메뉴 건너뛰기




Volumn 23, Issue 3, 2008, Pages 229-236

Application of real-time long and short polymerase chain reaction for sensitive monitoring of the fate of extracellular plasmid DNA introduced into river waters

Author keywords

DNA uptake; Extracellular DNA; In situ RCA; Real time long PCR

Indexed keywords


EID: 70349902258     PISSN: 13426311     EISSN: 13426311     Source Type: Journal    
DOI: 10.1264/jsme2.23.229     Document Type: Article
Times cited : (1)

References (46)
  • 1
    • 4143137442 scopus 로고    scopus 로고
    • 4 epsps transgene from Roundup Ready canola in the intestinal, ruminal, and fecal contents of sheep
    • Alexander, T.W., R. Sharma, M.Y. Deng, A.J. Whetsell, J.C. Jennings, Y. Wang, E. Okine, D. Damgaard, and T.A. McAllister. 2004. Use of quantitative real-time and conventional PCR to assess the stability of the cp4 epsps transgene from Roundup Ready canola in the intestinal, ruminal, and fecal contents of sheep. J. Biotechnol. 112:255-266.
    • (2004) J. Biotechnol. , vol.112 , pp. 255-266
    • Alexander, T.W.1    Sharma, R.2    Deng, M.Y.3    Whetsell, A.J.4    Jennings, J.C.5    Wang, Y.6    Okine, E.7    Damgaard, D.8    McAllister, T.A.9
  • 2
  • 3
    • 0034431467 scopus 로고    scopus 로고
    • Analysis of gene-specific DNA damage and repair using quantitative polymerase chain reaction
    • Ayala-Torres, S., Y. Cheng, T. Svoboda, J. Rosenblatt, and B.V. Houten. 2000. Analysis of gene-specific DNA damage and repair using quantitative polymerase chain reaction. Methods 22:135-147.
    • (2000) Methods , vol.22 , pp. 135-147
    • Ayala-Torres, S.1    Cheng, Y.2    Svoboda, T.3    Rosenblatt, J.4    Houten, B.V.5
  • 4
    • 0028211009 scopus 로고
    • PCR amplification of up to 35-kb DNA with high fidelity and high yield from lambda bacteriophage templates
    • Barnes, W.M. 1994. PCR amplification of up to 35-kb DNA with high fidelity and high yield from lambda bacteriophage templates. Proc. Natl. Acad. Sci. USA 91:2216-2220.
    • (1994) Proc. Natl. Acad. Sci. USA. , vol.91 , pp. 2216-2220
    • Barnes, W.M.1
  • 7
    • 0037294793 scopus 로고    scopus 로고
    • Measurement of oxida- tive damage at individual gene levels by quantitative PCR using 8- hydroxyguanine glycosylase (OGG1)
    • Choi, J., D.-Y. Kim, J.-W. Hyun, S.-H. Yoon, E.-M. Choi, K.-B. Hahm, K.-H. Rhee, and M.-H. Chung. 2003. Measurement of oxida- tive damage at individual gene levels by quantitative PCR using 8- hydroxyguanine glycosylase (OGG1). Mutat. Res. 523-524:225-235.
    • (2003) Mutat. Res. , vol.523-524 , pp. 225-235
    • Choi, J.1    Kim, D.-Y.2    Hyun, J.-W.3    Yoon, S.-H.4    Choi, E.-M.5    Hahm, K.-B.6    Rhee, K.-H.7    Chung, M.-H.8
  • 8
    • 0035159370 scopus 로고    scopus 로고
    • Evaluation of biological and physical protection against nuclease degradation of clay-bound plasmid DNA
    • Demanéche, S., L. Jocteur-Monrozier, H. Quiquampoix, and P. Simo- net. 2001. Evaluation of biological and physical protection against nuclease degradation of clay-bound plasmid DNA. Appl. Environ. Microbiol. 67:293-299.
    • (2001) Appl. Environ. Microbiol. , vol.67 , pp. 293-299
    • Demanéche, S.1    Jocteur-Monrozier, L.2    Quiquampoix, H.3
  • 9
    • 0031921638 scopus 로고    scopus 로고
    • Detection of nptll (kanamy- cin resistance) genes in genomes of transgenic plants by marker-rescue transformation
    • de Vries, J., and W. Wackernagel. 1998. Detection of nptll (kanamy- cin resistance) genes in genomes of transgenic plants by marker-rescue transformation. Mol. Gen. Genet. 257:606-613.
    • (1998) Mol. Gen. Genet. , vol.257 , pp. 606-613
    • De Vries, J.1    Wackernagel, W.2
  • 10
    • 0035916398 scopus 로고    scopus 로고
    • The natural transformation of the soil bacteria Pseudomonas stutzeri and acineto- bacter sp. by transgenic plant DNA strictly depends on homologous sequences in the recipient cells
    • de Vries, J., P. Meier, and W. Wackernagel. 2001. The natural transformation of the soil bacteria Pseudomonas stutzeri and Acineto- bacter sp. by transgenic plant DNA strictly depends on homologous sequences in the recipient cells. FEMS Microbiol. Lett. 195:211-215.
    • (2001) FEMS Microbiol. Lett. , vol.195 , pp. 211-215
    • De Vries, J.1    Meier, P.2    Wackernagel, W.3
  • 11
    • 0042530369 scopus 로고    scopus 로고
    • Spread of recombinant DNA by roots and pollen of transgenic potato plants, identified by highly specific biomonitoring using natural transformation of an acinetobacter sp
    • de Vries, J., M. Heine, K. Harms, and W. Wackernagel. 2003. Spread of recombinant DNA by roots and pollen of transgenic potato plants, identified by highly specific biomonitoring using natural transformation of an Acinetobacter sp. Appl. Environ. Microbiol. 69:4455-4462.
    • (2003) Appl. Environ. Microbiol. , vol.69 , pp. 4455-4462
    • De Vries, J.1    Heine, M.2    Harms, K.3    Wackernagel, W.4
  • 12
    • 0041734731 scopus 로고    scopus 로고
    • Realtime PCR provides improved detection and titer determination of bacteriophage
    • Edelman, D.C., and J. Barletta. 2003. Real-time PCR provides improved detection and titer determination of bacteriophage. Biotechniques 35:368-375.
    • (2003) Biotechniques , vol.35 , pp. 368-375
    • Edelman, D.C.1    Barletta, J.2
  • 13
    • 11344254823 scopus 로고    scopus 로고
    • Tracing residual recombinant feed molecules during digestion and rumen bacterial diversity in cattle fed transgene maize
    • Einspanier, R., B. Lutz, S. Rief, O. Berezina, V. Zverlov, W. Schwarz, and J. Mayer. 2004. Tracing residual recombinant feed molecules during digestion and rumen bacterial diversity in cattle fed transgene maize. Eur. Food Res. Technol. 218:269-273.
    • (2004) Eur. Food Res. Technol. , vol.218 , pp. 269-273
    • Einspanier, R.1    Lutz, B.2    Rief, S.3    Berezina, O.4    Zverlov, V.5    Schwarz, W.6    Mayer, J.7
  • 15
  • 16
    • 0001351054 scopus 로고    scopus 로고
    • Bacterial uptake and utilization of dissolved DNA
    • Jorgensen, N.O.G., and C.S. Jacobsen. 1996. Bacterial uptake and utilization of dissolved DNA. Aquat. Microb. Ecol. 11:263-270.
    • (1996) Aquat. Microb. Ecol. , vol.11 , pp. 263-270
    • Jorgensen, N.O.G.1    Jacobsen, C.S.2
  • 17
    • 70349971808 scopus 로고    scopus 로고
    • A combination of direct viable counting, fluorescence in situ hybridization, and green fluorescent protein gene expression for estimating plasmid transfer at the single cell level
    • Jorquera, M., N. Yamaguchi, K. Tani, and M. Nasu. 2006. A combination of direct viable counting, fluorescence in situ hybridization, and green fluorescent protein gene expression for estimating plasmid transfer at the single cell level. Microbes Environ. 21:101-111.
    • (2006) Microbes Environ , vol.21 , pp. 101-111
    • Jorquera, M.1    Yamaguchi, N.2    Tani, K.3    Nasu, M.4
  • 18
    • 70349976021 scopus 로고    scopus 로고
    • Stimulatory effect of glutamine and pyruvate on plasmid transfer between pseudomonas strains
    • Jorquera, M., N. Yamaguchi, K. Tani, and M. Nasu. 2007. Stimulatory effect of glutamine and pyruvate on plasmid transfer between Pseudomonas strains. Microbes Environ. 22:320-326.
    • (2007) Microbes Environ , vol.22 , pp. 320-326
    • Jorquera, M.1    Yamaguchi, N.2    Tani, K.3    Nasu, M.4
  • 19
    • 0031690236 scopus 로고    scopus 로고
    • RRNA-tar-geted fluorescent in situ hybridization analysis of bacterial community structure in river water
    • Kenzaka, T., N. Yamaguchi, K. Tani, and M. Nasu. 1998. rRNA-tar- geted fluorescent in situ hybridization analysis of bacterial community structure in river water. Microbiology 144:2085-2093.
    • (1998) Microbiology. , vol.144 , pp. 2085-2093
    • Kenzaka, T.1    Yamaguchi, N.2    Tani, K.3    Nasu, M.4
  • 20
    • 0035992649 scopus 로고    scopus 로고
    • Design of species-specific primers to identify 13 species of clostridium harbored in human intestinal tracts
    • Kikuchi, E., Y. Miyamoto, S. Narushima, and K. Ito. 2002. Design of species-specific primers to identify 13 species of Clostridium harbored in human intestinal tracts. Microbiol. Immunol. 46:353-358.
    • (2002) Microbiol. Immunol. , vol.46 , pp. 353-358
    • Kikuchi, E.1    Miyamoto, Y.2    Narushima, S.3    Ito, K.4
  • 21
    • 0035988627 scopus 로고    scopus 로고
    • Quantification using real-time PCR technology: Applications and limitations
    • Klein, D. 2002. Quantification using real-time PCR technology: applications and limitations. Trends Mol. Med. 8:257-260.
    • (2002) Trends Mol. Med. , vol.8 , pp. 257-260
    • Klein, D.1
  • 22
    • 0035852068 scopus 로고    scopus 로고
    • Detection of DNA adducts using a quantitative long PCR technique and the fluorogenic 5 nuclease assay (Taqman
    • Laws, G.M., T.R. Skopek, M.V. Reddy, R.D. Sorer, and W.E. Glaab. 2001. Detection of DNA adducts using a quantitative long PCR technique and the fluorogenic 5 nuclease assay (Taqman). Mutat. Res. 484:3-18.
    • (2001) Mutat. Res. , vol.484 , pp. 3-18
    • Laws, G.M.1    Skopek, T.R.2    Reddy, M.V.3    Sorer, R.D.4    Glaab, W.E.5
  • 23
    • 33646342766 scopus 로고    scopus 로고
    • Quantitative real-time polymerase chain reaction for determination of plasmid copy number in bacteria
    • Lee, C.L., D.S.W. Ow, and S.K.W. Oh. 2006. Quantitative real-time polymerase chain reaction for determination of plasmid copy number in bacteria. J. Microbiol. Methods 65:258-267.
    • (2006) J. Microbiol. Methods. , vol.65 , pp. 258-267
    • Lee, C.L.1    Ow, D.S.W.2    Oh, S.K.W.3
  • 24
    • 0028136885 scopus 로고
    • Bacterial gene-transfer by natural genetic-transformation in the environment
    • Lorenz, M.G., and W. Wackernagel. 1994. Bacterial gene-transfer by natural genetic-transformation in the environment. Microbiol. Rev. 58:563-602.
    • (1994) Microbiol. Rev. , vol.58 , pp. 563-602
    • Lorenz, M.G.1    Wackernagel, W.2
  • 25
    • 0037226743 scopus 로고    scopus 로고
    • Use of real-time quantitative PCR for the analysis of phi LC3 prophage stability in lactococci
    • Lunde, M., J.M. Blatny, D. Lillehaug, A.H. Aastveit, and I.F. Nes. 2003. Use of real-time quantitative PCR for the analysis of phi LC3 prophage stability in lactococci. Appl. Environ. Microbiol. 69:41-48.
    • (2003) Appl. Environ. Microbiol. , vol.69 , pp. 41-48
    • Lunde, M.1    Blatny, J.M.2    Lillehaug, D.3    Aastveit, A.H.4    Nes, I.F.5
  • 26
    • 5644238611 scopus 로고    scopus 로고
    • Simplified sample preparation using frame spotting method for direct counting of total bacteria by fluorescence microscopy
    • Maruyama, F., N. Yamaguchi, T. Kenzaka, K. Tani, and M. Nasu. 2004. Simplified sample preparation using frame spotting method for direct counting of total bacteria by fluorescence microscopy. J. Microbiol. Methods 59:427-431.
    • (2004) J. Microbiol. Methods. , vol.59 , pp. 427-431
    • Maruyama, F.1    Yamaguchi, N.2    Kenzaka, T.3    Tani, K.4    Nasu, M.5
  • 27
    • 29144504169 scopus 로고    scopus 로고
    • Visualization and enumeration of bacteria carrying a specific gene sequence by in situ rolling circle amplification
    • Maruyama, F., T. Kenzaka, N. Yamaguchi, K. Tani, and M. Nasu. 2005. Visualization and enumeration of bacteria carrying a specific gene sequence by in situ rolling circle amplification. Appl. Environ. Microbiol. 71:7933-7940.
    • (2005) Appl. Environ. Microbiol. , vol.71 , pp. 7933-7940
    • Maruyama, F.1    Kenzaka, T.2    Yamaguchi, N.3    Tani, K.4    Nasu, M.5
  • 28
    • 33748801467 scopus 로고    scopus 로고
    • Quantitative determination of free-DNA uptake in river bacteria at the single-cell level by in situ rolling-circle amplification
    • Maruyama, F., K. Tani, T. Kenzaka, N. Yamaguchi, and M. Nasu. 2006. Quantitative determination of free-DNA uptake in river bacteria at the single-cell level by in situ rolling-circle amplification. Appl. Environ. Microbiol. 72:6248-6256.
    • (2006) Appl. Environ. Microbiol. , vol.72 , pp. 6248-6256
    • Maruyama, F.1    Tani, K.2    Kenzaka, T.3    Yamaguchi, N.4    Nasu, M.5
  • 29
    • 0035955542 scopus 로고    scopus 로고
    • Estimation of the fate of dissolved DNA in thermally stratified lake water from the stability of exogenous plasmid DNA
    • Matsui, K., M. Honjo, and Z. Kawabata. 2001. Estimation of the fate of dissolved DNA in thermally stratified lake water from the stability of exogenous plasmid DNA. Aquat. Microbiol. Ecol. 26:95-102.
    • (2001) Aquat. Microbiol. Ecol. , vol.26 , pp. 95-102
    • Matsui, K.1    Honjo, M.2    Kawabata, Z.3
  • 30
    • 0038016731 scopus 로고    scopus 로고
    • Mechanisms of homology- facilitated illegitimate recombination for foreign DNA acquisition in transformable Pseudomonas stutzeri
    • Meier, P., and W. Wackernagel. 2003. Mechanisms of homologyfacilitated illegitimate recombination for foreign DNA acquisition in transformable Pseudomonas stutzeri. Mol. Microbiol. 48:1107-1118.
    • (2003) Mol. Microbiol. , vol.48 , pp. 1107-1118
    • Meier, P.1    Wackernagel, W.2
  • 31
    • 17444453992 scopus 로고    scopus 로고
    • Optimized strategy for rapid cytochrome P450 2D6 genotyping by real-time long PCR
    • Müller, B., K. Zöpf, J. Bachofer, and W. Steimer. 2003. Optimized strategy for rapid cytochrome P450 2D6 genotyping by real-time long PCR. Clin. Chem. 49:1624-1631.
    • (2003) Clin. Chem. , vol.49 , pp. 1624-1631
    • Müller, B.1    Zöpf, K.2    Bachofer, J.3    Steimer, W.4
  • 32
    • 33747490702 scopus 로고    scopus 로고
    • Influence of dissolved organic matter and inorganic nutrients on the biofilm bacterial community on artificial substrates in a northern Ohio, USA, stream
    • Olapade, O.A., and G.L. Leff. 2006. Influence of dissolved organic matter and inorganic nutrients on the biofilm bacterial community on artificial substrates in a northern Ohio, USA, stream. Can. J. Microbiol. 52:540-549.
    • (2006) Can. J. Microbiol. , vol.52 , pp. 540-549
    • Olapade, O.A.1    Leff, G.L.2
  • 33
    • 0030957269 scopus 로고    scopus 로고
    • Uptake and processing of DNA by acinetobacter calcoaceticus-a review
    • Palmen, R., and K.J. Hellingwerf. 1997. Uptake and processing of DNA by Acinetobacter calcoaceticus-a review. Gene 192:179-190.
    • (1997) Gene , vol.192 , pp. 179-190
    • Palmen, R.1    Hellingwerf, K.J.2
  • 34
    • 33646340437 scopus 로고    scopus 로고
    • The copy-number of plasmids and other genetic elements can be determined by SYBR-Green-based real-time PCR
    • Providenti, M.A., J.M. O'Brien, R.J. Ewing, E.S. Paterson, and M.L. Smith. 2006. The copy-number of plasmids and other genetic elements can be determined by SYBR-Green-based real-time PCR. J. Microbiol. Methods 65:476-487.
    • (2006) J. Microbiol. Methods. , vol.65 , pp. 476-487
    • Providenti, M.A.1    O'Brien, J.M.2    Ewing, R.J.3    Paterson, E.S.4    Smith, M.L.5
  • 35
    • 0037133288 scopus 로고    scopus 로고
    • Homologous recombination at the border: Insertion-deletions and the trapping of foreign DNA in Streptococcus pneumoniae
    • Prudhomme, M., V. Libante, and J.-P. Claverys. 2002. Homologous recombination at the border: insertion-deletions and the trapping of foreign DNA in Streptococcus pneumoniae. Proc. Natl. Acad. Soc. USA 99:2100-2105.
    • (2002) Proc. Natl. Acad. Soc. USA. , vol.99 , pp. 2100-2105
    • Prudhomme, M.1    Libante, V.2    Claverys, J.-P.3
  • 38
    • 0042009753 scopus 로고    scopus 로고
    • Quantitative analysis of gene-specific DNA damage in human spermatozoa
    • Sawyer, D.E., B.G. Mercer, A.M. Wiklendt, and R.J. Aitken. 2003. Quantitative analysis of gene-specific DNA damage in human spermatozoa. Mutat. Res. 529:21-34.
    • (2003) Mutat. Res. , vol.529 , pp. 21-34
    • Sawyer, D.E.1    Mercer, B.G.2    Wiklendt, A.M.3    Aitken, R.J.4
  • 39
    • 38949159128 scopus 로고    scopus 로고
    • Influence of flanking homology and insert size on the transformation frequency of acinetobacter baylyi BD413
    • Simpson, D.J., L.F. Dawson, J.C. Fry, H.J. Rogers, and M.J. Day. 2007. Influence of flanking homology and insert size on the transformation frequency of Acinetobacter baylyi BD413. Environ. Biosafety Res. 6:55-69.
    • (2007) Environ. Biosafety Res. , vol.6 , pp. 55-69
    • Simpson, D.J.1    Dawson, L.F.2    Fry, J.C.3    Rogers, H.J.4    Day, M.J.5
  • 41
    • 0001776426 scopus 로고    scopus 로고
    • Distribution and origin of dissolved DNA in lakes of different trophic states
    • Suida, W., R.J. Chróst, and H. Güde. 1998. Distribution and origin of dissolved DNA in lakes of different trophic states. Aquat. Microbial. Ecol. 15:89-96.
    • (1998) Aquat. Microbial. Ecol. , vol.15 , pp. 89-96
    • Suida, W.1    Chróst, R.J.2    Güde, H.3
  • 42
    • 0029956369 scopus 로고    scopus 로고
    • Long PCR and its application to hepatitis viruses: Amplification of hepatitis A, hepatitis B, and hepatitis C virus genomes
    • Tellier, R., J. Bukh, S.U. Emerson, R.H. Miller, and R.H. Purcell. 1996. Long PCR and its application to hepatitis viruses: amplification of hepatitis A, hepatitis B, and hepatitis C virus genomes. J. Clin. Microbiol. 34:3085-3091.
    • (1996) J. Clin. Microbiol. , vol.34 , pp. 3085-3091
    • Tellier, R.1    Bukh, J.2    Emerson, S.U.3    Miller, R.H.4    Purcell, R.H.5
  • 43
    • 23944475626 scopus 로고    scopus 로고
    • Mechanisms of, and barriers to, horizontal gene transfer between bacteria
    • Thomas, C.M., and K.M. Nielsen. 2005. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat. Rev. Microbiol. 3:711-721.
    • (2005) Nat. Rev. Microbiol. , vol.3 , pp. 711-721
    • Thomas, C.M.1    Nielsen, K.M.2
  • 44
    • 0028136885 scopus 로고
    • Bacterial gene transfer by natural genetic transformation in the environment
    • Lorenz, M.G., and W. Wackernagel. 1994. Bacterial gene transfer by natural genetic transformation in the environment. Microbiol. Rev. 58:563-602.
    • (1994) Microbiol. Rev. , vol.58 , pp. 563-602
    • Lorenz, M.G.1    Wackernagel, W.2
  • 45
    • 0030745194 scopus 로고    scopus 로고
    • Flow cytometric analysis of bacterial respiratory and enzymatic activity in the natural aquatic environment
    • Yamaguchi, N., and M. Nasu. 1997. Flow cytometric analysis of bacterial respiratory and enzymatic activity in the natural aquatic environment. J. Appl. Microbiol. 83:43-52.
    • (1997) J. Appl. Microbiol. , vol.83 , pp. 43-52
    • Yamaguchi, N.1    Nasu, M.2
  • 46
    • 0034466802 scopus 로고    scopus 로고
    • Improved direct viable count procedure for quantitative estimation of bacterial viability in freshwater environments
    • Yokomaku, D., N. Yamaguchi, and M. Nasu. 2000. Improved direct viable count procedure for quantitative estimation of bacterial viability in freshwater environments. Appl. Environ. Microbiol. 66:55445548.
    • (2000) Appl. Environ. Microbiol. , vol.66 , pp. 55445548
    • Yokomaku, D.1    Yamaguchi, N.2    Nasu, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.