My research program is housed within the BIO5 Institute at the University of Arizona. It focuses on four areas: Biological Instrumentation, Plant Gene Expression, Plant Functional Genomics, and Chemical Genomics and Translational Research. Work in my laboratory is supported by NSF, USDA, the International Rice Research Institute, and Science Foundation Arizona.
Our work in Biological Instrumentation incorporates flow cytometry and cell sorting, DNA and protein microarrays, Fluorescent Protein expression and targeting, and the development of novel high throughput assay platforms. Major research equipment in the laboratory includes a Beckman-Coulter MoFlo Flow Cytometer/Cell Sorter, a BioRad 1024MP Confocal/Multiphoton Microscope, Omnigrid OG100 and OG300 microarray printers, a Genetix QarrayMax printer, MDS Genepix 4100B and 4200AL microarray scanners, a Tecan hybridization station, and an Omix ArrayPlate Scanner and associated Zephyr and BioMek robotics.
Many of these instruments, associated technologies, and products are available as Research Services on a cost-recovery basis.
Work supported by USDA (Microarray-based QTL Mapping in Rice) is directed at the development of a high-throughput, low-cost platform for genotyping this important crop. For this purpose, we have employed insertion-deletion (Indel) sequences existing between the indica and japonica subspecies as the source of information for designing microarray elements. We have developed low-cost methods for fluorescent labeling of source genomic DNAs taken from parental lines, their hybrids, and subsequent back-cross and recombinant inbred lines . We are employing this platform, in combination with rice expression microarrays, to characterize eQLSs.
Work supported by the NSF-PGRP (Self-Assembling Autofluorescent Protein Microarrays) aims to develop a high throughput platform for characterizing protein interactions. This is based on in situ printing of microarray elements comprising a mixture of recombinant DNA constructions, encoding chimeric protein-GFP fusions, and an anti-GFP antibody. Proteins are produced from the DNA elements via cell-free transcription-translation, and are subsequently captured on the array surface by the antibodies. We are optimizing methods for protein production, and for detection of their interactions with other cellular components.
The SFAz-supported Center for Chemical Genomics and Translational Research is a novel partnership between the University of Arizona and High Throughput Genomics, a company located in Tucson. CGTR activities are based on a novel quantitative Nuclease Protection Assay (qNPA) for transcript levels. This microarray-based assay is more sensitive and has a greater dynamic range than competing platforms . It is particularly suited for screening large chemical libraries and for discovery of transcript signatures that are diagnostic of developmental and disease states.
One recently-completed project, entitled “Technology Development: Novel techniques for discovery of patterns of gene regulation within complex eukaryotic tissues”, developed new methods for the analysis of gene expression within minor subsets of specific cell-types within complex tissues [3-6].
We print and distribute microarrays produced by mechanical deposition of 70-mer single-stranded DNA elements. These are available to the academic and non-profit communities on a cost-recovery basis. Species include arabidopsis, maize, rice, tomato, pig, and bovine. We also provide hybridization services associated with these arrays, as well as a workshop offered yearly.
I teach Methods in Cell Biology & Genomics: PLS539 and am associated with a NSF-funded IGERT in Genomics.
I teach an Annual five-day Workshop on Microarrays. The next in the series will be offered from January 4-9, 2009.
- Edwards JD, Sweeney M, Janda J, Gaikwad A, Liu B, Leung H, Galbraith DW (2008). Development of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays, and its evaluation in rice. Plant Methods 2008, 4:13.
- Kris RM, Felder S, Deyholos M, Lambert GM, Botros I, Martel R, Seligmann B, Galbraith DW (2007). High-throughput, high-sensitivity analysis of gene expression in Arabidopsis thaliana. Plant Physiology 144: 1256-1266.
- Galbraith DW (2003). Global analysis of cell type-specific gene expression. Comparative and Functional Genomics 4:208-215.
- Zanetti ME, Chang I-F, Gong FC, Galbraith
- Zhang CQ, Gong FC, Lambert GM, Galbraith DW (2005). Cell type-specific characterization of nuclear DNA contents within complex tissues and organs. Plant Methods 1:7 doi:10.1186/1746-4811-1-7.
- Zhang CQ, Lambert GM, Barthelson RA, Galbraith DW (2008). Characterization of cell-specific gene expression through fluorescence-activated sorting of nuclei. Plant Physiology 147:30-40.