Bioinformatics is a modern information technology for computerized warehousing, visualization and analysis of biological data. The technology emerged in response to the explosive growth of biological information, in forms such as whole-genome sequences, whole-genome expression patterns and high-throughput structure characterization of proteins. One form of biological information, namely the multi-species interactions of a biological system, is of a higher-level complexity that naturally requires bioinformatics solutions. Development of bioinformatics systems of species interactions, however, is in its infancy compared with the proliferation of computing systems for genomics and proteomics. Lyme disease, the most prevalent vector-borne disease in the United States, is a model system for the study of species interactions between a pathogen (Borrelia burgdorferi), its vector (Ixodes ticks) and hosts (vertebrates). In this application, we propose to develop a database system for the study of biogeographic variations of Lyme disease as a multi-species infectious system. The database will host multiple Borrelia genomes, multi-locus sequence variations of Borrelia and Ixodes, as well as biogeographic and ecological information associated with the genome and sequence information. Genomes, sequence variations and biogeographic information will be collected from public databases and published studies. Tools for evolutionary analyses, such as phylogenetic reconstruction and tests of neutral evolution of sequence variations, will be developed and integrated with the database system. In addition, we will implement and curate a web interface to the database system. There are two specific aims for the proposed pilot project. First, we will develop a proof-of-concept database of Lyme disease biogeography, complete with Borrelia genome information, Borrelia and tick multi-locus genetic variations and ecological data on Borrelia-Tick-Host associations. Secondly, we will validate the utility of the database system by testing two evolutionary hypotheses, one on the co-evolutionary history of Borrelia and ticks, and the other on the Borrelia adaptive divergence between geographic localities. The project will pave the way for a bioinformatics system for automated analyses and visualization of biogeographic patterns of vector-borne infectious systems.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Minority Biomedical Research Support - MBRS (S06)
Project #
5S06GM060654-06
Application #
7063088
Study Section
Minority Programs Review Committee (MPRC)
Project Start
Project End
Budget Start
2005-04-01
Budget End
2006-03-31
Support Year
6
Fiscal Year
2005
Total Cost
$35,000
Indirect Cost
Name
Hunter College
Department
Type
DUNS #
620127915
City
New York
State
NY
Country
United States
Zip Code
10065
Luine, Victoria; Gomez, Juan; Beck, Kevin et al. (2017) Sex differences in chronic stress effects on cognition in rodents. Pharmacol Biochem Behav 152:13-19
Gupta, Rupal; Huang, Wenlin; Francesconi, Lynn C et al. (2017) Effect of positional isomerism and vanadium substitution on 51V magic angle spinning NMR Spectra Of Wells-Dawson polyoxotungstates. Solid State Nucl Magn Reson 84:28-33
Luine, Victoria (2016) Estradiol: Mediator of memories, spine density and cognitive resilience to stress in female rodents. J Steroid Biochem Mol Biol 160:189-95
Frankfurt, Maya; Luine, Victoria (2015) The evolving role of dendritic spines and memory: Interaction(s) with estradiol. Horm Behav 74:28-36
Luine, Victoria (2015) Recognition memory tasks in neuroendocrine research. Behav Brain Res 285:158-64
DeCicco, Jennifer M; O'Toole, Laura J; Dennis, Tracy A (2014) The late positive potential as a neural signature for cognitive reappraisal in children. Dev Neuropsychol 39:497-515
Luine, Victoria N (2014) Estradiol and cognitive function: past, present and future. Horm Behav 66:602-18
Garcia, Miguel; Ray, Sibnath; Brown, Isaiah et al. (2014) PakD, a putative p21-activated protein kinase in Dictyostelium discoideum, regulates actin. Eukaryot Cell 13:119-26
O'Toole, Laura J; DeCicco, Jennifer M; Berthod, Samantha et al. (2013) The N170 to angry faces predicts anxiety in typically developing children over a two-year period. Dev Neuropsychol 38:352-63
Garcia, Rebecca; Nguyen, Liem; Brazill, Derrick (2013) Dictyostelium discoideum SecG interprets cAMP-mediated chemotactic signals to influence actin organization. Cytoskeleton (Hoboken) 70:269-80

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