Gene capture and random amplification for quantitative recovery of homologous genes

Molecular and Cellular Probes

Volumn 21, Issue 2, 2007, Pages 140-147

  Crosby, Laurel D ^a   Criddle, Craig S ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

16S rRNA; Microarray; PCR; Probes; Quantitative; Random; rpoC

Indexed keywords

DNA DIRECTED RNA POLYMERASE; OLIGONUCLEOTIDE; RNA 16S;

ACCURACY; ARTICLE; CONCENTRATION RESPONSE; CONTROLLED STUDY; DNA DETERMINATION; DNA MICROARRAY; DNA PROBE; GENE AMPLIFICATION; GENE CAPTURE AND RANDOM AMPLIFICATION; GENE NUMBER; GENOME; MICROORGANISM; MOLECULAR PROBE; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; SAMPLING; SEQUENCE HOMOLOGY;

BASE SEQUENCE; DNA; DNA PRIMERS; DNA PROBES; GENE AMPLIFICATION; POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 33846096244     PISSN: 08908508     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mcp.2006.09.003     Document Type: Article

References (26)

1. Wilson K.H., Wilson W.J., Radosevich J.L., DeSantis T.Z., Viswanathan V.S., Kuczmarski T.A., et al. High-density microarray of small-subunit ribosomal DNA probes. Appl Environ Microbiol 68 5 (2002) 2535-2541
2. Palmer C., Bik E.M., Eisen M.B., Eckburg P.B., Sana T.R., Wolber P.K., et al. Rapid quantitative profiling of complex microbial populations. Nucl Acids Res 34 1 (2006) e5
3. von Wintzingerode F., Gobel U.B., and Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21 3 (1997) 213-229
4. Polz M.F., and Cavanaugh C.M. Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64 10 (1998) 3724-3730
5. Suzuki M.T., and Giovannoni S.J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62 2 (1996) 625-630
6. Jacobsen C.S. Microscale detection of specific bacterial DNA in soil with a magnetic capture-hybridization and PCR amplification assay. Appl Environ Microbiol 61 9 (1995) 3347-3352
7. Mangiapan G., Vokurka M., Schouls L., Cadranel J., Lecossier D., van Embden J., et al. Sequence capture-PCR improves detection of mycobacterial DNA in clinical specimens. J Clin Microbiol 34 5 (1996) 1209-1215
8. Stinear T., Davies J.K., Jenkin G.A., Hayman J.A., Oppedisano F., and Johnson P.D. Identification of Mycobacterium ulcerans in the environment from regions in Southeast Australia in which it is endemic with sequence capture-PCR. Appl Environ Microbiol 66 8 (2000) 3206-3213
9. Bohlander S.K., Espinosa R., Le Beau M.M., Rowley J.D., and Diaz M.O. A method for the rapid sequence-independent amplification of microdissected chromosomal material. Genomics 13 4 (1992) 1322-1324
10. Woese C.R. Bacterial evolution. Microbiol Rev 51 2 (1987) 221-271
11. DeLong E.F. Marine microbial diversity: the tip of the iceberg. Trends Biotechnol 15 6 (1997) 203-207
12. Maidak B.L., Larsen N., McCaughey M.J., Overbeek R., Olsen G.J., Fogel K., et al. The ribosomal database project. Nucl Acids Res 22 17 (1994) 3485-3487
13. Farrelly V., Rainey F.A., and Stackebrandt E. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol 61 7 (1995) 2798-2801
14. Acinas S.G., Marcelino L.A., Klepac-Ceraj V., and Polz M.F. Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186 9 (2004) 2629-2635
15. Crosby L.D., and Criddle C.S. Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques 34 4 (2003) 790-794 796, 798 passim
16. Forney L.J., Zhou X., and Brown C.J. Molecular microbial ecology: land of the one-eyed king. Curr Opin Microbiol 7 3 (2004) 210-220
17. Schloss P.D., and Handelsman J. Status of the microbial census. Microbiol Mol Biol Rev 68 4 (2004) 686-691
18. Harris J.K., Kelley S.T., Spiegelman G.B., and Pace N.R. The genetic core of the universal ancestor. Genome Res 13 3 (2003) 407-412
19. Dahllöf I., Baillie H., and Kjelleberg S. rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol 66 8 (2000) 3376-3380
20. Toledo G., and Palenik B. Synechococcus diversity in the California current as seen by RNA polymerase (rpoC1) gene sequences of isolated strains. Appl Environ Microbiol 63 11 (1997) 4298-4303
21. Zaychikov E., Martin E., Denissova L., Kozlov M., Markovtsov V., Kashlev M., et al. Mapping of catalytic residues in the RNA polymerase active center. Science 273 5271 (1996) 107-109
22. Dieci G., Hermann-Le Denmat S., Lukhtanov E., Thuriaux P., Werner M., and Sentenac A. A universally conserved region of the largest subunit participates in the active site of RNA polymerase III. EMBO J 14 15 (1995) 3766-3776
23. Hughes T.R., Mao M., Jones A.R., Buchard J., and Branton M.J. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nature Biotechnol 19 (2001) 342-347
24. Wang D., Coscoy L., Zylberberg M., Avila P.C., Boushey H.A., Ganem D., et al. Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci USA 99 24 (2002) 15687-15692
25. Vora G.J., Meador C.E., Stenger D.A., and Andreadis J.D. Nucleic acid amplification strategies for DNA microarray-based pathogen detection. Appl Environ Microbiol 70 5 (2004) 3047-3054
26. DeSantis T., Stone C.E., Murray S.R., Mcberg J.P., and Anderson G.L. Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray. FEMS Microbiol Lett 245 2 (2005) 271-278