title: Computational estimation of tricarboxylic acid cycle fluxes using noisy NMR data from cardiac biopsies.
abstract: BACKGROUND
  The aerobic energy metabolism of cardiac muscle cells is of major importance for the contractile function of the heart. Because energy metabolism is very heterogeneously distributed in heart tissue, especially during coronary disease, a method to quantify metabolic fluxes in small tissue samples is desirable. Taking tissue biopsies after infusion of substrates labeled with stable carbon isotopes makes this possible in animal experiments. However, the appreciable noise level in NMR spectra of extracted tissue samples makes computational estimation of metabolic fluxes challenging and a good method to define confidence regions was not yet available.
  
  
  RESULTS
  Here we present a computational analysis method for nuclear magnetic resonance (NMR) measurements of tricarboxylic acid (TCA) cycle metabolites. The method was validated using measurements on extracts of single tissue biopsies taken from porcine heart in vivo. Isotopic enrichment of glutamate was measured by NMR spectroscopy in tissue samples taken at a single time point after the timed infusion of 13C labeled substrates for the TCA cycle. The NMR intensities for glutamate were analyzed with a computational model describing carbon transitions in the TCA cycle and carbon exchange with amino acids. The model dynamics depended on five flux parameters, which were optimized to fit the NMR measurements. To determine confidence regions for the estimated fluxes, we used the Metropolis-Hastings algorithm for Markov chain Monte Carlo (MCMC) sampling to generate extensive ensembles of feasible flux combinations that describe the data within measurement precision limits. To validate our method, we compared myocardial oxygen consumption calculated from the TCA cycle flux with in vivo blood gas measurements for 38 hearts under several experimental conditions, e.g. during coronary artery narrowing.
  
  
  CONCLUSIONS
  Despite the appreciable NMR noise level, the oxygen consumption in the tissue samples, estimated from the NMR spectra, correlates with blood-gas oxygen uptake measurements for the whole heart. The MCMC method provides confidence regions for the estimated metabolic fluxes in single cardiac biopsies, taking the quantified measurement noise level and the nonlinear dependencies between parameters fully into account.
authors: Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam, de Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands. j.hettling@vu.nl.
authors: Hannes
authors: H
authors: Hettling
authors: David J C
authors: DJ
authors: Alders
authors: Jaap
authors: J
authors: Heringa
authors: Thomas W
authors: TW
authors: Binsl
authors: A B Johan
authors: AB
authors: Groeneveld
authors: Johannes H G M
authors: JH
authors: van Beek
mesh_terms: D000818:Animals; D001706:Biopsy; D002952:Citric Acid Cycle; D019295:Computational Biology / Q000379:methods*; D015925:Cryopreservation; D009682:Magnetic Resonance Spectroscopy; D009010:Monte Carlo Method; D009206:Myocardium / Q000166:cytology / Q000378:metabolism* / Q000473:pathology*; D013552:Swine; D013997:Time Factors
references: Am J Physiol Heart Circ Physiol. 2004 Sep;287(3):H1353-61
references: 15142850
references: PLoS Comput Biol. 2007 Oct;3(10):1871-78
references: 17922568
references: Am J Physiol Heart Circ Physiol. 2000 Nov;279(5):H2390-8
references: 11045976
references: Biochem J. 1981 Mar 15;194(3):867-75
references: 6796067
references: J Biol Chem. 1983 Nov 25;258(22):13785-94
references: 6643454
references: J Cereb Blood Flow Metab. 1995 Jan;15(1):12-25
references: 7798329
references: BMC Syst Biol. 2012 Jan 30;6:9
references: 22289253
references: FASEB J. 2009 Aug;23(8):2529-38
references: 19329759
references: Biochem J. 1970 May;117(4):677-95
references: 5449122
references: Bioinformatics. 2010 Mar 1;26(5):653-60
references: 20097912
references: Mol Syst Biol. 2006;2:62
references: 17102807
references: Arch Biochem Biophys. 2007 Jul 1;463(1):110-7
references: 17418801
references: Biophys J. 1995 Nov;69(5):2090-102
references: 8580353
references: Am J Physiol. 1990 Sep;259(3 Pt 2):H987-95
references: 1975735
references: Exp Physiol. 2007 May;92(3):541-8
references: 17303649
references: PLoS Comput Biol. 2011 Aug;7(8):e1002130
references: 21912519
references: Am J Physiol. 1997 Dec;273(6):E1228-42
references: 9435540
references: J Nucl Cardiol. 2000 May-Jun;7(3):228-34
references: 10888393
references: Radiology. 1999 Sep;212(3):739-47
references: 10478241
references: Circ Res. 1978 Jan;42(1):119-26
references: 618593
references: Metab Eng. 2006 Jul;8(4):324-37
references: 16631402
references: Proc Natl Acad Sci U S A. 1989 Aug;86(16):6426-30
references: 2762333
references: Adv Exp Med Biol. 1998;454:475-85
references: 9889927
references: Biochem Soc Trans. 2005 Dec;33(Pt 6):1421-2
references: 16246135
references: Circulation. 1993 Jan;87(1):270-82
references: 8419016
references: J Biol Chem. 1993 Dec 15;268(35):26296-301
references: 8253751
references: Am J Physiol Heart Circ Physiol. 2004 Jul;287(1):H351-62
references: 15001444
references: BMC Syst Biol. 2011 Mar 15;5:41
references: 21406095
references: Am J Physiol. 1999 Dec;277(6):E1111-21
references: 10600802
references: Am J Physiol Endocrinol Metab. 2003 Feb;284(2):E351-6
references: 12388135
references: J Stat Softw. 2007 Apr;19(4):1-24
references: 21494410
references: Am J Physiol Heart Circ Physiol. 2001 Oct;281(4):H1613-20
references: 11557551
references: Bioinformatics. 2006 Nov 1;22(21):2681-7
references: 16940326
references: MAGMA. 1996 Mar;4(1):35-46
references: 8774000
references: Bioinformatics. 2013 Jan 1;29(1):143-5
references: 23110970
references: Am J Physiol. 1999 Oct;277(4):H1630-40
references: 10516204
references: J Biol Chem. 2009 Feb 27;284(9):5457-61
references: 18940807
references: Circulation. 2007 Apr 17;115(15):2033-41
references: 17404155
references: J Biol Chem. 1995 Apr 7;270(14):7999-8008
references: 7713900
references: Microb Cell Fact. 2009 May 01;8:25
references: 19409084
references: Phys Biol. 2004 Dec;1(3-4):184-95
references: 16204838