The genomes of some pathogenic viruses are made up of RNA that can be involved directly in theproduction of proteins crucial to viral reproduction and infection. These fast-mutating RNA viruses showed ahigh incidence of cross-infections among different species by variant forms (Plant et al. 2005). It is feasible toperform computational analyses on the viral genome and obtain useful information which give clues to theorigin, natural reservoir, and evolution of the virus, contributing to the understanding of the immune responseto these viruses and the pathogenesis of viral diseases and facilitate the development of antiviral drugs. Wehave recently reported that regions in coronavirus RNA genomes with statistically significant clusters ofpalindromes are associated with the presence of stem-loops or pseudoknots (Chew et al 2004). These RNAstructures have been suggested to be responsible for frame-shifting mechanisms during gene expression,where two different proteins can be produced in the same region just by shifting the reading frame by onebase. We hypothesize that by exploiting the correlation between nonrandom clusters of close inversions withstem-loop and pseudoknot structures in RNA molecules, an efficient and utilitarian tool for predictingsecondary structures on RNA viral genomes can be developed using current heterogeneous Grid Computingtechnology. We propose a four-year project to evaluate this hypothesis focusing on coronaviruses andinfluenza viruses with specific aims to: (1) Establish a statistics-based algorithm to locate RNA segmentcontaining nonrandom clusters of close inversions. (2) Develop a strategy for cutting of the viral genomesequences into segments of length no greater than 200 bases. (3) Construct a software prototype for RNAsecondary structure prediction using Grid Computing technology. (4) Implement user facilities for thesoftware and predict genome structures in coronaviruses and Influenza viruses. For this project, ourobjective is to produce the prototype of an RNA secondary structure prediction system on a grid ofheterogeneous, distributed computers. The software will be publicly accessible through a web portal. Ourlong-term goal is to develop a set of open-source computational tools in a Grid Computing environment toaccurately predict genome structures and dynamics in RNA viruses and their interactions with cellular RNA.This will provide information to be used by virologists to design finely tuned experiments to study RNAviruses and their pathogenic interactions with their hosts, especially when time is limiting in combating new infectious viral diseases.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Minority Biomedical Research Support - MBRS (S06)
Project #
2S06GM008012-37
Application #
7282250
Study Section
Minority Programs Review Committee (MPRC)
Project Start
2007-06-01
Project End
2011-05-31
Budget Start
2007-06-01
Budget End
2008-05-31
Support Year
37
Fiscal Year
2007
Total Cost
$150,555
Indirect Cost
Name
University of Texas El Paso
Department
Type
DUNS #
132051285
City
El Paso
State
TX
Country
United States
Zip Code
79968
Rocha-Gutiérrez, Beatriz A; Lee, Wen-Yee; Shane Walker, W (2016) Mass balance and mass loading of polybrominated diphenyl ethers (PBDEs) in a tertiary wastewater treatment plant using SBSE-TD-GC/MS. Water Sci Technol 73:302-8
Vargas-Medrano, Javier; Sierra-Fonseca, Jorge A; Plenge-Tellechea, Luis F (2016) 1,2-Dichlorobenzene affects the formation of the phosphoenzyme stage during the catalytic cycle of the Ca(2+)-ATPase from sarcoplasmic reticulum. BMC Biochem 17:5
Buhaya, Munir H; Galvan, Steven; Maldonado, Rosa A (2015) Incidence of Trypanosoma cruzi infection in triatomines collected at Indio Mountains Research Station. Acta Trop 150:97-9
Vasquez, Miguel A; Iniguez, Eva; Das, Umashankar et al. (2015) Evaluation of ?,?-unsaturated ketones as antileishmanial agents. Antimicrob Agents Chemother 59:3598-601
Serna, Carylinda; Lara, Joshua A; Rodrigues, Silas P et al. (2014) A synthetic peptide from Trypanosoma cruzi mucin-like associated surface protein as candidate for a vaccine against Chagas disease. Vaccine 32:3525-32
Rodrigues, Marcio L; Nakayasu, Ernesto S; Almeida, Igor C et al. (2014) The impact of proteomics on the understanding of functions and biogenesis of fungal extracellular vesicles. J Proteomics 97:177-86
Dagda, Ruben K; Gasanov, Sardar E; Zhang, Boris et al. (2014) Molecular models of the Mojave rattlesnake (Crotalus scutulatus scutulatus) venom metalloproteinases reveal a structural basis for differences in hemorrhagic activities. J Biol Phys 40:193-216
Rico-Martínez, Roberto; Walsh, Elizabeth J (2013) Sexual Reproductive Biology of a Colonial Rotifer Sinantherina socialis (Rotifera: Monogononta): Do mating strategies vary between colonial and solitary rotifer species? Mar Freshw Behav Physiol 46:419-430
Jin, Seoweon; Staniswalis, Joan G; Mallawaarachchi, Indika (2013) Principal Differential Analysis with a Continuous Covariate: Low Dimensional Approximations for Functional Data. J Stat Comput Simul 83:
Dagda, Ruben K; Gasanov, Sardar; De La Oiii, Ysidro et al. (2013) Genetic Basis for Variation of Metalloproteinase-Associated Biochemical Activity in Venom of the Mojave Rattlesnake (Crotalus scutulatus scutulatus). Biochem Res Int 2013:251474

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