Services

Before bringing samples , please fill out the order form ,sample manifesto and E-mail to Hardik Shah, so we can give you an estimate for the services needed. You will have to provide a grant number to be charged for these services, you will not be charged until you receive your data. The order form, sample manifest form, and sample manifest guidelines can be downloaded using the window highlighted to the right of this introduction. Please bring the sample manifest along with the samples. You must review the markings on all tubes/samples so when a bar code is generated for your samples, there will be no confusion. 
  
For the modules listed below, information is organized for your review of the pertinent metabolic pathways. For example in module 1 there are “hyperlinks” in the Pubchem ID and subpathway columns. If you click the hotlink in pubchem, it will take you to pages of information about the metabolite, including structures. If you click on the subpathway hyperlink, you will get taken to the small molecule pathway diagram database, and you can visualize where your metabolite is relative to others in the pathway. Clicking on a metabolite in the figure will take you to the human metabolome database for more specific information about that metabolite. 

Module # 1 180 Metabolites 

The targeted metabolomics approach in this assay is based on measurements with the AbsoluteIDQ p180 kit (BIOCRATES Life Sciences AG, Innsbruck, Austria). This method allows simultaneous quantification of 188 metabolites using liquid chromatography and flow injection analysis–mass spectrometry. For an example of this Module’s utility, see Wang-Sattler et al Novel biomarkers for pre-diabetes identified by metabolomics, Molecular Systems Biology 8; 615; doi:10.1038/msb.2012.43.  

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Module # 2-150 Metabolites

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For an example by the SIMC facility, see Lv et al Advantages of Tandem LC-MS for the Rapid Assessment of Tissue-Specific Metabolic Complexity Using a Pentafluorophenylpropyl Stationary Phase J. Proteome Res. 2011, 10, 2104–2112 |dx.doi.org/10.1021/pr1011119  

 

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Module #4 Redox and Bioenergetics

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Module # 5 Acylcarnitines

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Module #6 Amino acids and Biogenic amines 

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Module # 7  GC/MS small molecule screen by electron impact ionization

GC/MS will identify at least 40 to 50 small metabolites, in the combined glycolytic/gluconeogenic, pentose and TCA cycle pathways. For an example by the SIMC facility, see Vaitheesvaran B, Yang L, Hartil K, Glaser S, Yazulla S, et al. (2012) Peripheral Effects of FAAH Deficiency on Fuel and Energy Homeostasis: Role of Dysregulated Lysine Acetylation. PLoS ONE 7(3): e33717. doi:10.1371/journal.pone.0033717 

Module # 8 Gas Chromatography/Flame Ionization detection for fatty acid profiling

Module #9 Estimates of de novo lipogenesis using deuterated water 

Detailed website information under development

Both fatty acid and cholesterol synthesis can be assessed in tissues, depending on the time frame for the study. 
For examples by the SIMC Facility see Haas et al, Hepatic Insulin Signaling Is Required for Obesity-Dependent Expression of SREBP-1c mRNA but Not for Feeding-Dependent Expression, Cell Metabolism 15, 873–884, 2012; Zhao et al Regulation of lipogenesis by cyclin-dependent kinase 8–mediated control of SREBP-1, J. Clin. Invest. 122:2417-27, 2012; Vaitheesvaran B, Yang L, Hartil K, Glaser S, Yazulla S, et al. (2012) Peripheral Effects of FAAH Deficiency on Fuel and Energy Homeostasis: Role of Dysregulated Lysine Acetylation. PLoS ONE 7(3): e33717 

 

Module #10 Hepatic Recycling Glucose Tolerance Test

Illustrative diagram of pathways for hepatic metabolism of the deuterium-labeled [2-2H1]/[6,6-2H2]glucose. Use of deutrated, instead of unlabeled glucose during a GTT allows for the estimation of hepatic and peripheral glucose disposal. Equal amounts of D1 and D2 glucose ( [2-2H1]- and [6,6-2H2] glucose) are given, at 1 mg glucose/gm body weight. De-deuteration of [2-2H1] glucose occurs during the equilibration of glucose-6-P (G-6-P) with fructose-6-P (F-6-P), which causes plasma D1/D2 levels to decrease. De-deuteration of [6,6-2H1]glucose does not occur until the deuterated glucose reaches the level of pyruvate.  Whole body glucose disposal (mainly peripheral) is reflected in the area under the curve of [6,6-2H2] glucose  during the GTT. Hepatic vs peripheral glucose disposal can be assessed from the differences in plasma [2-2H1]- and [6,6-2H2] glucose during the GTT. This test allows for non-invasive monitoring of peripheral and hepatic glucose disposal, and the mice can be used, after recovery, for additional phenotyping tests.  GK, glucokinase; G6Pase, glucose-6-phosphatase; PK, pyruvate kinase. Diagram from Xu et al Decreased Hepatic Futile Cycling Compensates for Increased Glucose Disposal in the Pten Heterodeficient Mouse, Diabetes 55: 3372-3380, 2006. More examples, done by the SIMC Facility: Vaitheesvaran, LeRoith and Kurland MKR mice have increased dynamic glucose disposal despite metabolic inflexibility, and hepatic and peripheral insulin insensitivity Diabetologia 53:2224–2232, 2010; Vaitheesvaran et al Advantages of dynamic ‘‘closed loop’’ stable isotope flux phenotyping over static ‘‘open loop’’ clamps in detecting silent genetic and dietary phenotypes Metabolomics 6:180–190, 2010; Zong et al Enhanced Energy Expenditure, Glucose Utilization, and Insulin Sensitivity in VAMP8 Null Mice Diabetes. 60: 30–38, 2011