Transcriptome analysis of HIV-1 virus in understanding the effect of antiretroviral drugs (cART) and methamphetamine on the virus

Ishwor Thapa, Oward S. Fox, Hundy R. Bastola

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

The use of methamphetamine and infection of HIV are both considered public health issues by the Centers of Disease Control and Prevention (CDC). Many studies have shown the effect of methamphetamine, HIV, and both to the central nervous system. The use of methamphetamine not only increases the tendency of HIV transmission, but also the severity of the infection, which may lead to neurodegeneration and neurocognitive disorders. Several studies have examined the gene expression changes in the host due to viral infection, antiretroviral treatment, and the use of methamphetamine, but there is a lack of understanding of their impact on the virus. We investigated their effect on the HIV-1 virus by analyzing the amount of reads obtained from RNA sequencing. We showed that the use of antiretroviral drugs reduced viral read levels, whereas methamphetamine increased them. The expression level of some of the HIV-1 genes such as gag, pol, and nef, inferred from the count of reads mapped to their genomic locations, showed different temporal states among our biological samples.

Original languageEnglish (US)
Title of host publicationProceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Editorslng. Matthieu Schapranow, Jiayu Zhou, Xiaohua Tony Hu, Bin Ma, Sanguthevar Rajasekaran, Satoru Miyano, Illhoi Yoo, Brian Pierce, Amarda Shehu, Vijay K. Gombar, Brian Chen, Vinay Pai, Jun Huan
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages962-968
Number of pages7
ISBN (Electronic)9781467367981
DOIs
StatePublished - Dec 16 2015
EventIEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 - Washington, United States
Duration: Nov 9 2015Nov 12 2015

Publication series

NameProceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015

Other

OtherIEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
CountryUnited States
CityWashington
Period11/9/1511/12/15

Fingerprint

Methamphetamine
Gene Expression Profiling
Viruses
HIV-1
Disease control
Neurology
Public health
RNA
Gene expression
Pharmaceutical Preparations
Genes
HIV
RNA Sequence Analysis
Virus Diseases
Centers for Disease Control and Prevention (U.S.)
HIV Infections
Central Nervous System
Public Health
Gene Expression
Infection

Keywords

  • HIV-1
  • Methamphetamine
  • RNA-Seq
  • antiretroviral drugs (cART)
  • transcriptome

ASJC Scopus subject areas

  • Software
  • Artificial Intelligence
  • Health Informatics
  • Biomedical Engineering

Cite this

Thapa, I., Fox, O. S., & Bastola, H. R. (2015). Transcriptome analysis of HIV-1 virus in understanding the effect of antiretroviral drugs (cART) and methamphetamine on the virus. In L. M. Schapranow, J. Zhou, X. T. Hu, B. Ma, S. Rajasekaran, S. Miyano, I. Yoo, B. Pierce, A. Shehu, V. K. Gombar, B. Chen, V. Pai, ... J. Huan (Eds.), Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 (pp. 962-968). [7359813] (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2015.7359813

Transcriptome analysis of HIV-1 virus in understanding the effect of antiretroviral drugs (cART) and methamphetamine on the virus. / Thapa, Ishwor; Fox, Oward S.; Bastola, Hundy R.

Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. ed. / lng. Matthieu Schapranow; Jiayu Zhou; Xiaohua Tony Hu; Bin Ma; Sanguthevar Rajasekaran; Satoru Miyano; Illhoi Yoo; Brian Pierce; Amarda Shehu; Vijay K. Gombar; Brian Chen; Vinay Pai; Jun Huan. Institute of Electrical and Electronics Engineers Inc., 2015. p. 962-968 7359813 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Thapa, I, Fox, OS & Bastola, HR 2015, Transcriptome analysis of HIV-1 virus in understanding the effect of antiretroviral drugs (cART) and methamphetamine on the virus. in LM Schapranow, J Zhou, XT Hu, B Ma, S Rajasekaran, S Miyano, I Yoo, B Pierce, A Shehu, VK Gombar, B Chen, V Pai & J Huan (eds), Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015., 7359813, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Institute of Electrical and Electronics Engineers Inc., pp. 962-968, IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Washington, United States, 11/9/15. https://doi.org/10.1109/BIBM.2015.7359813
Thapa I, Fox OS, Bastola HR. Transcriptome analysis of HIV-1 virus in understanding the effect of antiretroviral drugs (cART) and methamphetamine on the virus. In Schapranow LM, Zhou J, Hu XT, Ma B, Rajasekaran S, Miyano S, Yoo I, Pierce B, Shehu A, Gombar VK, Chen B, Pai V, Huan J, editors, Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. Institute of Electrical and Electronics Engineers Inc. 2015. p. 962-968. 7359813. (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015). https://doi.org/10.1109/BIBM.2015.7359813
Thapa, Ishwor ; Fox, Oward S. ; Bastola, Hundy R. / Transcriptome analysis of HIV-1 virus in understanding the effect of antiretroviral drugs (cART) and methamphetamine on the virus. Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. editor / lng. Matthieu Schapranow ; Jiayu Zhou ; Xiaohua Tony Hu ; Bin Ma ; Sanguthevar Rajasekaran ; Satoru Miyano ; Illhoi Yoo ; Brian Pierce ; Amarda Shehu ; Vijay K. Gombar ; Brian Chen ; Vinay Pai ; Jun Huan. Institute of Electrical and Electronics Engineers Inc., 2015. pp. 962-968 (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015).
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