A. James Clark School of Engineering
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The collections in this community comprise faculty research works, as well as graduate theses and dissertations.
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Item High-Throughput Time Series Metabolomic Analysis of a Systematically Perturbed Plant System(2007-04-27) Kanani, Harin H; Klapa, Maria I; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In the post-genomic era, availability of high-throughput profiling techniques enabled the measurement of entire cellular molecular fingerprints. Major characteristics of the high-throughput revolution were that (a) studying biological problems did not have to rely on prior hypotheses, while (b) parallel occurring phenomena, previously assumed disconnected, could now be simultaneously observed. Metabolomics is the newest of the "omics" techniques. It enables the quantification of hundreds of free metabolite pools, providing a metabolic fingerprint. Considering the importance of cellular metabolism, which is the net effect of changes at the genomic, transcriptomic and proteomic levels and of the cell with its environment, the metabolomic profile, is a fundamental determinant of cellular physiology. Obtaining accurate and complete metabolomic profiles is thus of great importance. However, being recent technology, metabolomics is currently at its standardization phase. As part of my PhD thesis research, I focused on addressing several current challenges in metabolomics technology development. Specifically a novel data correction, validation and normalization strategy for gas chromatography-mass spectrometry (GC-MS) metabolomic profiling analysis was developed, which dramatically increased the accuracy and reliability of GC-MS metabolomic profiles. The optimized metabolomics protocol was applied to study the short-term dynamic response of systematically perturbed Arabidopsis thaliana liquid culture system to study regulation of its primary metabolism. The biological system was studied under conditions of elevated CO2 stress, salt (NaCl) stress, sugar (trehalose) signal, and hormone (ethylene) signal, applied individually; the latter three stresses also applied in combination with the CO2 stress. Analysis of the obtained results required the appropriate application of multivariate statistical analysis techniques, which are developed mainly in transcriptomic analysis, into metabolomics analysis for the first time. The acquired results identified important new regulatory information about the biological systems resulting in new targets for metabolic engineering of plants. The large number of dynamic perturbation allowed re-construction of metabolic networks to identify possible novel metabolic pathways based on correlations between metabolic profiles. In addition, it demonstrates the advantages of dynamic, multiple-stress "omic" analysis for the elucidation of plant systems function. In this sense, it contributes in further advancing the computational and experimental metabolic engineering and systems biology toolbox.Item TIME SERIES METABOLIC PROFILING ANALYSIS OF THE SHORT TERM Arabidopsis thaliana RESPONSE TO ELEVATED CO2 USING GAS CHROMATOGRAPHY MASS SPECTROMETRY.(2004-08-30) Kanani, Harin Haridas; Klapa, Maria I; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Metabolic profiling has emerged as a high throughput technique for the quantitative analysis of the cellular physiological state at the metabolic level. It allows for the simultaneous relative quantification of hundreds of low molecular weight intra cellular metabolites. In this analysis, the polar metabolic profiles of A. thaliana liquid cultures (grown for 12 days, under light and 23°C) throughout 1-day treatment with 1% CO2, were measured using gas chromatography-mass spectrometry. Despite the advantages of time series analysis, this is the first plant metabolic profiling study of this type reported in the literature. The time series metabolic profiles were analyzed using multivariate statistical techniques. Data analysis revealed repression of photorespiration, repression of nitrogen assimilation and increase in structural carbohydrates. It is for the first time that the latter phenomenon is observed as a result of elevated CO2 in the plant environment.Item TIME SERIES TRANSCRIPTIONAL PROFILING ANALYSIS OF THE Arabidopsis thaliana USING FULL GENOME DNA MICROARRAY AND METABOLIC INFORMATION(2004-08-26) Dutta, Bhaskar; Klapa, Maria I; Quackenbush, John; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)With the advent of the DNA microarray technology, it became possible to study the expression of entire cellular genomes. Tanscriptional profiling alone can not provide a comprehensive picture of the cellular physiological state and it should be complemented by other cellular fingerprints. Transcriptional profiling combined with metabolic information of a systematically perturbed system can unravel the relationship between gene and metabolic regulation. In this context the transcriptional response of Arabidopsis thaliana liquid cultures (grown for 12 days under light and 23 sup oC) to 1-day treatment with 1% CO sub 2 was measured by full genome cDNA microarrays. The Time series gene expression profiles were analyzed in the context of the known Arabidopsis thaliana physiology using multivariate statistics. Data analysis revealed an increase in the rate of CO sub 2 fixation, biomass production and cell wall growth. The breadth of the information obtained from a single experiment validated the significance of the high throughput transcriptional profiling.