{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000383","ANALYSIS_ID":"AN000618","VERSION":"1","CREATED_ON":"April 22, 2016, 9:58 am"},

"PROJECT":{"PROJECT_TITLE":"Plasma Metabolomic Profiles Reflective of Glucose Homeostasis in Non-Diabetic and Type 2 Diabetic Obese African-American Women","PROJECT_SUMMARY":"Insulin resistance progressing to type 2 diabetes mellitus (T2DM) is marked by a broad perturbation of macronutrient intermediary metabolism. Understanding the biochemical networks that underlie metabolic homeostasis and how they associate with insulin action will help unravel diabetes etiology and should foster discovery of new biomarkers of disease risk and severity. We examined differences in plasma concentrations of >350 metabolites in fasted obese T2DM vs. obese non-diabetic African-American women, and utilized principal components analysis to identify 158 metabolite components that strongly correlated with fasting HbA1c over a broad range of the latter (r?=??0.631; p<0.0001). In addition to many unidentified small molecules, specific metabolites that were increased significantly in T2DM subjects included certain amino acids and their derivatives (i.e., leucine, 2-ketoisocaproate, valine, cystine, histidine), 2-hydroxybutanoate, long-chain fatty acids, and carbohydrate derivatives. Leucine and valine concentrations rose with increasing HbA1c, and significantly correlated with plasma acetylcarnitine concentrations. It is hypothesized that this reflects a close link between abnormalities in glucose homeostasis, amino acid catabolism, and efficiency of fuel combustion in the tricarboxylic acid (TCA) cycle. It is speculated that a mechanism for potential TCA cycle inefficiency concurrent with insulin resistance is “anaplerotic stress” emanating from reduced amino acid-derived carbon flux to TCA cycle intermediates, which if coupled to perturbation in cataplerosis would lead to net reduction in TCA cycle capacity relative to fuel delivery.","INSTITUTE":"University of California, Davis","DEPARTMENT":"Genome and Biomedical Sciences Facility","LABORATORY":"WCMC Metabolomics Core","LAST_NAME":"Fiehn","FIRST_NAME":"Oliver","ADDRESS":"1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616","EMAIL":"ofiehn@ucdavis.edu","PHONE":"(530) 754-8258","FUNDING_SOURCE":"NIH U24DK097154","PUBLICATIONS":"Plasma Metabolomic Profiles Reflective of Glucose Homeostasis in Non-Diabetic and Type 2 Diabetic Obese African-American Women"},

"STUDY":{"STUDY_TITLE":"Plasma Metabolomic Profiles Reflective of Glucose Homeostasis in Non-Diabetic and Type 2 Diabetic Obese African-American Women","STUDY_SUMMARY":"Insulin resistance progressing to type 2 diabetes mellitus (T2DM) is marked by a broad perturbation of macronutrient intermediary metabolism. Understanding the biochemical networks that underlie metabolic homeostasis and how they associate with insulin action will help unravel diabetes etiology and should foster discovery of new biomarkers of disease risk and severity. We examined differences in plasma concentrations of >350 metabolites in fasted obese T2DM vs. obese non-diabetic African-American women, and utilized principal components analysis to identify 158 metabolite components that strongly correlated with fasting HbA1c over a broad range of the latter (r?=??0.631; p<0.0001). In addition to many unidentified small molecules, specific metabolites that were increased significantly in T2DM subjects included certain amino acids and their derivatives (i.e., leucine, 2-ketoisocaproate, valine, cystine, histidine), 2-hydroxybutanoate, long-chain fatty acids, and carbohydrate derivatives. Leucine and valine concentrations rose with increasing HbA1c, and significantly correlated with plasma acetylcarnitine concentrations. It is hypothesized that this reflects a close link between abnormalities in glucose homeostasis, amino acid catabolism, and efficiency of fuel combustion in the tricarboxylic acid (TCA) cycle. It is speculated that a mechanism for potential TCA cycle inefficiency concurrent with insulin resistance is “anaplerotic stress” emanating from reduced amino acid-derived carbon flux to TCA cycle intermediates, which if coupled to perturbation in cataplerosis would lead to net reduction in TCA cycle capacity relative to fuel delivery.","INSTITUTE":"University of California, Davis","DEPARTMENT":"Genome and Biomedical Sciences Facility","LABORATORY":"WCMC Metabolomics Core","LAST_NAME":"Fiehn","FIRST_NAME":"Oliver","ADDRESS":"1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616","EMAIL":"ofiehn@ucdavis.edu","PHONE":"(530) 754-8258","STUDY_COMMENTS":"G/g and g/a are polymorphisms in the promoter region of the UCP3 gene that leads to the gene being enhanced and an increased chance of obesity in those with this polymorphism.","PUBLICATIONS":"Plasma Metabolomic Profiles Reflective of Glucose Homeostasis in Non-Diabetic and Type 2 Diabetic Obese African-American Women"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","GENOTYPE_STRAIN":"g/g vs. g/a","AGE_OR_AGE_RANGE":"19.3 - 87.1","HUMAN_RACE":"African American","HUMAN_ETHNICITY":"African American"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"889378",
"Sample ID":"090309bsesa82_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889382",
"Sample ID":"090309bsesa108_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889386",
"Sample ID":"090309bsesa83_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889390",
"Sample ID":"090309bsesa85_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889394",
"Sample ID":"090309bsesa70_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889398",
"Sample ID":"090309bsesa86_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889403",
"Sample ID":"090309bsesa68_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889407",
"Sample ID":"090309bsesa110_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889411",
"Sample ID":"090309bsesa66_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889415",
"Sample ID":"090309bsesa89_2",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889419",
"Sample ID":"090309bsesa69_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889423",
"Sample ID":"090309bsesa109_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889428",
"Sample ID":"090309bsesa105_1",
"Factors":{"Health Status":"non-diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889432",
"Sample ID":"090309bsesa107_1",
"Factors":{"Health Status":"non-diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889436",
"Sample ID":"090309bsesa111_1",
"Factors":{"Health Status":"non-diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889440",
"Sample ID":"090309bsesa71_1",
"Factors":{"Health Status":"non-diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889444",
"Sample ID":"090309bsesa57_1",
"Factors":{"Health Status":"non-diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889448",
"Sample ID":"090309bsesa81_1",
"Factors":{"Health Status":"non-diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889453",
"Sample ID":"090309bsesa74_1",
"Factors":{"Health Status":"non-diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889457",
"Sample ID":"090309bsesa91_1",
"Factors":{"Health Status":"non-diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889461",
"Sample ID":"090309bsesa103_1",
"Factors":{"Health Status":"non-diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889465",
"Sample ID":"090309bsesa76_1",
"Factors":{"Health Status":"non-diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889469",
"Sample ID":"090309bsesa93_2",
"Factors":{"Health Status":"non-diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889473",
"Sample ID":"090309bsesa102_1",
"Factors":{"Health Status":"non-diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889478",
"Sample ID":"090309bsesa72_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889482",
"Sample ID":"090309bsesa112_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889486",
"Sample ID":"090309bsesa97_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889490",
"Sample ID":"090309bsesa73_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889494",
"Sample ID":"090309bsesa90_2",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889498",
"Sample ID":"090309bsesa63_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889502",
"Sample ID":"090309bsesa94_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889506",
"Sample ID":"090309bsesa87_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889510",
"Sample ID":"090309bsesa62_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889514",
"Sample ID":"090309bsesa79_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889518",
"Sample ID":"090309bsesa80_2",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889522",
"Sample ID":"090309bsesa58_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889526",
"Sample ID":"090309bsesa104_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889530",
"Sample ID":"090309bsesa101_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889534",
"Sample ID":"090309bsesa64_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889538",
"Sample ID":"090309bsesa84_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/g"}
},
{
"Subject ID":"889542",
"Sample ID":"090309bsesa65_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889546",
"Sample ID":"090309bsesa77_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889550",
"Sample ID":"090309bsesa60_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889554",
"Sample ID":"090309bsesa96_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889558",
"Sample ID":"090309bsesa99_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889562",
"Sample ID":"090309bsesa106_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889566",
"Sample ID":"090309bsesa59_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889570",
"Sample ID":"090309bsesa67_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889574",
"Sample ID":"090309bsesa95_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889578",
"Sample ID":"090309bsesa100_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889582",
"Sample ID":"090309bsesa61_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889586",
"Sample ID":"090309bsesa88_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889590",
"Sample ID":"090309bsesa98_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889594",
"Sample ID":"090309bsesa75_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889598",
"Sample ID":"090309bsesa92_2",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
},
{
"Subject ID":"889602",
"Sample ID":"090309bsesa78_1",
"Factors":{"Health Status":"diabetic","UCP-3 Polymorphism":"g/a"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Blood was collected by arm venipuncture between ?08:00–09:00 into EDTA-treated collection tubes after an overnight fast (no food or drink since 20:00 the night before). Plasma was frozen at ?20°C for 1–7 days before transport to ?80°C freezers for longer-term storage.","COLLECTION_PROTOCOL_FILENAME":"Plasma_Metabolomic_Profiles_of_Type_2_Diabetic_Obese_Women.pdf","SAMPLE_TYPE":"Blood","COLLECTION_METHOD":"Venipuncture","BLOOD_SERUM_OR_PLASMA":"Plasma"},

"TREATMENT":{"TREATMENT_SUMMARY":"Volunteers were asked to avoid unusual activity and intentional exercise in the 3 days leading up to the study, and were instructed to continue to eat their habitual diet without unusual deviations. Patients with T2DM did not take doses of oral agents on the evening before and on the morning of study. Patients treated with insulin could take regular or rapid acting insulin at dinner the night before the study but were instructed to withhold any intermediate- or long-acting insulin on the evening before, and to avoid insulin injections on the morning of the study.","TREATMENT_PROTOCOL_FILENAME":"Plasma_Metabolomic_Profiles_of_Type_2_Diabetic_Obese_Women.pdf","HUMAN_FASTING":"12-13 hours"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"1. Switch on bath to pre-cool at –20°C (±2°C validity temperature range) 2. Gently rotate or aspirate the blood samples for about 10s to obtain a homogenised sample. 3. Aliquot 30?l of plasma sample to a 1.0 mL extraction solution. The extraction solution has to be prechilled using the ThermoElectron Neslab RTE 740 cooling bath set to -20°C. 4. Vortex the sample for about 10s and shake for 5 min at 4°C using the Orbital Mixing Chilling/Heating Plate. If you are using more than one sample, keep the rest of the sample on ice (chilled at <0°C with sodium chloride). 5. Centrifuge samples for 2min at 14000 rcf using the centrifuge Eppendorf 5415 D. 6. Aliquot two 450?L portions of the supernatant. One for analysis and one for a backup sample. Store the backup aliquot in -20°C freezer. 7. Evaporate one 450?L aliquots of the sample in the Labconco Centrivap cold trap concentrator to complete dryness. 8. The dried aliquot is then re-suspended with 450 ?L 50% acetonitrile (degassed as given above). 9. Centrifuged for 2 min at 14000 rcf using the centrifuge Eppendorf 5415. 10. Remove supernatant to a new Eppendorf tube. 11. Evaporate the supernatant to dryness in the Labconco Centrivap cold trap concentrator. 12. Submit to derivatization.","SAMPLEPREP_PROTOCOL_FILENAME":"PR_SP_SOP_blood-GCTOF-11082012.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 6890N","COLUMN_NAME":"Restek Corporation Rtx-5Sil MS","FLOW_RATE":"1 ml/min","COLUMN_TEMPERATURE":"50-330C","METHODS_FILENAME":"GCTOF_MS_primary_metabolism_10-15-2013_general.pdf","COLUMN_PRESSURE":"7.7 PSI","INJECTION_TEMPERATURE":"50 C ramped to 2580 C by 12C/s","SAMPLE_INJECTION":"0.5 uL","OVEN_TEMPERATURE":"50°C for 1 min, then ramped at 20°C/min to 330°C, held constant for 5 min","TRANSFERLINE_TEMPERATURE":"230C","WASHING_BUFFER":"Ethyl Acetate","SAMPLE_LOOP_SIZE":"30 m length x 0.25 mm internal diameter","RANDOMIZATION_ORDER":"Excel generated"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Leco Pegasus IV TOF","INSTRUMENT_TYPE":"GC-TOF","MS_TYPE":"EI","ION_MODE":"POSITIVE","ION_SOURCE_TEMPERATURE":"250 C","IONIZATION_ENERGY":"70 eV","MASS_ACCURACY":"Nominal","SOURCE_TEMPERATURE":"250 C","SCAN_RANGE_MOVERZ":"85-500 Da","SCANNING_CYCLE":"17 Hz","SCANNING_RANGE":"85-500 Da","SKIMMER_VOLTAGE":"1850 V"},

"MS_METABOLITE_DATA":{
"Units":"counts",

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