Brown, J. K., Lambert, G. M., Ghanim, M., Czosnek, H., & Galbraith, D. W. (2005). Nuclear DNA content of the whitefly Bemisia tabaci (Aleyrodidae: Hemiptera) estimated by flow cytometry. Bulletin of Entomological Research, 95(4), 309-312.
BIO5 Collaborators
Judith K Brown, David W Galbraith
PMID: 16048678;Abstract:
The nuclear DNA content of the whitefly Bemisia tabaci (Gennnadius) was estimated using flow cytometry. Male and female nuclei were stained with propidium iodide and their DNA content was estimated using chicken red blood cells and Arabidopsis thaliana L. (Brassicaceae) as external standards. The estimated nuclear DNA content of male and female B. tabaci was 1.04 and 2.06 pg, respectively. These results corroborated previous reports based on chromosome counting, which showed that B. tabaci males are haploid and females are diploid. Conversion between DNA content and genome size (1 pg DNA = 980 Mbp) indicate that the haploid genome size of B. tabaci is 1020 Mbp, which is approximately five times the size of the genome of the fruitfly Drosophila melanogaster Meigen. These results provide an important baseline that will facilitate genomics-based research for the B. tabaci complex. © CAB International, 2005.
Jiexun, L. i., Xin, L. i., Hua, S. u., Chen, H., & Galbraith, D. W. (2006). A framework of integrating gene relations from heterogeneous data sources: An experiment on Arabidopsis thaliana. Bioinformatics, 22(16), 2037-2043.
BIO5 Collaborators
Hsinchun Chen, David W Galbraith
PMID: 16820427;Abstract:
One of the most important goals of biological investigation is to uncover gene functional relations. In this study we propose a framework for extraction and integration of gene functional relations from diverse biological data sources, including gene expression data, biological literature and genomic sequence information. We introduce a two-layered Bayesian network approach to integrate relations from multiple sources into a genome-wide functional network. An experimental study was conducted on a test-bed of Arabidopsis thaliana. Evaluation of the integrated network demonstrated that relation integration could improve the reliability of relations by combining evidence from different data sources. Domain expert judgments on the gene functional clusters in the network confirmed the validity of our approach for relation integration and network inference. © 2006 Oxford University Press.
Galbraith, D. W. (2007). Analysis of Plant Gene Expression Using Flow Cytometry and Sorting. Flow Cytometry with Plant Cells: Analysis of Genes, Chromosomes and Genomes, 405-422.
Birnbaum, K., Jung, J. W., Wang, J. Y., Lambert, G. M., Hirst, J. A., Galbraith, D. W., & Benfey, P. N. (2005). Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines. Nature Methods, 2(8), 615-619.
PMID: 16170893;Abstract:
To investigate the relationship between developmental events and gene expression, cell-specific resolution of gene activity is critical. Such high-resolution data have been difficult to obtain at a genomic level because cells first need to be isolated, and then sufficient amounts of mRNA must be collected, or subsequently amplified, for a large-scale profiling analysis. Genomics methods have tremendous potential to infer developmental circuits and, in combination with genetic tools, to discover the unknown downstream targets of known developmental regulators. We have developed a method that can be used to isolate up to hundreds of thousands of plant cells of a specific cell type, with very high purity, which can then be used for microarray analysis. The method makes use of reporter lines expressing green fluorescent protein (GFP) in histologically defined cell types, of which large collections are now available (Table 1). The GFP Line of interest is bulked and the tissue is collected and rapidly converted into protoplasts. GFP-positive cells are then isolated using a fluorescence-activated cell sorter (FACS). Total RNA is isolated, labeled using standard procedures and applied to microarrays (Fig. 1). The technique has been used to generate expression profiles of cell types and tissues in the Arabidopsis thaliana root, although it can be used for any tissue whose cell walls can be readily digested. The protocol presented here has been optimized for roots.
Galbraith, D., Gong, F. C., Giddings, T. H., Meehl, J. B., Staehelin, L. A., & Galbraith, D. W. (1996). Z-membranes: artificial organelles for overexpressing recombinant integral membrane proteins. Proceedings of the National Academy of Sciences of the United States of America, 93(5).
We have expressed a fusion protein formed between the avian infectious bronchitis virus M protein and the bacterial enzyme beta-glucuronidase in transgenic tobacco cells. Electron microscope images of such cells demonstrate that overexpression of this fusion protein gives rise to a type of endoplasmic reticulum membrane domain in which adjacent membranes become zippered together apparently as a consequence of the oligomerizing action of beta-glucuronidase. These zippered (Z-) membranes lack markers of the endoplasmic reticulum (NADH cytochrome c reductase and ribosomes) and accumulate in the cells in the form of multilayered scroll-like structures (up to 2 micrometers in diameter; 20-50 per cell) without affecting plant growth. The discovery of Z-membranes has broad implications for biology and biotechnology in that they provide a means for accumulating large quantities of recombinant membrane proteins within discrete domains of native membranes.
