Galbraith, D. W., Herzenberg, L. A., & Anderson, M. T. (1999). Flow cytometric analysis of transgene expression in higher plants: Green fluorescent protein. Methods in Enzymology, 302, 296-315.
Luo, Q., Samanta, M. P., Köksal, F., Janda, J., Galbraith, D. W., Richardson, C. R., Ou-Yang, F., & Rock, C. D. (2009). Evidence for antisense transcription associated with microRNA target mRNAs in arabidopsis. PLoS Genetics, 5(4).
PMID: 19381263;PMCID: PMC2664332;Abstract:
Antisense transcription is a pervasive phenomenon, but its source and functional significance is largely unknown. We took an expression-based approach to explore microRNA (miRNA)-related antisense transcription by computational analyses of published whole-genome tiling microarray transcriptome and deep sequencing small RNA (smRNA) data. Statistical support for greater abundance of antisense transcription signatures and smRNAs was observed for miRNA targets than for paralogous genes with no miRNA cleavage site. Antisense smRNAs were also found associated with MIRNA genes. This suggests that miRNA-associated "transitivity" (production of small interfering RNAs through antisense transcription) is more common than previously reported. High-resolution (3 nt) custom tiling microarray transcriptome analysis was performed with probes 400 bp 5' upstream and 3' downstream of the miRNA cleavage sites (direction relative to the mRNA) for 22 select miRNA target genes. We hybridized RNAs labeled from the smRNA pathway mutants, including hen1-1, dcl1-7, hyl1-2, rdr6-15, and sgs3-14. Results showed that antisense transcripts associated with miRNA targets were mainly elevated in hen1- 1 and sgs3-14 to a lesser extent, and somewhat reduced in dcl11-7, hyl11-2, or rdr6-15 mutants. This was corroborated by semi-quantitative reverse transcription PCR; however, a direct correlation of antisense transcript abundance in MIR164 gene knockouts was not observed. Our overall analysis reveals a more widespread role for miRNA-associated transitivity with implications for functions of antisense transcription in gene regulation. HEN1 and SGS3 may be links for miRNA target entry into different RNA processing pathways. © 2009.
Jay, E., Harkins, K. R., Galbraith, D. W., & Bohnert, H. J. (1990). Developmentally regulated systemic endopolyploidy in succulents with small genomes. Science, 250(4977), 99-101.
Abstract:
Nuclei from Mesembryanthemum crystallinum (ice plant) exhibit multiple levels of ploidy in every tissue as revealed by flow microfluorometric analysis of isolated nuclei stained with mithramycin. Multiples of the haploid nuclear genome complement (1C) corresponding to 2C, 4C, 8C, 16C, 32C, and 64C were observed. The distribution of nuclei among the different ploidy levels is tissue-specific and in leaves is characteristic of the stage of development. This type of genome organization has been identified in eight other succulent CAM (crassulacean acid metabolism) plant species with small genomes. Multiploidy may be a common property of this type of plant.
Miyazaki, S., Fredricksen, M., Hollis, K. C., Poroyko, V., Shepley, D., Galbraith, D. W., Long, S. P., & Bohnert, H. J. (2004). Transcript expression profiles of Arabidopsis thaliana grown under controlled conditions and open-air elevated concentrations of CO 2 and of O 3. Field Crops Research, 90(1), 47-59.
Abstract:
Microarrays have significantly enhanced our ability to track transcripts and changes in gene expression under different conditions and environments. In order to find determinants of plant performance influenced by atmospheric changes, we tracked transcript profiles in Arabidopsis thaliana (L.) Heynh. grown in a field within SoyFACE. This facility (http://www.soyface.uiuc.edu/ index.htm) consists of a series of open-air rings within which either [CO 2] or [O 3] are elevated above current atmospheric concentrations by 1.5× and 1.2×, respectively. A microarray platform including ∼26,000 DNA elements was used to monitor transcript abundance and changes due to exposure to elevated [CO 2] and [O 3]. Transcripts from plants in growth chambers were further compared with material from plants grown in Free Air Concentration Enrichment (FACE) rings under ambient conditions. Most changes in gene expression were observed between growth chamber and ambient field conditions. Two to four times the number of transcripts were either up- or down-regulated between controlled versus field ambient conditions compared with high versus low [CO 2] or [O 3] contrasts. The differences showed a preponderance of regulated transcripts in categories such as chaperones and general defense reactions, altered (secondary) metabolic functions, redox control, energy provision, protein turnover, signaling and transcription. We discuss the results obtained in a model non-crop plant for their possible relevance in studies with crop species. © 2004 Elsevier B.V. All rights reserved.
Deyholos, M. K., & Galbraith, D. W. (2001). High-Density Microarrays for Gene Expression Analysis. Cytometry, 43(4), 229-238.
