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Detection and Quantification of Viral and Satellite RNAs in Plant Hosts

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RNA Abundance Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 883))

Abstract

Northern blotting is a valuable method for detection and quantification of RNA in the field of virology. Although many methods including a various versions of polymerase chain reaction have been developed over the years, Northern blotting has been still considered as a useful and effective method for the analysis of progeny RNA accumulation for viral and subviral pathogens, such as satellite RNAs, in plant hosts. Here, we describe a detailed Northern blot protocol for efficient detection and quantification of viral and satellite RNAs from plant hosts.

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References

  1. Noueiry AO, Ahlquist P (2003) Brome mosaic virus RNA replication: revealing the role of the host in RNA virus replication. Annu Rev Phytopathol 41:77–98

    Article  PubMed  CAS  Google Scholar 

  2. Gamarnik AV, Andino R (1998) Switch from translation to RNA replication in a ­positive-stranded RNA virus. Genes Dev 12:2293–2304

    Article  PubMed  CAS  Google Scholar 

  3. Lemm JA, Rumenapf T, Strauss EG, Strauss JH, Rice CM (1994) Polypeptide requirements for assembly of functional Sindbis virus replication complexes: a model for the temporal regulation of minus- and plus-strand RNA synthesis. EMBO J 13:2925–2934

    PubMed  CAS  Google Scholar 

  4. Marsh LE, Huntley CC, Pogue GP, Connell JP, Hall TC (1991) Regulation of (+):(−)-strand asymmetry in replication of brome mosaic virus RNA. Virology 182:76–83

    Article  PubMed  CAS  Google Scholar 

  5. Annamalai P, Rao AL (2007) In vivo packaging of brome mosaic virus RNA3, but not RNAs 1 and 2, is dependent on a cis-acting 3′ tRNA-like structure. J Virol 81:173–181

    Article  PubMed  CAS  Google Scholar 

  6. Wang WK, Sung TL, Tsai YC, Kao CL, Chang SM, King CC (2002) Detection of dengue virus replication in peripheral blood mononuclear cells from dengue virus type 2-infected patients by a reverse transcription-real-time PCR assay. J Clin Microbiol 40:4472–4478

    Article  PubMed  CAS  Google Scholar 

  7. Purcell MK, Hart SA, Kurath G, Winton JR (2006) Strand-specific, real-time RT-PCR assays for quantification of genomic and positive-sense RNAs of the fish rhabdovirus, infectious hematopoietic necrosis virus. J Virol Methods 132:18–24

    Article  PubMed  CAS  Google Scholar 

  8. Komurian-Pradel F, Perret M, Deiman B, Sodoyer M, Lotteau V, Paranhos-Baccala G, Andre P (2004) Strand specific quantitative real-time PCR to study replication of hepatitis C virus genome. J Virol Methods 116:103–106

    Article  PubMed  CAS  Google Scholar 

  9. Gu C, Zheng C, Shi L, Zhang Q, Li Y, Lu B, Xiong Y, Qu S, Shao J, Chang H (2007) Plus- and minus-stranded foot-and-mouth disease virus RNA quantified simultaneously using a novel real-time RT-PCR. Virus Genes 34:289–298

    Article  PubMed  CAS  Google Scholar 

  10. Lanford RE, Chavez D, Chisari FV, Sureau C (1995) Lack of detection of negative-strand hepatitis C virus RNA in peripheral blood mononuclear cells and other extrahepatic tissues by the highly strand-specific rTth reverse transcriptase PCR. J Virol 69:8079–8083

    PubMed  CAS  Google Scholar 

  11. Lanford RE, Sureau C, Jacob JR, White R, Fuerst TR (1994) Demonstration of in vitro infection of chimpanzee hepatocytes with hepatitis C virus using strand-specific RT/PCR. Virology 202:606–614

    Article  PubMed  CAS  Google Scholar 

  12. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY

    Google Scholar 

  13. Miller WA, Koev G (2000) Synthesis of subgenomic RNAs by positive-strand RNA viruses. Virology 273:1–8

    Article  PubMed  CAS  Google Scholar 

  14. Simon AE, Roossinck MJ, Havelda Z (2004) Plant virus satellite and defective interfering RNAs: new paradigms for a new century. Annu Rev Phytopathol 42:415–437

    Article  PubMed  CAS  Google Scholar 

  15. Levy JA, Fraenkel-Conrat H, Owens RA (1994) Virology, 3rd edn. Prentice Hall, Englewood Cliffs, NJ

    Google Scholar 

  16. Dimmock NJ, Easton AJ, Leppard K (2007) Introduction to modern virology, 6th edn. Blackwell, Malden, MA

    Google Scholar 

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Acknowledgments

This study was supported by a grant from the National Institutes of Health (1R21AI82301) to A.L.N. Rao.

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Authors and Affiliations

  1. Department of Plant Pathology and Microbiology, University of California, Riverside, CA, USA

    Sun-Jung Kwon, Jang-Kyun Seo & A. L. N. Rao

Authors
  1. Sun-Jung Kwon
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  2. Jang-Kyun Seo
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  3. A. L. N. Rao
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Corresponding author

Correspondence to A. L. N. Rao .

Editor information

Editors and Affiliations

  1. , Dept. Plant Pathology & Microbiology, University of California, University Avenue 900, Riverside, 92521, USA

    Hailing Jin

  2. , Division of Plant Sciences, University of Missouri, Agriculture Building 1-31, Columbia, 65211, Missouri, USA

    Walter Gassmann

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Kwon, SJ., Seo, JK., Rao, A.L.N. (2012). Detection and Quantification of Viral and Satellite RNAs in Plant Hosts. In: Jin, H., Gassmann, W. (eds) RNA Abundance Analysis. Methods in Molecular Biology, vol 883. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-839-9_10

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  • DOI: https://doi.org/10.1007/978-1-61779-839-9_10

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-838-2

  • Online ISBN: 978-1-61779-839-9

  • eBook Packages: Springer Protocols

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