메뉴 건너뛰기




Volumn 1, Issue 1, 2016, Pages

Infectio: A generic framework for computational simulation of virus transmission between cells

Author keywords

Advection; Cell population; Cellular automata; Convection; Diffusion; Fluorescence microscopy; Hybrid modeling; Infection spread; Multiscale modeling; Numerical simulation; Particle strength exchange; Phenotypic properties

Indexed keywords


EID: 84966700952     PISSN: None     EISSN: 23795042     Source Type: Journal    
DOI: 10.1128/mSphere.00078-15     Document Type: Article
Times cited : (9)

References (50)
  • 1
    • 73549093632 scopus 로고    scopus 로고
    • Virus movements on the plasma membrane support infection and transmission between cells
    • Burckhardt CJ, Greber UF. 2009. Virus movements on the plasma membrane support infection and transmission between cells. PLoS Pathog 5:e1000621. http://dx.doi.org/10.1371/journal.ppat.1000621
    • (2009) PLoS Pathog , vol.5
    • Burckhardt, C.J.1    Greber, U.F.2
  • 3
    • 80052395837 scopus 로고    scopus 로고
    • Cell-to-cell spread of HIV permits ongoing replication despite antiretroviral therapy
    • Sigal A, Kim JT, Balazs AB, Dekel E, Mayo A, Milo R, Baltimore D. 2011. Cell-to-cell spread of HIV permits ongoing replication despite antiretroviral therapy. Nature 477:95-98. http://dx.doi.org/10.1038/ nature10347
    • (2011) Nature , vol.477 , pp. 95-98
    • Sigal, A.1    Kim, J.T.2    Balazs, A.B.3    Dekel, E.4    Mayo, A.5    Milo, R.6    Baltimore, D.7
  • 5
    • 84908389414 scopus 로고    scopus 로고
    • Chemical induction of unfolded protein response enhances cancer cell killing through lytic virus infection
    • Prasad V, Suomalainen M, Pennauer M, Yakimovich A, Andriasyan V, Hemmi S, Greber UF. 2014. Chemical induction of unfolded protein response enhances cancer cell killing through lytic virus infection. J Virol 88:13086-13098. http://dx.doi.org/10.1128/JVI.02156-14
    • (2014) J Virol , vol.88 , pp. 13086-13098
    • Prasad, V.1    Suomalainen, M.2    Pennauer, M.3    Yakimovich, A.4    Andriasyan, V.5    Hemmi, S.6    Greber, U.F.7
  • 7
    • 54149119141 scopus 로고    scopus 로고
    • Avoiding the void: cell-to-cell spread of human viruses
    • Sattentau Q. 2008. Avoiding the void: cell-to-cell spread of human viruses. Nat Rev Microbiol 6:815-826. http://dx.doi.org/10.1038/nrmicro1972
    • (2008) Nat Rev Microbiol , vol.6 , pp. 815-826
    • Sattentau, Q.1
  • 8
    • 77957658175 scopus 로고    scopus 로고
    • Quasispecies theory and the behavior of RNA viruses
    • Lauring AS, Andino R. 2010. Quasispecies theory and the behavior of RNA viruses. PLoS Pathog 6:e1001005. http://dx.doi.org/10.1371/ journal.ppat.1001005
    • (2010) PLoS Pathog , vol.6
    • Lauring, A.S.1    Andino, R.2
  • 9
    • 0031792462 scopus 로고    scopus 로고
    • Virus assembly and disassembly: the adenovirus cysteine protease as a trigger factor
    • Greber UF. 1998. Virus assembly and disassembly: the adenovirus cysteine protease as a trigger factor. Rev Med Virol 8:213-222. http:// dx.doi.org/10.1002/(SICI)1099-1654(1998100)8:4<213::AID-RMV225>3.0.CO;2-W
    • (1998) Rev Med Virol , vol.8 , pp. 213-222
    • Greber, U.F.1
  • 10
    • 84901989727 scopus 로고    scopus 로고
    • How cells tune viral mechanics-insights from biophysical measurements of influenza virus
    • Greber UF. 2014. How cells tune viral mechanics-insights from biophysical measurements of influenza virus. Biophys J 106:2317-2321. http://dx.doi.org/10.1016/j.bpj.2014.04.025
    • (2014) Biophys J , vol.106 , pp. 2317-2321
    • Greber, U.F.1
  • 11
    • 58049202272 scopus 로고    scopus 로고
    • Innate immunity to virus infection
    • Takeuchi O, Akira S. 2009. Innate immunity to virus infection. Immunol Rev 227:75-86. http://dx.doi.org/10.1111/j.1600-065X.2008.00737.x
    • (2009) Immunol Rev , vol.227 , pp. 75-86
    • Takeuchi, O.1    Akira, S.2
  • 12
    • 77954097645 scopus 로고    scopus 로고
    • Immunity and immunopathology to viruses: what decides the outcome?
    • Rouse BT, Sehrawat S. 2010. Immunity and immunopathology to viruses: what decides the outcome? Nat Rev Immunol 10:514-526. http://dx.doi.org/10.1038/nri2802
    • (2010) Nat Rev Immunol , vol.10 , pp. 514-526
    • Rouse, B.T.1    Sehrawat, S.2
  • 13
    • 79960316181 scopus 로고    scopus 로고
    • Chemotactic antiviral cytokines promote infectious apical entry of human adenovirus into polarized epithelial cells
    • Lutschg V, Boucke K, Hemmi S, Greber UF. 2011. Chemotactic antiviral cytokines promote infectious apical entry of human adenovirus into polarized epithelial cells. Nat Commun 2:391. http://dx.doi.org/10.1038/ ncomms1391
    • (2011) Nat Commun , vol.2 , pp. 391
    • Lutschg, V.1    Boucke, K.2    Hemmi, S.3    Greber, U.F.4
  • 14
    • 84881029265 scopus 로고    scopus 로고
    • Virus interactions with endocytic pathways in macrophages and dendritic cells
    • Mercer J, Greber UF. 2013. Virus interactions with endocytic pathways in macrophages and dendritic cells. Trends Microbiol 21:380-388. http://dx.doi.org/10.1016/j.tim.2013.06.001
    • (2013) Trends Microbiol , vol.21 , pp. 380-388
    • Mercer, J.1    Greber, U.F.2
  • 16
    • 0008899802 scopus 로고
    • Cytopathology of virus infections: particular reference to tissue culture studies
    • Enders JF. 1954. Cytopathology of virus infections: particular reference to tissue culture studies. Annu Rev Microbiol 8:473-502. http:// dx.doi.org/10.1146/annurev.mi.08.100154.002353
    • (1954) Annu Rev Microbiol , vol.8 , pp. 473-502
    • Enders, J.F.1
  • 17
    • 50849129909 scopus 로고    scopus 로고
    • Vesicular egress of non-enveloped lytic parvoviruses depends on gelsolin functioning
    • Bär S, Daeffler L, Rommelaere J, Nüesch JP. 2008. Vesicular egress of non-enveloped lytic parvoviruses depends on gelsolin functioning. PLoS Pathog 4:e1000126. http://dx.doi.org/10.1371/journal.ppat.1000126
    • (2008) PLoS Pathog , vol.4
    • Bär, S.1    Daeffler, L.2    Rommelaere, J.3    Nüesch, J.P.4
  • 18
    • 34548434746 scopus 로고    scopus 로고
    • Junctional gating: the Achilles' heel of epithelial cells in pathogen infection
    • Greber UF, Gastaldelli M. 2007. Junctional gating: the Achilles' heel of epithelial cells in pathogen infection. Cell Host Microbe 2:143-146. http://dx.doi.org/10.1016/j.chom.2007.08.004
    • (2007) Cell Host Microbe , vol.2 , pp. 143-146
    • Greber, U.F.1    Gastaldelli, M.2
  • 19
    • 76749169041 scopus 로고    scopus 로고
    • Repulsion of superinfecting virions: a mechanism for rapid virus spread
    • Doceul V, Hollinshead M, van der Linden L, Smith GL. 2010. Repulsion of superinfecting virions: a mechanism for rapid virus spread. Science 327:873-876. http://dx.doi.org/10.1126/science.1183173
    • (2010) Science , vol.327 , pp. 873-876
    • Doceul, V.1    Hollinshead, M.2    van der Linden, L.3    Smith, G.L.4
  • 20
    • 0033578669 scopus 로고    scopus 로고
    • Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures
    • Benson SD, Bamford JK, Bamford DH, Burnett RM. 1999. Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures. Cell 98:825-833. http://dx.doi.org/10.1016/S0092-8674(00)81516-0
    • (1999) Cell , vol.98 , pp. 825-833
    • Benson, S.D.1    Bamford, J.K.2    Bamford, D.H.3    Burnett, R.M.4
  • 21
    • 84866173314 scopus 로고    scopus 로고
    • Cell-free transmission of human adenovirus by passive mass transfer in cell culture simulated in a computer model
    • Yakimovich A, Gumpert H, Burckhardt CJ, Lütschg VA, Jurgeit A, Sbalzarini IF, Greber UF. 2012. Cell-free transmission of human adenovirus by passive mass transfer in cell culture simulated in a computer model. J Virol 86:10123-10137. http://dx.doi.org/10.1128/JVI.01102-12
    • (2012) J Virol , vol.86 , pp. 10123-10137
    • Yakimovich, A.1    Gumpert, H.2    Burckhardt, C.J.3    Lütschg, V.A.4    Jurgeit, A.5    Sbalzarini, I.F.6    Greber, U.F.7
  • 24
    • 0036932713 scopus 로고    scopus 로고
    • The formation and function of extracellular enveloped vaccinia virus
    • Smith GL, Vanderplasschen A, Law M. 2002. The formation and function of extracellular enveloped vaccinia virus. J Gen Virol 83:2915-2931. http://dx.doi.org/10.1099/0022-1317-83-12-2915
    • (2002) J Gen Virol , vol.83 , pp. 2915-2931
    • Smith, G.L.1    Vanderplasschen, A.2    Law, M.3
  • 26
    • 0026625607 scopus 로고
    • Role of cell-associated enveloped vaccinia virus in cell-to-cell spread
    • PubMed
    • Blasco R, Moss B. 1992. Role of cell-associated enveloped vaccinia virus in cell-to-cell spread. J Virol 66:4170-4179. PubMed
    • (1992) J Virol , vol.66 , pp. 4170-4179
    • Blasco, R.1    Moss, B.2
  • 27
    • 0033780474 scopus 로고    scopus 로고
    • A complex of N-WASP and WIP integrates signalling cascades that lead to actin polymerization
    • Moreau V, Frischknecht F, Reckmann I, Vincentelli R, Rabut G, Stewart D, Way M. 2000. A complex of N-WASP and WIP integrates signalling cascades that lead to actin polymerization. Nat Cell Biol 2:441-448. http://dx.doi.org/10.1038/35017080
    • (2000) Nat Cell Biol , vol.2 , pp. 441-448
    • Moreau, V.1    Frischknecht, F.2    Reckmann, I.3    Vincentelli, R.4    Rabut, G.5    Stewart, D.6    Way, M.7
  • 28
    • 0028866712 scopus 로고
    • Actin-based motility of vaccinia virus
    • Cudmore S, Cossart P, Griffiths G, Way M. 1995. Actin-based motility of vaccinia virus. Nature 378:636-638. http://dx.doi.org/10.1038/ 378636a0
    • (1995) Nature , vol.378 , pp. 636-638
    • Cudmore, S.1    Cossart, P.2    Griffiths, G.3    Way, M.4
  • 29
    • 0032565358 scopus 로고    scopus 로고
    • Role for the vaccinia virus A36R outer envelope protein in the formation of virus-tipped actioncontaining microvilli and cell-to-cell virus spread
    • Wolffe EJ, Weisberg AS, Moss B. 1998. Role for the vaccinia virus A36R outer envelope protein in the formation of virus-tipped actioncontaining microvilli and cell-to-cell virus spread. Virology 244:20-26. http://dx.doi.org/10.1006/viro.1998.9103
    • (1998) Virology , vol.244 , pp. 20-26
    • Wolffe, E.J.1    Weisberg, A.S.2    Moss, B.3
  • 30
    • 0019199323 scopus 로고
    • Significance of extracellular enveloped virus in the in vitro and in vivo dissemination of vaccinia
    • Payne LG. 1980. Significance of extracellular enveloped virus in the in vitro and in vivo dissemination of vaccinia. J Gen Virol 50:89-100. http://dx.doi.org/10.1099/0022-1317-50-1-89
    • (1980) J Gen Virol , vol.50 , pp. 89-100
    • Payne, L.G.1
  • 31
    • 84946925907 scopus 로고    scopus 로고
    • Plaque2.0-A high-throughput analysis framework to score virus-cell transmission and clonal cell expansion
    • Yakimovich A, Andriasyan V, Witte R, Wang IH, Prasad V, Suomalainen M, Greber UF. 2015. Plaque2.0-A high-throughput analysis framework to score virus-cell transmission and clonal cell expansion. PLoS One 10:e0138760. http://dx.doi.org/10.1371/journal.pone.0138760
    • (2015) PLoS One , vol.10
    • Yakimovich, A.1    Andriasyan, V.2    Witte, R.3    Wang, I.H.4    Prasad, V.5    Suomalainen, M.6    Greber, U.F.7
  • 34
    • 84968481687 scopus 로고
    • The weighted particle method for convection-diffusion equations Part 1 the case of an isotropic viscosity
    • Degond P, Mas-Gallic S. 1989. The weighted particle method for convection-diffusion equations. Part 1: the case of an isotropic viscosity. Math Comput 53:485-507. http://dx.doi.org/10.1090/S0025-5718-1989-0983559-9
    • (1989) Math Comput , vol.53 , pp. 485-507
    • Degond, P.1    Mas-Gallic, S.2
  • 36
    • 0017291489 scopus 로고
    • A complexity measure
    • McCabe TJ. 1976. A complexity measure. IEEE Trans Softw Eng 2:308-320. http://dx.doi.org/10.1109/TSE.1976.233837
    • (1976) IEEE Trans Softw Eng , vol.2 , pp. 308-320
    • McCabe, T.J.1
  • 37
    • 0033346610 scopus 로고    scopus 로고
    • A critique of software defect prediction models
    • Fenton NE, Neil M. 1999. A critique of software defect prediction models. IEEE Trans Softw Eng 25:675-689. http://dx.doi.org/10.1109/ 32.815326
    • (1999) IEEE Trans Softw Eng , vol.25 , pp. 675-689
    • Fenton, N.E.1    Neil, M.2
  • 39
    • 7644242473 scopus 로고    scopus 로고
    • A simple cellular automaton model for influenza A viral infections
    • Beauchemin C, Samuel J, Tuszynski J. 2005. A simple cellular automaton model for influenza A viral infections. J Theor Biol 232:223-234. http://dx.doi.org/10.1016/j.jtbi.2004.08.001
    • (2005) J Theor Biol , vol.232 , pp. 223-234
    • Beauchemin, C.1    Samuel, J.2    Tuszynski, J.3
  • 40
    • 33344460430 scopus 로고    scopus 로고
    • A probability cellular automaton model for hepatitis B viral infections
    • Xiao X, Shao S-H, Chou K-C. 2006. A probability cellular automaton model for hepatitis B viral infections. Biochem Biophys Res Commun 342:605-610. http://dx.doi.org/10.1016/j.bbrc.2006.01.166
    • (2006) Biochem Biophys Res Commun , vol.342 , pp. 605-610
    • Xiao, X.1    Shao, S.-H.2    Chou, K.-C.3
  • 41
    • 42749102416 scopus 로고    scopus 로고
    • Dynamics of HIV infection: A cellular automata approach
    • Zorzenon dos Santos RM, Coutinho S. 2001. Dynamics of HIV infection: A cellular automata approach. Phys Rev Lett 87:168102. http:// dx.doi.org/10.1103/PhysRevLett.87.168102
    • (2001) Phys Rev Lett , vol.87
    • Zorzenon dos Santos, R.M.1    Coutinho, S.2
  • 42
    • 63049110384 scopus 로고    scopus 로고
    • Towards predictive computational models of oncolytic virus therapy: basis for experimental validation and model selection
    • Wodarz D, Komarova N. 2009. Towards predictive computational models of oncolytic virus therapy: basis for experimental validation and model selection. PLoS One 4:e4271. http://dx.doi.org/10.1371/ journal.pone.0004271
    • (2009) PLoS One , vol.4
    • Wodarz, D.1    Komarova, N.2
  • 43
    • 84855348940 scopus 로고    scopus 로고
    • Early infection and spread of a conditionally replicating adenovirus under conditions of plaque formation
    • Hofacre A, Wodarz D, Komarova NL, Fan H. 2012. Early infection and spread of a conditionally replicating adenovirus under conditions of plaque formation. Virology 423:89-96. http://dx.doi.org/10.1016/ j.virol.2011.11.014
    • (2012) Virology , vol.423 , pp. 89-96
    • Hofacre, A.1    Wodarz, D.2    Komarova, N.L.3    Fan, H.4
  • 44
    • 84864048651 scopus 로고    scopus 로고
    • Complex spatial dynamics of oncolytic viruses in vitro: mathematical and experimental approaches
    • Wodarz D, Hofacre A, Lau JW, Sun Z, Fan H, Komarova NL. 2012. Complex spatial dynamics of oncolytic viruses in vitro: mathematical and experimental approaches. PLoS Comput Biol 8:e1002547. http:// dx.doi.org/10.1371/journal.pcbi.1002547
    • (2012) PLoS Comput Biol , vol.8
    • Wodarz, D.1    Hofacre, A.2    Lau, J.W.3    Sun, Z.4    Fan, H.5    Komarova, N.L.6
  • 45
    • 70349655451 scopus 로고    scopus 로고
    • Chlamydial infection and spatial ascension of the female genital tract: a novel hybrid cellular automata and continuum mathematical model
    • Mallet DG, Heymer K-J, Rank RG, Wilson DP. 2009. Chlamydial infection and spatial ascension of the female genital tract: a novel hybrid cellular automata and continuum mathematical model. FEMS Immunol Med Microbiol 57:173-182. http://dx.doi.org/10.1111/j.1574-695X.2009.00596.x
    • (2009) FEMS Immunol Med Microbiol , vol.57 , pp. 173-182
    • Mallet, D.G.1    Heymer, K.-J.2    Rank, R.G.3    Wilson, D.P.4
  • 46
    • 59149087387 scopus 로고    scopus 로고
    • A multiscale mathematical model for oncolytic virotherapy
    • Paiva LR, Binny C, Ferreira SC, Martins ML. 2009. A multiscale mathematical model for oncolytic virotherapy. Cancer Res 69:1205-1211. http://dx.doi.org/10.1158/0008-5472.CAN-08-2173
    • (2009) Cancer Res , vol.69 , pp. 1205-1211
    • Paiva, L.R.1    Binny, C.2    Ferreira, S.C.3    Martins, M.L.4
  • 49
    • 24144448719 scopus 로고    scopus 로고
    • Effects of organelle shape on fluorescence recovery after photobleaching
    • Sbalzarini IF, Mezzacasa A, Helenius A, Koumoutsakos P. 2005. Effects of organelle shape on fluorescence recovery after photobleaching. Biophys J 89:1482-1492. http://dx.doi.org/10.1529/biophysj.104.057885
    • (2005) Biophys J , vol.89 , pp. 1482-1492
    • Sbalzarini, I.F.1    Mezzacasa, A.2    Helenius, A.3    Koumoutsakos, P.4
  • 50
    • 0038315334 scopus 로고    scopus 로고
    • Comparison of virus production in chicken embryo fibroblasts infected with the WR, IHD-J and MVA strains of vaccinia virus: IHD-J is most efficient in trans-Golgi network wrapping and extracellular enveloped virus release
    • Meiser A, Boulanger D, Sutter G, Krijnse Locker J. 2003. Comparison of virus production in chicken embryo fibroblasts infected with the WR, IHD-J and MVA strains of vaccinia virus: IHD-J is most efficient in trans-Golgi network wrapping and extracellular enveloped virus release. J Gen Virol 84:1383-1392. http://dx.doi.org/10.1099/vir.0.19016-0
    • (2003) J Gen Virol , vol.84 , pp. 1383-1392
    • Meiser, A.1    Boulanger, D.2    Sutter, G.3    Krijnse Locker, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.