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@ARTICLE{Ning:7048,
      author       = {Ning, J. and Liebich, J. and Kästner, M. and Zhou, J. Z.
                      and Schäffer, A. and Burauel, P.},
      title        = {{D}ifferent influences of {DNA} purity indices and quantity
                      on {PCR}-based {DGGE} and functional gene microarray in soil
                      microbial community study},
      journal      = {Applied Microbiology and Biotechnology},
      volume       = {82},
      issn         = {0175-7598},
      address      = {Berlin},
      publisher    = {Springer},
      reportid     = {PreJuSER-7048},
      pages        = {983 - 993},
      year         = {2009},
      note         = {The manuscript is a joint approach within the working group
                      "Biodiversity" of the Helmholtz Association, Germany. The
                      authors would like to thank Eva Mareike Seeger, Mareike
                      Braeckevelt, and Heidrun Paschke in the group of the
                      Department of Bioremediation (UFZ, Germany) for the help
                      during the sampling at the SAFIRA plant in Bitterfeld and
                      the group in the Institute for Environmental Genomics
                      (Oklahoma, USA) for providing the microarray chips, as well
                      as Dr. Naixin Li for the valuable discussion. The
                      construction of microarray chips and its functional gene
                      array predecessors is supported by the Environmental Stress
                      Pathway Project (ESPP) of the Virtual Institute for
                      Microbial Stress and Survival (http://vimss. lbl. gov)
                      supported by the U. S. Department of Energy, Office of
                      Science, Office of Biological and Environmental Research,
                      Genomics: GTL Program, through contract DE- AC0205CH11231
                      with Lawrence Berkeley National Laboratory.},
      abstract     = {Based on the comparative study of the DNA extracts from two
                      soil samples obtained by three commercial DNA extraction
                      kits, we evaluated the influence of the DNA quantity and
                      purity indices (the absorbance ratios A260/280 and A260/230,
                      as well as the absorbance value A320 indicating the amount
                      of humic substances) on polymerase chain reaction
                      (PCR)-based denaturing gradient gel electrophoresis (DGGE)
                      and a functional gene microarray used in the study of
                      microbial communities. Numbers and intensities of the DGGE
                      bands are more affected by the A260/280 and A320 values than
                      by the ratio A260/230 and conditionally affected by the DNA
                      yield. Moreover, we demonstrated that the DGGE band pattern
                      was also affected by the preferential extraction due to
                      chemical agents applied in the extraction. Unlike DGGE,
                      microarray is more affected by the A260/230 and A320 values.
                      Until now, the successful PCR performance is the mostly used
                      criterion for soil DNA purity. However, since PCR was more
                      influenced by the A260/280 ratio than by A260/230, it is not
                      accurate enough any more for microbial community assessed by
                      non-PCR-based methods such as microarray. This study
                      provides some useful hints on how to choose effective DNA
                      extraction method for the subsequent assessment of microbial
                      community.},
      keywords     = {Bacteriological Techniques: methods / Biodiversity / DNA,
                      Bacterial: isolation $\&$ purification / Electrophoresis,
                      Gel, Two-Dimensional: methods / Humic Substances: analysis /
                      Oligonucleotide Array Sequence Analysis: methods /
                      Polymerase Chain Reaction: methods / Reagent Kits,
                      Diagnostic: standards / Reproducibility of Results / Soil
                      Microbiology / DNA, Bacterial (NLM Chemicals) / Humic
                      Substances (NLM Chemicals) / Reagent Kits, Diagnostic (NLM
                      Chemicals) / J (WoSType)},
      cin          = {ICG-4},
      ddc          = {570},
      cid          = {I:(DE-Juel1)VDB793},
      pnm          = {Terrestrische Umwelt},
      pid          = {G:(DE-Juel1)FUEK407},
      shelfmark    = {Biotechnology $\&$ Applied Microbiology},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:19247649},
      UT           = {WOS:000264460500020},
      doi          = {10.1007/s00253-009-1912-0},
      url          = {https://juser.fz-juelich.de/record/7048},
}