Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
Citations
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Cites background from "Profiling of complex microbial popu..."
...%) out of 8889 ‘DGGE’ sequences found belong to the 300–600 nucleotide length class....
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...The large number of sequences with 300 and 600 bases is typical for diversity studies that use single reads or fingerprint techniques like DGGE (25)....
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...A text search for ‘DGGE’ across all fields of the SSU Parc database using ARB showed that 8241 (93...
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5,346 citations
Additional excerpts
...Primer pairs were: (i): S-D-Bact-0341b-S-17, 50-CCTACGGGNGGCWGCAG-30 (32), and S-D-Bact-0785-a-A-21, 50-GACTACHVGGGTATCTA ATCC-3 (32); and (ii): S-D-Bact-0008-a-S-16, 50-AGAG TTTGATCMTGGC-30 (33), and S-D-Bact-0907-a-A-20, 50-CCGTCAATTCMTTTGAGTTT-30 (34)....
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2,475 citations
Cites methods from "Profiling of complex microbial popu..."
...Classification of bacterial/archaeal 16S rRNA gene sequences was made using the Greengenes (13_8 release) [5] reference sequence database preclustered at 99% ID, with amplicons for the domain of interest extracted using primers 27F/1492R [27], 515F/806R [28], or 27F/534R [29] with q2-feature-classifier’s extract_reads method....
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...The bacterial primers used were 27F/1492R [27] to simulate full-length 16S rRNA gene sequences, 515F/806R [28] to simulate 16S rRNA gene V4 domain sequences, and 27F/534R [29] to simulate 16S rRNA gene V1–3 domain sequences; the fungal primers used were BITSf/B58S3r [30] to simulate ITS1 internal transcribed spacer DNA sequences....
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2,383 citations
Cites methods from "Profiling of complex microbial popu..."
...More recently, techniques dependent on DNA melting behavior (20, 21) or single-strand DNA conformation (14) have been developed as a means of circumventing library construction....
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References
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"Profiling of complex microbial popu..." refers methods in this paper
...The variable V3 region of 16S rDNA was enzymatically amplified in the PCR (17) with primers to conserved regions of the 16S rRNA genes (13)....
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4,110 citations
"Profiling of complex microbial popu..." refers methods in this paper
...To analyze the microbial populations for the presence of specific bacteria, the DGGE separation patterns were stained with ethidium bromide, photographed, and subsequently hybridized, after being transferred to a nylon membrane, to an oligonucleotide probe specific for sulfate-reducing bacteria (1)....
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2,699 citations
"Profiling of complex microbial popu..." refers background in this paper
...This temperature, which is 1)°C abovc the cxpectcd ainncaling temperature, was decreased by 1°C cvery sccond cyclc until a touchdown at 55°C, at which temperatture five aidditional cycles were carried out (5)....
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2,636 citations