3D Spatially Resolved Models of the Intracellular Dynamics of the Hepatitis C Genome Replication Cycle
AuthorsKnodel, Markus M.
KAUST DepartmentApplied Mathematics and Computational Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Extreme Computing Research Center
Permanent link to this recordhttp://hdl.handle.net/10754/625833
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AbstractMathematical models of virus dynamics have not previously acknowledged spatial resolution at the intracellular level despite substantial arguments that favor the consideration of intracellular spatial dependence. The replication of the hepatitis C virus (HCV) viral RNA (vRNA) occurs within special replication complexes formed from membranes derived from endoplasmatic reticulum (ER). These regions, termed membranous webs, are generated primarily through specific interactions between nonstructural virus-encoded proteins (NSPs) and host cellular factors. The NSPs are responsible for the replication of the vRNA and their movement is restricted to the ER surface. Therefore, in this study we developed fully spatio-temporal resolved models of the vRNA replication cycle of HCV. Our simulations are performed upon realistic reconstructed cell structures-namely the ER surface and the membranous webs-based on data derived from immunostained cells replicating HCV vRNA. We visualized 3D simulations that reproduced dynamics resulting from interplay of the different components of our models (vRNA, NSPs, and a host factor), and we present an evaluation of the concentrations for the components within different regions of the cell. Thus far, our model is restricted to an internal portion of a hepatocyte and is qualitative more than quantitative. For a quantitative adaption to complete cells, various additional parameters will have to be determined through further in vitro cell biology experiments, which can be stimulated by the results deccribed in the present study.
CitationKnodel M, Reiter S, Targett-Adams P, Grillo A, Herrmann E, et al. (2017) 3D Spatially Resolved Models of the Intracellular Dynamics of the Hepatitis C Genome Replication Cycle. Viruses 9: 282. Available: http://dx.doi.org/10.3390/v9100282.
SponsorsWe thank Andreas Vogel, Michael Lampe, Martin Rupp and Konstantinos Xylouris (G-CSC) for technical help and helpful discussions, Wouter van Beerendonk (Huygens SVI, Netherlands) for his very friendly support in Huygens usage, backgrounds, and licensing. The HLRS Stuttgart is acknowledged for the supplied computing time on the Hermit and Hornet super computers . The authors acknowledge the Goethe-University Frankfurt and the Politecnico di Torino for general support and computational resources. This work has been supported in part by the “Fondazione Cassa di Risparmio di Torino” (Italy), through the “La Ricerca dei Talenti” (HR Excellence in Research) programme. The Authors wish to express their sincere thanks to the anonymous Referees for their thorough and critical reviews of our work.
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