-apartheid campaigner.
Dr. R. Adron Harris was the featured speaker at the 2009 Distinguished Speakers Series hosted by the Mind Science Foundation (MSF), held March 16, 2009, in San Antonio. A private foundation, the MSF funds cutting-edge research and educational programs focused on the mind, brain and human consciousness. Dr. Harris spoke on the molecular biology of alcoholism and the complex relationships between genes, addiction and the brain. In addition to the lecture, Dr. Harris and Dr. Paul Inmundson, MSF Board Vice-Chair and Acting Executive Director, were interviewed on San Antonio’s morning show, Great Day SA.
Dr. Mark Harnett (Morikawa lab) completed a distinguished graduate career in May 2009. His honors and awards include a first-author publication in the highly rated peer-reviewed journal Neuron, a Fred Murphy Jones & Lindsey Bruce Endowed Fellowship, a Graduate School Continuing Fellowship and a National Science Foundation Predoctoral Fellowship. Dr. Harnett begins a position as a postdoctoral fellow with Dr. Jeffrey C. Magee at Janelia Farm Research Campus, Howard Hughes Medical Institute, in September 2009.
Honors & Awards
Dr. Michael Spinetta (Schallert lab), who received his doctoral degree in August 2008, received one of three Outstanding Dissertation Awards of $5,000 each from the Graduate School Awards Program, sponsored by the University Co-op. Graduate Studies Committee Chairs submit nominations to recognize outstanding doctoral dissertations. The title of Dr. Spinetta's thesis: Ethanol and Retrograde Amnesia: Can Rats Have Blackouts and Does Caffeine Help?
Two researchers received the prestigious National Research Service Award (NRSA) for Postdoctoral and Predoctoral Fellows from The National Institute of Alcohol Abuse & Alcoholism (NIAAA):
Dr. Regina Mangieri (Gonzales Lab)
"The Role of the Endogenous Cannabinoid System in Ethanol Self-administration"
Brian Welsh (Mihic Lab)
"Single Channel Characterization of Ethanol Action on the Glycine Receptor"
In addition to the NRSA, Mr. Welsh received a David Bruton, Jr. Graduate School Fellowship with a stipend of $1,000 for the 2009-2010 academic year.
Doctoral Awards
Dr. Michelle Dupre (Mihic Lab), December 2, 2009
The Structure of the TM2-3 Linker in the Alpha1 Glyr and its Role in Gating and Modulation
Dr. Mark Harnett (Morikawa Lab), May 12, 2009
Burst Timing-Dependent Plasticity of NMDA Receptor-Mediated Synaptic Transmission in Midbrain Dopamine Neurons: A Putative Cellular Substrate for Reward Learning
Dr. Elaina Howard (Gonzales Lab), May 11, 2009
Dopamine Concentrations in Nucleus Accumbens Subregions are Differentially Affected by Ethanol Administration
Dr. Martin Job (Gonzales Lab), February 23, 2009
The Etiology of Fragmentary Blackouts: Memory Processes and Neural Activations
Dr. The-Sheng Ma (Schallert Lab), May 1, 2009
Rodent Ultrasonic Mating Call as a Biomarker for Oromotor Deficits in Parkinsonian Animal Model
Dr. Angela Ozburn (Harris/Blednov Lab), April 23, 2009
Comparison of Ethanol-Related Behaviors and FosB Mapping in Hybrid Mice with Distinct Drinking Patterns
