Systems Biology - Methods - Metabolomics
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Projects by Edward and Peter :
The microorganism Desulfovibrio vulgaris Hildenborough (D. vulgaris), because of its metabolic versatility, its ability to remediate heavy metals and radionuclides, is of particular interest to the DOE. However, the effective implementation of remediation strategies and the use of natural attenuation for the cleanup of heavy metal waste in DOE sites is dependent upon understanding critical chemical, physical, and biological processes. Thus, an understanding of regulatory mechanisms and cellular responses to different environmental factors affecting the metal remediation activity, in situ, is of great importance. One approach to study such mechanisms within D. vulgaris is to quantify all metabolites within the organism at a given point in time (metabolomics).
Since the metabolome is further down the line from gene function, it can reflect more closely the activities of a cell at the functional level than the transcript and the proteome. We are currently utilizing novel capillary electrophoretic separations with mid-to-high resolution mass spectrometry (CE-TOFMS and CE-FTICRMS) to bring us closer to the goal of metabolomics within D. vulgaris. This approach has proven successful in identifying metabolites from most classes of compound, including amino acids, coenzyme As, nucleosides, nucleotides and organic acids. The use of GC-MS will also enable us to address the neutral fraction of the metabolite pool.
Project by David
Pathway engineering and optimization in microbes has necessarily grown to include bioanalytical chemistry. The so-called 'omic techniques (e.g., genomics) provide direct information about the genotype, however all useful pathway engineering is performed to create new phenotypes. Most of the 'omic techniques can hint at what might be happening at the metabolic level--which is a microbe's phenotype--so a direct assay of the metabolome would be beneficial. Metabolomics in microbes is a relatively new and underdeveloped 'omic technique that we are improving and using to address strain optimization from a phenotype-orientated approach.
Project by Sandra
The goals of this project are to develop new and utilize existing methods to quantify and identify metabolites in Shewanella oneidensis MR-1 and to develop strategies to perturb metabolite levels in order to study the influences of metabolism on cellular function.
