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Investigating Hepatitis C Virus Infection Using Super-Resolution Microscopy

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Hepatitis C Virus Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1911))

Abstract

Super-resolution microscopy (SRM) can provide a window on the nanoscale events of virus replication. Here we describe a protocol for imaging hepatitis C virus-infected cells using localization SRM. We provide details on sample preparation, immunostaining, data collection, and super-resolution image reconstruction. We have made all efforts to generalize the protocol to make it accessible to all budding super-resolution microscopists.

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References

  1. Grove J (2014) Super-resolution microscopy: a virus' eye view of the cell. Viruses 6:1365–1378

    Article  Google Scholar 

  2. Sydor AM, Czymmek KJ, Puchner EM, Mennella V (2015) Super-resolution microscopy: from single molecules to supramolecular assemblies. Trends Cell Biol 25:730–748

    Article  CAS  Google Scholar 

  3. Galbraith CG, Galbraith JA (2011) Super-resolution microscopy at a glance. J Cell Sci 124:1607–1611

    Article  CAS  Google Scholar 

  4. Bates M, Huang B, Dempsey GT, Zhuang X (2007) Multicolor super-resolution imaging with photo-switchable fluorescent probes. Science 317:1749–1753

    Article  CAS  Google Scholar 

  5. Betzig E, Patterson GH, Sougrat R et al (2006) Imaging intracellular fluorescent proteins at nanometer resolution. Science 313:1642–1645

    Article  CAS  Google Scholar 

  6. Holm T, Klein T, Löschberger A et al (2014) A blueprint for cost-efficient localization microscopy. ChemPhysChem 15:651–654

    Article  CAS  Google Scholar 

  7. Sage D, Kirshner H, Pengo T et al (2015) Quantitative evaluation of software packages for single-molecule localization microscopy. Nat Methods 12:717–724

    Article  CAS  Google Scholar 

  8. Gustafsson N, Culley S, Ashdown G et al (2016) Fast live-cell conventional fluorophore nanoscopy with ImageJ through super-resolution radial fluctuations. Nat Commun 7:12471

    Article  CAS  Google Scholar 

  9. Lindenbach BD, Evans MJ, Syder AJ et al (2005) Complete replication of hepatitis C virus in cell culture. Science 309:623–626

    Article  CAS  Google Scholar 

  10. Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9:671–675

    Article  CAS  Google Scholar 

  11. Schindelin J, Arganda-Carreras I, Frise E et al (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods 9:676–682

    Article  CAS  Google Scholar 

  12. Zhang M, Chang H, Zhang Y et al (2012) Rational design of true monomeric and bright photoactivatable fluorescent proteins. Nat Methods 9:727–729

    Article  CAS  Google Scholar 

  13. Uno S-N, Tiwari DK, Kamiya M et al (2015) A guide to use photocontrollable fluorescent proteins and synthetic smart fluorophores for nanoscopy. Microscopy 64:263–277

    Article  CAS  Google Scholar 

  14. Dempsey GT, Vaughan JC, Chen KH et al (2011) Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging. Nat Methods 8:1027–1036

    Article  CAS  Google Scholar 

  15. Durisic N, Cuervo LL, Lakadamyali M (2014) Quantitative super-resolution microscopy: pitfalls and strategies for image analysis. Curr Opin Chem Biol 20C:22–28

    Article  Google Scholar 

  16. Durisic N, Laparra-Cuervo L, Sandoval-Álvarez Á et al (2014) Single-molecule evaluation of fluorescent protein photoactivation efficiency using an in vivo nanotemplate. Nat Methods 11:156–162

    Article  CAS  Google Scholar 

  17. Metcalf DJ, Edwards R, Kumarswami N, Knight AE (2013) Test samples for optimizing STORM super-resolution microscopy. J Vis Exp 79. https://doi.org/10.3791/50579

  18. Ji C, Lou X (2016) Single-molecule Super-resolution Imaging of Phosphatidylinositol 4,5-bisphosphate in the Plasma Membrane with Novel Fluorescent Probes. J Vis Exp 116. https://doi.org/10.3791/54466

  19. Paul D, Madan V, Bartenschlager R (2014) Hepatitis C Virus RNA Replication and Assembly: Living on the Fat of the Land. Cell Host Microbe 16:569–579

    Article  CAS  Google Scholar 

  20. Wang H, Tai AW (2016) Mechanisms of Cellular Membrane Reorganization to Support Hepatitis C Virus Replication. Viruses 8:e142

    Article  Google Scholar 

  21. Romero-Brey I, Merz A, Chiramel A et al (2012) Three-dimensional architecture and biogenesis of membrane structures associated with hepatitis C virus replication. PLoS Pathog 8:e1003056

    Article  CAS  Google Scholar 

  22. Camus G, Herker E, Modi AA et al (2013) Diacylglycerol acyltransferase-1 localizes hepatitis C virus NS5A protein to lipid droplets and enhances NS5A interaction with the viral capsid core. J Biol Chem 288:9915–9923

    Article  CAS  Google Scholar 

  23. Tam J, Cordier GA, Borbely JS et al (2014) Cross-talk-free multi-color STORM imaging using a single fluorophore. PLoS One 9:e101772

    Article  Google Scholar 

  24. Valley CC, Liu S, Lidke DS, Lidke KA (2015) Sequential Superresolution Imaging of Multiple Targets Using a Single Fluorophore. PLoS One 10:e0123941

    Article  Google Scholar 

  25. Shroff H, Galbraith CG, Galbraith JA et al (2007) Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes. Proc Natl Acad Sci U S A 104:20308–20313

    Article  CAS  Google Scholar 

  26. Lelek M, Di Nunzio F, Henriques R et al (2012) Superresolution imaging of HIV in infected cells with FlAsH-PALM. Proc Natl Acad Sci U S A 109:8564–8569

    Article  CAS  Google Scholar 

  27. Pereira PM, Almada P, Henriques R (2015) High-content 3D multicolor super-resolution localization microscopy. Methods Cell Biol 125:95–117

    Article  Google Scholar 

  28. Chandradoss SD, Haagsma AC, Lee YK et al (2014) Surface passivation for single-molecule protein studies. J Vis Exp 86. https://doi.org/10.3791/50549

  29. Whelan DR, Bell TDM (2015) Image artifacts in Single Molecule Localization Microscopy: why optimization of sample preparation protocols matters. Sci Rep 5:7924

    Article  CAS  Google Scholar 

  30. Tanaka KAK, Suzuki KGN, Shirai YM et al (2010) Membrane molecules mobile even after chemical fixation. Nat Methods 7:865–866

    Article  CAS  Google Scholar 

  31. Stone MB, Veatch SL (2014) Far-red organic fluorophores contain a fluorescent impurity. ChemPhysChem 15:2240–2246

    Article  CAS  Google Scholar 

  32. Nahidiazar L, Agronskaia AV, Broertjes J et al (2016) Optimizing imaging conditions for demanding multi-color super resolution localization microscopy. PLoS One 11:e0158884

    Article  Google Scholar 

  33. Barna L, Dudok B, Miczán V et al (2016) Correlated confocal and super-resolution imaging by VividSTORM. Nat Protoc 11:163–183

    Article  CAS  Google Scholar 

  34. van de Linde S, Sauer M (2014) How to switch a fluorophore: from undesired blinking to controlled photoswitching. Chem Soc Rev 43:1076–1087

    Article  Google Scholar 

  35. Fox-Roberts P, Marsh R, Pfisterer K et al (2017) Local dimensionality determines imaging speed in localization microscopy. Nat Commun 8:13558

    Article  CAS  Google Scholar 

  36. Ovesny M, Křižek P, Borkovec J et al (2014) ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging. Bioinformatics 30:2389–2390

    Article  CAS  Google Scholar 

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Acknowledgments

We would like to thank Ricardo Henriques and Lucas Walker for advice and technical support. JG is supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (107653/Z/15/Z). PMP is supported by a Biotechnology and Biological Sciences Research Council grant (BB/M022374/1). CJ is a Commonwealth Scholar, funded by the UK government. The imaging systems used in this work were funded by the Medical Research Council (MR/K015826/1).

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Correspondence to Joe Grove .

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Pereira, P.M., Jacobs, C., Grove, J. (2019). Investigating Hepatitis C Virus Infection Using Super-Resolution Microscopy. In: Law, M. (eds) Hepatitis C Virus Protocols . Methods in Molecular Biology, vol 1911. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8976-8_17

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  • DOI: https://doi.org/10.1007/978-1-4939-8976-8_17

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8975-1

  • Online ISBN: 978-1-4939-8976-8

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