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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Postdoctoral Individual National Research Service Award (F32)
Project #
1F32GM065690-01
Application #
6487643
Study Section
Special Emphasis Panel (ZRG1-F08 (20))
Program Officer
Wolfe, Paul B
Project Start
2002-09-01
Project End
Budget Start
2002-09-01
Budget End
2003-08-31
Support Year
1
Fiscal Year
2002
Total Cost
$36,592
Indirect Cost
Name
New York University
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
004514360
City
New York
State
NY
Country
United States
Zip Code
10012
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