Abstract The application of metabolomics to human and animal model systems is poised to provide great insight into our understanding of disease etiology and the metabolic changes that are associated with these conditions. However, metabolomic studies have also revealed that there is significant, inherent biological variation in human samples and even in samples from animal model systems where the animals are housed under carefully controlled conditions. This inherent biological variability is an important consideration for all metabolomics analyses. In this study, we examined the biological variation in 1H NMR-based metabolic profiling of two model systems, the yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans. Using relative standard deviations (RSD) as a measure of variability, our results reveal that both model systems have significant amounts of biological variation. The C. elegans metabolome possesses greater metabolic variance with average RSD values of 29 and 39%, depending on the food source that was used. The S. cerevisiae exometabolome RSD values ranged from 8% to 12% for the four strains examined. We also determined whether biological variation occurs between pairs of phenotypically identical yeast strains. Multivariate statistical analysis allowed us to discriminate between pair members based on their metabolic phenotypes. Our results highlight the variability of the metabolome that exists even for less complex model systems cultured under defined conditions. We also highlight the efficacy of metabolic profiling for defining these subtle metabolic alterations.
Content Type Journal Article
Pages 1-10
DOI 10.1007/s10858-011-9492-6
Authors
Samuel S. W. Szeto, Department of Biochemistry, School of Molecular and Systems Medicine, University of Alberta, Edmonton, AB T6G 2H7, Canada
Stacey N. Reinke, Department of Biochemistry, School of Molecular and Systems Medicine, University of Alberta, Edmonton, AB T6G 2H7, Canada
Bernard D. Lemire, Department of Biochemistry, School of Molecular and Systems Medicine, University of Alberta, Edmonton, AB T6G 2H7, Canada
Mutations in the Saccharomyces cerevisiae succinate dehydrogenase result in distinct metabolic phenotypes revealed through (1)H NMR-based metabolic footprinting.
Mutations in the Saccharomyces cerevisiae succinate dehydrogenase result in distinct metabolic phenotypes revealed through (1)H NMR-based metabolic footprinting.
Mutations in the Saccharomyces cerevisiae succinate dehydrogenase result in distinct metabolic phenotypes revealed through (1)H NMR-based metabolic footprinting.
J Proteome Res. 2010 Dec 3;9(12):6729-39
Authors: Szeto SS, Reinke SN, Sykes BD, Lemire BD
Metabolomics is a powerful method of examining the intricate connections between mutations, metabolism, and disease. Metabolic...
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Metabolic profiling of cadmium-induced effects in one pioneer intertidal halophyte Suaeda salsa by NMR-based metabolomics.
Metabolic profiling of cadmium-induced effects in one pioneer intertidal halophyte Suaeda salsa by NMR-based metabolomics.
Metabolic profiling of cadmium-induced effects in one pioneer intertidal halophyte Suaeda salsa by NMR-based metabolomics.
Ecotoxicology. 2011 May 15;
Authors: Liu X, Yang C, Zhang L, Li L, Liu S, Yu J, You L, Zhou D, Xia C, Zhao J, Wu H
Cadmium is a non-essential element to living organisms and has become the severe contaminant in both seawater and sediment in the intertidal zones of the Bohai Sea. The halophyte, Suaeda salsa...
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05-17-2011 06:21 PM
Metabolic profiling of vitamin C deficiency in Guloâ??/â?? mice using proton NMR spectroscopy
Metabolic profiling of vitamin C deficiency in Guloâ??/â?? mice using proton NMR spectroscopy
Abstract Nutrient deficiencies are an ongoing problem in many populations and ascorbic acid is a key vitamin whose mild or acute absence leads to a number of conditions including the famously debilitating scurvy. As such, the biochemical effects of ascorbate deficiency merit ongoing scrutiny, and the Gulo knockout mouse provides a useful model for the metabolomic examination of vitamin C deficiency. Like humans, these animals are incapable of synthesizing ascorbic acid but with dietary...
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In Vivo NMR Metabolic Profiling of Fabrea salina Reveals Sequential Defense Mechanisms against Ultraviolet Radiation.
In Vivo NMR Metabolic Profiling of Fabrea salina Reveals Sequential Defense Mechanisms against Ultraviolet Radiation.
In Vivo NMR Metabolic Profiling of Fabrea salina Reveals Sequential Defense Mechanisms against Ultraviolet Radiation.
Biophys J. 2011 Jan 5;100(1):215-24
Authors: Marangoni R, Paris D, Melck D, Fulgentini L, Colombetti G, Motta A
Fabrea salina is a hypersaline ciliate that is known to be among the strongest ultraviolet (UV)-resistant microorganisms; however, the molecular mechanisms of this resistance are almost unknown. By means...
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12-31-2010 07:03 PM
NMR Metabolomic Profiling Reveals New Roles of SUMOylation in DNA Damage Response.
NMR Metabolomic Profiling Reveals New Roles of SUMOylation in DNA Damage Response.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles NMR Metabolomic Profiling Reveals New Roles of SUMOylation in DNA Damage Response.
J Proteome Res. 2010 Aug 9;
Authors: Cano KE, Li YJ, Chen Y
Post-translational modifications by the Small Ubiquitin-like Modifier (SUMO) family of proteins have been established as critical events in the cellular response to a wide range of DNA damaging reagents and radiation;...
CSA variation: how reliable model-free dynamics is
The following paper shows, in particular, how site-specific variations of 15N chemical shift anisotropy (CSA) can cause under- and overestimation of protein mobility that is inferred from the order parameter of model-free analysis.
Limited variations in 15N CSA magnitudes and orientations in ubiquitin are revealed by joint analysis of longitudinal and transverse NMR relaxation.
Damberg P, Jarvet J, Graslund A.
Department of Biochemistry and Biophysics, Stockholm University, Svante Arrheniusv.12, S-106 91 Stockholm, Sweden.
J Am Chem Soc. 2005 Feb 16;127(6):1995-2005.
1H NMR-based metabolic profiling reveals inherent biological variation in yeast and nematode model systems
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