Current Laboratory Members
USDA: Microarray-based QTL Mapping in
NSF: Self-Assembling Autofluorescent
SFAz: Center for
Chemical Genomics and Translational research.
NSF: Plant Functional Genomics Methods
Analysis of Cell Type-Specific Gene Expression
Conference on Genomics & Bioinformatics (2002)
Microarray Short Course (2006)
Scholarly Societies and Journals
International Society for Advancement of
American Society of Plant Biologists
Cytometry Part A
Microarray Workshop. Tucson, Arizona, January 3-8, 2010.
31st Annual Course in Flow
Cytometry, Bowdoin College, June 14-20, 2008
in Cell Biology & Genomics: PLS539
College of Agriculture and Life Sciences
School of Plant Sciences
Library (Web of Science; E-Journals)
Recommendations for Scientists
Tucson Weather, Panorama,
Music and other Fun Stuff
Tucson Chamber Artists
Tucson Symphony Orchestra
of the Bard Part I, Part II
How did I
get into this situation?
Joined at the Hippo
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.
of these instruments, associated technologies, and products are available
as Research Services on a cost-recovery basis.
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
work supported by USDA (Microarray-based QTL Mapping in
directed at the development of a high-throughput, low-cost platform for
genotyping this important crop. For this purpose, we 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 .
Work supported by the NSF-PGRP (Self-Assembling Autofluorescent
Protein Microarrays) aimed 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 have
optimized methods for protein production, and for detection of their
interactions with other cellular components.
A final recently-completed
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
I teach Plant Biochemistry: PLS448, Methods in Cell Biology &
Genomics: PLS539, and am associated with a NSF-funded IGERT in Genomics.
I organize in Tucson an Annual five-day Workshop on
Microarrays. The next in the series is scheduled in January, 2011. Contact
me for more details.
1. 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.
2. 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.
3. Zanetti ME, Chang I-F, Gong FC,
Galbraith DW, Bailey-Serres J (2005).
Immunopurification of polyribosomal complexes of arabidopsis for
global analysis of gene expression. Plant Physiology 138:624-635.
4. 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
5. Zhang CQ, Lambert GM, Barthelson RA,
Galbraith DW (2008). Characterization of cell-specific gene expression
through fluorescence-activated sorting of nuclei. Plant Physiology
A., Zanetti, M.E., Jang, C.J.H., Galbraith, D.W., Girke,
T., and Bailey-Serres, J. (2009). Profiling translatomes of discrete cell
populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proceedings of the
National Academy of Sciences U.S.A. 106:18849-18854.
Questions and comments should be addressed to: David