참고문헌
- Ye, R. W., T. Wang, L. Bedzyk, and K. M. Croker (2001) Applications of DNA microarrays in microbial systems. J. Microbiol. Meth. 47: 257-272 https://doi.org/10.1016/S0167-7012(01)00308-6
- Conway, T. and G. K. Schoolnik (2003) Microarray expression profiling: capturing a genome-wide portrait of the transcriptome. Mol. Microbiol. 47: 879-889 https://doi.org/10.1046/j.1365-2958.2003.03338.x
- Rhodius, V. A. and R. A. LaRossa (2003) Uses and pitfalls of microarrays for studying transcriptional regulation. Curr. Opin. Microbiol. 6: 114-119 https://doi.org/10.1016/S1369-5274(03)00034-1
- Dharmadi, Y. and R. Gonzalez (2004) DNA microarrays: experimental issues, data analysis, and application to bacterial systems. Biotechnol. Progr. 20: 1309-1324 https://doi.org/10.1021/bp0400240
- Jones, D. T. and D. R. Woods (1986) Acetone-butanol fermentation revisited. Microbiol. Rev. 50: 484-524
- Tomas, C. A., K. V. Alsaker, H. P. J. Bonarius, W. T. Hendriksen, H. Yang, J. A. Beamish, C. J. Parades, and E. T. Papoutsakis (2003) DNA-array based transcriptional analysis of asporogenous, non-solventogenic Clostridium acetobutylicum strains SKO1 and M5. J. Bacteriol. 185: 4539-4547 https://doi.org/10.1128/JB.185.15.4539-4547.2003
- Alsaker, K. V., T. R. Spitzer, and E. T. Papoutsakis (2004) Transcriptional analysis of spo0A overexpression in Clostridium acetobutylicum and its effect on the cell's response to butanol stress. J. Bacteriol. 186: 1959-1971 https://doi.org/10.1128/JB.186.7.1959-1971.2004
- Tomas, C. A., N. E. Welker, and E. T. Papoutsakis (2003) Overexpression of groESL in Clostridium acetobutylicum results in increased solvent production and tolerance, prolonged metabolism, and large changes in the cell's transcriptional program. Appl. Environ. Microbiol. 69: 4951-4965 https://doi.org/10.1128/AEM.69.8.4951-4965.2003
- Tummala, S. B., S. G. Junne, C. J. Paredes, and E. T. Papoutsakis (2003) Transcriptional analysis of product-concentration driven changes in cellular programs of recombinant Clostridium acetobutylicum strains. Biotechnol. Bioeng. 84: 842-854 https://doi.org/10.1002/bit.10851
- Tomas, C. A., J. A. Beamish, and E. T. Papoutsakis (2004) Transcriptional analysis of butanol stress and tolerance in Clostridium acetobutylicum. J. Bacteriol. 186: 2006-2018 https://doi.org/10.1128/JB.186.7.2006-2018.2004
- Hegde, P., R. Qi, K. Abernathy, C. Gay, S. Dharap, R. Gaspard, J. E. Hughes, E. Snesrud, N. Lee, and J. Quackenbush (2000) A concise guide to cDNA microarray analysis. Biotechniques 29: 548-562
- Yang, H., H. Haddad, C. Tomas, K. Alsaker, and E. T. Papoutsakis (2003) A segmental nearest neighbor normalization and gene identification method gives superior results for DNA-array analysis. P. Natl. Acad. Sci. USA 100: 1122-1127 https://doi.org/10.1073/pnas.0237337100
- Xu, D., G. S. Li, L. Y. Wu, J. Z. Zhou, and Y. Xu (2002) PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis. Bioinformatics 18: 1432-1437 https://doi.org/10.1093/bioinformatics/18.11.1432
- Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman (1990) Basic Local Alignment Search Tool. J. Mol. Biol. 215: 403-410
- Rozen, S. and H. Skaletsky (2000) Primer3 on the WWW for general users and for biologist programmers. pp 365-386. In: S. Krawetz, S. Misener, (eds.). Methods in Molecular Biology. Humana Press, Totowa, NJ
- Richmond, C. S., J. D. Glasner, R. Mau, H. F. Jin, and F. R. Blattner (1999) Genome-wide expression profiling in Escherichia coli K-12. Nucleic Acids Res. 27: 3821-3835 https://doi.org/10.1093/nar/27.19.3821
- Raghavachari, N., Y. P. Bao, G. S. Li, X. Y. Xie, and U. R. Müller (2003) Reduction of autofluorescence on DNA microarrays and slide surfaces by treatment with sodium borohydride. Anal. Biochem. 312: 101-105 https://doi.org/10.1016/S0003-2697(02)00440-2
- Eisen, M. B., P. T. Spellman, P. O. Brown, and D. Botstein (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA. 95: 14863-14868 https://doi.org/10.1073/pnas.95.25.14863
- Clark, S. W., G. N. Bennett, and F. B. Rudolph (1989) Isolation and characterization of mutants of Clostridium acetobutylicum ATCC 824 deficient in acetoacetyl-coenzyme A:acetate/butyrate:coenzyme A transferase (EC 2.8.3.9) and in other solvent pathway enzymes. Appl. Environ. Microbiol. 55: 970-976
- Wiesenborn, D. P., F. B. Rudolph, and E. T. Papoutsakis (1988) Thiolase from Clostridium acetobutylicum ATCC 824 and its role in the synthesis of acids and solvents. Appl. Environ. Microbiol. 54: 2717-2722
- Tummala, S. B., N. E. Welker, and E. T. Papoutsakis (2003) Design of antisense RNA constructs for downregulation of the acetone formation pathway of Clostridium acetobutylicum. J. Bacteriol. 185: 1923-1934 https://doi.org/10.1128/JB.185.6.1923-1934.2003
- Buday, Z., J. C. Linden, and M. N. Karim (1990) Improved acetone butanol fermentation analysis using subambient HPLC column temperature. Enzyme Microb. Tech. 12: 24-27 https://doi.org/10.1016/0141-0229(90)90175-P
- Wei, Y., J. M. Lee, C. Richmond, F. R. Blattner, J. A. Rafalski, and R. A. LaRossa (2001) High-density microarray-mediated gene expression profiling of Escherichia coli. J. Bacteriol. 183: 545-556 https://doi.org/10.1128/JB.183.2.545-556.2001
- Schena, M., D. Shalon, R. Heller, A. Chai, P. O. Brown, and R. W. Davis (1996) Parallel human genome analysis: microarray-based expression monitoring of 1,000 genes. Proc. Natl. Acad. Sci. USA 93: 10614-10619 https://doi.org/10.1073/pnas.93.20.10614
- Chhabra, S. R., K. R. Shockley, S. B. Conners, K. L. Scott, R. D. Wolfinger, and R. M. Kelly (2003) Carbohydrateinduced differential gene expression patterns in the hyperthermophilic bacterium Thermotoga maritima. J. Biol.Chem. 278: 7540-7552 https://doi.org/10.1074/jbc.M211748200
- Worley, J., K. Bechtol, S. Penn, D. Roach, D. Hanzel, M. Trounstine, and D. Barker (2000) A systems approach to fabricating and analyzing DNA microarrays. In: M. Schena, editor. Microarray Biochip Technology. Eaton Publishing, Natick, MA, USA
- Yuen, P. K., G. Li, Y. Bao, and U. R. Muller (2003) Microfluidic devices for fluidic circulation and mixing improve hybridization signal intensity on DNA arrays. Lab Chip 3: 46-50 https://doi.org/10.1039/b210274a
- Adey, N. B., M. Lei, M. T. Howard, J. D. Jensen, D. A. Mayo, D. L. Butel, S. C. Coffin, T. C. Moyer, D. E. Slade, M. K. Spute, A. M. Hancock, G. T. Eisenhoffer, B. K. Dalley, and M. R. McNeely (2002) Gains in sensitivity with a device that mixes microarray hybridization solution in a 25-micron-thick chamber. Anal. Chem. 74: 6413-6417 https://doi.org/10.1021/ac026082m
- Gadgil, C., A. Yeckel, J. J. Derby, and W. S. Hu (2004) A diffusion-reaction model for DNA microarray assays. J. Biotechnol. 114: 31-45 https://doi.org/10.1016/j.jbiotec.2004.05.008
- Borden, J. R., C. J. Paredes, and E. T. Papoutsakis (2005) Diffusion, mixing, and associated dye effects in DNAmicroarray hybridizations. Biophys. J. In press
- ;olling, J., G. Breton, M. V. Omelchenko, K. S. Makarova, Q. Zeng, R. Gibson, H. M. Lee, J. Dubois, D. Qiu, J. Hitti, Y. Wolf, R. L. Tatusov, F. Sabathe, L. Doucette-Stamm, P. Soucaille, M. J. Daly, G. N. Bennett, E. V. Koonin, and D. R. Smith (2001) Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J. Bacteriol. 183: 4823-4838 https://doi.org/10.1128/JB.183.16.4823-4838.2001
- Cornillot, E., R. V. Nair, E. T. Papoutsakis, and P. Soucaille (1997) The genes for butanol and acetone formation in Clostridium acetobutylicum ATCC 824 reside on a large plasmid whose loss leads to degeneration of the strain. J. Bacteriol. 179: 5442-5447 https://doi.org/10.1128/jb.179.17.5442-5447.1997
- Stim-Herndon, K. P., R. Nair, E. T. Papoutsakis, and G. N. Bennett (1996) Analysis of degenerate variants of Clostridium acetobutylicum ATCC 824. Anaerobe 2: 11-18 https://doi.org/10.1006/anae.1996.0002
- Tseng, G. C., M. K. Oh, L. Rohlin, J. C. Liao, and W. H. Wong (2001) Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res. 29: 2549-2557 https://doi.org/10.1093/nar/29.12.2549
- Harris, L. M., N. E. Welker, and E. T. Papoutsakis (2002) Northern, morphological, and fermentation analysis of spo0A inactivation and overexpression in Clostridium acetobutylicum ATCC 824. J. Bacteriol. 184: 3586-3597 https://doi.org/10.1128/JB.184.13.3586-3597.2002
- Strauch, M. A., G. B. Spiegelman, M. Perego, W. C. Johnson, D. Burbulys, and J. A. Hoch (1989) The transition state transcription regulator abrB of Bacillus subtilis is a DNA-binding protein. EMBO J. 8: 1615-1621
- Strauch, M., V. Webb, G. Spiegelman, and J. A. Hoch (1990) The Spo0A protein of Bacillus subtilis is a repressor of the abrB gene. Proc. Natl. Acad. Sci. USA 87: 1801-1805
- Molle, V., M. Fujita, S. T. Jensen, P. Eichenberger, J. E. Gonzalez-Pastor, J. S. Liu, and R. Losick (2003) The Spo0A regulon of Bacillus subtilis. Mol. Microbiol. 50: 1683-1701 https://doi.org/10.1046/j.1365-2958.2003.03818.x
- Scotcher, M. C., F. B. Rudolph, and G. N. Bennett (2005) Expression of abrB310 and sinR, and effects of decreased abrB310 expression on the transition from acidogenesis to solventogenesis, in Clostridium acetobutylicum ATCC 824. Appl. Environ. Microbiol. 71: 1987-1995 https://doi.org/10.1128/AEM.71.4.1987-1995.2005
- Ravagnani, A., K. C. Jennert, E. Steiner, R. Grunberg, J. R. Jefferies, S. R. Wilkinson, D. I. Young, E. C. Tidswell, D. P. Brown, P. Youngman, J. G. Morris, and M. Young (2000) Spo0A directly controls the switch from acid to solvent production in solvent-forming clostridia. Mol. Microbiol. 37: 1172-1185 https://doi.org/10.1046/j.1365-2958.2000.02071.x
- Helmann, J. D. and C. P. Moran Jr (2002) RNA polymerase and sigma factors. pp 289-312. In: A. L. Sonenshein, J. A. Hoch, R. Losick, (eds.). Bacillus subtilis and Its Closest Relatives: From Genes to Cells. ASM Press, Washington, D.C., USA
- Schaffer, S., N. Isci, B. Zickner, and P. Durre (2002) Changes in protein synthesis and identification of proteins specifically induced during solventogenesis in Clostridium acetobutylicum. Electrophoresis 23: 110-121 https://doi.org/10.1002/1522-2683(200201)23:1<110::AID-ELPS110>3.0.CO;2-G
- Eymann, C., A. Dreisbach, D. Albrecht, J. Bernhardt, D. Becher, S. Gentner, L. T. Tam, K. Büttner, G. Buurman, C. Scharf, S. Venz, U. Völker, and M. Hecker (2004) A comprehensive proteome map of growing Bacillus subtilis cells. Proteomics 4: 2849-2876 https://doi.org/10.1002/pmic.200400907
- Kanehisa, M., S. Goto, S. Kawashima, Y. Okuno, and M. Hattori (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res. 32: D277-D280 https://doi.org/10.1093/nar/gkh063