A. James Clark School of Engineering

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Author: search.filters.author.Dutta, Bhaskar

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    Individual vs. combinatorial effect of elevated CO2 conditions and salinity stress on Arabidopsis thaliana liquid cultures: Comparing the early molecular response using time-series transcriptomic and metabolomic analyses
    (2010-12-29) Kanani, Harin; Dutta, Bhaskar; Klapa, Maria I
    Background: In this study, we investigated the individual and combinatorial effect of elevated CO2 conditions and salinity stress on the dynamics of both the transcriptional and metabolic physiology of Arabidopsis thaliana liquid hydroponic cultures over the first 30 hours of continuous treatment. Both perturbations are of particular interest in plant and agro-biotechnological applications. Moreover, within the timeframe of this experiment, they are expected to affect plant growth to opposite directions. Thus, a major objective was to investigate whether this expected “divergence” was valid for the individual perturbations and to study how it is manifested under the combined stress at two molecular levels of cellular function, using high-throughput analyses. Results: We observed that a) high salinity has stronger effect than elevated CO2 at both the transcriptional and metabolic levels, b) the transcriptional responses to the salinity and combined stresses exhibit strong similarity, implying a robust transcriptional machinery acting to the salinity stress independent of the co-occurrence of elevated CO2 , c) the combinatorial effect of the two perturbations on the metabolic physiology is milder than of the salinity stress alone. Metabolomic analysis suggested that the beneficial role of elevated CO2 on salt-stressed plants within the timeframe of this study should be attributed to the provided additional resources; these allow the plants to respond to high salinity without having to forfeit other major metabolic functions, and d) 9 h-12 h and 24 h of treatment coincide with significant changes in the metabolic physiology under any of the investigated stresses. Significant differences between the acute and longer term responses were observed at both molecular levels. Conclusions: This study contributes large-scale dynamic omic data from two levels of cellular function for a plant system under various stresses. It provides an additional example of the power of integrated omic analyses for the comprehensive study of the molecular physiology of complex biological systems. Moreover, taking into consideration the particular interest of the two investigated perturbations in plant biotechnology, enhanced understanding of the molecular physiology of the plants under these conditions could lead to the design of novel metabolic engineering strategies to increase the resistance of commercial crops to salinity stress.
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    Time-Series Transcriptomic Analysis of a Systematically Perturbed Arabidopsis thaliana Liquid Culture System: A Systems Biology Perspective
    (2007-05-16) Dutta, Bhaskar; Klapa, Maria I; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Revealing the gene regulation network has been one of the main objectives of biological research. Studying such a complex, multi-scale and multi-parametric problem requires educated fingerprinting of cellular physiology at different molecular levels under systematically designed perturbations. Conventional biology lacked the means for holistic analysis of biological systems. In the post-genomic era, advances in robotics and biology lead to the development of high-throughput molecular fingerprinting technologies. Transcriptional profiling analysis using DNA microarrays has been the most widely used among them. My Ph.D. thesis concerns the dynamic, transcriptional profiling analysis of a systematically perturbed plant system. Specifically, Arabidopsis thaliana liquid cultures were subjected to three different stresses, i.e. elevated CO2 stress, salt (NaCl) stress and sugar (trehalose) applied individually, while the latter two stresses were also applied in combination with the CO2 stress. The transcriptional profiling of these conditions involved carrying out 320 microarray hybridizations, generating thus a vast amount of transcriptomic data for Arabidopsis thaliana liquid culture system. To upgrade the dynamic information content in the data, I developed a statistical analysis strategy that enables at each time point of a time-series the identification of genes whose expression changes in statistically significant amount due to the applied stress. Additional algorithms allow for further exploration of the dynamic significance analysis results to extract biologically relevant conclusions. All algorithms have been incorporated in a software suite called MiTimeS, written in C++. MiTimeS can be applied accordingly to analyze time-series data from any other high-throughput molecular fingerprint. The experimental design combined with existing multivariate statistical analysis techniques and MiTimeS revealed a wealth of biologically relevant dynamic information that had been unobserved before. Due to the high-throughput nature of the analysis, the study enabled the simultaneous identification and correlation of parallel-occurring phenomena induced by the applied stress. Stress responses comparisons indicated that transcriptional response of the biological system to combined stresses is usually not the cumulative effect of individual responses. In addition to the significance of the study for the analysis of the particular plant system, the experimental and analytical strategies used provide a systems biology methodological framework for any biological system, in general.
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    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.