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Virus Imaging Tools

Year 2020, Volume: 4 Issue: 2, 75 - 83, 29.08.2020

Abstract

Viruses are very small physical particles that can not be observed with a normal microscope. Only the largest virus, the poxvirus can be seen in the light microscope. Other tools are required for a detailed examination of viruses in ultrastructural size. Especially for the last 20 years, these advanced and ongoing tools have been used in the investigation of the biological molecules and biological processes of viruses. With the help of virus imaging tools, viruses can be identified in clinical samples, thereby explaining the detailed life cycle of the virus. Thus, these tools help the creation of new and safe vaccines and antiviral medicine. In this review, electron microscopy (EM) tools were given as scanning electron microscopy (SEM), transmission electron microscopy (TEM), cryo-electron microscopy (Cryo-EM) since generally used tools based on EM. Besides EM-based tools, X-ray crystallography which is the basis for cryo-EM and atomic force microscopy (AFM) that is relatively economic and easy to apply compared to other microscopies were also described.

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Thanks

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References

  • Acharya, R., Fry, E., Stuart, D., Fox, G., Rowlands, D., & Brown, F. (1990). The structure of FMDV: implications for its physical and biological properties. Veterinary Microbiology, 23(6), 21-34.
  • Auer, M. (2000) Three dimensional Cryo-EM as a powerful structural tool in moleculer medicine. Journal of Moleculer Medicine, 78 (4), 191-202.
  • Balthazar, J. M., Souza, S. L. T., Tusset, A. M., & Bueno, A. M. (2013). Microcantilever chaotic motion suppression in tapping mode atomic force microscope. Proceedings of the Institution of Mechanical Engineers Part C Journal of Mechanical Engineering Science 1989-1996, 203-210.
  • Bartenschaler, R., & Romea–Brey, I. (2015). Viral İnfection at high magnification: 3D electron microscopy methods to analyze the architecture of infected cells. Viruses. 7(12), 6316-6345.
  • Binnig, C. F., Quate, C., & Gerber, H. (1986). Atomic Force Microscope. Physical Review Letters. 56 (3), 930-933.
  • Briggs, J. A., Watson, B., Gowen, B. E., & Fuller, S. D. (2004). Cryoelectron microscopy of mouse mammary tumor virus; Journal of Virology, 78(3), 2606-2608.
  • Büttner, F. M., Renner-Schnecka, M., & Stehle, T., (2015). X-ray crystallography and its impact on understanding bacterial cell wall remodeling processes. International Journal of Medical Microbiology, 305(2), 209-216.
  • Carter, C. W. J., & Robert, M. S. (1997). Methods in enzymology: Macromolecular crystallography part A 1st ed., Cambridge, Massachusetts, US: National Academic  Press.
  • Cherry, S. R., & Gambhir, S. S. (2001). Use of positron emission tomography in animal research. ILAR Journal, 42(3), 219-232.
  • Cook, S. C., Griffin, D. E. (2003). Luciferase imaging of a neurotropic viral infection in intact animals. Journal of Virology, 77(9). 5333-5338.
  • Colton, R. J., Baselt, R. D., Dufrene, Y., Green, J. B. D., & Li, J. U. (1997). Scanning probe microscopy. Current Opinion in Chemical Biology, 1(3), 370-377.
  • Commike, T., & Chiu, W. (2000). Reconstruction principles of icosahedral virus structure determination using electron cryomicroscopy. Micron, 31(6), 687-711.
  • David, B. W., & Carter, B. C. (2009). Transmission electron microscopy (TEM), A textbook for material science, New York US: Springer.
  • Gelderblom, H. R.,& Hazelton, P. R. (2003). Electron microscopy for rapid diagnosis of emerging infectious agents. Emerging İnfectious Disease, 9(3), 294-303.
  • Gao, Y., Yan, L., Huang, Y., Liu, F., Zhao, Y., Cao, L., Wang, T., Sun, Q., Ming, Z., Zhang, L., Ge, J., Zheng, L., Zhang, Y., Wang, H., Zhu, Y., Zhu, C., Hu, T., Hua, T., Zhang, B., Yang, X., Li, J., Yang, H., Liu, Z., Xu, W., Guddat, L. W., Wang, Q., Lou, Z., & Ra, Z. (2020). Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science. 10.1126/science.abb7498
  • Goldsmith, C. S., & Mille, S. E. (2009). Modern uses of electron microscopy for detection of viruses. Clinical Microbiology Review, 22(4) 552-563.
  • Haan K., Ballard, Z., Rivenson, Y., Wu., Y., & Ozcan, A. (2019). Resolution enhancement in SEM using deep learning. Scientific Reports, 9(8) 12050.
  • Hewat, E. A., Verdaguer, N., Blakemore, W., Brookes, S., & King, A. (1997). Structure of the complex of an Fab fragment of a neutralizing antibody with FMD virus: positioning of a highly mobile antigenic loop, The EMBO Journal, 16(7), 1492-1500.
  • Kienberger, F., Zhu, R., Moser, R., Blaas, D., & Hinterdorfer, P. (2004). Monitoring RNA release from human rhinovirus by dynamic force microscopy. Journal of Virology, 78(7) 3203-3209.
  • Kiselyova, O. I., Yaminsky, I. V., Karger, E. M., Frolava, O. Y., Dorakhov, Y. L., & Atabekov, J. G. (2001). Visualization by atomic force microscopy of tobacco mosaic virus movement protein-RNA complexes formed in vitro. Journal General Virology, 82(6), 1503-1508.
  • Kim, J. M., Chung, Y. S., Jo, H. J., Lee, N. J. Kim, M. S., Woo, S. H., Park, S., Kim, S. J. W., Kim, H. M., & Hana, M. G. (2020). Identification of coronavirus isolated from a patient in Korea with COVID-19, Osong Public Health and Research Perspectives, 11(6), 3-7.
  • Kuznetsov, Y. G., & Mcpearson, A. (2011). Atomic force microscopy in imaging of viruses and virus infected cells. Microbiology Moleculer Biology Review, 75(2),268-285.
  • Kuznetsov, Y. G., Malkin, A. J., Lucas, R. W., Plomp, M., & McPherson, A. (2001). Imaging of viruses by atomic force microscopy. Journal General Virology, 82(6)2025-2034.
  • Malkin, A. J., McPearson, A., & Gershon, P. D. (2003). Structure of intracelluler mature vaccinia virus visualized by in situ atomic force microscopy, Journal of Virology, 77(11)6332-6340.
  • Parker, S. D., Joseph, S. W., & Hunter, E. (2001). Analysis of Mason Pfizer Monkey virus gag particules by SEM. Journal of Virology, 75(19) 9543-9548.
  • Quinn, C., Lu, M., Suiter, C. L., Hou, G., Zhang, H., & Polenava, T. (2015). Magic angle spinning NMR of viruses. Progress in Nulcear Magnetic Resonance Spectroscopy, 4(4), 21-40.
  • Raza, M. (2012). Syntesis of hydrogenated amorphous carbon (a-C:H) thin films by HIPIMS-based process. PhD thesis, Linköping University, Sweden.
  • Roingeard, P. (2008). Viral detection by electron microscopy: past, present and future. Biology of the Cell,100(8), 491-501.
  • Roingeard, P., Raynal, P., Eymiex, S., & Blanchard, E. (2018) Virus detection by transmission electron microscopy: still useful for diagnosis and a plus for biosafety. Reviews in Medical Virology, 29(1)e2019.
  • Risco, C., & Carrascosa, J. L. (1999). Visualization of viral assembly in the infected cell; Histology Histopathology, 14(3), 905-926.
  • Risco, C., Rodriguez, J. R., Lopez-Iglesias, C., Carracose, J. L., Esteban, M., Rodriquez, D. (2002). Endoplasmic reticulum–golgi intermediate compartment membranes and vimentin filaments participate in vaccinia virus assembly, Journal of Virology, 76(4), 1839-1855.
  • Szatanek, R., Krzyworzeka, M. B., Zimoch, J., Lekka, M., Siedlar, M., Baran, J. (2017). The methods of choice for extracellular vesicles (EVs) characterization. International Journal of Moleculer Science, 18(6),1153
  • Stewart, P. L., Fuller, S. D., & Burnett, R. M. (1993). Difference imaging of adenovirus: bridging the resolution gap between X-ray crystallography and electron microscopy. EMBO Journal, 127 2589-2599.
  • Utagawa E. T. (2004). Small round structured viruses (SRSVs) and TEM; African Journal Biotechnology, 3, 8-11. Edward, K., Wagner, M. J., Hewlett, D., Bloom, D. C., & Camerini, D. (2003). Basic Virology. 3rd ed. New Jersey, US: Blackwell.
  • Wery, P., & Schevitz, R. W. (1997). New trends in macromoleculer X-ray crystallography, Current Opinion Chemical Biology, 1(3), 365-369.
  • Yu, Z., & Bajaj, C. (2005). Automatic ultrastructure segmenttaion of reconstructed cryo-EM maps of icosehedral viruses. IEEE Transactions on image processing. 9, 1324-1337.
  • Zaitsev, B. N., Durymanov, A. G., & Generalow, V. M. (2002). AFM of the interaction of erytrocyte membrane and virus particules, state research center of virology and biotechnology "Vector" Koltsovo Proceedings, Novabirsk region.
Year 2020, Volume: 4 Issue: 2, 75 - 83, 29.08.2020

Abstract

Project Number

-

References

  • Acharya, R., Fry, E., Stuart, D., Fox, G., Rowlands, D., & Brown, F. (1990). The structure of FMDV: implications for its physical and biological properties. Veterinary Microbiology, 23(6), 21-34.
  • Auer, M. (2000) Three dimensional Cryo-EM as a powerful structural tool in moleculer medicine. Journal of Moleculer Medicine, 78 (4), 191-202.
  • Balthazar, J. M., Souza, S. L. T., Tusset, A. M., & Bueno, A. M. (2013). Microcantilever chaotic motion suppression in tapping mode atomic force microscope. Proceedings of the Institution of Mechanical Engineers Part C Journal of Mechanical Engineering Science 1989-1996, 203-210.
  • Bartenschaler, R., & Romea–Brey, I. (2015). Viral İnfection at high magnification: 3D electron microscopy methods to analyze the architecture of infected cells. Viruses. 7(12), 6316-6345.
  • Binnig, C. F., Quate, C., & Gerber, H. (1986). Atomic Force Microscope. Physical Review Letters. 56 (3), 930-933.
  • Briggs, J. A., Watson, B., Gowen, B. E., & Fuller, S. D. (2004). Cryoelectron microscopy of mouse mammary tumor virus; Journal of Virology, 78(3), 2606-2608.
  • Büttner, F. M., Renner-Schnecka, M., & Stehle, T., (2015). X-ray crystallography and its impact on understanding bacterial cell wall remodeling processes. International Journal of Medical Microbiology, 305(2), 209-216.
  • Carter, C. W. J., & Robert, M. S. (1997). Methods in enzymology: Macromolecular crystallography part A 1st ed., Cambridge, Massachusetts, US: National Academic  Press.
  • Cherry, S. R., & Gambhir, S. S. (2001). Use of positron emission tomography in animal research. ILAR Journal, 42(3), 219-232.
  • Cook, S. C., Griffin, D. E. (2003). Luciferase imaging of a neurotropic viral infection in intact animals. Journal of Virology, 77(9). 5333-5338.
  • Colton, R. J., Baselt, R. D., Dufrene, Y., Green, J. B. D., & Li, J. U. (1997). Scanning probe microscopy. Current Opinion in Chemical Biology, 1(3), 370-377.
  • Commike, T., & Chiu, W. (2000). Reconstruction principles of icosahedral virus structure determination using electron cryomicroscopy. Micron, 31(6), 687-711.
  • David, B. W., & Carter, B. C. (2009). Transmission electron microscopy (TEM), A textbook for material science, New York US: Springer.
  • Gelderblom, H. R.,& Hazelton, P. R. (2003). Electron microscopy for rapid diagnosis of emerging infectious agents. Emerging İnfectious Disease, 9(3), 294-303.
  • Gao, Y., Yan, L., Huang, Y., Liu, F., Zhao, Y., Cao, L., Wang, T., Sun, Q., Ming, Z., Zhang, L., Ge, J., Zheng, L., Zhang, Y., Wang, H., Zhu, Y., Zhu, C., Hu, T., Hua, T., Zhang, B., Yang, X., Li, J., Yang, H., Liu, Z., Xu, W., Guddat, L. W., Wang, Q., Lou, Z., & Ra, Z. (2020). Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science. 10.1126/science.abb7498
  • Goldsmith, C. S., & Mille, S. E. (2009). Modern uses of electron microscopy for detection of viruses. Clinical Microbiology Review, 22(4) 552-563.
  • Haan K., Ballard, Z., Rivenson, Y., Wu., Y., & Ozcan, A. (2019). Resolution enhancement in SEM using deep learning. Scientific Reports, 9(8) 12050.
  • Hewat, E. A., Verdaguer, N., Blakemore, W., Brookes, S., & King, A. (1997). Structure of the complex of an Fab fragment of a neutralizing antibody with FMD virus: positioning of a highly mobile antigenic loop, The EMBO Journal, 16(7), 1492-1500.
  • Kienberger, F., Zhu, R., Moser, R., Blaas, D., & Hinterdorfer, P. (2004). Monitoring RNA release from human rhinovirus by dynamic force microscopy. Journal of Virology, 78(7) 3203-3209.
  • Kiselyova, O. I., Yaminsky, I. V., Karger, E. M., Frolava, O. Y., Dorakhov, Y. L., & Atabekov, J. G. (2001). Visualization by atomic force microscopy of tobacco mosaic virus movement protein-RNA complexes formed in vitro. Journal General Virology, 82(6), 1503-1508.
  • Kim, J. M., Chung, Y. S., Jo, H. J., Lee, N. J. Kim, M. S., Woo, S. H., Park, S., Kim, S. J. W., Kim, H. M., & Hana, M. G. (2020). Identification of coronavirus isolated from a patient in Korea with COVID-19, Osong Public Health and Research Perspectives, 11(6), 3-7.
  • Kuznetsov, Y. G., & Mcpearson, A. (2011). Atomic force microscopy in imaging of viruses and virus infected cells. Microbiology Moleculer Biology Review, 75(2),268-285.
  • Kuznetsov, Y. G., Malkin, A. J., Lucas, R. W., Plomp, M., & McPherson, A. (2001). Imaging of viruses by atomic force microscopy. Journal General Virology, 82(6)2025-2034.
  • Malkin, A. J., McPearson, A., & Gershon, P. D. (2003). Structure of intracelluler mature vaccinia virus visualized by in situ atomic force microscopy, Journal of Virology, 77(11)6332-6340.
  • Parker, S. D., Joseph, S. W., & Hunter, E. (2001). Analysis of Mason Pfizer Monkey virus gag particules by SEM. Journal of Virology, 75(19) 9543-9548.
  • Quinn, C., Lu, M., Suiter, C. L., Hou, G., Zhang, H., & Polenava, T. (2015). Magic angle spinning NMR of viruses. Progress in Nulcear Magnetic Resonance Spectroscopy, 4(4), 21-40.
  • Raza, M. (2012). Syntesis of hydrogenated amorphous carbon (a-C:H) thin films by HIPIMS-based process. PhD thesis, Linköping University, Sweden.
  • Roingeard, P. (2008). Viral detection by electron microscopy: past, present and future. Biology of the Cell,100(8), 491-501.
  • Roingeard, P., Raynal, P., Eymiex, S., & Blanchard, E. (2018) Virus detection by transmission electron microscopy: still useful for diagnosis and a plus for biosafety. Reviews in Medical Virology, 29(1)e2019.
  • Risco, C., & Carrascosa, J. L. (1999). Visualization of viral assembly in the infected cell; Histology Histopathology, 14(3), 905-926.
  • Risco, C., Rodriguez, J. R., Lopez-Iglesias, C., Carracose, J. L., Esteban, M., Rodriquez, D. (2002). Endoplasmic reticulum–golgi intermediate compartment membranes and vimentin filaments participate in vaccinia virus assembly, Journal of Virology, 76(4), 1839-1855.
  • Szatanek, R., Krzyworzeka, M. B., Zimoch, J., Lekka, M., Siedlar, M., Baran, J. (2017). The methods of choice for extracellular vesicles (EVs) characterization. International Journal of Moleculer Science, 18(6),1153
  • Stewart, P. L., Fuller, S. D., & Burnett, R. M. (1993). Difference imaging of adenovirus: bridging the resolution gap between X-ray crystallography and electron microscopy. EMBO Journal, 127 2589-2599.
  • Utagawa E. T. (2004). Small round structured viruses (SRSVs) and TEM; African Journal Biotechnology, 3, 8-11. Edward, K., Wagner, M. J., Hewlett, D., Bloom, D. C., & Camerini, D. (2003). Basic Virology. 3rd ed. New Jersey, US: Blackwell.
  • Wery, P., & Schevitz, R. W. (1997). New trends in macromoleculer X-ray crystallography, Current Opinion Chemical Biology, 1(3), 365-369.
  • Yu, Z., & Bajaj, C. (2005). Automatic ultrastructure segmenttaion of reconstructed cryo-EM maps of icosehedral viruses. IEEE Transactions on image processing. 9, 1324-1337.
  • Zaitsev, B. N., Durymanov, A. G., & Generalow, V. M. (2002). AFM of the interaction of erytrocyte membrane and virus particules, state research center of virology and biotechnology "Vector" Koltsovo Proceedings, Novabirsk region.
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Details

Primary Language English
Subjects Veterinary Surgery
Journal Section Review Articles
Authors

Beyhan Sareyyüpoğlu 0000-0002-0279-1673

Project Number -
Publication Date August 29, 2020
Published in Issue Year 2020 Volume: 4 Issue: 2

Cite

APA Sareyyüpoğlu, B. (2020). Virus Imaging Tools. Journal of Istanbul Veterinary Sciences, 4(2), 75-83.

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