Abstract
The recent rapid developments in genomics tools, technologies, and bioinformatics have revolutionized gene expression analysis. It is now routine to measure gene expression modulation at the genomic level. GeneCalling® technology is an open architecture system capable of assaying more than 95% of genes expressed in a tissue. Unlike the closed systems, GeneCalling is not dependent upon an existing sequence or clone database. GeneCalling uses as low as 50 pg of the cDNA from samples and identifies cDNA fragments that are differentially modulated within a set of samples. With the use of 96 pairs of restriction enzymes, more than 30,000 cDNA fragments are routinely assayed to identify those that are differentially modulated. Specific processes, such as SeqCalling™, Trace Poisoning, and GeneCall Poisoning, are set up to not only confirm the known genes, but also to clone and analyze unknown and novel genes that have an interesting expression profile. GeneCalling has been successfully applied to expression profiling of several plant and fungal species, and resulted in identification and characterization of genes that are useful in commercial applications towards improving agriculturally important traits in plants.
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References
Eikhom, T. S., Abraham, K. A., and Dowben, R. M. (1975) Ribosomal RNA metabolism in synchronized plasmacytoma cells. Exp. Cell Res. 91, 301–309.
Green, C. D., Simons, J. F., Taillon, B. E., and Lewin, D. A. (2001) Open systems: panoramic views of gene expression. J. Immunol. Methods 250, 67–79.
Rothberg, J. M., Deem, M. W., and Simpson, J. W. (1999) Method and apparatus for identifying, classifying, or quantifying DNA sequences in a sample without sequencing. U.S.A. Patent 5,871,697.
Bruce, W., Folkerts, O., Gamaat, C., Crasta, O., Roth, B., and Bowen, B. (2000) Expression profiling of the maize flavonoid pathway genes controlled by estradiol-inducible transcription factors CRC and P. Plant Cell 12, 65–80.
Mysore, K., Crasta, O. R., Tuori, R. P., Folkerts, O., Swirsky, P. B., and Martin, G. B. (2002) Comprehensive transcript profiling of Pto-and Prf-mediated host defense responses to infection by Pseudomonas syringae pv. tomato. Plant J. 32, 299–315.
Duvick, J., Gilliam, J., Maddox, J., Crasta, O., and Folkerts, O. (2001) Amino polyol amine oxidase polynucleotides and related polypeptides and methods of use. U.S.A. Patent 6,211,435.
Duvick, J., Maddox, J., Gilliam, J., Folkerts, O., and Crasta, O. R. (2002) Compositions and methods for fumonisin detoxification. U.S.A. Patent 6,388,171.
Garnaat, C., Crasta, O., Li, Y., et al. (2000) An auxin inducible promoter for conditional complementation of male-sterile maize. Poster presented at the symposium, “Frontiers in Sexual Plant Reproduction.” October 28–29, 2000, University at Albany, SUNY, Albany, NY.
Duvick, J., Simmons, C., Crasta, O., and Folkerts, O. (2002) Use of beta-glucosidase to enhance disease resistance and resistance to insects in crop plants. U.S.A. Patent 6,433,249.
Bruce, W., Desbons, P., Crasta, O., and Folkerts, O. (2001) Gene expression profiling of two related maize inbred lines with contrasting root-lodging traits. J. Exp. Bot. 52, 459–468.
Kollipara, K., Saab, I. N., Wych, R. D., Lauer, M. J., and Singletary, G. W. (2002) Expression profiling of reciprocal maize hybrids divergent for cold germination and desiccation. Plant Physiol. 129, 974–992.
Simmons, C. R., Grant, S., Altier, D. J., et al. (2001) Maize rhm1 resistance to Bipolaris maydis is associated with few differences in pathogenesis-related proteins and global mRNA profiles. Mol. Plant-Microbe Inter. 14, 947–954.
Shimkets, R. A., Lowe, D. G., Tai, J. T., et al. (1999) Gene expression analysis by transcript profiling coupled to a gene database query. Nat. Biotechnol. 17, 798–803.
Bader, J., Gold, S., Gusev, U., et al. (2002) Method of analyzing a nucleic acid. U.S.A. Patent Application 20020015951.
Gould-Rothberg, B., Ramesh, T. M., and Burgess, C. E. (2000) Integrating expression-based drug response and SNP-based pharmacogenetic strategies into a single comprehensive pharmacogenomics program. Drug Dev. Res. 49, 54–64.
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© 2003 Humana Press Inc., Totowa, NJ
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Crasta, O.R., Folkerts, O. (2003). Open Architecture Expression Profiling of Plant Transcriptomes and Gene Discovery Using GeneCalling® Technology. In: Grotewold, E. (eds) Plant Functional Genomics. Methods in Molecular Biology™, vol 236. Humana Press. https://doi.org/10.1385/1-59259-413-1:381
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DOI: https://doi.org/10.1385/1-59259-413-1:381
Publisher Name: Humana Press
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