메뉴 건너뛰기




Volumn 77, Issue 1, 2011, Pages 41-47

Relative and absolute quantitative real-time PCR-based quantifications of hcnC and phlD gene transcripts in natural soil spiked with Pseudomonas sp. strain LBUM300

Author keywords

[No Author keywords available]

Indexed keywords

ARTIFICIAL RNA; BACTERIAL CELLS; COMPLEX MATRICES; COPY NUMBER; FIELD SOIL; GENE TRANSCRIPTS; IN-CONTROL; IN-VITRO; NATURAL SOILS; NONSTERILE; PRODUCTION OF HYDROGEN; PSEUDOMONAS SP; Q-RT-PCR; QUANTITATIVE REAL TIME PCR; RELATIVE QUANTIFICATION; RNA EXTRACTION; SAMPLING DATES; TECHNICAL PROBLEM; TRANSCRIPTIONAL ACTIVITY; TRANSCRIPTIONAL ANALYSIS;

EID: 79251606607     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01387-10     Document Type: Article
Times cited : (28)

References (39)
  • 1
    • 0004034258 scopus 로고    scopus 로고
    • Agriculture and Agri-Food Canada, 3rd ed. NRC Research Press, Ottawa, Ontario, Canada
    • Agriculture and Agri-Food Canada. 1998. The Canadian System of Soil Classification, 3rd ed. NRC Research Press, Ottawa, Ontario, Canada.
    • (1998) The Canadian System of Soil Classification
  • 3
    • 33144468213 scopus 로고    scopus 로고
    • Degradation of 4-chloro-2-methylphenoxyacetic acid in top- and subsoil is quantitatively linked to the class III tfdA gene
    • Bælum, J., T. Henriksen, H. C. B. Hansen, and C. S. Jacobsen. 2006. Degradation of 4-chloro-2-methylphenoxyacetic acid in top- and subsoil is quantitatively linked to the class III tfdA gene. Appl. Environ. Microbiol. 72:1476-1486.
    • (2006) Appl. Environ. Microbiol. , vol.72 , pp. 1476-1486
    • Bælum, J.1    Henriksen, T.2    Hansen, H.C.B.3    Jacobsen, C.S.4
  • 4
    • 44849121863 scopus 로고    scopus 로고
    • Direct analysis of tfdA gene expression by indigenous bacteria in phenoxy acid amended agricultural soil
    • Bælum, J., M. H. Nicolaisen, W. E. Holben, B. W. Strobel, J. Sørensen, and C. S. Jacobsen. 2008. Direct analysis of tfdA gene expression by indigenous bacteria in phenoxy acid amended agricultural soil. ISME J. 2:677-687.
    • (2008) ISME J. , vol.2 , pp. 677-687
    • Bælum, J.1    Nicolaisen, M.H.2    Holben, W.E.3    Strobel, B.W.4    Sørensen, J.5    Jacobsen, C.S.6
  • 5
    • 0034769121 scopus 로고    scopus 로고
    • Expression of prostaglandin D synthetase during development in the mouse testis
    • Baker, P. J., and P. J. O'Shaughnessy. 2001. Expression of prostaglandin D synthetase during development in the mouse testis. Reproduction 122:553-559.
    • (2001) Reproduction , vol.122 , pp. 553-559
    • Baker, P.J.1    O'shaughnessy, P.J.2
  • 6
    • 0033598832 scopus 로고    scopus 로고
    • Global GacA-steered control of cyanide and exoprotease production in Pseudomonas fluorescens involves specific ribosome binding sites
    • Blumer, C., S. Heeb, G. Pessi, and D. Haas. 1999. Global GacA-steered control of cyanide and exoprotease production in Pseudomonas fluorescens involves specific ribosome binding sites. Proc. Natl. Acad. Sci. U. S. A. 96:14073-14078.
    • (1999) Proc. Natl. Acad. Sci. U. S. A. , vol.96 , pp. 14073-14078
    • Blumer, C.1    Heeb, S.2    Pessi, G.3    Haas, D.4
  • 7
    • 0031470882 scopus 로고    scopus 로고
    • Rapid and direct method for extraction of RNA from soil
    • Borneman, J., and E. W. Triplett. 1997. Rapid and direct method for extraction of RNA from soil. Soil Biol. Biochem. 29:1621-1624.
    • (1997) Soil Biol. Biochem. , vol.29 , pp. 1621-1624
    • Borneman, J.1    Triplett, E.W.2
  • 8
    • 34247645532 scopus 로고    scopus 로고
    • Universal reference method for real-time PCR gene expression analysis of preimplantation embryos
    • Bower, N. I., R. J. Moser, J. R. Hill, and S. A. Lehnert. 2007. Universal reference method for real-time PCR gene expression analysis of preimplantation embryos. Biotechniques 42:199-206.
    • (2007) Biotechniques , vol.42 , pp. 199-206
    • Bower, N.I.1    Moser, R.J.2    Hill, J.R.3    Lehnert, S.A.4
  • 9
    • 0242668357 scopus 로고    scopus 로고
    • MRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil
    • Bürgmann, H., F. Widmer, W. V. Sigler, and J. Zeyer. 2003. mRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil. Appl. Environ. Microbiol. 69: 1928-1935.
    • (2003) Appl. Environ. Microbiol. , vol.69 , pp. 1928-1935
    • Bürgmann, H.1    Widmer, F.2    Sigler, W.V.3    Zeyer, J.4
  • 10
    • 0033775615 scopus 로고    scopus 로고
    • Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays
    • Bustin, S. A. 2000. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J. Mol. Endocrinol. 25:169-193.
    • (2000) J. Mol. Endocrinol. , vol.25 , pp. 169-193
    • Bustin, S.A.1
  • 12
    • 26844512816 scopus 로고    scopus 로고
    • Real-time reverse transcription PCR (qRT-PCR) and its potential use in clinical diagnosis
    • Bustin, S. A., and R. Mueller. 2005. Real-time reverse transcription PCR (qRT-PCR) and its potential use in clinical diagnosis. Clin. Sci. 109:365-379.
    • (2005) Clin. Sci. , vol.109 , pp. 365-379
    • Bustin, S.A.1    Mueller, R.2
  • 13
    • 0018725851 scopus 로고
    • The relationship between growth phase and cyanogenesis in Pseudomonas aeruginosa
    • Castric, P. A., R. F. Ebert, and K. F. Castric. 1979. The relationship between growth phase and cyanogenesis in Pseudomonas aeruginosa. Curr. Microbiol. 2:287-292.
    • (1979) Curr. Microbiol. , vol.2 , pp. 287-292
    • Castric, P.A.1    Ebert, R.F.2    Castric, K.F.3
  • 14
    • 0037343190 scopus 로고    scopus 로고
    • Phenazines and their role in biocontrol by Pseudomonas bacteria
    • Chin-A-Woeng, T. F. C., G. V. Bloemberg, and B. J. J. Lugtenberg. 2003. Phenazines and their role in biocontrol by Pseudomonas bacteria. New Phytol. 157:503-523.
    • (2003) New Phytol. , vol.157 , pp. 503-523
    • Chin-A-Woeng, T.F.C.1    Bloemberg, G.V.2    Lugtenberg, B.J.J.3
  • 15
    • 77949401095 scopus 로고    scopus 로고
    • A versatile internal control for use as DNA in real-time PCR and as RNA in real-time reverse transcription PCR assays
    • Deer, D. M., K. A. Lampel, and N. González-Escalona. 2010. A versatile internal control for use as DNA in real-time PCR and as RNA in real-time reverse transcription PCR assays. Lett. Appl. Microbiol. 50:366-372.
    • (2010) Lett. Appl. Microbiol. , Issue.50 , pp. 366-372
    • Deer, D.M.1    Lampel, K.A.2    González-Escalona, N.3
  • 16
    • 41449100793 scopus 로고    scopus 로고
    • Improved normalization of real-time reverse transcriptase polymerase chain reaction data using an external RNA control
    • Ellefsen, S., K.-O. Stensløkken, G. K. Sandvik, T. A. Kristensen, and G. E. Nilsson. 2008. Improved normalization of real-time reverse transcriptase polymerase chain reaction data using an external RNA control. Anal. Biochem. 376:83-93.
    • (2008) Anal. Biochem. , vol.376 , pp. 83-93
    • Ellefsen, S.1    Stensløkken, K.-O.2    Sandvik, G.K.3    Kristensen, T.A.4    Nilsson, G.E.5
  • 18
    • 0034468557 scopus 로고    scopus 로고
    • Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition
    • Griffiths, R. I., A. S. Whiteley, A. G. O'Donnell, and M. J. Bailey. 2000. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl. Environ. Microbiol. 66:5488-5491.
    • (2000) Appl. Environ. Microbiol. , vol.66 , pp. 5488-5491
    • Griffiths, R.I.1    Whiteley, A.S.2    O'donnell, A.G.3    Bailey, M.J.4
  • 19
    • 1842614298 scopus 로고    scopus 로고
    • Quantification of gene expression in methanotrophs by competitive reverse transcription-polymerase chain reaction
    • Han, J.-I., and J. D. Semrau. 2004. Quantification of gene expression in methanotrophs by competitive reverse transcription-polymerase chain reaction. Environ. Microbiol. 6:388-399.
    • (2004) Environ. Microbiol. , vol.6 , pp. 388-399
    • Han, J.-I.1    Semrau, J.D.2
  • 21
    • 34047260936 scopus 로고    scopus 로고
    • Quantification of mRNA in Salmonella sp. seeded soil and chicken manure using magnetic capture hybridization RT-PCR
    • Jacobsen, C. S., and W. E. Holben. 2007. Quantification of mRNA in Salmonella sp. seeded soil and chicken manure using magnetic capture hybridization RT-PCR. J. Microbiol. Methods 69:315-321.
    • (2007) J. Microbiol. Methods , vol.69 , pp. 315-321
    • Jacobsen, C.S.1    Holben, W.E.2
  • 23
    • 38549112329 scopus 로고    scopus 로고
    • Transcription dynamics of the functional tfdA gene during MCPA herbicide degradation by Cupriavidus necator AEO106 (pRO101) in agricultural soil
    • Nicolaisen, M. H., J. Bælum, C. S. Jacobsen, and J. Sørensen. 2008. Transcription dynamics of the functional tfdA gene during MCPA herbicide degradation by Cupriavidus necator AEO106 (pRO101) in agricultural soil. Environ. Microbiol. 10:571-579.
    • (2008) Environ. Microbiol. , vol.10 , pp. 571-579
    • Nicolaisen, M.H.1    Bælum, J.2    Jacobsen, C.S.3    Sørensen, J.4
  • 25
    • 17344392308 scopus 로고    scopus 로고
    • A new mathematical model for relative quantification in real-time RT-PCR
    • Pfaffl, M. W. 2001. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29:e45.
    • (2001) Nucleic Acids Res. , vol.29
    • Pfaffl, M.W.1
  • 26
    • 0034694128 scopus 로고    scopus 로고
    • Effect of experimental treatment on housekeeping gene expression: Validation by real-time, quantitative RT-PCR
    • Schmittgen, T. D., and B. A. Zakrajsek. 2000. Effect of experimental treatment on housekeeping gene expression: validation by real-time, quantitative RT-PCR. J. Biochem. Biophys. Methods 46:69-81.
    • (2000) J. Biochem. Biophys. Methods , vol.46 , pp. 69-81
    • Schmittgen, T.D.1    Zakrajsek, B.A.2
  • 27
    • 0033974559 scopus 로고    scopus 로고
    • Autoinduction of 2,4-diacetylphloroglucinol biosynthesis in the biocontrol agent Pseudomonas fluorescens CHA0 and repression by the bacterial metabolites salicylate and pyoluteorin
    • Schnider-Keel, U., A. Seematter, M. Maurhofer, C. Blumer, B. Duffy, C. Gigot-Bonnefoy, C. Reimmann, R. Notz, G. Défago, D. Haas, and C. Keel. 2000. Autoinduction of 2,4-diacetylphloroglucinol biosynthesis in the biocontrol agent Pseudomonas fluorescens CHA0 and repression by the bacterial metabolites salicylate and pyoluteorin. J. Bacteriol. 182:1215-1225.
    • (2000) J. Bacteriol. , vol.182 , pp. 1215-1225
    • Schnider-Keel, U.1    Seematter, A.2    Maurhofer, M.3    Blumer, C.4    Duffy, B.5    Gigot-Bonnefoy, C.6    Reimmann, C.7    Notz, R.8    Défago, G.9    Haas, D.10    Keel, C.11
  • 28
    • 0036069298 scopus 로고    scopus 로고
    • RNA isolation from soil for bacterial community and functional analysis: Evaluation of different extraction and soil conservation protocols
    • Sessitsch, A., S. Gyamfi, N. Stralis-Pavese, A. Weilharter, and U. Pfeifer. 2002. RNA isolation from soil for bacterial community and functional analysis: evaluation of different extraction and soil conservation protocols. J. Microbiol. Methods 51:171-179.
    • (2002) J. Microbiol. Methods , vol.51 , pp. 171-179
    • Sessitsch, A.1    Gyamfi, S.2    Stralis-Pavese, N.3    Weilharter, A.4    Pfeifer, U.5
  • 29
    • 0026527458 scopus 로고
    • Isolation of 2,4-diacetylphloroglucinol from a fluorescent pseudomonad and investigation of physiological parameters influencing its production
    • Shanahan, P., D. J. O'Sullivan, P. Simpson, J. D. Glennon, and F. O'Gara. 1992. Isolation of 2,4-diacetylphloroglucinol from a fluorescent pseudomonad and investigation of physiological parameters influencing its production. Appl. Environ. Microbiol. 58:353-358.
    • (1992) Appl. Environ. Microbiol. , vol.58 , pp. 353-358
    • Shanahan, P.1    O'sullivan, D.J.2    Simpson, P.3    Glennon, J.D.4    O'gara, F.5
  • 30
    • 3242784271 scopus 로고    scopus 로고
    • Detection and quantification of gene expression in environmental bacteriology
    • Sharkey, F. H., I. M. Banat, and R. Marchant. 2004. Detection and quantification of gene expression in environmental bacteriology. Appl. Environ. Microbiol. 70:3795-3806.
    • (2004) Appl. Environ. Microbiol. , vol.70 , pp. 3795-3806
    • Sharkey, F.H.1    Banat, I.M.2    Marchant, R.3
  • 31
    • 0037227141 scopus 로고    scopus 로고
    • Exogenous reference RNA for normalization of real-time quantitative PCR
    • Smith, R. D., B. Brown, P. Ikonomi, and A. N. Schechter. 2003. Exogenous reference RNA for normalization of real-time quantitative PCR. Biotechniques 34:88-91.
    • (2003) Biotechniques , vol.34 , pp. 88-91
    • Smith, R.D.1    Brown, B.2    Ikonomi, P.3    Schechter, A.N.4
  • 32
    • 0037109753 scopus 로고    scopus 로고
    • Quantitative real-time reverse transcription polymerase chain reaction: Normalization to rRNA or single housekeeping genes is inappropriate for human tissue biopsies
    • Tricarico, C., P. Pinzani, S. Bianchi, M. Paglierani, V. Distante, M. Pazzagli, S. A. Bustin, and C. Orlando. 2002. Quantitative real-time reverse transcription polymerase chain reaction: normalization to rRNA or single housekeeping genes is inappropriate for human tissue biopsies. Anal. Biochem. 309: 293-300.
    • (2002) Anal. Biochem. , vol.309 , pp. 293-300
    • Tricarico, C.1    Pinzani, P.2    Bianchi, S.3    Paglierani, M.4    Distante, V.5    Pazzagli, M.6    Bustin, S.A.7    Orlando, C.8
  • 33
    • 0345195995 scopus 로고    scopus 로고
    • Determination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis
    • von Wintzingerode, F., U. B. Göbel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229.
    • (1997) FEMS Microbiol. Rev. , vol.21 , pp. 213-229
    • Von Wintzingerode, F.1    Göbel, U.B.2    Stackebrandt, E.3
  • 34
    • 0033541685 scopus 로고    scopus 로고
    • MRNA quantification by real time TaqMan polymerase chain reaction: Validation and comparison with RNase protection
    • Wang, T., and M. J. Brown. 1999. mRNA quantification by real time TaqMan polymerase chain reaction: validation and comparison with RNase protection. Anal. Biochem. 269:198-201.
    • (1999) Anal. Biochem. , vol.269 , pp. 198-201
    • Wang, T.1    Brown, M.J.2
  • 37
    • 24944534978 scopus 로고    scopus 로고
    • Real-time PCR for mRNA quantitation
    • Wong, M. L., and J. F. Medrano. 2005. Real-time PCR for mRNA quantitation. Biotechniques 39:75-85.
    • (2005) Biotechniques , vol.39 , pp. 75-85
    • Wong, M.L.1    Medrano, J.F.2
  • 38
    • 33750324141 scopus 로고    scopus 로고
    • Real-time RT-PCR detection of bovine viral diarrhoea virus in whole blood using an external RNA reference
    • Young, N. J., C. J. Thomas, M. E. Collins, and J. Brownlie. 2006. Real-time RT-PCR detection of bovine viral diarrhoea virus in whole blood using an external RNA reference. J. Virol. Methods 138:218-222.
    • (2006) J. Virol. Methods , vol.138 , pp. 218-222
    • Young, N.J.1    Thomas, C.J.2    Collins, M.E.3    Brownlie, J.4
  • 39
    • 69949096465 scopus 로고    scopus 로고
    • Transcription level of messenger RNA per gene copy determined with dual-spike-in strategy
    • Zhang, Y., Z. Wei, Y.-Y. Li, Y. Chen, W. Shen, and C. Lu. 2009. Transcription level of messenger RNA per gene copy determined with dual-spike-in strategy. Anal. Biochem. 394:202-208.
    • (2009) Anal. Biochem. , vol.394 , pp. 202-208
    • Zhang, Y.1    Wei, Z.2    Li, Y.-Y.3    Chen, Y.4    Shen, W.5    Lu, C.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.