Literature DB >> 16085891

Fluorophore-labeled primers improve the sensitivity, versatility, and normalization of denaturing gradient gel electrophoresis.

Josh D Neufeld1, William W Mohn.   

Abstract

Denaturing gradient gel electrophoresis (DGGE) is widely used in microbial ecology. We tested the effect of fluorophore-labeled primers on DGGE band migration, sensitivity, and normalization. The fluorophores Cy5 and Cy3 did not visibly alter DGGE fingerprints; however, 6-carboxyfluorescein retarded band migration. Fluorophore modification improved the sensitivity of DGGE fingerprint detection and facilitated normalization of samples from multiple gels by the application of intralane standards.

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Year:  2005        PMID： 16085891      PMCID： PMC1183338          DOI： 10.1128/AEM.71.8.4893-4896.2005

Source DB:  PubMed          Journal:  Appl Environ Microbiol        ISSN： 0099-2240            Impact factor:   4.792


  11 in total

Review 1.  DGGE/TGGE a method for identifying genes from natural ecosystems.

Authors:  G Muyzer
Journal:  Curr Opin Microbiol       Date:  1999-06       Impact factor: 7.934

2.  Diversity and distribution of DNA sequences with affinity to ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in the Arctic Ocean.

Authors:  N Bano; J T Hollibaugh
Journal:  Appl Environ Microbiol       Date:  2000-05       Impact factor: 4.792

3.  Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis.

Authors:  M M Moeseneder; J M Arrieta; G Muyzer; C Winter; G J Herndl
Journal:  Appl Environ Microbiol       Date:  1999-08       Impact factor: 4.792

4.  Widespread distribution in polar oceans of a 16S rRNA gene sequence with affinity to Nitrosospira-like ammonia-oxidizing bacteria.

Authors:  James T Hollibaugh; Nasreen Bano; Hugh W Ducklow
Journal:  Appl Environ Microbiol       Date:  2002-03       Impact factor: 4.792

5.  Phylogenetic composition of Arctic Ocean archaeal assemblages and comparison with Antarctic assemblages.

Authors:  Nasreen Bano; Shomari Ruffin; Briana Ransom; James T Hollibaugh
Journal:  Appl Environ Microbiol       Date:  2004-02       Impact factor: 4.792

6.  Influence of depth and sampling time on bacterial community structure in an upland grassland soil.

Authors:  Robert I Griffiths; Andrew S Whiteley; Anthony G O'Donnell; Mark J Bailey
Journal:  FEMS Microbiol Ecol       Date:  2003-02-01       Impact factor: 4.194

7.  Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA.

Authors:  J R Marchesi; T Sato; A J Weightman; T A Martin; J C Fry; S J Hiom; D Dymock; W G Wade
Journal:  Appl Environ Microbiol       Date:  1998-02       Impact factor: 4.792

8.  Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean.

Authors:  Nasreen Bano; James T Hollibaugh
Journal:  Appl Environ Microbiol       Date:  2002-02       Impact factor: 4.792

9.  A molecular technique for identification of bacteria using small subunit ribosomal RNA sequences.

Authors:  E Avaniss-Aghajani; K Jones; D Chapman; C Brunk
Journal:  Biotechniques       Date:  1994-07       Impact factor: 1.993

10.  Characterization of humus microbial communities in adjacent forest types that differ in nitrogen availability.

Authors:  S E Leckie; C E Prescott; S J Grayston; J D Neufeld; W W Mohn
Journal:  Microb Ecol       Date:  2004-04-19       Impact factor: 4.552
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  6 in total

Review 1.  Genotypic microbial community profiling: a critical technical review.

Authors:  Andreas Nocker; Mark Burr; Anne K Camper
Journal:  Microb Ecol       Date:  2007-03-08       Impact factor: 4.552

2.  PCR-denaturing gradient gel electrophoresis of complex microbial communities: a two-step approach to address the effect of gel-to-gel variation and allow valid comparisons across a large dataset.

Authors:  Panagiotis Tourlomousis; E Katherine Kemsley; Karyn P Ridgway; Michael J Toscano; Thomas J Humphrey; Arjan Narbad
Journal:  Microb Ecol       Date:  2009-12-03       Impact factor: 4.552

3.  A New Standard-Based Polynomial Interpolation (SBPIn) method to address gel-to-gel variability for the comparison of multiple denaturing gradient gel electrophoresis profile matrices.

Authors:  Alexis Valentín-Vargas; Jon Chorover; Raina M Maier
Journal:  J Microbiol Methods       Date:  2012-12-09       Impact factor: 2.363

4.  Isolation of Methylophaga spp. from marine dimethylsulfide-degrading enrichment cultures and identification of polypeptides induced during growth on dimethylsulfide.

Authors:  Hendrik Schäfer
Journal:  Appl Environ Microbiol       Date:  2007-02-23       Impact factor: 4.792

5.  Application of sequence-dependent electrophoresis fingerprinting in exploring biodiversity and population dynamics of human intestinal microbiota: what can be revealed?

Authors:  Geert Huys; Tom Vanhoutte; Peter Vandamme
Journal:  Interdiscip Perspect Infect Dis       Date:  2008-12-14

6.  Fluorescent-BOX-PCR for resolving bacterial genetic diversity, endemism and biogeography.

Authors:  Lorenzo Brusetti; Iana Malkhazova; Maher Gtari; Isabella Tamagnini; Sara Borin; Maya Merabishvili; Nina Chanishvili; Diego Mora; Francesca Cappitelli; Daniele Daffonchio
Journal:  BMC Microbiol       Date:  2008-12-15       Impact factor: 3.605
  6 in total

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