Global Metabolomics and Isotopically-Labeled Metabolomics for Metabolic Flux Analysis
Metabolomics is another key aspect of an integrated systems biology approach to understanding engineered and basal strains under different conditions to enable learning that leads to the next set of Designs for DBTL. Global metabolomics is the derivatization GC-MS analysis of the intracellular metabolome. The extracellular metabolites can be analyzed separately to assess substrate utilization and secretion of target molecules as well as side-products.
13C Metabolic Flux Analysis (MFA) involves the use of 13C labeled substrates and subsequent metabolomics and metabolic modeling analysis discussed in the Modeling and Machine Learning Capability to determine fluxes through pathways.
LC-MS and NMR methods are techniques complementary to our standard GC-MS metabolomics analysis. They are useful for examining large hydrophilic molecules and can be utilized for verification of structures of complex or novel intermediates or target molecules.
There are three GC-MS instruments devoted to metabolomics and one LC-MS. High resolution instruments for isotopically labelled metabolite assignments, enabling 13C-MFA. Multiple NMR instruments of moderate to high fields with diverse probes available.
Preference for this activity is ~50 mg of wet cell weight per sample, quadruplicate biological replicates, and sample sets of 48-60 though twice that number can be accommodated.
References and Additional Information:
MF Romine, DA Rodionov, Y Maezato, LN Anderson, P Nandhikonda, IA Rodionova, A Carre, X Li, C Xu, TRW Clauss, YM Kim, TO Metz, AT Wright. (2017) Elucidation of roles for vitamin B12 in regulation of folate, ubiquinone, and methionine metabolism. PNAS, 114(7): E1205-E1214
AM Snijders, SA Langley, YM Kim, CJ Brislawn, C Noecker, EM Zink, SJ Fansler, CP Casey, DR Miller, Y Huang, GH Karpen, SE Celniker, JB Brown, E Borenstein, JK Jansson, TO Metz, JH Mao (2016) Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome. Nature Microbiology, 2:16221
YM Kim, S Nowack, MT Olsen, ED Becraft, JM Wood, V Thiel, I Klapper, M Kühl, JK Fredrickson, DA Bryant, DM Ward, TO Metz (2015) Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms. Frontiers in Microbiology 6:209
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