Taking arrays from the lab to the field: Trying to make sense of the unknown

BioTechniques

Volumn 38, Issue 4, 2005, Pages 591-600

  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

ARRAYS; CHEMICAL ANALYSIS; ENVIRONMENTAL ENGINEERING; MICROBIOLOGY; MICROORGANISMS; SUSTAINABLE DEVELOPMENT; TECHNOLOGY TRANSFER;

ENVIRONMENTAL MICROBIOLOGY; ENVIRONMENTAL SAMPLES; MICROARRAY TECHNOLOGIES; TECHNOLOGY DEVELOPMENT;

NUCLEIC ACIDS;

ANALYTIC METHOD; COMPARATIVE STUDY; DNA MICROARRAY; ENVIRONMENTAL FACTOR; FIELD EXPERIMENT; HYPOTHESIS; LABORATORY; MICROFLORA; MICROORGANISM DETECTION; NONHUMAN; QUANTITATIVE ANALYSIS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; REVIEW; SAMPLING;

EID: 17244365943     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/05384PS01     Document Type: Review

References (59)

1. Sayler, G.S. and A.C. Layton. 1990. Environmental application of nucleic acid hybridization. Annu. Rev. Microbiol. 44:625-648.
2. Ogram, A.V. and G.S. Sayler. 1988. The use of gene probes in the rapid analysis of natural microbial communities. J. Indust. Microbiol. 3:281-292.
3. Steffan, R.J. and R.M. Atlas. 1991. Polymerase chain reaction: applications in environmental microbiology. Annu. Rev. Microbiol. 45:137-161.
4. Olson, B.H. and Y.-L. Tasi. 1992. Molecular approaches to environmental management, p. 239-263. In R. Mitchell (Ed.), Environmental Microbiology. John Wiley & Sons, New York.
5. Stahl, D.A. 1997. Molecular approaches for the measurement of density, diversity, and phylogeny, p. 102-114. In C.J. Hurst, G.R. Knudsen, M.J. McInerney, L.D. Stetzenbach, and M.V. Walter (Eds.), Manual of Environmental Microbiology. ASM Press, Washington, D.C.
6. Muyzer, G., E.C. De Waal, and A.G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
7. Power, M., J.R. van der Meer, R. Tchelet, T. Egli, and R. Eggen. 1998. Molecular-based methods can contribute to assessments of toxicological risks and bioremediation strategies. J. Microbiol. Methods 32:107-119.
8. Stapleton, R.D., S. Ripp, L. Jimenez, S. Cheol-Koh, J.T. Fleming, I.R. Gregory, and G.S. Sayler. 1998. Nucleic acid analytical approaches in bioremediation: site assessment and characterization. J. Microbiol. Methods 32:165-178.
9. 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.
10. Lee, J.-M., S. Zhang, S. Saha, S.S. Anna, C. Jiang, and J. Perkins. 2001. RNA expression analysis using an antisense Bacillus subtilis genome array. J. Bacteriol. 183:7371-7380.
11. Adamczyk, J., M. Hesselsoe, N. Iversen, M. Horn, A. Lehner, P.H. Nielsen, M. Sehloter, P. Roslev, et al. 2003. The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Appl. Environ. Microbiol. 69:6875-6887.
12. Rudi, K., S.L. Flateland, J.F. Hanssen, G. Bengtsson, and H. Nissen. 2002. Development and evaluation of a 16S ribosomal DNA array-based approach for describing complex microbial communities in ready-to-eat vegetable salads packed in a modified atmosphere. Appl. Environ. Microbiol. 68:1146-1156.
13. Rhee, S.-K., X. Liu, L. Wu, S.C. Chong, X. Wan, and J. Zhou. 2004. Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl. Environ. Microbiol. 70:4303-4317.
14. Wu, L., D.K. Thompson, G. Li, R.A. Hurt, J.M. Tiedje, and J. Zhou. 2001. Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl. Environ. Microbiol. 67:5780-5790.
15. Castiglioni, B., E. Rizzi, A. Frosini, K. Sivonen, P. Rajaniemi, A. Rantala, M.A. Mugnai, S. Ventura, et al. 2004. Development of a universal microarray based on the ligation detection reaction and 16S rRNA genepolymorphism to target diversity of Cyanobacteria. Appl. Environ. Microbiol. 70:7161-7172.
16. Jenkins, B.D., G.F. Steward, S.M. Short, B.B. Ward, and J.P. Zehr. 2004. Fingerprinting diazotroph communities in the Chesapeake Bay by using a DNA macroarray. Appl. Environ. Microbiol. 70:1767-1776.
17. Steward, G.F., B.D. Jenkins, B.B. Ward, and J.P. Zehr. 2004. Development and testing of a DNA macroarray to assess nitrogenase (nifH) gene diversity. Appl. Environ. Microbiol. 70:1455-1465.
18. Brown, P.O. and D. Botstein. 1999. Exploring the new world of the genome with DNA microarrays. Nat. Genet. 21(1 Suppl):33-31.
19. Chee, M., R. Yang, E. Hubbell, A. Berno, X.C. Huang, D. Stern, J. Winkler, D.J. Lockhart, et al. 1996. Accessing genetic information with high-density DNA arrays. Science 274:610-614.
20. Sosnowski, R.G., E. Tu, W.F. Butler, J.P. O'Connell, and M.J. Heller. 1997. Rapid determination of single base mismatch mutations in DNA hybrids by direct electric field control. Proc. Natl. Acad. Sci. USA 94:1119-1123.
21. Fulton, R.J., R.L. McDade, P.L. Smith, L.J. Kienker, and J.R. Kettman, Jr. 1997. Advanced multiplexed analysis with the Flow-Metrix™ system. Clin.Chem. 43:1749-1756.
22. Walt, D.R. 2000. Bead-based fiber-optic arrays. Science 287:451-452.
23. Ali, M.F., R. Kirby, A.P. Goodey, M.D. Rodriguez, A.D. Ellington, D.P. Neikirk, and J.T. McDevitt. 2003. DNA hybridization and discrimination of single-nucleotide mismatches using chip-based microbead arrays. Anal. Chem. 75:4732-4739.
24. Yershov, G., V. Barsky, A. Belgovskiy, E. Kirillov, E. Kreindlin, I. Ivanov, S. Parinov, D. Guschin, et al. 1996. DNA analysis and diagnostics on oligonucleotide microchips. Proc. Natl. Acad. Sci. USA 93:4913-4918.
25. Peplies, J., F.O. Glöckner, and R. Amann. 2003. Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl. Environ. Microbiol. 69:1397-1407.
26. Alvarez, J., S. Porwollik, I. Laconcha, V. Gisakis, A.B. Vivanco, I. Gonzalez, S. Echenagusia, N. Zabala, et al. 2003. Detection of Salmonella enterica serovar California strain spreading in Spanish feed mills and genetic characterization with DNA microarrays. Appl. Environ. Microbiol. 69:7531-7534.
27. Dennis, P., E.A. Edwards, S.N. Liss, and R. Fulthorpe. 2003. Monitoring gene expression in mixed microbial communities by using DNA microarrays. Appl. Environ. Microbiol. 69:769-778.
28. Gonzalez, S.F., M.J. Krug, M.E. Nielsen, Y. Santos, and D.R. Call. 2004. Simultaneous detection of marine fish pathogens by using multiplex PCR and a DNA microarray. J. Clin. Microbiol. 42:1414-1419.
29. Sebat, J.L., F.S. Colwell, and R.L. Crawford. 2003. Metagenomic profiling: microarray analysis of an environmntal genomic library. Appl. Environ. Microbiol. 69:4927-4934.
30. Vora, G.J., C.E. Meador, D.A. Stenger, and J.D. Andreadis. 2004. Nucleic acid amplification strategies for DNA microarray-based pathogen detection. Appl. Environ. Microbiol. 70:3047-3054.
31. Rondon, M.R., P.R. August, A.D. Bettermann, S.F. Brady, T.H. Grossman, M.R. Lilies, K.A. Loiacono, B.A. Lynch, et al. 2000. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66:2541-2547.
32. Venter, J.C., K. Remington, J.F. Heidelberg, A.L. Halpern, D. Rusch, J.A. Eisen, D. Wu, I. Paulsen, et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74.
33. Nielsen, H.B. and S. Knudsen. 2002. Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays. Bioinformatics 18:321-322.
34. Held, G.A., G. Grinstein, and Y. Tu. 2003. Modeling of DNA microarray data by using physical properties of hybridization. Proc. Natl. Acad. Sci. USA 100:7575-7580.
35. Siegmund, K.H., U.E. Steiner, and C. Richert. 2003. ChipCheck - a program predicting total hybridization equilibria for DNA binding to small oligonucleotide microarrays. J. Chem. Inf. Comput. Sci. 43:2153-2162.
36. Chandler, D.P. and A.E. Jarrell. 2004. Automated purification and suspension array detection of 16S rRNA from soil and sediment extracts using tunable surface microparticles. Appl. Environ. Microbiol. 70:2621-2631.
37. 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.
38. Chandler, D.P., G.J. Newton, J.A. Small, and D.S. Daly. 2003. Sequence vs. structure for the direct detection of 16S rRNA on planar oligonucleotide microarrays. Appl. Environ. Microbiol. 69:2950-2958.
39. Lane, S., J. Evermann, F. Loge, and D.R. Call. 2004. Amplicon secondary structure prevents target hybridization to oligonucleotide microarrays. Biosens. Bioelectron. 20:728-735.
40. Murray, A.E., D. Lies, G. Li, K. Nealson, J. Zhou, and J.M. Tiedje. 2001. DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes. Proc. Natl. Acad. Sci. USA 98:9853-9858.
41. Rajashekara, G., J.D. Glasner, D.A. Glover, and G.A. Splitter. 2004. Comparative whole-genome hybridization reveals genomic islands in Brucella species. J. Bacteriol. 186:5040-5051.
42. Ji, W., W. Zhou, K. Gregg, N. Yu, S. Davis, and S. Davis. 2004. A method for cross-species gene expression analysis with high-density oligonucleotide arrays. Nucleic Acids Res. 32:e93.
43. Brody, E.N., M.C. Willis, J.D. Smith, S. Jayasena, D. Zichi, and L. Gold. 1999. The use of aptamers in large arrays for molecular diagnostics. Mol. Diagn. 4:381-388.
44. Potyrailo, R.A., R.C. Conrad, A.D. Ellington, and G.M. Hieftje. 1998. Adapting selected nucleic acid ligands (aptamers) to biosensors. Anal. Chem. 70:3419-3425.
45. Jayasena, S.D. 1999. Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin. Chem. 45:1628-1650.
46. Bhanot, G., Y. Louzoun, J. Zhu, and C. DeLisi. 2003. The importance of thermodynamic equilibrium for high throughput gene expression arrays. Biophys. J. 84:124-135.
47. Dai, H., M. Meyer, S. Stepaniants, M. Ziman, and R. Stoughton. 2002. Use of hybridization kinetics for differentiating specific from non-specific binding to oligonucleotide microarrays. Nucleic Acids Res. 30:e86.
48. Livshits, M.A. and A.D. Mirzabekov. 1996. Theoretical analysis of the kinetics of DNA hybridization with gel-immobilized oligonucleotides. Biophys. J. 71:2795-2801.
49. Livshits, M.A., V.L. Florentiev, and A.D. Mirzabekov. 1994. Dissociation of duplexes formed by hybridization of DNA with gel-immobilized oligonucleotides. J. Biomol. Struct. Dyn. 11:783-795.
50. Fotin, A.V., A.L. Drobyshev, D.Y. Proudnikov, A.N. Perov, and A.D. Mirzabekov. 1998. Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips. Nucleic Acids Res. 26:1515-1521.
51. 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.
52. 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.
53. Fukushima, H., Y. Tsunomori, and R. Seki. 2003. Duplex real-time SYBR green PCR assays for detection of 17 species of food- or waterborne pathogens in stools. J. Clin. Microbiol. 41:5134-5146.
54. Li, E.S.Y., J.K.K. Ng, J.-H. Wu, and W.-T. Liu. 2004. Evaluating single-base-pair discriminating capability of planar oligonucleotide microchips using a non-equilibrium dissociation approach. Environ. Microbiol. 6:1197-1202.
55. Stomakhin, A.A., V.A. Vasiliskov, E. Timofeev, D. Schulga, R.J. Cotter, and A.D. Mirzabekov. 2000. DNA sequence analysis by hybridization with oligonucleotide microchips: MALDI mass spectrometry identification of 5mers contiguously stacked to microchip oligonucleotides. Nucleic Acids Res. 28:1193-1198.
56. Gupta, V., A. Cherkassky, P. Chatis, R. Joseph, A.L. Johnson, J. Broadbent, T. Erickson, and J. DiMeo. 2003. Directly labeled mRNA produces highly precise and unbiased differential gene expression data. Nucleic Acids Res. 31:e13.
57. Lu, J., C.M. Strohsahl, B.L. Miller, and L.J. Rothberg. 2004. Reflective interferometric detection of label-free oligonucleotides. Anal. Chem. 76:4416-4420.
58. Wang, H., J. Li, H. Liu, Q. Liu, Q. Mei, Y. Wang, J. Zhu, N. He, et al. 2002. Label-free hybridization detection of a single nucleotide mismatch by immobilization of molecular beacons on an agarose film. Nucleic Acids Res. 30:e61.
59. Polz, M.F. and C.M. Cavanaugh. 1998. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64:3724-3730.