Skip to main content
Springer Nature Link
Log in

An Information Theoretic Approach to the Study of Genome Sequences: An Application to the Evolution of HIV

  • Conference paper
  • First Online:
Unconventional Models of Computation (UMC 2002)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2509))

Included in the following conference series:

  • 443 Accesses

Abstract

When a V3 sequence obtained on the n-th year after infection with human immunodeficiency virus type 1 (HIV-1) was supposed to change into a V3 sequence on the n+1-th year, the variation between the above two sequences was analyzed by means of entropic chaos degree. The entropic chaos degree measures chaotic aspects of the dynamics causing the variation of sequence. If it is large, then the dynamics produces the large complexity, in other words, the variation of sequences becomes large.

As a results, the chaos degree for the dynamics changing the V3 region showed the specific variation patterns throughout from the early stages of infection to death. That is, the variation patterns indicated that the entropic chaos degree is useful to measure the stage of disease progression after HIV-1 infection.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

  1. Cleland A, Watson HG, Robertson P, Ludlam CA, Leigh Brown AJ (1996) Evolution of Zidovudine Resistance-Associated Genotypes in Human Immunodeficiency Virus Type 1-infected Patients, Journal of Acqired Immune Deficiency Syndromes and Human Retrovirology, 12(1): 6–18

    Google Scholar 

  2. Takahashi H, Nakagawa Y, Pendleton C.D., Houghten R.A, Yokomuro K, Germain R.N Berzofsky J.A (1992) Induction of Brosadly Cross-Reactive Cytotoxic T-Cells Recognizing an HIV-1 Envelope Determinant. Science, Vol. 255: 333–336

    Article  Google Scholar 

  3. Holmes E C, Zhang LQ, Simmonds P, Ludlam CA, Leigh-Brown AJ (1992) Convergent and divergent sequence evolution in the surface envelope glycoprotein of Human immunodeficiency virus type 1 within a single infected patient. Proc. Natl. Acad. Sci. U.S.A. 89: 4835–4839

    Article  Google Scholar 

  4. Ida S, Gatanaga H, Shioda T, Nagai Y, Kobayashi N, Shimada K, Kimura S, Iwamoto A, Oka S (1997) HIV type 1 V3 variation dynamics in vivo: long-term persistence of non-syncytium-inducing genotypes and transient presence of syncytium-inducing genotypes during the course of progressive AIDS. AIDS Res. Hum. Retroviruses 13(18): 1597–1609

    Article  Google Scholar 

  5. Inoue K, Ohya M and Sato K: Application of chaos degree to some dynamical systems, to appear in Chaos, Solitons & Fractals

    Google Scholar 

  6. Javaherian K, Langlois A.J, McDanal C, Ross K.L, Eckler L.I., Jellis C.L, Proty A.T, Rusche J.R, Bolognesi D.P, Putwey S.D., Matthews T.J.(1989) Principal Newtralizing Domain of the Human Immunodeficiency Virus Type 1 Envelope Protein, Proc. Natl. Acad. Sci. USA, Vol. 86: 6768–6772

    Article  Google Scholar 

  7. John W. Mellors, Lawrence A. Kingsley, Charles r. Rinaldo, John A. Todd, Brad S. Hoo, Robert P. Kokka, Phalguni Gupta (1995) Quantitation of HIV-1 RNA in Plasma Predict Outcome after Seroconversion, Ann. Intern. Med., 122: 573–579

    Google Scholar 

  8. Leigh Brown AJ, Cleland A(1996) Independent evolution of the env and pol genes of HIV-1 during zidovudine therapy. AIDS 10(10): 1067–1073

    Article  Google Scholar 

  9. Markham, R.B., Wang, W.C., Weisstein, A.E., Wang, Z., Munoz, A., Templeton, A., Margolick, J., Vlahov, D., Quinn, T., Farzadegan, H., Yu, X.F. (1998) Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc. Natl. Acad. Sci. U.S.A. 95(21): 12568–12573

    Article  Google Scholar 

  10. Ohya M (1998) Complexities and their applications to characterization of chaos, International Jornal of Theoretical Physics, 37,1: 495–505

    Article  MATH  MathSciNet  Google Scholar 

  11. Poss M, Rodrigo A.G., Gosink J.J., Learn G.H., de Vange Panteleeff D., Martin H.L. Jr., Bwayo J., Kreiss J.K., Overbaugh J (1998) Evolution of envelope sequences from the genital tract and peripheral blood of women infected with clade A human immunodeficiency virus type 1. J. Virol. 72(10): 8240–8251

    Google Scholar 

  12. Sato K., Miyazaki S., Ohya M. (1998) Analysis of HIV by entropy evolution rate. Amino Acids14: 343–352

    Article  Google Scholar 

  13. van’t Wout A.B, Ran L.J., Kuiken C.L., Kootstra N.A., Pals S.T., Schuitemaker, H. (1998) Analysis of the temporal relationship between human immunodeficiency virus type 1 quasispecies in sequential blood samples and various organs obtained at autopsy. J. Virol. 72(1): 488–496

    Google Scholar 

  14. van’t Wout, A.B., Blaak, H., Ran, L.J., Brouwer, M., Kuiken, C.L., Schuitemkaer, H. (1998) Evolution of syncytium-inducing and non-syncytium-inducing biological virus clones in relation to replication kinetics during the course of HIV-1 infection. J. Virol. 72(6): 5099–5107

    Google Scholar 

  15. Wolfs T.W., Zwart G., Bakker M., Valk M., Kuiken C., Goudsmit J. (1991) Naturally occurring mutations within HIV-1 V3 genomic RNA lead to antigenic variation dependent on a single amino scid substitution. Virology185: 195–205

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Information Sciences, Tokyo University of Science, Noda City, Chiba, 278-8510, Japan

    Masanori Ohya

Authors
  1. Masanori Ohya
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

Copyright information

© 2002 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Ohya, M. (2002). An Information Theoretic Approach to the Study of Genome Sequences: An Application to the Evolution of HIV. In: Unconventional Models of Computation. UMC 2002. Lecture Notes in Computer Science, vol 2509. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45833-6_5

Download citation

  • DOI: https://doi.org/10.1007/3-540-45833-6_5

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-44311-7

  • Online ISBN: 978-3-540-45833-3

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation