메뉴 건너뛰기




Volumn 91, Issue 6, 2015, Pages

Re-evaluation of dioxygenase gene phylogeny for the development and validation of a quantitative assay for environmental aromatic hydrocarbon degraders

Author keywords

Dioxygenases; phylogeny; quantitative PCR; Rieske centre

Indexed keywords

CATALYST; ENZYME ACTIVITY; GENE EXPRESSION; PHYLOGENY; QUANTITATIVE ANALYSIS;

EID: 84949238906     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1093/femsec/fiv049     Document Type: Article
Times cited : (18)

References (69)
  • 1
    • 0036682224 scopus 로고    scopus 로고
    • PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database
    • Ashelford KE, Weightman AJ, Fry JC. PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database. Nucleic Acids Res 2002;30: 3481-9.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3481-3489
    • Ashelford, K.E.1    Weightman, A.J.2    Fry, J.C.3
  • 2
    • 0028953835 scopus 로고
    • The evolutionary relationship of biphenyl dioxygenase from Gram-positive Rhodococcus globerulus P6 to multicomponent dioxygenases from Gramnegative bacteria
    • Asturias JA, Diaz E, Timmis KN. The evolutionary relationship of biphenyl dioxygenase from Gram-positive Rhodococcus globerulus P6 to multicomponent dioxygenases from Gramnegative bacteria. Gene 1995;156:11-8.
    • (1995) Gene , vol.156 , pp. 11-18
    • Asturias, J.A.1    Diaz, E.2    Timmis, K.N.3
  • 3
    • 0037641131 scopus 로고    scopus 로고
    • Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR
    • Baldwin BR, Nakatsu CH, Nies L. Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR. Appl Environ Microb 2003;69:3350-8.
    • (2003) Appl Environ Microb , vol.69 , pp. 3350-3358
    • Baldwin, B.R.1    Nakatsu, C.H.2    Nies, L.3
  • 4
    • 21344459064 scopus 로고    scopus 로고
    • Bioremediation of polycyclic aromatic hydrocarbons: current knowledge and future directions
    • Bamforth SM, Singleton I. Bioremediation of polycyclic aromatic hydrocarbons: current knowledge and future directions. J Chem Technol Biot 2005;80:723-36.
    • (2005) J Chem Technol Biot , vol.80 , pp. 723-736
    • Bamforth, S.M.1    Singleton, I.2
  • 5
    • 0002557598 scopus 로고
    • Phthalate dioxygenase reductase and related flavin-iron-sulfur containing electron transferases
    • Batie CJ, Ballou DP, Correll CC. Phthalate dioxygenase reductase and related flavin-iron-sulfur containing electron transferases. Chem Biochem Flavoenzymes 1991;3:543-56.
    • (1991) Chem Biochem Flavoenzymes , vol.3 , pp. 543-556
    • Batie, C.J.1    Ballou, D.P.2    Correll, C.C.3
  • 6
    • 79954550877 scopus 로고    scopus 로고
    • Mechanisms of chemical carcinogenicity and mutagenicity: a review with implications for predictive toxicology
    • Benigni R, Bossa C. Mechanisms of chemical carcinogenicity and mutagenicity: a review with implications for predictive toxicology. Chem Rev 2011;111:2507-36.
    • (2011) Chem Rev , vol.111 , pp. 2507-2536
    • Benigni, R.1    Bossa, C.2
  • 9
    • 0038771927 scopus 로고    scopus 로고
    • Molecular characterization of dioxygenases from polycyclic aromatic hydrocarbondegrading Mycobacterium spp
    • Brezna B, Khan AA, Cerniglia CE. Molecular characterization of dioxygenases from polycyclic aromatic hydrocarbondegrading Mycobacterium spp. FEMS Microbiol Lett 2003;223:177-83.
    • (2003) FEMS Microbiol Lett , vol.223 , pp. 177-183
    • Brezna, B.1    Khan, A.A.2    Cerniglia, C.E.3
  • 10
    • 64149097786 scopus 로고    scopus 로고
    • The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments
    • Bustin SA, Benes V, Garson JA, et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 2009;55:611-22.
    • (2009) Clin Chem , vol.55 , pp. 611-622
    • Bustin, S.A.1    Benes, V.2    Garson, J.A.3
  • 11
    • 70349410312 scopus 로고    scopus 로고
    • Influence of vegetation on the in situ bacterial community and polycyclic aromatic hydrocarbon (PAH) degraders in aged PAHcontaminated or thermal-desorption-treated soil
    • Cebron A, Beguiristain T, Faure P, et al. Influence of vegetation on the in situ bacterial community and polycyclic aromatic hydrocarbon (PAH) degraders in aged PAHcontaminated or thermal-desorption-treated soil. Appl Environ Microb 2009;75:6322-30.
    • (2009) Appl Environ Microb , vol.75 , pp. 6230-6322
    • Cebron, A.1    Beguiristain, T.2    Faure, P.3
  • 12
    • 42249095068 scopus 로고    scopus 로고
    • Real-Time PCR quantification of PAH-ring hydroxylating dioxygenase (PAH-RHD alpha) genes from Gram positive and Gram negative bacteria in soil and sediment samples
    • Cebron A, Norini MP, Beguiristain T, et al. Real-Time PCR quantification of PAH-ring hydroxylating dioxygenase (PAH-RHD alpha) genes from Gram positive and Gram negative bacteria in soil and sediment samples. J Microbiol Methods 2008;73:148-59.
    • (2008) J Microbiol Methods , vol.73 , pp. 148-159
    • Cebron, A.1    Norini, M.P.2    Beguiristain, T.3
  • 13
    • 33847168352 scopus 로고
    • Biodegradation of polycyclic aromatic hydrocarbons
    • Cerniglia CE. Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation 1992;3:351-68.
    • (1992) Biodegradation , vol.3 , pp. 351-368
    • Cerniglia, C.E.1
  • 14
    • 33644865858 scopus 로고    scopus 로고
    • Improved quantitative realtime PCR assays for enumeration of harmful algal species in field samples using an exogenous DNA reference standard
    • Coyne KJ, Handy SM, Demir E, et al. Improved quantitative realtime PCR assays for enumeration of harmful algal species in field samples using an exogenous DNA reference standard. Limnol Oceanogr-Meth 2005;3:381-91.
    • (2005) Limnol Oceanogr-Meth , vol.3 , pp. 381-391
    • Coyne, K.J.1    Handy, S.M.2    Demir, E.3
  • 15
    • 0035380609 scopus 로고    scopus 로고
    • Isolation and characterization of polycyclic aromatic hydrocarbon-degrading bacteria associated with the rhizosphere of salt marsh plants
    • Daane LL, Harjono I, Zylstra GJ, et al. Isolation and characterization of polycyclic aromatic hydrocarbon-degrading bacteria associated with the rhizosphere of salt marsh plants. Appl Environ Microb 2001;67:2683-91.
    • (2001) Appl Environ Microb , vol.67 , pp. 2683-2691
    • Daane, L.L.1    Harjono, I.2    Zylstra, G.J.3
  • 16
    • 84864518655 scopus 로고    scopus 로고
    • Improved real-time PCR estimation of gene copy number in soil extracts using an artificial reference
    • Daniell TJ, Davidson J, Alexander CJ, et al. Improved real-time PCR estimation of gene copy number in soil extracts using an artificial reference. J Microbiol Methods 2012;91:38-44.
    • (2012) J Microbiol Methods , vol.91 , pp. 38-44
    • Daniell, T.J.1    Davidson, J.2    Alexander, C.J.3
  • 17
    • 34547674725 scopus 로고    scopus 로고
    • Comparative quantitative prevalence of Mycobacteria and functionally abundant nidA, nahAc, and nagAc dioxygenase genes in coal tar contaminated sediments
    • DeBruyn JM, Chewning CS, Sayler GS. Comparative quantitative prevalence of Mycobacteria and functionally abundant nidA, nahAc, and nagAc dioxygenase genes in coal tar contaminated sediments. Environ Sci Technol 2007;41:5426-32.
    • (2007) Environ Sci Technol , vol.41 , pp. 5426-5432
    • DeBruyn, J.M.1    Chewning, C.S.2    Sayler, G.S.3
  • 18
    • 77954692062 scopus 로고    scopus 로고
    • Soil type-dependent responses to phenanthrene as revealed by determining the diversity and abundance of polycyclic aromatic hydrocarbon ringhydroxylating dioxygenase genes by using a novel PCR detection system
    • Ding GC, Heuer H, Zuhlke S, et al. Soil type-dependent responses to phenanthrene as revealed by determining the diversity and abundance of polycyclic aromatic hydrocarbon ringhydroxylating dioxygenase genes by using a novel PCR detection system. Appl Environ Microb 2010;76:4765-71.
    • (2010) Appl Environ Microb , vol.76 , pp. 4765-4771
    • Ding, G.C.1    Heuer, H.2    Zuhlke, S.3
  • 19
    • 3242764705 scopus 로고    scopus 로고
    • Abundance of dioxygenase genes similar to Ralstonia sp strain U2 nagAc is correlated with naphthalene concentrations in coal tar-contaminated freshwater sediments
    • Dionisi HM, Chewning CS, Morgan KH, et al. Abundance of dioxygenase genes similar to Ralstonia sp strain U2 nagAc is correlated with naphthalene concentrations in coal tar-contaminated freshwater sediments. Appl Environ Microb 2004;70:3988-95.
    • (2004) Appl Environ Microb , vol.70 , pp. 3988-3995
    • Dionisi, H.M.1    Chewning, C.S.2    Morgan, K.H.3
  • 20
    • 33750087103 scopus 로고    scopus 로고
    • Real-time PCR
    • New York: Taylor
    • Dorak MT. Real-time PCR. New York: Taylor, Francis Group, 2006.
    • (2006)
    • Dorak, M.T.1
  • 22
    • 27544477399 scopus 로고    scopus 로고
    • Rieske business: structurefunction of Rieske non-heme oxygenases
    • Ferraro DJ, Gakhar L, Ramaswamy S. Rieske business: structurefunction of Rieske non-heme oxygenases. Biochem Bioph Res Co 2005;338:175-90.
    • (2005) Biochem Bioph Res Co , vol.338 , pp. 175-190
    • Ferraro, D.J.1    Gakhar, L.2    Ramaswamy, S.3
  • 23
    • 0042914355 scopus 로고    scopus 로고
    • Novel maltotriose esters enhance biodegradation of Aroclor 1242 by Burkholderia cepacia LB400
    • Ferrer M, Golyshin P, Timmis KN. Novel maltotriose esters enhance biodegradation of Aroclor 1242 by Burkholderia cepacia LB400. World J Microbiol Biotechnol 2003;19:637-43.
    • (2003) World J Microbiol Biotechnol , vol.19 , pp. 637-643
    • Ferrer, M.1    Golyshin, P.2    Timmis, K.N.3
  • 24
    • 0037394251 scopus 로고    scopus 로고
    • Larger PAHs pose big risk
    • Fetzer J. Larger PAHs pose big risk. Environ Sci Technol 2003;37:121A.
    • (2003) Environ Sci Technol , vol.37 , pp. 121A
    • Fetzer, J.1
  • 25
    • 0034029015 scopus 로고    scopus 로고
    • Aromatic hydrocarbon dioxygenases in environmental biotechnology
    • Gibson DT, Parales RE. Aromatic hydrocarbon dioxygenases in environmental biotechnology. Curr Opin Biotech 2000;11: 236-43.
    • (2000) Curr Opin Biotech , vol.11 , pp. 236-243
    • Gibson, D.T.1    Parales, R.E.2
  • 26
    • 34547644103 scopus 로고    scopus 로고
    • Characterization of biphenyl dioxygenase of Pandoraea pnomenusa B-356 as a potent polychlorinated biphenyl-degrading enzyme
    • Gómez-Gil L, Kumar P, Barriault D, et al. Characterization of biphenyl dioxygenase of Pandoraea pnomenusa B-356 as a potent polychlorinated biphenyl-degrading enzyme. J Bacteriol 2007;189:5705-15.
    • (2007) J Bacteriol , vol.189 , pp. 5705-5715
    • Gómez-Gil, L.1    Kumar, P.2    Barriault, D.3
  • 27
    • 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 RI, Whiteley AS, O'Donnell AG, et al. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl Environ Microb 2000;66: 5488-91.
    • (2000) Appl Environ Microb , vol.66 , pp. 5488-5491
    • Griffiths, R.I.1    Whiteley, A.S.2    O'Donnell, A.G.3
  • 28
    • 0037506334 scopus 로고    scopus 로고
    • Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria
    • Habe H, Omori T. Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria. Biosci Biotech Bioch 2003;67:225-43.
    • (2003) Biosci Biotech Bioch , vol.67 , pp. 225-243
    • Habe, H.1    Omori, T.2
  • 29
    • 39649117992 scopus 로고    scopus 로고
    • Enrichment, isolation, and phylogenetic identification of polycyclic aromatic hydrocarbon-degrading bacteria from Elizabeth River sediments
    • Hilyard EJ, Jones-Meehan JM, Spargo BJ, et al. Enrichment, isolation, and phylogenetic identification of polycyclic aromatic hydrocarbon-degrading bacteria from Elizabeth River sediments. Appl Environ Microb 2008;74:1176-82.
    • (2008) Appl Environ Microb , vol.74 , pp. 1176-1182
    • Hilyard, E.J.1    Jones-Meehan, J.M.2    Spargo, B.J.3
  • 30
    • 79958257334 scopus 로고    scopus 로고
    • Comparison of the specificities and efficacies of primers for aromatic dioxygenase gene analysis of environmental samples
    • Iwai S, Johnson TA, Chai BL, et al. Comparison of the specificities and efficacies of primers for aromatic dioxygenase gene analysis of environmental samples. Appl Environ Microb 2011;77:3551-7.
    • (2011) Appl Environ Microb , vol.77 , pp. 3551-3557
    • Iwai, S.1    Johnson, T.A.2    Chai, B.L.3
  • 31
    • 34247513062 scopus 로고    scopus 로고
    • Characterization of two biphenyl dioxygenases for biphenyl/PCB degradation in a PCB degrader, Rhodococcus sp strain RHA1
    • Iwasaki T, Takeda H, Miyauchi K, et al. Characterization of two biphenyl dioxygenases for biphenyl/PCB degradation in a PCB degrader, Rhodococcus sp strain RHA1. Biosci Biotech Bioch 2007;71:993-1002.
    • (2007) Biosci Biotech Bioch , vol.71 , pp. 993-1002
    • Iwasaki, T.1    Takeda, H.2    Miyauchi, K.3
  • 32
    • 8744222675 scopus 로고    scopus 로고
    • Pore size dependence on growth temperature is a common characteristic of the major outer membrane protein OprF in psychrotrophic and mesophilic Pseudomonas species
    • Jaouen T, Dé E, Chevalier S, et al. Pore size dependence on growth temperature is a common characteristic of the major outer membrane protein OprF in psychrotrophic and mesophilic Pseudomonas species. Appl Environ Microbiol 2004;70:6665-9.
    • (2004) Appl Environ Microbiol , vol.70 , pp. 6665-6669
    • Jaouen, T.1    Dé, E.2    Chevalier, S.3
  • 33
    • 0347264753 scopus 로고    scopus 로고
    • Crystal structure of naphthalene dioxygenase: Side-on binding of dioxygen to iron
    • Karlsson A, Parales JV, Parales RE, et al. Crystal structure of naphthalene dioxygenase: Side-on binding of dioxygen to iron. Science 2003;299:1039-42.
    • (2003) Science , vol.299 , pp. 1039-1042
    • Karlsson, A.1    Parales, J.V.2    Parales, R.E.3
  • 35
    • 43149093388 scopus 로고    scopus 로고
    • A new classification system for bacterial Rieske non-heme iron aromatic ring-hydroxylating oxygenases
    • Kweon O, Kim S-J, Baek S, et al. A new classification system for bacterial Rieske non-heme iron aromatic ring-hydroxylating oxygenases. BMC Biochem 2008;9:11.
    • (2008) BMC Biochem , vol.9 , pp. 11
    • Kweon, O.1    Kim, S.-J.2    Baek, S.3
  • 36
    • 0034019871 scopus 로고    scopus 로고
    • Quantification of phnAc and nahAc in contaminated New Zealand soils by competitive PCR
    • Laurie AD, Lloyd-Jones G. Quantification of phnAc and nahAc in contaminated New Zealand soils by competitive PCR. Appl Environ Microb 2000;66:1814-7.
    • (2000) Appl Environ Microb , vol.66 , pp. 1814-1817
    • Laurie, A.D.1    Lloyd-Jones, G.2
  • 37
    • 33845873289 scopus 로고    scopus 로고
    • Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
    • Letunic I, Bork P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 2007;23:127-8.
    • (2007) Bioinformatics , vol.23 , pp. 127-128
    • Letunic, I.1    Bork, P.2
  • 38
    • 0032925832 scopus 로고    scopus 로고
    • Analysis of catabolic genes for naphthalene and phenanthrene degradation in contaminated New Zealand soils
    • Lloyd-Jones G, Laurie AD, Hunter DWF, et al. Analysis of catabolic genes for naphthalene and phenanthrene degradation in contaminated New Zealand soils. FEMS Microbiol Ecol 1999;29:69-79.
    • (1999) FEMS Microbiol Ecol , vol.29 , pp. 69-79
    • Lloyd-Jones, G.1    Laurie, A.D.2    Hunter, D.W.F.3
  • 39
    • 33746191929 scopus 로고    scopus 로고
    • The complete genome of Rhodococcus sp RHA1 provides insights into a catabolic powerhouse
    • McLeod MP, Warren RL, Hsiao WWL, et al. The complete genome of Rhodococcus sp RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci U S A 2006;103:15582-7.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 15582-15587
    • McLeod, M.P.1    Warren, R.L.2    Hsiao, W.W.L.3
  • 40
    • 84860495991 scopus 로고    scopus 로고
    • Effect of activated carbon amendment on bacterial community structure and functions in a PAH impacted urban soil
    • Meynet P, Hale SE, Davenport RJ, et al. Effect of activated carbon amendment on bacterial community structure and functions in a PAH impacted urban soil. Environ Sci Technol 2012;46:5057-66.
    • (2012) Environ Sci Technol , vol.46 , pp. 5057-5066
    • Meynet, P.1    Hale, S.E.2    Davenport, R.J.3
  • 41
    • 0019519171 scopus 로고
    • Searches for ultimate chemical carcinogens and their reactions with cellular macromolecules
    • Miller EC, Miller JA. Searches for ultimate chemical carcinogens and their reactions with cellular macromolecules. Cancer 1981;47:2327-45.
    • (1981) Cancer , vol.47 , pp. 2327-2345
    • Miller, E.C.1    Miller, J.A.2
  • 42
    • 1842509857 scopus 로고    scopus 로고
    • Convenient determination of DNA extraction efficiency using an external DNA recovery standard and quantitative-competitive PCR
    • Mumy KL, Findlay RH. Convenient determination of DNA extraction efficiency using an external DNA recovery standard and quantitative-competitive PCR. J Microbiol Methods 2004;57:259-68.
    • (2004) J Microbiol Methods , vol.57 , pp. 259-268
    • Mumy, K.L.1    Findlay, R.H.2
  • 43
    • 33745132697 scopus 로고    scopus 로고
    • Microbial dioxygenase gene population shifts during polycyclic aromatic hydrocarbon biodegradation
    • Ni Chadhain SM, Norman RS, Pesce KV, et al. Microbial dioxygenase gene population shifts during polycyclic aromatic hydrocarbon biodegradation. Appl Environ Microb 2006;72: 4078-87.
    • (2006) Appl Environ Microb , vol.72 , pp. 4078-4087
    • Ni Chadhain, S.M.1    Norman, R.S.2    Pesce, K.V.3
  • 45
    • 33845383312 scopus 로고    scopus 로고
    • A targeted real-time PCR assay for studying naphthalene degradation in the environment
    • Nyyssonen M, Piskonen R, Itavaara M. A targeted real-time PCR assay for studying naphthalene degradation in the environment. Microbial Ecol 2006;52:533-43.
    • (2006) Microbial Ecol , vol.52 , pp. 533-543
    • Nyyssonen, M.1    Piskonen, R.2    Itavaara, M.3
  • 46
    • 74249111651 scopus 로고    scopus 로고
    • A study of PCR inhibition mechanisms using real time PCR
    • Opel KL, Chung D, McCord BR. A study of PCR inhibition mechanisms using real time PCR. J Forensic Sci 2010;55:25-33.
    • (2010) J Forensic Sci , vol.55 , pp. 25-33
    • Opel, K.L.1    Chung, D.2    McCord, B.R.3
  • 48
    • 0037826062 scopus 로고    scopus 로고
    • The role of active-site residues in naphthalene dioxygenase
    • Parales RE. The role of active-site residues in naphthalene dioxygenase. J Ind Microbiol Biot 2003;30:271-8.
    • (2003) J Ind Microbiol Biot , vol.30 , pp. 271-278
    • Parales, R.E.1
  • 49
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. P Natl Acad Sci USA 1988;85:2444-8.
    • (1988) P Natl Acad Sci USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 50
    • 0032534926 scopus 로고    scopus 로고
    • Biodegradation of bicyclic and polycyclic aromatic hydrocarbons in anaerobic enrichments
    • Rockne KJ, Strand SE. Biodegradation of bicyclic and polycyclic aromatic hydrocarbons in anaerobic enrichments. Environ Sci Technol 1998;32:3962-7.
    • (1998) Environ Sci Technol , vol.32 , pp. 3962-3967
    • Rockne, K.J.1    Strand, S.E.2
  • 51
    • 0003903343 scopus 로고    scopus 로고
    • Molecular Cloning: A Laboratory Manual
    • NewYork: Cold Spring Harbor Laboratory Press
    • Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning: A Laboratory Manual. NewYork: Cold Spring Harbor Laboratory Press, 2001.
    • (2001)
    • Sambrook, J.1    Fritsch, E.F.2    Maniatis, T.3
  • 52
    • 0029128756 scopus 로고
    • A novel transformation of polychlorinated-biphenyl by Rhodococcus sp. strain RHA1
    • Seto M, Kimbara K, Shimura M, et al. A novel transformation of polychlorinated-biphenyl by Rhodococcus sp. strain RHA1. Appl Environ Microb 1995;61:3353-8.
    • (1995) Appl Environ Microb , vol.61 , pp. 3353-3358
    • Seto, M.1    Kimbara, K.2    Shimura, M.3
  • 54
    • 84877037742 scopus 로고    scopus 로고
    • Comparison of methods for the characterization and quantification of carbon forms in estuarine and marine sediments fromcoal mining regions
    • Siavalas G, Werner D, Karapanagioti HK, et al. Comparison of methods for the characterization and quantification of carbon forms in estuarine and marine sediments fromcoal mining regions. Org Geochem 2013;59:61-74.
    • (2013) Org Geochem , vol.59 , pp. 61-74
    • Siavalas, G.1    Werner, D.2    Karapanagioti, H.K.3
  • 55
    • 4143146355 scopus 로고    scopus 로고
    • Molecular characterization of a phenanthrene degradation pathway in Mycobacterium vanbaalenii PYR-1
    • Stingley RL, Khan AA, Cerniglia CE. Molecular characterization of a phenanthrene degradation pathway in Mycobacterium vanbaalenii PYR-1. Biochem Bioph Res Co 2004;322:133-46.
    • (2004) Biochem Bioph Res Co , vol.322 , pp. 133-146
    • Stingley, R.L.1    Khan, A.A.2    Cerniglia, C.E.3
  • 56
    • 0035379677 scopus 로고    scopus 로고
    • Application of the 5' fluorogenic exonuclease assay (TaqMan) for quantitative ribosomal DNA and rRNA analysis in sediments
    • Stults JR, Snoeyenbos-West O, Methe B, et al. Application of the 5' fluorogenic exonuclease assay (TaqMan) for quantitative ribosomal DNA and rRNA analysis in sediments. Appl Environ Microb 2001;67:2781-9.
    • (2001) Appl Environ Microb , vol.67 , pp. 2781-2789
    • Stults, J.R.1    Snoeyenbos-West, O.2    Methe, B.3
  • 57
    • 3342920601 scopus 로고    scopus 로고
    • Prospects for inferring very large phylogenies by using the neighbor-joining method
    • Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. P Natl Acad Sci USA 2004;101:11030-5.
    • (2004) P Natl Acad Sci USA , vol.101 , pp. 11030-11035
    • Tamura, K.1    Nei, M.2    Kumar, S.3
  • 58
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura K, Peterson D, Peterson N, et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28:2731-9.
    • (2011) Mol Biol Evol , vol.28 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3
  • 59
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL?X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson JD, Gibson TJ, Plewniak F, et al. The CLUSTAL?X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25:4876-82.
    • (1997) Nucleic Acids Res , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3
  • 60
    • 60349117029 scopus 로고    scopus 로고
    • Development of real-time PCR assay for detection and quantification of Sinorhizobium meliloti in soil and plant tissue
    • Trabelsi D, Pini F, Aouani ME, et al. Development of real-time PCR assay for detection and quantification of Sinorhizobium meliloti in soil and plant tissue. Lett Appl Microbiol 2009;48:355-61.
    • (2009) Lett Appl Microbiol , vol.48 , pp. 355-361
    • Trabelsi, D.1    Pini, F.2    Aouani, M.E.3
  • 61
    • 84949270957 scopus 로고    scopus 로고
    • Emergency planning and community right-to-know act- Section 313
    • Washington DC: Office of Environmental Information
    • USEPA. Emergency planning and community right-to-know act- Section 313. Guidance for Reporting Toxic Chemicals: Polycyclic Aromatic Compounds Category. Washington DC: Office of Environmental Information, 2001.
    • (2001) Guidance for Reporting Toxic Chemicals: Polycyclic Aromatic Compounds Category
  • 62
    • 79958812689 scopus 로고    scopus 로고
    • Development of a Relative Potency Factor (RPF) Approach for Polycyclic Aromatic Hydrocarbon (PAH) Mixtures
    • Washington, DC: U.S. Environmental Protection
    • USEPA. Development of a Relative Potency Factor (RPF) Approach for Polycyclic Aromatic Hydrocarbon (PAH) Mixtures. Washington, DC: U.S. Environmental Protection, 2010.
    • (2010)
  • 63
    • 70449358972 scopus 로고    scopus 로고
    • Accurate quantification of microorganisms in PCR-inhibiting environmental DNA extracts by a novel internal amplification control approach using biotrove openarrays
    • van Doorn R, Klerks MM, van Gent-Pelzer MPE, et al. Accurate quantification of microorganisms in PCR-inhibiting environmental DNA extracts by a novel internal amplification control approach using biotrove openarrays. Appl Environ Microb 2009;75:7253-60.
    • (2009) Appl Environ Microb , vol.75 , pp. 7253-7260
    • van Doorn, R.1    Klerks, M.M.2    van Gent-Pelzer, M.P.E.3
  • 64
    • 84875885665 scopus 로고    scopus 로고
    • Analysis of the microbial gene landscape and transcriptome for aromatic pollutants and alkane degradation using a novel internally calibratedmicroarray system
    • Vilchez-Vargas R, Geffers R, Suarez-Diez M, et al. Analysis of the microbial gene landscape and transcriptome for aromatic pollutants and alkane degradation using a novel internally calibratedmicroarray system. Environ Microbiol 2013;15: 1016-39.
    • (2013) Environ Microbiol , vol.15 , pp. 1016-1039
    • Vilchez-Vargas, R.1    Geffers, R.2    Suarez-Diez, M.3
  • 65
    • 0037015403 scopus 로고    scopus 로고
    • Mechanism and applications of Rieske non-heme iron dioxygenases
    • Wackett LP. Mechanism and applications of Rieske non-heme iron dioxygenases. Enzyme Microbial Technol 2002;31:577-87.
    • (2002) Enzyme Microbial Technol , vol.31 , pp. 577-587
    • Wackett, L.P.1
  • 66
    • 0032906465 scopus 로고    scopus 로고
    • In situ, real-time catabolic gene expression: extraction and characterization of naphthalene dioxygenase mRNA transcripts from groundwater
    • Wilson MS, Bakermans C, Madsen EL. In situ, real-time catabolic gene expression: extraction and characterization of naphthalene dioxygenase mRNA transcripts from groundwater. Appl Environ Microb 1999;65:80-7.
    • (1999) Appl Environ Microb , vol.65 , pp. 80-87
    • Wilson, M.S.1    Bakermans, C.2    Madsen, E.L.3
  • 67
    • 70349907086 scopus 로고    scopus 로고
    • Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer
    • Yagi JM, Madsen EL. Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer. Appl Environ Microb 2009;75:6478-87.
    • (2009) Appl Environ Microb , vol.75 , pp. 6478-6487
    • Yagi, J.M.1    Madsen, E.L.2
  • 68
    • 33746199793 scopus 로고    scopus 로고
    • Genomic DNA functions as a universal external standard in quantitative real-time PCR
    • Yun JJ, Heisler LE, Hwang IIL, et al. Genomic DNA functions as a universal external standard in quantitative real-time PCR. Nucleic Acids Res 2006;34:10.
    • (2006) Nucleic Acids Res , vol.34 , pp. 10
    • Yun, J.J.1    Heisler, L.E.2    Hwang, I.I.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.