This proposal will investigate the global regulation of genes in Arabidopsis as a result of changes in light, carbon, and nitrogen. Computer sciences will aid heavily in this study. """"""""Combinatorial design"""""""" will be used to predict which microarray experiments (out of 64 possible) need to be done to get """"""""good"""""""" coverage of the experimental space. Since this will be the first use of """"""""combinatorial design"""""""" in this manner, the use of """"""""combinatorial design"""""""" itself will be tested. Northern blots of all 64 treatments will be done to determine the regulation of GLN2 and ASN1, two of the main genes involved in nitrogen metabolism. The results of the Northern blots will be compared to the predictions of """"""""combinatorial design"""""""" to determine how successful """"""""combinatorial design"""""""" was. Microarray experiments will then be done on the samples needed to give """"""""good"""""""" coverage of the experimental space. Another computer algorithm will be used to analyze the microarray data to determine genes that are expressed to similar extents by the same treatments, which suggest these genes are co-regulated. The function of the proteins encoded by genes whose expression changes in the treatments will be determined. This part of the study will rely heavily on web based tools, like PSI/PHI BLAST, to determine the function of proteins with unknown functions. Once, the function of the proteins has been determined the affected biochemical pathways will be determined. This information will be used to construct a database that can be queried to determine which biochemical pathways are affected in certain growth conditions.
| Thum, Karen E; Shin, Michael J; Palenchar, Peter M et al. (2004) Genome-wide investigation of light and carbon signaling interactions in Arabidopsis. Genome Biol 5:R10 |
| Palenchar, Peter M; Kouranov, Andrei; Lejay, Laurence V et al. (2004) Genome-wide patterns of carbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen (CN)-signaling hypothesis in plants. Genome Biol 5:R91 |
