Skip to main content
SpringerLink
Log in

On the Potential for Multiscale Oscillatory Behavior in HIV

  • Chapter
  • First Online:
Global Virology II - HIV and NeuroAIDS

  • 806 Accesses

Abstract

This chapter summarizes several theoretical studies on the potential for oscillatory behavior of HIV infection at molecular and cellular levels. It discusses the biological relevance of oscillatory systems in the HIV life cycle and touches upon broader perspectives for further theoretical and experimental exploration of system dynamics. The potential interference of HIV oscillatory dynamics at different scales and levels as well as interaction and coevolution with the complex host immune system is also discussed.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Coffin JM (1995) HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science 267(5197):483–489

    Article  CAS  PubMed  Google Scholar 

  2. Sloot PMA, Coveney PV, Ertaylan G, Müller V, Boucher CA, Bubak M (2009) HIV decision support: from molecule to man. Philos Transact A Math Phys Eng Sci 367(1898):2691–2703

    Article  CAS  Google Scholar 

  3. Peterlin BM, Trono D (2003) Hide, shield and strike back: how HIV-infected cells avoid immune eradication. Nat Rev Immunol 3(2):97–107

    Article  CAS  PubMed  Google Scholar 

  4. Gougeon M-L (2003) Apoptosis as an HIV strategy to escape immune attack. Nat Rev Immunol 3(5):392–404

    Article  CAS  PubMed  Google Scholar 

  5. Malim MH, Emerman M (2008) HIV-1 accessory proteins – ensuring viral survival in a hostile environment. Cell Host Microbe 3(6):388–398

    Article  CAS  PubMed  Google Scholar 

  6. Appay V, Sauce D (2008) Immune activation and inflammation in HIV-1 infection: causes and consequences. J Pathol 214(2):231–241

    Article  CAS  PubMed  Google Scholar 

  7. Perelson AS, Ribeiro RM (2013) Modeling the within-host dynamics of HIV infection. BMC Biol 11:96

    Article  PubMed  PubMed Central  Google Scholar 

  8. Perelson AS (2002) Modelling viral and immune system dynamics. Nat Rev Immunol 2(1):28–36

    Article  CAS  PubMed  Google Scholar 

  9. Perelson AS, Neumann AU, Markowitz M, Leonard JM, Ho DD (1996) HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science 271(5255):1582–1586

    Article  CAS  PubMed  Google Scholar 

  10. Bonhoeffer S, May RM, Shaw GM, Nowak MA (1997) Virus dynamics and drug therapy. Proc Natl Acad Sci U S A 94(13):6971–6976

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Ribeiro RM, Bonhoeffer S (2000) Production of resistant HIV mutants during antiretroviral therapy. Proc Natl Acad Sci U S A 97(14):7681–7686

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Hammond BJ (1993) Quantitative study of the control of HIV-1 gene expression. J Theor Biol 163(2):199–221

    Article  CAS  PubMed  Google Scholar 

  13. Reddy B, Yin J (1999) Quantitative intracellular kinetics of HIV type 1. AIDS Res Hum Retrovir 15(3):273–283

    Article  CAS  PubMed  Google Scholar 

  14. Kim H, Yin J (2005) Robust growth of human immunodeficiency virus type 1 (HIV-1). Biophys J 89(4):2210–2221

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Tameru B, Habtemariam T, Nganwa D, Ayanwale L, Beyene G, Robnett V, Wilson W (2008) Computational modelling of intracellular viral kinetics and CD4+ cellular population dynamics of HIV/AIDS. Adv Syst Sci Appl 8(1):40–45

    PubMed  PubMed Central  Google Scholar 

  16. Zarrabi N, Mancini E, Tay J, Shahand S, Sloot PMA (2010) Modeling HIV-1 intracellular replication: two simulation approaches. Procedia Comput Sci 1(1):555–564

    Article  Google Scholar 

  17. Likhoshvai VA, Khlebodarova TM, Bazhan SI, Gainova IA, Chereshnev VA, Bocharov GA (2014) Mathematical model of the tat-rev regulation of HIV-1 replication in an activated cell predicts the existence of oscillatory dynamics in the synthesis of viral components. BMC Genomics 15(Suppl 12):S1

    Article  PubMed  PubMed Central  Google Scholar 

  18. Karn J, Stoltzfus CM (2012) Transcriptional and posttranscriptional regulation of HIV-1 gene expression. Cold Spring Harb Perspect Med 2(2):a006916

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  19. Purcell DF, Martin MA (1993) Alternative splicing of human immunodeficiency virus type 1 mRNA modulates viral protein expression, replication, and infectivity. J Virol 67(11):6365–6378

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Laspia MF, Rice AP, Mathews MB (1989) HIV-1 tat protein increases transcriptional initiation and stabilizes elongation. Cell 59(2):283–292

    Article  CAS  PubMed  Google Scholar 

  21. Marciniak RA, Calnan BJ, Frankel AD, Sharp PA (1990) HIV-1 tat protein trans-activates transcription in vitro. Cell 63(4):791–802

    Article  CAS  PubMed  Google Scholar 

  22. Feinberg MB, Baltimore D, Frankel AD (1991) The role of tat in the human immunodeficiency virus life cycle indicates a primary effect on transcriptional elongation. Proc Natl Acad Sci U S A 88(9):4045–4049

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Bohan CA, Kashanchi F, Ensoli B, Buonaguro L, Boris-Lawrie KA, Brady JN (1992) Analysis of tat transactivation of human immunodeficiency virus transcription in vitro. Gene Expr 2(4):391–407

    CAS  PubMed  Google Scholar 

  24. Graeble MA, Churcher MJ, Lowe AD, Gait MJ, Karn J (1993) Human immunodeficiency virus type 1 transactivator protein, tat, stimulates transcriptional read-through of distal terminator sequences in vitro. Proc Natl Acad Sci U S A 90(13):6184–6188

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Harrich D, Hsu C, Race E, Gaynor RB (1994) Differential growth kinetics are exhibited by human immunodeficiency virus type 1 TAR mutants. J Virol 68(9):5899–5910

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Chojnacki J, Müller B (2013) Investigation of HIV-1 assembly and release using modern fluorescence imaging techniques. Traffic Cph Den 14(1):15–24

    Article  CAS  Google Scholar 

  27. Richard N, Iacampo S, Cochrane A (1994) HIV-1 rev is capable of shuttling between the nucleus and cytoplasm. Virology 204(1):123–131

    Article  CAS  PubMed  Google Scholar 

  28. Love DC, Sweitzer TD, Hanover JA (1998) Reconstitution of HIV-1 rev nuclear export: independent requirements for nuclear import and export. Proc Natl Acad Sci U S A 95(18):10608–10613

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Pond SJK, Ridgeway WK, Robertson R, Wang J, Millar DP (2009) HIV-1 rev protein assembles on viral RNA one molecule at a time. Proc Natl Acad Sci U S A 106(5):1404–1408

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Felber BK, Drysdale CM, Pavlakis GN (1990) Feedback regulation of human immunodeficiency virus type 1 expression by the rev protein. J Virol 64(8):3734–3741

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Weinberger LS, Dar RD, Simpson ML (2008) Transient-mediated fate determination in a transcriptional circuit of HIV. Nat Genet 40(4):466–470

    Article  CAS  PubMed  Google Scholar 

  32. Hong H-W, Lee S-W, Myung H (2013) Induced degradation of Tat by nucleocapsid (NC) via the proteasome pathway and its effect on HIV transcription. Virus 5(4):1143–1152

    Article  CAS  Google Scholar 

  33. Jablonski JA, Amelio AL, Giacca M, Caputi M (2010) The transcriptional transactivator tat selectively regulates viral splicing. Nucleic Acids Res 38(4):1249–1260

    Article  CAS  PubMed  Google Scholar 

  34. Lata S, Ali A, Sood V, Raja R, Banerjea AC (2015) HIV-1 Rev downregulates Tat expression and viral replication via modulation of NAD(P)H:quinine oxidoreductase 1 (NQO1). Nat Commun 6:7244

    Article  CAS  PubMed  Google Scholar 

  35. Barkai N, Leibler S (2000) Circadian clocks limited by noise. Nature 403(6767):267–268

    CAS  PubMed  Google Scholar 

  36. Hasty J, Dolnik M, Rottschäfer V, Collins JJ (2002) Synthetic gene network for entraining and amplifying cellular oscillations. Phys Rev Lett 88(14):148101

    Article  PubMed  CAS  Google Scholar 

  37. Leite MCA, Wang Y (2010) Multistability, oscillations and bifurcations in feedback loops. Math Biosci Eng MBE 7(1):83–97

    Article  PubMed  Google Scholar 

  38. Stricker J, Cookson S, Bennett MR, Mather WH, Tsimring LS, Hasty J (2008) A fast, robust and tunable synthetic gene oscillator. Nature 456(7221):516–519

    Article  CAS  PubMed  Google Scholar 

  39. Cao Y, Wang H, Ouyang Q, Tu Y (2015) The free energy cost of accurate biochemical oscillations. Nat Phys 11(9):772–778

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Leloup J-C, Goldbeter A (2003) Toward a detailed computational model for the mammalian circadian clock. Proc Natl Acad Sci U S A 100(12):7051–7056

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Hayot F, Jayaprakash C (2006) NF-kappaB oscillations and cell-to-cell variability. J Theor Biol 240(4):583–591

    Article  CAS  PubMed  Google Scholar 

  42. Krishna S, Jensen MH, Sneppen K (2006) Minimal model of spiky oscillations in NF-kappaB signaling. Proc Natl Acad Sci U S A 103(29):10840–10845

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Pigolotti S, Krishna S, Jensen MH (2007) Oscillation patterns in negative feedback loops. Proc Natl Acad Sci U S A 104(16):6533–6537

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Jensen PB, Pedersen L, Krishna S, Jensen MH (2010) A Wnt oscillator model for somitogenesis. Biophys J 98(6):943–950

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Hoffmann A, Levchenko A, Scott ML, Baltimore D (2002) The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. Science 298(5596):1241–1245

    Article  CAS  PubMed  Google Scholar 

  46. Nelson DE, Ihekwaba AEC, Elliott M, Johnson JR, Gibney CA, Foreman BE, Nelson G, See V, Horton CA, Spiller DG, Edwards SW, McDowell HP, Unitt JF, Sullivan E, Grimley R, Benson N, Broomhead D, Kell DB, White MRH (2004) Oscillations in NF-kappaB signaling control the dynamics of gene expression. Science 306(5696):704–708

    Article  CAS  PubMed  Google Scholar 

  47. Wang Y, Paszek P, Horton CA, Kell DB, White MR, Broomhead DS, Muldoon MR (2011) Interactions among oscillatory pathways in NF-kappa B signaling. BMC Syst Biol 5:23

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  48. Hirata H, Yoshiura S, Ohtsuka T, Bessho Y, Harada T, Yoshikawa K, Kageyama R (2002) Oscillatory expression of the bHLH factor Hes1 regulated by a negative feedback loop. Science 298(5594):840–843

    Article  CAS  PubMed  Google Scholar 

  49. Kageyama R, Yoshiura S, Masamizu Y, Niwa Y (2007) Ultradian oscillators in somite segmentation and other biological events. Cold Spring Harb Symp Quant Biol 72:451–457

    Article  CAS  PubMed  Google Scholar 

  50. Bose I, Ghosh B (2007) The p53-MDM2 network: from oscillations to apoptosis. J Biosci 32(5):991–997

    Article  CAS  PubMed  Google Scholar 

  51. Perelson A, Nelson P (1999) Mathematical analysis of HIV-1 dynamics in vivo. SIAM Rev 41(1):3–44

    Article  Google Scholar 

  52. Nowak MA, May R (2001) Virus dynamics: mathematical principles of immunology and virology, 1st edn. Oxford University Press, Oxford/New York

    Google Scholar 

  53. De Leenheer P, Smith H (2003) Virus dynamics: a global analysis. SIAM J Appl Math 63(4):1313–1327

    Google Scholar 

  54. Muldowney JS (1990) Compound matrices and ordinary differential equations. Rocky Mt J Math 20(4):857–872

    Article  Google Scholar 

  55. Li M, Muldowney J (1996) A geometric approach to global-stability problems. SIAM J Math Anal 27(4):1070–1083

    Article  Google Scholar 

  56. Wang L, Li MY (2006) Mathematical analysis of the global dynamics of a model for HIV infection of CD4+ T cells. Math Biosci 200(1):44–57

    Article  CAS  PubMed  Google Scholar 

  57. Ellermeyer S, Wang L (2006) HIV infection and CD4+ T cell dynamics. Discrete Contin Dyn Syst - Ser B 6(6):1417–1430

    Article  Google Scholar 

  58. Smith HL (2008) Monotone dynamical systems: an introduction to the theory of competitive and cooperative systems. American Mathematical Society, Providence

    Book  Google Scholar 

  59. van den Driessche P, Watmough J (2002) Reproduction numbers and sub-threshold endemic equilibria for compartmental models of disease transmission. Math Biosci 180:29–48

    Article  PubMed  Google Scholar 

  60. Hutten S, Wälde S, Spillner C, Hauber J, Kehlenbach RH (2009) The nuclear pore component Nup358 promotes transportin-dependent nuclear import. J Cell Sci 122(Pt 8):1100–1110

    Article  CAS  PubMed  Google Scholar 

  61. Hutten S, Kehlenbach RH (2006) Nup214 is required for CRM1-dependent nuclear protein export in vivo. Mol Cell Biol 26(18):6772–6785

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Voit EO (2000) Computational analysis of biochemical systems: a practical guide for biochemists and molecular biologists, 1st edn. Cambridge University Press, New York

    Google Scholar 

  63. Carlotti F, Dower SK, Qwarnstrom EE (2000) Dynamic shuttling of nuclear factor kappa B between the nucleus and cytoplasm as a consequence of inhibitor dissociation. J Biol Chem 275(52):41028–41034

    Article  CAS  PubMed  Google Scholar 

  64. Lipniacki T, Paszek P, Brasier ARAR, Luxon B, Kimmel M (2004) Mathematical model of NF-kappaB regulatory module. J Theor Biol 228(2):195–215

    Article  CAS  PubMed  Google Scholar 

  65. Slice LW, Codner E, Antelman D, Holly M, Wegrzynski B, Wang J, Toome V, Hsu MC, Nalin CM (1992) Characterization of recombinant HIV-1 tat and its interaction with TAR RNA. Biochemistry (Mosc) 31(48):12062–12068

    Article  CAS  Google Scholar 

  66. Singh J, Padgett RA (2009) Rates of in situ transcription and splicing in large human genes. Nat Struct Mol Biol 16(11):1128–1133

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Audibert A, Weil D, Dautry F (2002) In vivo kinetics of mRNA splicing and transport in mammalian cells. Mol Cell Biol 22(19):6706–6718

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Kessler O, Jiang Y, Chasin LA (1993) Order of intron removal during splicing of endogenous adenine phosphoribosyltransferase and dihydrofolate reductase pre-mRNA. Mol Cell Biol 13(10):6211–6222

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Robert-Guroff M, Popovic M, Gartner S, Markham P, Gallo RC, Reitz MS (1990) Structure and expression of tat-, rev-, and nef-specific transcripts of human immunodeficiency virus type 1 in infected lymphocytes and macrophages. J Virol 64(7):3391–3398

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Efthymiadis A, Briggs LJ, Jans DA (1998) The HIV-1 tat nuclear localization sequence confers novel nuclear import properties. J Biol Chem 273(3):1623–1628

    Article  CAS  PubMed  Google Scholar 

  71. Malim MH, Cullen BR (1991) HIV-1 structural gene expression requires the binding of multiple rev monomers to the viral RRE: implications for HIV-1 latency. Cell 65(2):241–248

    Article  CAS  PubMed  Google Scholar 

  72. Daugherty MD, Booth DS, Jayaraman B, Cheng Y, Frankel AD (2010) HIV Rev response element (RRE) directs assembly of the Rev homooligomer into discrete asymmetric complexes. Proc Natl Acad Sci U S A 107(28):12481–12486

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Mann DA, Mikaélian I, Zemmel RW, Green SM, Lowe AD, Kimura T, Singh M, Butler PJ, Gait MJ, Karn J (1994) A molecular rheostat. Co-operative rev binding to stem I of the rev-response element modulates human immunodeficiency virus type-1 late gene expression. J Mol Biol 241(2):193–207

    Article  CAS  PubMed  Google Scholar 

  74. Felber BK, Hadzopoulou-Cladaras M, Cladaras C, Copeland T, Pavlakis GN (1989) Rev protein of human immunodeficiency virus type 1 affects the stability and transport of the viral mRNA. Proc Natl Acad Sci U S A 86(5):1495–1499

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Kubota S, Duan L, Furuta RA, Hatanaka M, Pomerantz RJ (1996) Nuclear preservation and cytoplasmic degradation of human immunodeficiency virus type 1 rev protein. J Virol 70(2):1282–1287

    CAS  PubMed  PubMed Central  Google Scholar 

  76. Veloso A, Kirkconnell KS, Magnuson B, Biewen B, Paulsen MT, Wilson TE, Ljungman M (2014) Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications. Genome Res 24(6):896–905

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, Herschlag D (2003) Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 100(7):3889–3894

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Wada Y, Ohta Y, Xu M, Tsutsumi S, Minami T, Inoue K, Komura D, ‘ichi Kitakami J, Oshida N, Papantonis A, Izumi A, Kobayashi M, Meguro H, Kanki Y, Mimura I, Yamamoto K, Mataki C, Hamakubo T, Shirahige K, Aburatani H, Kimura H, Kodama T, Cook PR, Ihara S (2009) A wave of nascent transcription on activated human genes. Proc Natl Acad Sci U S A 106(43):18357–18361

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Boireau S, Maiuri P, Basyuk E, de la Mata M, Knezevich A, Pradet-Balade B, Bäcker V, Kornblihtt A, Marcello A, Bertrand E (2007) The transcriptional cycle of HIV-1 in real-time and live cells. J Cell Biol 179(2):291–304

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Maiuri P, Knezevich A, Bertrand E, Marcello A (2011) Real-time imaging of the HIV-1 transcription cycle in single living cells. Methods San Diego Calif 53(1):62–67

    Article  CAS  Google Scholar 

  81. Richter S, Cao H, Rana TM (2002) Specific HIV-1 TAR RNA loop sequence and functional groups are required for human cyclin T1-tat-TAR ternary complex formation. Biochemistry (Mosc) 41(20):6391–6397

    Article  CAS  Google Scholar 

  82. Allen TD, Cronshaw JM, Bagley S, Kiseleva E, Goldberg MW (2000) The nuclear pore complex: mediator of translocation between nucleus and cytoplasm. J Cell Sci 113(Pt 10):1651–1659

    CAS  PubMed  Google Scholar 

  83. Grünwald D, Singer RH (2010) In vivo imaging of labelled endogenous β-actin mRNA during nucleocytoplasmic transport. Nature 467(7315):604–607

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  84. MacKay VL, Li X, Flory MR, Turcott E, Law GL, Serikawa KA, Xu XL, Lee H, Goodlett DR, Aebersold R, Zhao LP, Morris DR (2004) Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone. Mol Cell Proteomics MCP 3(5):478–489

    Article  CAS  PubMed  Google Scholar 

  85. Malim MH, Cullen BR (1993) Rev and the fate of pre-mRNA in the nucleus: implications for the regulation of RNA processing in eukaryotes. Mol Cell Biol 13(10):6180–6189

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Dowling D, Nasr-Esfahani S, Tan CH, O’Brien K, Howard JL, Jans DA, j Purcell DF, Stoltzfus CM, Sonza S (2008) HIV-1 infection induces changes in expression of cellular splicing factors that regulate alternative viral splicing and virus production in macrophages. Retrovirology 5:18

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  87. Gear CW (1971) The automatic integration of ordinary differential equations. Commun ACM 14(3):176–179

    Article  Google Scholar 

  88. Klatt NR, Chomont N, Douek DC, Deeks SG (2013) Immune activation and HIV persistence: implications for curative approaches to HIV infection. Immunol Rev 254(1):326–342

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  89. Canini L, Perelson AS (2014) Viral kinetic modeling: state of the art. J Pharmacokinet Pharmacodyn 41(5):431–443

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Banks HT, Flores KB, Hu S, Rosenberg E, Buzon M, Yu X, Lichterfeld M (2015) Immuno-modulatory strategies for reduction of HIV reservoir cells. J Theor Biol 372:146–158

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Kumberger P, Frey F, Schwarz US, Graw F (2016) Multiscale modeling of pathogen replication and spread. FEBS Lett 2016 590(13):1972–1986

    Google Scholar 

  92. Mishchenko EL, Bezmaternykh KD, Likhoshvai VA, Ratushny AV, Khlebodarova TM, Yu Sournina N, Ivanisenko VA, Kolchanov NA (2007) Mathematical model for suppression of subgenomic hepatitis C virus RNA replication in cell culture. J Bioinforma Comput Biol 5:593–609

    Article  CAS  Google Scholar 

  93. Chatterjee A, Smith PF, Perelson AS (2013) Hepatitis C viral kinetics: the past, present, and future. Clin Liver Dis 17(1):13–26

    Article  PubMed  PubMed Central  Google Scholar 

  94. Li MY, Shu H (2012) Global dynamics of a mathematical model for HTLV-I infection of CD4+ T cells with delayed CTL response. Nonlinear Anal Real World Appl 13(3):1080–1092

    Article  CAS  Google Scholar 

  95. Elemans M, Florins A, Willems L, Asquith B (2014) Rates of CTL killing in persistent viral infection in vivo. PLoS Comput Biol 10(4):e1003534

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  96. Beauchemin CAA, Handel A (2011) A review of mathematical models of influenza a infections within a host or cell culture: lessons learned and challenges ahead. BMC Public Health 11(Suppl 1):S7

    Article  PubMed  PubMed Central  Google Scholar 

  97. Murillo LN, Murillo MS, Perelson AS (2013) Towards multiscale modeling of influenza infection. J Theor Biol 332:267–290

    Article  PubMed  PubMed Central  Google Scholar 

  98. Manchanda H, Seidel N, Krumbholz A, Sauerbrei A, Schmidtke M, Guthke R (2014) Within-host influenza dynamics: a small-scale mathematical modeling approach. Biosystems 118:51–59

    Article  PubMed  Google Scholar 

  99. Goyal A, Murray JM (2016) Dynamics of in vivo hepatitis D virus infection. J Theor Biol 398:9–19

    Article  PubMed  Google Scholar 

  100. Schiffer JT, Swan DA, Corey L, Wald A (2013) Rapid viral expansion and short drug half-life explain the incomplete effectiveness of current herpes simplex virus 2-directed antiviral agents. Antimicrob Agents Chemother 57(12):5820–5829

    Article  PubMed  PubMed Central  Google Scholar 

  101. Carrillo-Bustamante P, Keşmir C, de Boer RJ (2014) Quantifying the protection of activating and inhibiting NK cell receptors during infection with a CMV-like virus. Front Immunol 5:20

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  102. Fallahi-Sichani M, El-Kebir M, Marino S, Kirschner DE, Linderman JJ (2011) Multiscale computational modeling reveals a critical role for TNF-α receptor 1 dynamics in tuberculosis granuloma formation. J Immunol Baltim Md 1950 186(6):3472–3483

    CAS  Google Scholar 

  103. Linderman JJ, Kirschner DE (2015) In silico models of M. Tuberculosis infection provide a route to new therapies. Drug Discov Today Dis Models 15:37–41

    Article  PubMed  Google Scholar 

  104. Antia R, Yates A, de Roode JC (2008) The dynamics of acute malaria infections. I. Effect of the parasite’s red blood cell preference. Proc Biol Sci 275(1641):1449–1458

    Article  PubMed  PubMed Central  Google Scholar 

  105. Adekunle AI, Pinkevych M, McGready R, Luxemburger C, White LJ, Nosten F, Cromer D, Davenport MP (2015) Modeling the dynamics of plasmodium vivax infection and hypnozoite reactivation in vivo. PLoS Negl Trop Dis 9(3):e0003595

    Article  PubMed  PubMed Central  Google Scholar 

  106. Schaefer MR, Wonderlich ER, Roeth JF, Leonard JA, Collins KL (2008) HIV-1 Nef targets MHC-I and CD4 for degradation via a final common beta-COP-dependent pathway in T cells. PLoS Pathog 4(8):e1000131

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  107. Schwartz O, Maréchal V, Le Gall S, Lemonnier F, Heard JM (1996) Endocytosis of major histocompatibility complex class I molecules is induced by the HIV-1 Nef protein. Nat Med 2(3):338–342

    Article  CAS  PubMed  Google Scholar 

  108. Hosseini I, Mac Gabhann F (2012) Multi-scale modeling of HIV infection in vitro and APOBEC3G-based anti-retroviral therapy. PLoS Comput Biol 8(2):e1002371

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Holmes M, Zhang F, Bieniasz PD (2015) Single-cell and single-cycle analysis of HIV-1 replication. PLoS Pathog 11(6):e1004961

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  110. Chen B-C, Legant WR, Wang K, Shao L, Milkie DE, Davidson MW, Janetopoulos C, Wu XS, Hammer JA, Liu Z, English BP, Mimori-Kiyosue Y, Romero DP, Ritter AT, Lippincott-Schwartz J, Fritz-Laylin L, Mullins RD, Mitchell DM, Bembenek JN, Reymann A-C, Böhme R, Grill SW, Wang JT, Seydoux G, Tulu US, Kiehart DP, Betzig E (2014) Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science 346(6208):1257998

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  111. Li D, Shao L, Chen B-C, Zhang X, Zhang M, Moses B, Milkie DE, Beach JR, Hammer JA, Pasham M, Kirchhausen T, Baird MA, Davidson MW, Xu P, Betzig E (2015) ADVANCED IMAGING. Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics. Science 349(6251):aab3500

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  112. Legant WR, Shao L, Grimm JB, Brown TA, Milkie DE, Avants BB, Lavis LD, Betzig E (2016) High-density three-dimensional localization microscopy across large volumes. Nat Methods 13(4):359–365

    Article  PubMed  PubMed Central  CAS  Google Scholar 

Download references

Acknowledgments

We thank Fred D. Mast, Samuel A. Danziger, and John D. Aitchison for critical reading of the manuscript and for discussion. AVR is supported by the National Institutes of Health (P41GM109824 and P50 GM076547). PDL is supported by the National Science Foundation (DMS grant 1411853). SIB is supported by the Russian Foundation for Basic Research (Grant 14-04-91164). GAB is supported by the Russian Foundation for Basic Research (Grant 14-01-00477) and the Russian Science Foundation (Grant 15-11-00029). TMK and VAL are supported by Russian Foundation for Basic Research (Grant No 16-01-00237a) and Budget Project (No 0324-2016-0008).

Conflict of interest The authors report no conflicts of interest.

Author information

Authors and Affiliations

  1. The Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute) and Institute for Systems Biology, Seattle, WA, USA

    Alexander V. Ratushny

  2. Oregon State University, Corvallis, OR, USA

    Patrick De Leenheer

  3. State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia

    Sergei I. Bazhan

  4. Institute of Numerical Mathematics, Russian Academy of Sciences, Moscow, Russia

    Gennady A. Bocharov

  5. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia

    Tamara M. Khlebodarova & Vitaly A. Likhoshvai

  6. Novosibirsk State University, Novosibirsk, Russia

    Vitaly A. Likhoshvai

Authors
  1. Alexander V. Ratushny
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Patrick De Leenheer
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sergei I. Bazhan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Gennady A. Bocharov
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Tamara M. Khlebodarova
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Vitaly A. Likhoshvai
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Alexander V. Ratushny .

Editor information

Editors and Affiliations

  1. Department of Internal Medicine, Division of Infectious Diseases and International Health, University of South Florida, Tampa, Florida, USA

    Paul Shapshak

  2. Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, California, USA

    Andrew J. Levine

  3. Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA

    Brian T. Foley

  4. Department of Internal Medicine, Division of Infectious Diseases and International Health, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA

    Charurut Somboonwit

  5. Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, California, USA

    Elyse Singer

  6. Department of Oral Biology and Medicine, UCLA School of Dentistry, Los Angeles, California, USA

    Francesco Chiappelli

  7. Department of Internal Medicine, Division of Infectious Diseases and International Health, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA

    John T. Sinnott

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media LLC

About this chapter

Cite this chapter

Ratushny, A.V., De Leenheer, P., Bazhan, S.I., Bocharov, G.A., Khlebodarova, T.M., Likhoshvai, V.A. (2017). On the Potential for Multiscale Oscillatory Behavior in HIV. In: Shapshak, P., et al. Global Virology II - HIV and NeuroAIDS. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-7290-6_34

Download citation

Publish with us

Policies and ethics

Search

Navigation