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The University of Oklahoma Health Sciences Center Laboratory For The University of Oklahoma Health Sciences Center Labor atory for Genomics and Bioinformatics Vol. 4, No. 3 September 2006 http://microgen.ouhsc.edu University of Oklahoma Health Sciences Center/405-271-2337 Technology seminars to illustrate new equipment This fall, we are sponsoring three October 9, Dr. Ed Horton will discuss how technology seminars that will be offered you can take advantage of our Beckman during the regular seminar series for the Proteomelab (“Applying Intact Protein In this issue Department of Microbiology and Partitioning and Fractionation to Biomarker Immunology. These seminars, at noon on Discovery”; see related article on page 3). • Technology seminars 1 Mondays, are designed to bring you up to Lastly, Dr. Charles Greaves will discuss on • Featured Project: date on new technology that we offer in our October 30 a new microarray technology that Intergenetics SNP core facility or technology that we are we are considering (“Custom Microarrays for Genotyping 1 thinking about adding to our repertoire. On Application Specific Studies”). We hope OK INBRE September 25, Dr. Wendy VanScyoc will that you will be able to attend, as we will be discuss the use of surface plasmon resonance sending around surveys after each seminar, • INBRE News 2 (“Next Generation Surface Plasmon assessing how useful this has been, and • INBRE Summer Resonance Biosensor Technology for the whether you are interested in having these Undergraduate Research Production of High Quality Kinetic technologies in the core facility. Thanks for Program 4 Information in Protein Interactions”). On your support! -Dave Dyer & Allison Gillaspy OUHSC COBRE Featured project: InterGenetics SNP Genotyping • COBRE News 4 InterGenetics Incorporated (IGI) is • COBRE operating platform as that for the only FDA Investigator Focus 2 offering a new service to provide high approved cystic fibrosis mutation carrier throughput single nucleotide polymorphism screening test. New Services! (SNP) genotyping to academic investigators One of the factors that makes this new and biotechnology companies. IGI is a service possible is access to robust, accurate • The Beckman biotechnology- and bioinformatics-based and timely DNA sequencing provided by the ProteomeLab 3 company in the PHF Research Park located OUHSC core facility. Development of adjacent to the OUHSC. IGI has significant accurate SNP genotyping assays using ASPE expertise in developing and implementing requires a modest sample of individuals for Services and rates 6 multiplexed SNP assays through its whom SNP genotypes have been determined Acknowledgements development of a test for genetic by a method other than ASPE. It also is The OUHSC Laboratory for predisposition to breast cancer. Over a critical to know the locations of nearby Genomics and Bioinformatics million individual SNP genotype SNPs, to avoid problems in PCR and/or is partially supported by determinations were made by IGI over the ASPE primer design. Direct DNA USPHS grants 5P20-RR-15564 course of this and other projects. IGI is sequencing is the gold standard for finding (COBRE) and 5P20-RR- making available this expertise in SNP and characterizing such SNPs. Thus, 016478 (INBRE), from the genotyping to other investigators. development of each new assay begins with a National Center for Research Initiating and operating a large-scale SNP small resequencing project. Resources of the National genotyping project can be expensive and If you are contemplating a SNP genotyping Institutes of Health. Additional time consuming. Capital equipment costs are project, IGI will deliver timely, efficient and support is provided by the large and technical operators usually require competitively priced user-friendly service. OUHSC Office of the Provost. extensive training. IGI allows you to avoid And, IGI technical staff will be glad to guide these costs, shortening the time required for you through the process of designing your data acquisition and permitting you to SNP genotyping application. Interested concentrate on data analysis and investigators can contact IGI at 405-271- interpretation. IGI’s core technology uses 1720 or visit their website at allele specific primer extension (ASPE) www.intergenetics.com. mounted onto a bead-based assay system Contributed by David Ralph, Ph.D. with a readout linked to a flow cytometer. CSO, IGI This robust technology uses the same Page 2 OUHSC Laboratory for Genomics and Bioinformatics INBRE News by Edgar Scott, M.S. This summer, I had the pleasure of refines a specific scoring matrix that models mentoring Craig Covey from Oklahoma City the query sequence and sequence relatives Community College during the INBRE and can be used in successive searches to Summer Undergraduate Research Program find distantly related sequences. He then (see page 5). His research focused on using processed the two data sets separately with a bioinformatic tools to identify unique motif searching program called MEME sequence motifs in a family of bacterial (Maximum Expectation maximization for metal ion sensor proteins. The Ferric uptake Motif Elicitation). MEME uses the regulator (Fur) protein and the Zinc uptake expectation maximization algorithm to regulator (Zur) protein are related proteins identify conserved characters in a group of that regulate the uptake of iron and zinc, protein or DNA sequences. The program respectively. Their amino acid sequences are outputs conserved regions as local multiple so similar that it is difficult to distinguish sequence alignments with a bit score to between the proteins. Craig's project quantify the degree of conservation within attempted to identify unique amino acid that alignment. motifs from a group of Fur/Zur homologues This analysis showed that the Fur and Zur that might be useful for distinguishing Fur proteins have a strong sequence motif that http://okinbre.org/ from Zur. overlaps both the DNA binding domain and Craig proceeded in several steps. He first portions of a metal-binding domain. acquired amino acid sequences of Unfortunately, the sequence logos of the experimentally-characterized Fur and Zur motifs for the two proteins did not proteins from the UniProt Knowledgebase. distinguish Fur from Zur. However, the To this, he added sequences homologous to exercise was good for Craig’s introduction Zur and Fur using Protein Specific Iterative to bioinformatics and suggested several BLAST (PSI-BLAST) at NCBI. Through possible avenues for additional several iterations, PSI-BLAST creates and investigation. COBRE Investigator Fo cus: John West, Ph.D. Defining the impact of HIV-1 fitness on virus transmission from mother to child Infections with HIV-1 subtype C are survive in a given environment (fitness), and responsible for more than 50% of new between fitness and disease progression. infections and this continues to increase, We use a combination of genetic, particularly in the developing countries of phylogenetic, molecular, immunological and sub-Saharan Africa, India and China. The biochemical approaches to investigate primary routes of infection are unprotected relationships between Env evolution and heterosexual contact and mother-to-child biological function, including replication or transmission. transmission fitness. We employ Untreated mothers transmit HIV-1 to their fluorescent-tagged HIVs (containing infants in approximately 30% of deliveries. variants of Env) in dual-infection Of the remaining 70%, 15% become infected competition experiments to define through breast-feeding. My laboratory replication fitness. We also are developing focuses on mother-to-child transmission organotypic culture systems to evaluate viral because this represents one of few instances transmission fitness across mucosal barriers. where the donor, recipient, the direction and These experiments will facilitate our John West, Ph.D. timing of transmission are known. understanding of the determinants of HIV-1 Assistant Professor Transmission of HIV-1 is a function of the transmission, evolution and disease. Such OUHSC Department of envelope glycoprotein (Env) that mediates information will be essential in the design of Microbiology and Immunology fusion of the viral membrane with a target treatments or preventatives that limit or cell. Because the viral replicase lacks proof- redirect viral Env evolution such that lasting reading capability, the Env proteins are protection can be achieved. tremendously diverse, creating a swarm of For more information, contact: nearly identical but distinct individuals called John T. West, Ph.D. a ‘quasispecies’. This diversity lends Dept. of Microbiology and Immunology incredible plasticity to the virus to adapt to OU Health Sciences Center selective pressures. Recent data suggest a Email: [email protected] link between HIV Env and viral ability to Tel: 405-271-2570 OUHSC Laboratory for Genomics and Bioinformatics Page 3 The Beckman PF2D ProteomeLab in Practice In our last newsletter, we announced the be collected if the entire first dimension were availability of the Beckman PF2D fractionated, and because the fraction ProteomeLab for proteomics separations by collector is not large enough for that many our core facility. Bob Hurst’s lab has fractions, someone has to change out the full extensive experience with the PF2D, tubes for empty ones. This either means improving the throughput and accuracy of someone does this at 4AM, or the the instrument. Bob and coworkers have a fractionation requires some three days. recent paper published online with Biomed Running in “mapping
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