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.
Inan, G., Zhang, Q., Li, P. H., Wang, Z. L., Cao, Z. Y., Zhang, H., Zhang, C. Q., Quist, T. M., Goodwin, S. M., Zhu, J. H., Shi, H. H., Damsz, B., Charbaji, T., Gong, Q. Q., Ma, S. S., Fredricksen, M., Galbraith, D. W., Jenks, M. A., Rhodes, D., , Hasegawa, P. M., et al. (2004). Salt cress. A halophyte and cryophyte Arabidopsis relative model system and its applicability to molecular genetic analyses of growth and development of extremophiles. PLANT PHYSIOLOGY, 135(3), 1718-1737.
Bohnert, H. J., Ayoubi, P., Borchert, C., Bressan, R. A., Burnap, R. L., Cushman, J. C., Cushman, M. A., Deyholos, M., Fischer, R., Galbraith, D. W., Hasegawa, P. M., Jenks, M., Kawasaki, S., Koiwa, H., Kore-eda, S., Lee, B. -., Michalowski, C. B., Misawa, E., Nomura, M., , Ozturk, N., et al. (2001). A genomics approach towards salt stress tolerance. Plant Physiology and Biochemistry, 39(3-4), 295-311.
Abstract:
Abiotic stresses reduce plant productivity. We focus on gene expression analysis following exposure of plants to high salinity, using salt-shock experiments to mimic stresses that affect hydration and ion homeostasis. The approach includes parallel molecular and genetic experimentation. Comparative analysis is employed to identify functional isoforms and genetic orthologs of stress-regulated genes common to cyanobacteria, fungi, algae and higher plants. We analyze global gene expression profiles monitored under salt stress conditions through abundance profiles in several species: in the cyanobacterium Synechocystis PCC6803, in unicellular (Saccharomyces cerevisiae) and multicellular (Aspergillus nidulans) fungi, the eukaryotic alga Dunaliella salina, the halophytic land plant Mesembryanthemum crystallinum, the glycophytic Oryza sativa and the genetic model Arabidopsis thaliana. Expanding the gene count, stress brings about a significant increase of transcripts for which no function is known. Also, we generate insertional mutants that affect stress tolerance in several organisms. More than 400 000 T-DNA tagged lines of A. thaliana have been generated, and lines with altered salt stress responses have been obtained. Integration of these approaches defines stress phenotypes, catalogs of transcripts and a global representation of gene expression induced by salt stress. Determining evolutionary relationships among these genes, mutants and transcription profiles will provide categories and gene clusters, which reveal ubiquitous cellular aspects of salinity tolerance and unique solutions in multicellular species. © 2001 Éditions scientifiques et médicales Elsevier SAS.
Galbraith, D. W., Lambert, G. M., Macas, J., & Dolezel, J. (2001). Analysis of nuclear DNA content and ploidy in higher plants.. Current protocols in cytometry / editorial board, J. Paul Robinson, managing editor ... [et al.], Chapter 7, Unit 7.6.
PMID: 18770733;Abstract:
This is the first of a series of units discussing the application of cytometry to plant material. Techniques commonly used for mammalian nuclei evaluation need considerable modification to be successful with plant material. David Galbraith and his colleagues bring together many years of knowledge in plant cytometry. Their unit provides detailed protocols on measuring DNA content, ploidy, and cell cycle status of plant tissue using both conventional laser based instruments as well as arc lamp cytometers. This unit provides an excellent starting point for those interested in doing cytometry with plants.
