Title

Bioinformatics models in drug abuse and Neuro-AIDS: Using and developing databases

Authors

Paul Shapshak^1*, Robert Duncan², Jadwiga Turchan³, Avindra Nath⁴, Alireza Minagar⁵, Pandjassarame Kangueane⁶, Wade Davis⁷, Francesco Chiappelli⁸, Fatten Elkomy⁹, Raman Seth⁹, Toni Kazic⁹

Affiliation

¹Psychiatry & Behavioral Sciences, ²Epidemiology, University of Miami Miller Medical School, Miami, FL; ³Anatomy, University of Kentucky Medical School, Lexington, KY; ⁴Neurology, Johns Hopkins University Medical School, Baltimore, MD; ⁵Neurology, State University Health Sciences Center, Shreveport, LA; ⁶Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore; ⁷Health Management and Informatics, University of Missouri, Columbia, MO; ⁸Dentistry, School of Dentistry, UCLA, Los Angeles, CA; ⁹Computer Science, Engineering School, University of Missouri, Columbia, MO.  Tel: 

E-mail*

pshapsha@med.miami.edu; * Corresponding author

Phone

305-243-3917

Fax

305-243-5572

Article Type

Hypothesis

Date

received February 4, 2006; accepted February 22, 2006; published online February 22, 2006

The magnitude of the problems of drug abuse and Neuro-AIDS warrants the development of novel approaches for testing hypotheses in diagnosis and treatment ranging from cell culture models to developing databases.  In this study, cultured neurons were treated with/without HIV-TAT, ENV, or cocaine in a 2x2x2 expression study design. RNA was purified, labeled, and expression data were produced and analyzed using ANOVA.  Thus, we identified 35 genes that were significantly expressed across treatment conditions. A diagram is presented showing examples of molecular relationships involving a significantly expressed gene in the current study (SOX2). Also, we use this information to discuss examples of gene expression interactions as a means to portray significance and complexity of gene expression studies in Drug Abuse and Neuro-AIDS.  Furthermore, we discuss here that critical interactions remain undetected, which may be unravelled by developing robust database systems containing large datasets and gleaned information from collaborating scientists . Hence, we are developing a public domain database we named The Agora database , that will served as a shared infrastructure to query, deposit, and review information related to drug abuse and dementias including Neuro-AIDS).  A workflow of this database is also outlined in this paper.

Keywords

cocaine; HIV-1 gp120; HIV-1 tat; Neuro-AIDS; neuron; Gene Expression; public international database; The Agora

Citation

Shapshak et al., Bioinformation 1(3): 86-88 (2006)

Edited by

P. A. Reche

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.