My program focuses on three main areas: Biological Instrumentation, Developmental Plant Gene Expression, and Plant Functional Genomics. My research support is from NSF, and my research instrumentation has been purchased via support from NSF, DOD, and DOE.  I am P.I. on one project funded by the NSF Initiative in Plant Genomics.  Entitled Technology Development: Novel techniques for discovery of patterns of gene regulation within complex eukaryotic tissues, this project seeks to develop new methods for the analysis of gene expression within minor subsets of specific cell types within complex tissues.  It is a collaboration with Julia Bailey-Serres at U.C. Davis, and employs many of the flow sorting techniques outlined below.

This I am also a co-investigator on an additional grant from the NSF Initiative in Plant Genomics, entitled Maize Gene Discovery, Sequencing, and Phenotypic Analysis, which is designed to provide scientific resources to the research community, in the form of EST sequences, insertional mutants, and genomic information. I was also a co-investigator on another, completed, project funded by the same NSF Initiative , entitled Genomics of Plant Stress Tolerance. This aimed to characterize those plant genes that are responsive to abiotic stress, particularly osmotic and salt stress.  My role in the latter two projects centers around the twin techniques of  microarray analysis and functional genomics.  

Our research interests in the area of bioinstrumentation center around the technologies of flow cytometry and cell sorting as applied to higher plant cell systems. We are involved in developing new types of flow cytometric instrumentation, based on digital signal processing, which enable extraction of novel types of optical information from biological cells.  We are also developing intelligent systems, based on neural networks, for the classification of different cell types from flow cytometric data.

In terms of the analysis of plant gene expression and of functional genomics, we are developing flow sorting methods for the general identification of genes expressed within specific cell types, particularly during development and as a function of the cell division cycle. We have been focusing on the expression in plants of a novel reporter gene, encoding the Green-Fluorescent Protein of the jellyfish Aequorea victoria (photograph courtesy John Blinks; please seek permission to use this image from him, not me!  Also, note this image does not illustrate the fluorescence emission of GFP -- for a complete discussion of Aequorea taxonomy and fluorescence imaging in vivo, follow this link).

In combination with the targeting of GFP to the nucleus, we have devised a novel method for the analysis of cell type-specific gene expression.  Termed "NEST" (Nuclear Expressed Sequence Tag) analysis,  this method is based on the characterization of the spectrum of transcripts found within individual flow sorted nuclei.  NEST analysis is rapid, convenient, and accurate, and can be applied to any eukaryotic species that has transcriptionally active nuclei.  For this work, we employ a Cytomation MoFlo Flow Cytometer/Cell Sorter, a Partec PAII Flow Cytometer, and a BioRad 1024MP Confocal/Multiphoton Microscope.

Our further interests in the area of functional genomics include development of methods for massively parallel analysis of transcription.  Our involvement in this area started with the development of cheap hardware and software modifications to the Biomek Laboratory Automation Workstation (Beckman Instruments) for microarray production.  We now print microarrays containing up to 30,000 DNA elements (cDNAs, ESTs, or synthesized oligonucleotides) spaced at 160 micron intervals on coated glass slides, using Omnigrid Arrayers from Genemachines/Genomic Solutions.  

We are employing microarrays in a variety of different projects, including the analysis of cell type-specific gene expression in plants and, in collaboration with the UA College of Medicine, also in animal tissues and organs.  Other projects involving microarrays include the analysis of plant stress responses, and the characterization of the cytochrome P450 gene superfamily of Arabidopsis.

In the area of research training, I am involved in a NSF-funded IGERT in Functional Genomics. Further details of this program can be found by following that link.