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Research Outline :
Functional Characterization of Wavelet Events in the Arabidopsis Genome The structure and evolution of plant genomes can be studied in detail following the published availability of high-quality and comprehensive genome sequences for the model species Arabidopsis thaliana and, more recently, the model crop species Oryza sativa (Rice). Strategies have been developed for the numerical representation of genome sequence data in, which allows for the analysis of sequence patterning using numerical signal processing algorithms such as Wavelet Analysis. We have applied these strategies to Arabidopsis to identify Wavelet events that define perturbations in sequence pattern in the genome as a matter of evolutionary interest. We are also pursuing functional studies of Wavelet events via the identification of lines of Arabidopsis that are variant for select wavelet events – with special emphasis on events that lie outside known or predicted genes or other transcript units and their associated cis-regulatory regions.
Molecular Function of ASK Proteins in the Regulation of Plant Development The model plant Arabidopsis thaliana is a powerful system for the genetic investigation of plant patterning and development. Recently, a number of plant growth and developmental response pathways including auxin signalling, pathogen response, florigenesis and maintenance of circadian rhythm have been found to be regulated by genes encoding components of the SCF complexes in this organism. SCF complexes, as E3 ubiquitin ligases, direct the post-translational ubiquitination and degradation of target proteins. The Arabidopsis genome contains an unusually large number of genes that encode known or predicted subunits of SCF. Among these are an estimated 21 independent genes (ASK genes) that encode Skp1-like subunits in this species. We and others have provided evidence that ASK proteins in Arabidopsis may be functionally specialized, since certain of the subunits exhibit selective protein:protein interactions with other components of SCF complexes, as revealed by yeast 2-hybrid approaches. We are characterizing loss-of-function alleles of members of the ASK gene family, both alone and in combination, for their affect on Arabidopsis morphology and development. In the long term, we seek to understand the functional contribution of individual members of this protein family, and to understand in molecular terms their role the unique adaptive strategy inherent to plants.
Development of Whole-Genome Mutational Resources in Arabidopsis The power of reverse genetics in plant model systems like Arabidopsis has been fully realized with the advent of large insertion-mutagenesis populations such as the Salk/NRC, Syngenta and GABI T-DNA mutant collections. Together, these resources tag about 80% of known or predicted genes in Arabidopsis. Notwithstanding the number of independent insertions involved in the unified T-DNA insertion collection (about 150,000 lines), there is gathering evidence that a significant subset of these are less than fully genetically penetrant as evidenced by the absence of discernible phenotypes. In some cases, evidence of genetic redundancy has provided a ready explanation for the lack of phenotype for select insertions, where in other cases the evidence points to partial inactivation of gene expression or gene product function. Overall, about 30% of known and predicted genes likely exhibit partial inactivation phenotypes across the consolidated Arabidopsis collection. We are developing a complimentary resource based on plant lines subjected to fast-neutron (FN) irradiation, where chromosomal deletions are the dominant lesion We anticipate the FN resource to present a complimentary source of genetic variation that will likely expand the availability of true null mutations in select genes.
Currently the lab has two main research themes:
1- Functional Analysis of SKP1 orthologs in Arabidopsis:
2-Castor as a Next-Generation Crop for the Biorenewable Chemical and Energy Sectors: