Poster: Education

Abs # 15: Undergraduate student involvement in bioinformatics: genetic analysis of T-DNA insertional mutant plants as an education tool

Presenter:	Mercier, Richard W, rmercier@canr.cag.uconn.edu
Authors	Mercier, Richard W (A)   Kastal, Edit  (A)   Sutyak, Katia E. (A)   Maclean, Ian  (A)   Berkowitz, Gerald A. (A)
Affiliations:	(A): University of Connecticut

Whole-genome sequencing and advancements in the generation of 'knockouts' in single target genes have recently augmented the power of genetics as a tool for understanding the molecular basis of organism function. The sequencing of the Arabidopsis genome, and the public availability of T-DNA knockout plants provide researchers with powerful tools to associate specific gene products with a myriad of cell and organism functions. The NSF-funded Salk Institute Genomic Analysis Laboratory (SIGnAL) collection of T-DNA Arabidopsis lines provides powerful research tools for study of gene function. In addition, accessing and using this public resource can provide an opportunity for undergraduate students to embrace the power of bioinformatics as a learning tool. Using the SALK website, our team has been examining T-DNA insertion knockout mutants corresponding to 14 of 20 cyclic nucleotide-gated channels (CNGCs). This information was analyzed using bioinformatic tools available through NCBI, Munich Information for Protein Sequences, TAIR, and PlantsP. Utilizing a PCR strategy in tandem with Southern blots the various mutant lines are being characterized. In all cases a single insertional tag, homozygous for the gene of interest, must be identified and/or generated. Despite the vast technological capabilities available and in use, the importance of human involvement in the screening process remains paramount. The genome map, and the putative site of the insertional tag in mutant lines at present can have errors; as a result, the computational results must be reexamined, and molecular biology conducted manually. This will be discussed. A comprehensive gene profile for plant CNGCs is being assembled using the aforementioned bioinformatic tools. Supported by NSF award 0090675.