Lee, T., Kim, Y., Thi, T., Song, S. I., Kim, J., Kang, K. Y., Gynheung, A. n., Jung, K., Galbraith, D. W., Kim, M., Yoon, U., & Nahm, B. H. (2009). RiceArrayNet: A database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice. Plant Physiology, 151(1), 16-33.
PMID: 19605550;PMCID: PMC2735985;Abstract:
Microarray data can be used to derive understanding of the relationships between the genes involved in various biological systems of an organism, given the availability of databases of gene expression measurements from the complete spectrum of experimental conditions and materials. However, there have been no reports, to date, of such a database being constructed for rice (Oryza sativa). Here, we describe the construction of such a database, called RiceArrayNet (RAN; http://www.ggbio.com/arraynet/), which provides information on coexpression between genes in terms of correlation coefficients (γ values). The average number of coexpressed genes is 214, with SD of 440 at γ ≥ 0.5. Given the correlation between genes in a gene pair, the degrees of closeness between genes can be visualized in a relational tree and a relational network. The distribution of correlated genes according to degree of stringency shows how each gene is related to other genes. As an application of RAN, the 16-member L7Ae ribosomal protein family was explored for coexpressed genes and gene expression values within and between rice and Arabidopsis (Arabidopsis thaliana), and common and unique features in coexpression partners and expression patterns were observed for these family members. We observed a correlation pattern between Os01g0968800, a drought-responsive element-binding transcription factor, Os02g0790500, a trehalose-6-phosphate synthase, and Os06g0219500, a small heat shock factor, reflecting the fact that genes responding to the same biological stresses are regulated together. The RAN database can be used as a tool to gain insight into a particular gene by examining its coexpression partners. © 2009 American Society of Plant Biologists.
Baisakh, N., Ramana, R. M., Rajasekaran, K., Subudhi, P., Janda, J., Galbraith, D., Vanier, C., & Pereira, A. (2012). Enhanced salt stress tolerance of rice plants expressing a vacuolar H+-ATPase subunit c1 (SaVHAc1) gene from the halophyte grass Spartina alterniflora. Plant Biotechnology Journal, 10, 453-464.
Zanetti, M. E., Chang, I., Gong, F., Galbraith, D. W., & Bailey-Serres, J. (2005). Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression. Plant Physiology, 138(2), 624-635.
PMID: 15955926;PMCID: PMC1150383;Abstract:
Immunoaffinity purification of polyribosomes (polysomes) from crude leaf extracts of Arabidopsis (Arabidopsis thaliana) was achieved with transgenic genotypes that overexpress a translational fusion of a ribosomal protein (RP) with a His6-FLAG dual epitope tag. In plants with a cauliflower mosaic virus 35S:HF-RPL18 transgene immunopurification with anti-FLAG agarose beads yielded 60-Svedberg ribosomal subunits, intact 80-Svedberg monosomes and polysomes. Sucrose density gradient fractionation of the purified complexes demonstrated that the distribution of polysome size was similar in crude cell extracts and the purified complexes. The immunopurified complexes included putative cytosolic KPs of Arabidopsis and ribosome-associated proteins, as well as full-length transcripts of high and low abundance. Whole-genome profiling using long DNA oligonucleotide-based microarrays provided a high level of reproducibility between polysomal mRNA samples immunopurified from two independent biological replicates (r approximately 0.90). Comparison of immunopurified and total cellular RNA samples revealed that for most of the genes, the mRNAs were associated with the epitope-tagged polysomal complexes, with an average relative level of association of 62.06% + 4.39%. The results demonstrate that the immunopurification of polysomes can be a valuable tool for the quantification of mRNAs present in translation complexes in plant cells. This technology can be extended to evaluation of mRNA populations at the cell- or tissue-specific level by regulation of the tagged RP with distinct promoters. © 2005 American Society of Plant Biologists.
Sheen, J., Hwang, S., Niwa, Y., Kobayashi, H., & Galbraith, D. W. (1995). Green-fluorescent protein as a new vital marker in plant cells. Plant Journal, 8(5), 777-784.
PMID: 8528289;Abstract:
The green-fluorescent protein (GFP) from jellyfish Aequorea victoria has been used as a convenient new vital marker in various heterologous systems. However, it has been problematic to express GFP in higher eukaryotes, especially in higher plants. This paper reports that either a strong constitutive or a heat-shock promoter can direct the expression of GFP which is easily detectable in maize mesophyll protoplasts. In this single-cell system, bright green fluorescence emitted from GFP is visible when excited with UV or blue light even in the presence of blue fluorescence from the vacuole or the red chlorophyll autofluorescence from chloroplasts using a fluorescence microscope. No exogenous substrate, co-factor, or other gene product is required. GFP is very stable in plant cells and shows little photobleaching. Viable cells can be obtained after fluorescence-activated cell sorting based on GFP. The paper further reports that GFP can be detected in intact tissues after delivering the constructs into Arabidopsis leaf and root by microprojectile bombardment. The successful detection of GFP in plant cells relies on the use of a universal transcription enhancer from maize or the translation enhancer from tobacco mosaic virus (TMV) to boost the expression. This new reporter could be used to monitor gene expression, signal transduction, co-transfection, transformation, protein trafficking and localization, protein-protein interaction, cell separation and purification, and cell lineage in higher plants.
Nicolini, A. M., Toth, T. D., Kim, S. Y., Mandel, M. A., Galbraith, D. W., & Yoon, J. (2017). Mie scatter and interfacial tension based real-time quantification of colloidal emulsion nucleic acid amplification. Advanced Biosystems, 1(10), 1700098. doi:10.1002/adbi.201700098
This work demonstrates for the first time rapid, real-time Mie scatter sensing of colloidal emulsion nucleic acid amplification directly from emulsion droplets. Loop-mediated isothermal amplification is used in this study, and, to our knowledge, has not previously been used in a colloidal emulsion platform. Interfacial tension values (γ) associated with bulk protein adsorption and denaturation at the oil–water interface exhibit characteristic changes in the absence or presence of amplification. In the presence of target and amplicon, emulsions maintain a constant 300–400 nm diameter, whereas emulsions formed with no target control show a rapid decrease in droplet diameter to 100 nm over the first 20 min of incubation. This method is validated using whole bacteria (Staphylococcus aureus MSSA and Escherichia coli O157:H7) and whole virus (Potato virus Y and Zika virus) samples suspended in water, buffer, or serum-like matrices. Short-term formation of colloidal emulsion is quantified via 60° scatter monitoring, where the initial slope of scattering intensity is utilized to confirm target amplification in less than 5 min. The unique benefits of this method render it more cost-effective and field-deployable than existing methods, while being adaptable to a multitude of targets, sample matrices, and nucleic acid amplification tests.
