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References

The Course Faculty compiled the following list of references that may be useful when learning about isotope tracers in metabolic research.

Mass spectrometry

Antoniewicz MR, Kelleher JK, Stephanopoulos G. Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. Metab Eng. 2007;9(1):68-86. Epub 2006/11/08. doi: 10.1016/j.ymben.2006.09.001. PubMed PMID: 17088092; PMCID: PMC1994654.

Shah V, Herath K, Previs SF, Hubbard BK, Roddy TP. Headspace analyses of acetone: a rapid method for measuring the 2H-labeling of water. Anal Biochem. 2010;404(2):235-7. Epub 2010/05/22. doi: 10.1016/j.ab.2010.05.010. PubMed PMID: 20488158.

NMR

Merritt ME, Harrison C, Storey C, Jeffrey FM, Sherry AD, Malloy CR. Hyperpolarized 13C allows a direct measure of flux through a single enzyme-catalyzed step by NMR. Proc Natl Acad Sci U S A. 2007;104(50):19773-7. Epub 2007/12/07. doi: 10.1073/pnas.0706235104. PubMed PMID: 18056642; PMCID: PMC2148374.

Sherry AD, Malloy CR, Zhao P, Thompson JR. Alterations in substrate utilization in the reperfused myocardium: a direct analysis by 13C NMR. Biochemistry. 1992;31(20):4833-7. Epub 1992/05/26. doi: 10.1021/bi00135a014. PubMed PMID: 1350466.

Jin ES, Jones JG, Burgess SC, Merritt ME, Sherry AD, Malloy CR. Comparison of [3,4-13C2]glucose to [6,6-2H2]glucose as a tracer for glucose turnover by nuclear magnetic resonance. Magn Reson Med. 2005;53(6):1479-83. Epub 2005/05/21. doi: 10.1002/mrm.20496. PubMed PMID: 15906303.

Merritt M, Bretthorst GL, Burgess SC, Sherry AD, Malloy CR. Sources of plasma glucose by automated Bayesian analysis of 2H NMR spectra. Magn Reson Med. 2003;50(4):659-63. Epub 2003/10/03. doi: 10.1002/mrm.10577. PubMed PMID: 14523948.

Jones JG, Solomon MA, Cole SM, Sherry AD, Malloy CR. An integrated (2)H and (13)C NMR study of gluconeogenesis and TCA cycle flux in humans. Am J Physiol Endocrinol Metab. 2001;281(4):E848-56. Epub 2001/09/12. doi: 10.1152/ajpendo.2001.281.4.E848. PubMed PMID: 11551863.

Berry D, Loy A. Stable-Isotope Probing of Human and Animal Microbiome Function. Trends Microbiol. 2018;26(12):999-1007. Epub 2018/07/14. doi: 10.1016/j.tim.2018.06.004. PubMed PMID: 30001854; PMCID: PMC6249988.

Brook MS, Wilkinson DJ. Contemporary stable isotope tracer approaches: Insights into skeletal muscle metabolism in health and disease. Exp Physiol. 2020;105(7):1081-9. Epub 2020/05/04. doi: 10.1113/EP087492. PubMed PMID: 32362047.

Dufner D, Previs SF. Measuring in vivo metabolism using heavy water. Curr Opin Clin Nutr Metab Care. 2003;6(5):511-7. Epub 2003/08/13. doi: 10.1097/00075197-200309000-00004. PubMed PMID: 12913668.

Jang C, Chen L, Rabinowitz JD. Metabolomics and Isotope Tracing. Cell. 2018;173(4):822-37. Epub 2018/05/05. doi: 10.1016/j.cell.2018.03.055. PubMed PMID: 29727671; PMCID: PMC6034115.

Kim IY, Park S, Kim Y, Kim HJ, Wolfe RR. Tracing metabolic flux in vivo: basic model structures of tracer methodology. Exp Mol Med. 2022;54(9):1311-22. Epub 2022/09/09. doi: 10.1038/s12276-022-00814-z. PubMed PMID: 36075950; PMCID: PMC9534847.

Mahon AD, Timmons BW. Application of stable isotope tracers in the study of exercise metabolism in children: a primer. Pediatr Exerc Sci. 2014;26(1):3-10. Epub 2014/03/26. doi: 10.1123/pes.2013-0074. PubMed PMID: 24662114.

McCabe BJ, Previs SF. Using isotope tracers to study metabolism: application in mouse models. Metab Eng. 2004;6(1):25-35. Epub 2004/01/22. doi: 10.1016/j.ymben.2003.09.003. PubMed PMID: 14734253.

Wilkinson DJ, Brook MS, Smith K, Atherton PJ. Stable isotope tracers and exercise physiology: past, present and future. J Physiol. 2017;595(9):2873-82. Epub 2016/09/10. doi: 10.1113/JP272277. PubMed PMID: 27610950; PMCID: PMC5407962.

Information on the heated-hand vein technique

Dr. Dwight Matthews' theory and the use of a heated-hand box

Brooks DC, Black PR, Arcangeli MA, Aoki TT, Wilmore DW. The heated dorsal hand vein: an alternative arterial sampling site. JPEN J Parenter Enteral Nutr. 1989;13(1):102-5. Epub 1989/01/01. doi: 10.1177/0148607189013001102. PubMed PMID: 2926973.

Jensen MD, Heiling VJ. Heated hand vein blood is satisfactory for measurements during free fatty acid kinetic studies. Metabolism. 1991;40(4):406-9. Epub 1991/04/01. doi: 10.1016/0026-0495(91)90152-m. PubMed PMID: 2011082.

Nauck MA, Blietz RW, Qualmann C. Comparison of hyperinsulinaemic clamp experiments using venous, 'arterialized' venous or capillary euglycaemia. Clin Physiol. 1996;16(6):589-602. Epub 1996/11/01. doi: 10.1111/j.1475-097x.1996.tb00736.x. PubMed PMID: 8937798.

Nauck MA, Liess H, Siegel EG, Niedmann PD, Creutzfeldt W. Critical evaluation of the 'heated-hand-technique' for obtaining 'arterialized' venous blood: incomplete arterialization and alterations in glucagon responses. Clin Physiol. 1992;12(5):537-52. Epub 1992/09/01. doi: 10.1111/j.1475-097x.1992.tb00357.x. PubMed PMID: 1395446.

Norwich KH. Sites of infusion and sampling for measurement of rates of production in steady state. Am J Physiol. 1992;263(5 Pt 1):E817-22. Epub 1992/11/01. doi: 10.1152/ajpendo.1992.263.5.E817. PubMed PMID: 1443112.

Zello GA, Smith JM, Pencharz PB, Ball RO. Development of a heating device for sampling arterialized venous blood from a hand vein. Ann Clin Biochem. 1990;27 ( Pt 4):366-72. Epub 1990/07/01. doi: 10.1177/000456329002700414. PubMed PMID: 2403236.

Jones JG, Solomon MA, Cole SM, Sherry AD, Malloy CR. An integrated (2)H and (13)C NMR study of gluconeogenesis and TCA cycle flux in humans. Am J Physiol Endocrinol Metab. 2001;281(4):E848-56. Epub 2001/09/12. doi: 10.1152/ajpendo.2001.281.4.E848. PubMed PMID: 11551863.

Nauck MA, Blietz RW, Qualmann C. Comparison of hyperinsulinaemic clamp experiments using venous, 'arterialized' venous or capillary euglycaemia. Clin Physiol. 1996;16(6):589-602. Epub 1996/11/01. doi: 10.1111/j.1475-097x.1996.tb00736.x. PubMed PMID: 8937798.

Chung ST, Chacko SK, Sunehag AL, Haymond MW. Measurements of Gluconeogenesis and Glycogenolysis: A Methodological Review. Diabetes. 2015;64(12):3996-4010. Epub 2015/11/26. doi: 10.2337/db15-0640. PubMed PMID: 26604176; PMCID: PMC4657587.

Liu D, Moberg E, Kollind M, Lins PE, Adamson U, Macdonald IA. Arterial, arterialized venous, venous and capillary blood glucose measurements in normal man during hyperinsulinaemic euglycaemia and hypoglycaemia. Diabetologia. 1992;35(3):287-90. Epub 1992/03/01. doi: 10.1007/bf00400932. PubMed PMID: 1563586.

Previs SF, Brunengraber H. Methods for measuring gluconeogenesis in vivo. Curr Opin Clin Nutr Metab Care. 1998;1(5):461-5. Epub 1999/11/24. doi: 10.1097/00075197-199809000-00016. PubMed PMID: 10565394.

Stephenson EJ, Stayton AS, Sethuraman A, Rao PK, Meyer A, Gomes CK, Mulcahy MC, McAllan L, Puchowicz MA, Pierre JF, Bridges D, Han JC. Chronic intake of high dietary sucrose induces sexually dimorphic metabolic adaptations in mouse liver and adipose tissue. Nat Commun. 2022;13(1):6062. Epub 2022/10/14. doi: 10.1038/s41467-022-33840-6. PubMed PMID: 36229459; PMCID: PMC9561177 clinical trial investigator for Rhythm Pharmaceuticals, and a consultant for Novo Nordisk. J.F.P. is a co-founder and shareholder of AVnovum Therapeutics, Inc. The remaining authors declare no competing interests.

Browning JD, Burgess SC. Use of (2)H(2)O for estimating rates of gluconeogenesis: determination and correction of error due to transaldolase exchange. Am J Physiol Endocrinol Metab. 2012;303(11):E1304-12. Epub 2012/10/04. doi: 10.1152/ajpendo.00306.2012. PubMed PMID: 23032685; PMCID: PMC3774082.

Deja S, Fu X, Fletcher JA, Kucejova B, Browning JD, Young JD, Burgess SC. Simultaneous tracers and a unified model of positional and mass isotopomers for quantification of metabolic flux in liver. Metab Eng. 2020;59:1-14. Epub 2020/01/01. doi: 10.1016/j.ymben.2019.12.005. PubMed PMID: 31891762; PMCID: PMC7108978.

Hudson JL, Cotter M, Herndon DN, Wolfe RR, Borsheim E. Comparison of Arterial-Venous Balance and Tracer Incorporation Methods for Measuring Muscle Fractional Synthesis and Fractional Breakdown Rates. J Burn Care Res. 2022;43(1):156-62. Epub 2021/04/29. doi: 10.1093/jbcr/irab059. PubMed PMID: 33908606; PMCID: PMC8737081.

Jaleel A, Short KR, Asmann YW, Klaus KA, Morse DM, Ford GC, Nair KS. In vivo measurement of synthesis rate of individual skeletal muscle mitochondrial proteins. Am J Physiol Endocrinol Metab. 2008;295(5):E1255-68. Epub 2008/09/04. doi: 10.1152/ajpendo.90586.2008. PubMed PMID: 18765679; PMCID: PMC2584812.

Kobak KA, Lawrence MM, Pharaoh G, Borowik AK, Peelor FF, 3rd, Shipman PD, Griffin TM, Van Remmen H, Miller BF. Determining the contributions of protein synthesis and breakdown to muscle atrophy requires non-steady-state equations. J Cachexia Sarcopenia Muscle. 2021;12(6):1764-75. Epub 2021/08/22. doi: 10.1002/jcsm.12772. PubMed PMID: 34418329; PMCID: PMC8718081.

Moran A, Toffolo G, Schiavon M, Vella A, Klaus K, Cobelli C, Nair KS. A novel triple-tracer approach to assess postprandial protein turnover. Am J Physiol Endocrinol Metab. 2018;315(4):E469-E77. Epub 2018/06/06. doi: 10.1152/ajpendo.00012.2018. PubMed PMID: 29870679; PMCID: PMC6230707.

Short KR, Vittone JL, Bigelow ML, Proctor DN, Nair KS. Age and aerobic exercise training effects on whole body and muscle protein metabolism. Am J Physiol Endocrinol Metab. 2004;286(1):E92-101. Epub 2003/09/25. doi: 10.1152/ajpendo.00366.2003. PubMed PMID: 14506079.

Yoo H, Antoniewicz MR, Stephanopoulos G, Kelleher JK. Quantifying reductive carboxylation flux of glutamine to lipid in a brown adipocyte cell line. J Biol Chem. 2008;283(30):20621-7. Epub 2008/03/28. doi: 10.1074/jbc.M706494200. PubMed PMID: 18364355; PMCID: PMC2475696.

Jensen MD, Heiling VJ. Heated hand vein blood is satisfactory for measurements during free fatty acid kinetic studies. Metabolism. 1991;40(4):406-9. Epub 1991/04/01. doi: 10.1016/0026-0495(91)90152-m. PubMed PMID: 2011082.

Jensen MD, Rogers PJ, Ellman MG, Miles JM. Choice of infusion-sampling mode for tracer studies of free fatty acid metabolism. Am J Physiol. 1988;254(5 Pt 1):E562-5. Epub 1988/05/01. doi: 10.1152/ajpendo.1988.254.5.E562. PubMed PMID: 3364559.

Bederman IR, Foy S, Chandramouli V, Alexander JC, Previs SF. Triglyceride synthesis in epididymal adipose tissue: contribution of glucose and non-glucose carbon sources. J Biol Chem. 2009;284(10):6101-8. Epub 2008/12/31. doi: 10.1074/jbc.M808668200. PubMed PMID: 19114707; PMCID: PMC2649080.

Donnelly KL, Smith CI, Schwarzenberg SJ, Jessurun J, Boldt MD, Parks EJ. Sources of fatty acids stored in liver and secreted via lipoproteins in patients with nonalcoholic fatty liver disease. J Clin Invest. 2005;115(5):1343-51. Epub 2005/05/03. doi: 10.1172/JCI23621. PubMed PMID: 15864352; PMCID: PMC1087172.

Govatati S, Pichavaram P, Mani AM, Kumar R, Sharma D, Dienel A, Meena S, Puchowicz MA, Park EA, Rao GN. Novel role of xanthine oxidase-dependent H(2)O(2) production in 12/15-lipoxygenase-mediated de novo lipogenesis, triglyceride biosynthesis and weight gain. Redox Biol. 2021;47:102163. Epub 2021/10/17. doi: 10.1016/j.redox.2021.102163. PubMed PMID: 34655995; PMCID: PMC8577505.

Hodson L, McQuaid SE, Humphreys SM, Milne R, Fielding BA, Frayn KN, Karpe F. Greater dietary fat oxidation in obese compared with lean men: an adaptive mechanism to prevent liver fat accumulation? Am J Physiol Endocrinol Metab. 2010;299(4):E584-92. Epub 2010/07/16. doi: 10.1152/ajpendo.00272.2010. PubMed PMID: 20628024; PMCID: PMC2957864.

Kumari R, Irudayam MJ, Al Abdallah Q, Jones TL, Mims TS, Puchowicz MA, Pierre JF, Brown CW. SMAD2 and SMAD3 differentially regulate adiposity and the growth of subcutaneous white adipose tissue. FASEB J. 2021;35(12):e22018. Epub 2021/11/04. doi: 10.1096/fj.202101244R. PubMed PMID: 34731499.

Magkos F, Patterson BW, Mittendorfer B. Reproducibility of stable isotope-labeled tracer measures of VLDL-triglyceride and VLDL-apolipoprotein B-100 kinetics. J Lipid Res. 2007;48(5):1204-11. Epub 2007/02/28. doi: 10.1194/jlr.D600048-JLR200. PubMed PMID: 17325388.

Parks EJ, Hellerstein MK. Thematic review series: patient-oriented research. Recent advances in liver triacylglycerol and fatty acid metabolism using stable isotope labeling techniques. J Lipid Res. 2006;47(8):1651-60. Epub 2006/06/03. doi: 10.1194/jlr.R600018-JLR200. PubMed PMID: 16741290.

Ranea-Robles P, Chen H, Stauffer B, Yu C, Bhattacharya D, Friedman SL, Puchowicz M, Houten SM. The peroxisomal transporter ABCD3 plays a major role in hepatic dicarboxylic fatty acid metabolism and lipid homeostasis. J Inherit Metab Dis. 2021;44(6):1419-33. Epub 2021/09/27. doi: 10.1002/jimd.12440. PubMed PMID: 34564857; PMCID: PMC8578467.

Ranea-Robles P, Pavlova NN, Bender A, Pereyra AS, Ellis JM, Stauffer B, Yu C, Thompson CB, Argmann C, Puchowicz M, Houten SM. A mitochondrial long-chain fatty acid oxidation defect leads to transfer RNA uncharging and activation of the integrated stress response in the mouse heart. Cardiovasc Res. 2022;118(16):3198-210. Epub 2022/04/08. doi: 10.1093/cvr/cvac050. PubMed PMID: 35388887; PMCID: PMC9799058.

Sonnenberg GE, Keller U. Sampling of arterialized heated-hand venous blood as a noninvasive technique for the study of ketone body kinetics in man. Metabolism. 1982;31(1):1-5. Epub 1982/01/01. PubMed PMID: 6804743

Deuterated water for GNG

Katanik J, McCabe BJ, Brunengraber DZ, Chandramouli V, Nishiyama FJ, Anderson VE, Previs SF. Measuring gluconeogenesis using a low dose of 2H2O: advantage of isotope fractionation during gas chromatography. Am J Physiol Endocrinol Metab. 2003;284(5):E1043-8. Epub 2003/02/13. doi: 10.1152/ajpendo.00485.2002. PubMed PMID: 12582010.

Deuterated water for Lipid and Protein Synthesis

Dufner DA, Bederman IR, Brunengraber DZ, Rachdaoui N, Ismail-Beigi F, Siegfried BA, Kimball SR, Previs SF. Using 2H2O to study the influence of feeding on protein synthesis: effect of isotope equilibration in vivo vs. in cell culture. Am J Physiol Endocrinol Metab. 2005;288(6):E1277-83. Epub 2005/01/27. doi: 10.1152/ajpendo.00580.2004. PubMed PMID: 15671077.

Gasier HG, Fluckey JD, Previs SF. The application of 2H2O to measure skeletal muscle protein synthesis. Nutr Metab (Lond). 2010;7:31. Epub 2010/04/23. doi: 10.1186/1743-7075-7-31. PubMed PMID: 20409307; PMCID: PMC2873296.

Herath K, Bhat G, Miller PL, Wang SP, Kulick A, Andrews-Kelly G, Johnson C, Rohm RJ, Lassman ME, Previs SF, Johns DG, Hubbard BK, Roddy TP. Equilibration of (2)H labeling between body water and free amino acids: enabling studies of proteome synthesis. Anal Biochem. 2011;415(2):197-9. Epub 2011/05/21. doi: 10.1016/j.ab.2011.04.031. PubMed PMID: 21596013.

Previs SF, Herath K, Nawrocki AR, Rodriguez CG, Slipetz D, Singh SB, Kang L, Bhat G, Roddy TP, Conarello S, Terebetski J, Erion MD, Kelley DE. Using [(2)H]water to quantify the contribution of de novo palmitate synthesis in plasma: enabling back-to-back studies. Am J Physiol Endocrinol Metab. 2018;315(1):E63-e71. Epub 2018/01/20. doi: 10.1152/ajpendo.00010.2017. PubMed PMID: 29351479.

Kelleher JK, Nickol GB. Isotopomer Spectral Analysis: Utilizing Nonlinear Models in Isotopic Flux Studies. Methods Enzymol. 2015;561:303-30. Epub 2015/09/12. doi: 10.1016/bs.mie.2015.06.039. PubMed PMID: 26358909.

Zhang GF, Sadhukhan S, Tochtrop GP, Brunengraber H. Metabolomics, pathway regulation, and pathway discovery. J Biol Chem. 2011;286(27):23631-5. Epub 2011/05/14. doi: 10.1074/jbc.R110.171405. PubMed PMID: 21566142; PMCID: PMC3129142.

Ragavan M, Kirpich A, Fu X, Burgess SC, McIntyre LM, Merritt ME. A comprehensive analysis of myocardial substrate preference emphasizes the need for a synchronized fluxomic/metabolomic research design. Am J Physiol Heart Circ Physiol. 2017;312(6):H1215-h23. Epub 2017/04/16. doi: 10.1152/ajpheart.00016.2017. PubMed PMID: 28411229; PMCID: PMC5495932.

INCA

Rahim M, Ragavan M, Deja S, Merritt ME, Burgess SC, Young JD. INCA 2.0: A tool for integrated, dynamic modeling of NMR- and MS-based isotopomer measurements and rigorous metabolic flux analysis. Metab Eng. 2022;69:275-85. Epub 2021/12/30. doi: 10.1016/j.ymben.2021.12.009. PubMed PMID: 34965470; PMCID: PMC8789327.

Young JD. INCA: a computational platform for isotopically non-stationary metabolic flux analysis. Bioinformatics. 2014;30(9):1333-5. Epub 2014/01/15. doi: 10.1093/bioinformatics/btu015. PubMed PMID: 24413674; PMCID: PMC3998137.

Tools

tcaCalc (free access) - The tcaCALC program performs an isotopomer analysis to estimate relative pathway fluxes in biological systems at metabolic and isotopic steady state.

INCA - is a MATLAB-based software package for isotopomer network modeling and metabolic flux analysis.

MatLab - combines a desktop environment tuned for iterative analysis and design processes with a programming language that expresses matrix and array mathematics directly

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