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Quantitative PCR of environmental samples

  • Janet K. Jansson
  • Thomas Leser

Abstract

The polymerase chain reaction (PCR) is currently the most sensitive method for detection of specific DNA in environmental samples. Sensitivities in the range of 1–100 cells per gram of sediment or soil have been reported [24, 31, 32]. Ultimately, sensitivity of detection by PCR is dependent on several factors such as the target copy number and/or enhancement by use of nested primers or DNA probes.

Keywords

Polymerase Chain Reaction Polymerase Chain Reaction Reaction Quantitative Polymerase Chain Reaction Polymerase Chain Reaction Cycle Competitive Polymerase Chain Reaction 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    Ausubel FM, Brent R, Kingston RE, Moore DD, Smith JA, Seidman JG, Struhl K (1988) Preparation and analysis of DNA. In: Ausubel FM (ed) Current Protocols in Molecular Biology, pp. 2.4.1–2.4.5. John Wiley & Sons, Inc., New York.Google Scholar
  2. 2.
    Becker-André M, Hahlbrock K (1989) Absolute mRNA quantification using the polymerase chain reaction (PCR). A novel approach by a PCR aided transcript titration assay (PATTY). Nucl Acids Res 17: 9437–9446.CrossRefGoogle Scholar
  3. 3.
    Bennet PV, Sutherland BM (1993) Quantitative detection of single-copy genes in nanogram samples of human genomic DNA. BioTechniques 15: 520–525.Google Scholar
  4. 4.
    Celi FS, Zenilman ME, Shuldiner AR (1993) A rapid and versatile method to synthesize internal standards for competitive PCR. Nucl Acids Res 21: 1047.CrossRefGoogle Scholar
  5. 5.
    Clementi M, Menzo S, Bagnarelli P, Manzin A, Valenza A, Varaldo PE (1993) Quantitative PCR and RT-PCR in virology. PCR Meth Applic 2: 191–196.CrossRefGoogle Scholar
  6. 6.
    Coen D (1994) Quantification of DNAs by the polymerase chain reaction using an internal control. In: Mullis KB, Ferré F, Gibbs RA (eds) The Polymerase Chain Reaction, pp. 89–96. Birkhäuser, Boston.CrossRefGoogle Scholar
  7. 7.
    Diviacco S, Norio P, Zentilin L, Menzo S, Clementi M, Biamonti G, Riva S, Falaschi A, Giacca M (1992) A novel procedure for quantitative polymerase chain reaction by coamplification of competitive templates. Gene 122: 313–320.CrossRefGoogle Scholar
  8. 8.
    Du Breuil RM, Patel JM, Mendelow BV (1993) Quantitation of β-actin-specific mRNA transcripts using xeno-competitive PCR. PCR Meth Applic 3: 57–59.CrossRefGoogle Scholar
  9. 9.
    Ferré F (1992) Quantitative or semi-quantitative PCR: Reality versus myth. PCR Meth Applic 2: 1–9.CrossRefGoogle Scholar
  10. 10.
    Ferré F, Marchese A, Pessoli P, Griffin S, Buston E, Boyer V (1994) Quantitative PCR: An overview. In: Mullis KB, Ferré F, Gibbs RA (eds) The Polymerase Chain Reaction, pp. 67–88. Birkhäuser, Boston.CrossRefGoogle Scholar
  11. 11.
    Förster E (1994) An improved general method to generate internal standards for competitive PCR. BioTechniques 16: 18–19.Google Scholar
  12. 12.
    Förster E (1994) Rapid generation of internal standards for competitive PCR by low-stringency primer annealing. BioTechniques 16: 1006–1008.Google Scholar
  13. 13.
    Galea E, Feinstein DL (1992) Rapid synthesis of DNA deletion constructs for mRNA quantitation: analysis of astrocyte mRNAs. PCR Meth Applic 2: 66–69.CrossRefGoogle Scholar
  14. 14.
    Holben WE, Jansson JK, Chelm BK, Tiedje JM (1988) DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl Environ Microbiol 54: 703–711.Google Scholar
  15. 15.
    Jalava T, Lehtovaara P, Kallio A, Ranki M, Söderlund H (1993) Quantification of Hepatitis B Virus DNA by competitive amplification and hybridization on microplates. BioTechniques 15: 134–139.Google Scholar
  16. 16.
    Jansson JK (1995) Tracking genetically engineered microorganisms in nature. Current Opinion Biotechnol 6: 275–283.CrossRefGoogle Scholar
  17. 17.
    Katz ED, Di Cesare JL, Picozza E, Anderson MS (1993) General aspects of PCR quantitation. Amplifications 10: 7–8.Google Scholar
  18. 18.
    Keller MA, Cassel DL, Rappaport EF, McKenzie SE, Schwartz E, Surrey S (1993) Fluorescence-based RT PCR analysis: Determination of the ratio of soluble to membrane-bound forms of FcyRIIA transcripts in hematopoietic cell lines. PCR Meth Applic 3: 32–38.CrossRefGoogle Scholar
  19. 19.
    Leser TD, Boye M, Hendriksen NB (1995) Survival and activity of Pseudomonas sp. Strain B13(FR1) in a marine microcosms determined by quantitative PCR and an rRNA-targeting probe and its effect on the indigenous bacterioplankton. Appl Environ Microbiol 61: 1201–1207.Google Scholar
  20. 20.
    Leser TD (1995) Quantitation of Pseudomonas sp. strain B13(FR1) in the marine environment by competitive polymerase chain reaction. J Microbiol Meth 22: 249–262.CrossRefGoogle Scholar
  21. 21.
    Lundeberg J, Wahlberg J, Uhlén M (1991) Rapid colorimetric quantification of PCR-amplified DNA. BioTechniques 10: 68–75.Google Scholar
  22. 22.
    Martin CS, Butler L, Bronstein I (1995) Quantitation of PCR products with chemiluminescence. BioTechniques 18: 908–913.Google Scholar
  23. 23.
    McCulloch RK, Choong CS, Hurley DM (1995) An evaluation of competitor type and size for use in the determination of mRNA by competitive PCR. PCR Meth Applic 4: 219–226.CrossRefGoogle Scholar
  24. 24.
    Möller A, Gustafsson K, Jansson JK (1994) Specific monitoring by PCR amplification and bioluminescence of firefly luciferase gene-tagged bacteria added to environmental samples. FEMS Microbiol Ecol 15: 193–206.CrossRefGoogle Scholar
  25. 25.
    Möller A, Jansson JK (submitted) Quantitation of genetically-tagged cyanobacteria in Battic Sea sediment by competitive PCR.Google Scholar
  26. 26.
    Piatak Jr M, Luk K-C, Williams B, Lifson JD (1993) Quantitative competitive polymerase chain reaction for accurate quantitation of HIV DNA and RNA species. BioTechniques 14: 70–80.Google Scholar
  27. 27.
    Reischl U, Kochanowski B (1995) Quantitative PCR. Mol Biotechnol 3: 55–71.CrossRefGoogle Scholar
  28. 28.
    Siebert PD, Larrick JW (1993) PCR MIMICS: Competitive DNA fragments for use as internal standards in quantitative PCR: BioTechniques 14: 244–249.Google Scholar
  29. 29.
    Simon L, Levesque RC, Lalonde M (1992) Rapid quantitation by PCR of endomycorrhizal fungi colonizing roots. PCR Meth Applic 2: 76–80.CrossRefGoogle Scholar
  30. 30.
    Smalla K, Cresswell N, Mendonca-Hagler LC, Wolters A, Van Elsas JD (1993) Rapid DNA extraction protocol from soil for polymerase chain reaction-mediated amplification. J Appl Bacteriol 74: 78–85.CrossRefGoogle Scholar
  31. 31.
    Steffan RJ, Atlas RM (1988) DNA amplification to enhance detection of genetically engineered bacteria in environmental samples. Appl Environ Microbiol 34: 2185–2191.Google Scholar
  32. 32.
    Tebbe CC, Vahjen W (1993) Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and yeast. Appl Environ Microbiol 59: 2657–2665.Google Scholar
  33. 33.
    Thiery R, Boutin P, Arnauld C, Jestin A (1995) Efficient production of internal standard DNA for quantitative PCR using an automated sequencer. BioTechniques 18: 212–213.Google Scholar
  34. 34.
    Überla K, Platzer C, Daimantstein T, Blankenstein T (1991) Generation of competitor DNA fragments for quantitative PCR. PCR Meth Applic 1: 136–139.CrossRefGoogle Scholar
  35. 35.
    Wang AM, Doyle MV, Mark DF (1989) Quantitation of mRNA by the polymerase chain reaction. Proc Natl Acad Sci 86: 9717–9721.CrossRefGoogle Scholar
  36. 36.
    Zachar V, Thomas RA, Goustin AS (1993) Absolute quantification of target DNA: a simple competitive PCR for efficient analysis of multiple samples. Nucl Acids Res 21: 2017–2018.CrossRefGoogle Scholar
  37. 37.
    Zar JH (1984) Biostatistical Analysis, 2nd Ed. Prentice-Hall International Editions, Englewood Cliffs, NJ.Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 1996

Authors and Affiliations

  • Janet K. Jansson
    • 1
  • Thomas Leser
    • 2
  1. 1.Department of Biochemistry, Arrhenius LaboratoriesStockholm UniversityStockholmSweden
  2. 2.National Veterinary LaboratoryCopenhagenDenmark

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