Automated purification and suspension array detection of 16S rRNA from soil and sediment extracts by using tunable surface microparticles

Applied and Environmental Microbiology

Volumn 70, Issue 5, 2004, Pages 2621-2631

  Chandler, Darrell P ^a   Jarrell, Ann E ^b  

^a ARGONNE NATIONAL LABORATORY   (United States)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATION; EXTRACTION; FLUORESCENCE; PURIFICATION; QUENCHING; SEDIMENTS; SOILS;

INTEGRATED BIODETECTION SYSTEMS; TUNABLE SURFACE MICROPARTICLES;

RNA;

BUFFER; CHAPERONE; RESIN; RNA 16S;

MICROBIOLOGY;

ARTICLE; AUTOMATION; BACTERIAL FLORA; BIOLOGICAL MONITORING; BIOSENSOR; CONTROLLED STUDY; CROSS HYBRIDIZATION; EXTRACTION; FLOW CYTOMETRY; FLUORESCENCE; MOLECULAR GENETICS; NONHUMAN; NONPHOTOCHEMICAL QUENCHING; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; PARTICLE SIZE; RNA ANALYSIS; RNA DEGRADATION; RNA HYBRIDIZATION; RNA PURIFICATION; RNA SEQUENCE; SAMPLE; SEDIMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SOIL ANALYSIS; SURFACE PROPERTY; SYSTEM ANALYSIS; TECHNIQUE;

AUTOMATION; DESULFOVIBRIO; DNA PROBES; FLOW CYTOMETRY; GEOBACTER; GEOLOGIC SEDIMENTS; MICROSPHERES; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PARTICLE SIZE; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY;

ALEXA; BACTERIA (MICROORGANISMS);

EID: 2442659512     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.70.5.2621-2631.2004     Document Type: Article

References (30)

1. Alm, E. W., D. B. Oerther, N. Larsen, D. A. Stahl, and L. Raskin. 1996. The oligonucleotide probe database. Appl. Environ. Microbiol. 62:3557-3559.
2. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (ed.). 1995. Current protocols in molecular biology. John Wiley & Sons, Inc., New York, N.Y.
3. Bavykin, S. G., J. P. Akowski, V. M. Zakhariev, V. E. Barksy, A. N. Perov, and A. D. Mirzabekov. 2001. Portable system for microbial sample preparation and oligonucleotide microarray analysis. Appl. Environ. Microbiol. 67: 922-928.
4. Belgrader, P., W. Bennett, D. Hadley, G. Long, R. Mariella, Jr., F. Milanovich, S. Nasarabadi, W. Nelson, J. Richards, and P. Stratton. 1998. Rapid pathogen detection using a microchip PCR array instrument. Clin. Chem. 44:2191-2194.
5. Belosludtsev, Y., I. Belosludtsev, B. Iverson, S. Lemeshko, R. Wiese, M. Hogan, and T. Powdrill. 2001. Nearly instantaneous, cation-independent, high selectivity nucleic acid hybridization to DNA microarrays. Biochem. Biophys. Res. Commun. 282:1263-1267.
6. 2 or formate uptake. Appl. Environ. Microbiol. 55:1735-1741.
7. Brockman, F. J. 1995. Nucleic acid-based methods for monitoring the performance of in situ bioremediation. Mol. Ecol. 4:567-578.
8. Chandler, D. P., D. A. Holman, F. J. Brockman, J. W. Grate, and C. J. Bruckner-Lea. 2000. Renewable microcolumns for solid-phase nucleic acid separations and analysis from environmental samples. Trends Anal. Chem. 19:314-321.
9. Chandler, D. P., and A. E. Jarrell. 2003. Enhanced nucleic acid capture and flow cytometry detection with peptide nucleic acid probes and tunable surface microparticles. Anal. Biochem. 312:182-190.
10. Chandler, D. P., G. J. Newton, J. A. Small, and D. S. Daly. 2003. Sequence versus structure for the direct detection of 16S rRNA on planar oligonucleotide microarrays. Appl. Environ. Microbiol. 69:2950-2958.
11. Chandler, D. P., J. R. Stults, S. Cebula, B. L. Schuck, D. W. Weaver, K. K. Anderson, M. Egholm, and F. J. Brockman. 2000. Affinity purification of DNA and RNA from environmental samples with peptide nucleic acid clamps. Appl. Environ. Microbiol. 66:3438-3445.
12. a. Eggers, M. D., W. J. Balch, L. G. Mendoza, R. Gangadharan, A. K. Mallik, G. McMahon, M. E. Hogan, D. Xaio, T. R. Powdrill, B. Iverson, G. E. Fox, R. C. Willson, K. I. Maillard, J. L. Siefert, and N. Singh. 1997. Advanced approach to simultaneous monitoring of multiple bacteria in space, p. 1-8. Proceedings of the 27th International Conference on Environmental Systems, SAE International, Warrendale, Pa.
13. El Fantroussi, S., H. Urakawa, A. E. Bernhard, J. J. Kelly, P. A. Noble, H. Smidt, G. M. Yershov, and D. A. Stahl. 2003. Direct profiling of environmental microbial populations by thermal dissociation analysis of native ribosomal RNAs hybridized to oligonucleotide microarrays. Appl. Environ. Microbiol. 69:2377-2382.
14. Gilles, P. N., D. J. Wu, C. B. Foster, P. J. Dillon, and S. J. chanock. 1999. Single nucleotide polymorphic discrimination by an electronic dot blot assay on semiconductor microchips. Nat. Biotechnol. 17:365-370.
15. Iannone, M. A., J. D. Taylor, J. Chen, M.-S. Li, P. Rivers, K. A. Slentz-Kesler, and M. P. Weiner. 2000. Multiplexed single nucleotide polymorphism genotyping by oligonucleotide ligation and flow cytometry. Cytometry 39:131-140.
16. Khandurina, J., T. E. McKnight, S. C. Jacobson, L. C. Waters, R. S. Foote, and J. M. Ramsey. 2000. Integrated system for rapid PCR-based DNA analysis in microfluidic devices. Anal. Chem. 72:2995-3000.
17. Lewin, B. 1990. Genes IV. Oxford University Press, New York, N.Y.
18. Liu, W. T., A. D. Mirzabekov, and D. A. Stahl. 2001. Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach. Environ. Microbiol. 3:619-629.
19. Maidak, B. L., J. R. Cole, C. T. Parker, Jr., G. M. Garrity, N. Larsen, B. Li, T. G. Lilburn, M. J. McCaughey, G. J. Olsen, R. Overbeek, S. Pramanik, T. M. Schmidt, J. M. Tiedje, and C. R. Woese. 1999. A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res. 27:171-173.
20. Maldonado-Rodriguez, R., M. Espinosa-Lara, A. Calixto-Suárez, W. G. Beattie, and K. L. Beattie. 1999. Hybridization of glass-tethered oligonucleotide probes to target strands preannealed with labeled auxiliary oligonucleotides. Mol. Biotechnol. 11:1-12.
21. Nasarabadi, S., F. Milanovich, J. Richards, and P. Belgrader. 1999. Simultaneous detection of TaqMan probes containing FAM and TAMRA reporter fluorophores. BioTechniques 27:1116-1118.
22. Neidhardt, F. C., J. L. Ingraham, and M. Schaechter. 1990. Physiology of the bacterial cell: a molecular approach. Sinauer Associates, Inc., Sunderland, Mass.
23. Ogram, A., W. Sun, F. J. Brockman, and J. K. Fredrickson. 1995. Isolation and characterization of RNA from low-biomass deep-subsurface sediments. Appl. Environ. Microbiol. 61:763-768.
24. Small, J. A., D. R. Call, F. J. Brockman, T. M. Straub, and D. P. Chandler. 2001. Direct detection of 16S rRNA in soil extracts using oligonucleotide microarrays. Appl. Environ. Microbiol. 67:4708-4716.
25. Spiro, A., and M. Lowe. 2002. Quantitation of DNA sequences in environmental PCR products by a multiplexed, bead-based method. Appl. Environ. Microbiol. 68:1010-1013.
26. Spiro, A., M. Lowe, and D. Brown. 2000. A bead-based method for multiplexed identification and quantitation of DNA sequences using flow cytometry. Appl. Environ. Microbiol. 66:4258-4265.
27. Tebbe, C. C., and W. Vahjen. 1993. Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast. Appl. Environ. Microbiol. 59:2657-2665.
28. Wilson, K. H., W. J. Wilson, J. L. Radosevich, T. Z. DeSantis, V. S. Viswanathan, T. A. Kuczmarski, and G. L. Andersen. 2002. High-density microarray of small-subunit ribosomal DNA probes. Appl. Environ. Microbiol. 68:2535-2541.
29. Wintzingerode, F. V., U. B. Göbel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229.
30. Woolley, A. T., G. F. Sensabaugh, and R. A. Mathies. 1997. High-speed DNA genotyping using microfabricated capillary array electrophoresis chips. Anal. Chem. 69:2181-2186.