This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The tools used for high throughput DNA sequencing, comparative genomics, SNP analysis, and the analysis of gene expression have become nearly indispensable in contemporary biomedical research. As a result of our current COBRE support we have been able to establish a high throughput multi-user DNA Sequence Analysis Core facility;the only one at the University of Idaho. This facility has greatly benefited both COBRE researchers and the larger biomedical research community at the University. In order for the University to remain competitive in biomedical research, and for COBRE funded researchers to achieve the aims of the proposed research projects, we must not only maintain the current capabilities of the core, but also add the capability to rapidly do whole genome re-sequencing and gene expression analysis. The existing DNA Sequence Analysis Core Facility provides researchers access to the instruments, equipment, and facilities needed for the analysis of nucleic acid sequences. The Core Facility occupies 850 sq. feet of newly renovated space in Life Sciences South. It is equipped with the major instrumentation and computational resources described below, as well as wet lab benches, biosafety cabinets, thermocyclers, centrifuges, microfuges, freezers, refrigerators, and other minor equipment needed for sample preparation. A portion of the laboratory is dedicated to data analysis and bioinformatics and has high-end workstations and printers that are linked via the internet to the software and hardware resources of the Bioinformatics Core Facility on campus. A technician oversees operation and maintenance of the instruments, and provides instruction, guidance, and trouble-shooting assistance to users of the facility. The major instrumentation now available in the Core Facility includes the following: Nimblegen Hybridization System. The Hybridization system is a four-bay system that can accommodate multiple array types to achieve consistent and reproducible microarray hybridization results GenePix 4000B Microarray Scanner. The GenePix Scanner is capable of scanning and quantifying DNA microarray slides from multiple different vendors including Nimblegen and Agilant microarrays Genome Sequencer FLX Titanium Series Instrument. The Genome Sequencer FLX Instrument, powered by GS FLX Titanium and Standard series reagents, features a groundbreaking combination of long reads, exceptional accuracy and high throughput. Applications include de novo sequencing, resequencing of whole genomes and target DNA regions, metagenomics and RNA analysis. + Applied Biosystems PRISM 3730 DNA Analyzer. The ABI 3730 is a 48 capillary system that can accommodate two array lengths, 50cm and 36cm for DNA fragment analysis applications such as microsatellites, AFLP, SNP analysis, mutation detection and traditional DNA sequencing + Applied Biosystems PRISM 3100 DNA Analyzer. The ABI 3100 is a fluorescence based DNA analysis system in which 16 electrophoresis capillaries are operated in parallel. The instrument is almost exclusively used for DNA fragment analysis. + Qiagen BioRobot 3000. The Qiagen BioRobot allows for high throughput sample processing using a 96-well microplate format. The customized workstation is equipped with a 4 microplate shaker system for efficient cell resuspension or lysis, two vacuum manifolds for simultaneous purification of 192 samples, a high-speed pipetting system with four dilutor units, one cooling and heating Peltier system for performing heat-dependent steps, and a T-grip robotic arm for moving items such as microplates between locations on the worktable. + Two Macintosh Power Mac G5 computers both of which have dual 2GHz processors with 512kb of cache per processor. For memory and storage each computer is equipped with 1GB of RAM, two 250GB hard drives and a Pioneer DVD-RW/CD-RW disc drive. This computer is connected to the high speed IBEST network with an internal gigabit Ethernet network card. + One Macintosh Mac Pro computer with two quad-Core Intel Xeon 2.8GHz processors with 12MB of cache per processor. For memory and storage it is equipped with 4GB of RAM, two 500GB hard drives and a Pioneer DVD-RW/DVR disc drive. This computer is connected to the high speed IBEST network with an internal gigabit Ethernet network card. + One Dell Computer with a Intel Pentium 4 CPU 1.6GHz processor with 256kb of cache For memory and storage it is equipped with 256MB of RAM, a 76GB hard drive and a CD-R/CD-RW disc drive. It is setup to run Ubuntu Linux and is also connected to the high speed IBEST network. + One Dell Computer with an Intel Pentium 4 3GHz processor. For memory and storage it is equipped with 1GB of RAM, a 300GB hard Drive and a DVD/CD-R disc drive. It is currently running Windows XP and is also connected to the high speed IBEST network. One Dell Computer with Dual Intel Xeon 2.26 Ghz Quad Core Processors. For memory and storage it is equiped with 24GB of RAM and 1TB Hard Drive and DVD/CD-R disc drive. It is currently running Ubuntu Linux 9.04 and is also connected to the high speed IBEST network.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Exploratory Grants (P20)
Project #
5P20RR016448-09
Application #
8359573
Study Section
National Center for Research Resources Initial Review Group (RIRG)
Project Start
2011-02-01
Project End
2012-01-31
Budget Start
2011-02-01
Budget End
2012-01-31
Support Year
9
Fiscal Year
2011
Total Cost
$388,223
Indirect Cost
Name
University of Idaho
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
075746271
City
Moscow
State
ID
Country
United States
Zip Code
83844
Marx, Hannah E; Dentant, C├ędric; Renaud, Julien et al. (2017) Riders in the sky (islands): using a mega-phylogenetic approach to understand plant species distribution and coexistence at the altitudinal limits of angiosperm plant life. J Biogeogr 44:2618-2630
Sarver, Brice A J; Demboski, John R; Good, Jeffrey M et al. (2016) Comparative Phylogenomic Assessment of Mitochondrial Introgression among Several Species of Chipmunks (TAMIAS). Genome Biol Evol :
Stockmann, Chris; Ampofo, Krow; Pavia, Andrew T et al. (2016) Clinical and Epidemiological Evidence of the Red Queen Hypothesis in Pneumococcal Serotype Dynamics. Clin Infect Dis 63:619-626
Loftie-Eaton, Wesley; Yano, Hirokazu; Burleigh, Stephen et al. (2016) Evolutionary Paths That Expand Plasmid Host-Range: Implications for Spread of Antibiotic Resistance. Mol Biol Evol 33:885-97
Yano, Hirokazu; Wegrzyn, Katarznya; Loftie-Eaton, Wesley et al. (2016) Evolved plasmid-host interactions reduce plasmid interference cost. Mol Microbiol 101:743-56
Chernikova, Diana A; Koestler, Devin C; Hoen, Anne Gatewood et al. (2016) Fetal exposures and perinatal influences on the stool microbiota of premature infants. J Matern Fetal Neonatal Med 29:99-105
Uribe-Convers, Simon; Settles, Matthew L; Tank, David C (2016) A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae). PLoS One 11:e0148203
Garud, Nandita R; Messer, Philipp W; Buzbas, Erkan O et al. (2015) Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps. PLoS Genet 11:e1005004
Metzger, Genevieve; Espindola, Anahi; Waits, Lisette P et al. (2015) Genetic Structure across Broad Spatial and Temporal Scales: Rocky Mountain Tailed Frogs (Ascaphus montanus; Anura: Ascaphidae) in the Inland Temperate Rainforest. J Hered 106:700-10
Loftie-Eaton, Wesley; Suzuki, Haruo; Bashford, Kelsie et al. (2015) Draft Genome Sequence of Pseudomonas sp. nov. H2. Genome Announc 3:

Showing the most recent 10 out of 193 publications