flux balance analysis (fba) with a minimal import strategy  (Micom Laboratories)

Journal: Nature Communications

Article Title: Intracellular sodium elevation reprograms cardiac metabolism

doi: 10.1038/s41467-020-18160-x

Figure Lengend Snippet: a Myocardial 13 C NMR assessment of oxidative metabolism—% contribution of 13 C-U palmitate, 13 C 1,6 glucose and the remnant unlabelled 13 C substrate pool (triglycerides, glycogen, pyruvate, lactate, ketone bodies). 13 C NMR assessment of oxidative metabolism after 30 min administration of CGP37157 in 13 C-KH metab buffer—PLM 3SA ( n = 6) vs PLM WT ( n = 7) hearts. (* P < 0.03 PLM 3SA palmitate oxidation vs PLM WT , P < 0.02 PLM 3SA glucose oxidation vs PLM WT , t = 3.7 df = 8). b Representative 13 C spectrum from perfused mouse heart: full 13 C glutamate spectrum. Multiplet peak patterns of 13 C glutamate C2, C4, C3 glutamate resonances. c Metabolomic profile—metabolite fold change normalized to control concentration (PLM WT levels = 1) with propagated errors (SEM). 1 H NMR metabolomic analysis: NAD, ATP + ADP, PCr, creatine, carnitine, phosphocholine, choline, acetyl carnitine, acetate, aspartate, glutamine, glutamate, glycine, alanine. GS-MS/MS analysis: pyruvate, lactate, citrate, isocitrate, α-ketoglutarate, succinate, fumarate, malate (PLM 3SA n = 5, PLM WT n = 8; lactate PLM 3SA n = 12, PLM WT n = 10, succinate, glutamate PLM 3SA n = 14 PLM WT n = 10, aspartate PLM 3SA n = 13 PLM WT n = 10) (* P < 0.05 vs PLM WT , succinate, citrate, glutamine, alanine P < 0.005 vs PLM WT by t -test, two tailed, df = 10). d Representative 1 H metabolomic NMR spectra. e Myocardial energetic reserve (PCr/ATP) ratio determined by 31 P NMR spectroscopy (PLM 3SA n = 14, PLM WT n = 7, P < 0.22, vs control by t -test, two tailed, t = 1.2, df = 19). f Representative 31 P spectra of PLM WT and PLM 3SA hearts. g Impact of 30 min perfusion with 1μM CGP37157 in KH metab buffer on 1 H NMR metabolomic profile of PLM 3SA versus PLM WT hearts. Metabolite fold change vs control (control = 1) with propagated error of mean. ( n = 8/group PLM 3SA and PLM WT ). ** P < 0.05 vs PLM WT ,succinate, citrate, glutamine, alanine P < 0.005 vs PLM WT by t -test, two tailed, df = 10. Data are mean ± SEM. Source data are provided as a Source Data file.

Article Snippet: Flux distributions were calculated by Flux balance analysis (FBA) using the mammalian network of cardiac metabolism, CardioNet.

Techniques: Control, Concentration Assay, Tandem Mass Spectroscopy, Two Tailed Test, Structural Proteomics

Journal: Nature Communications

Article Title: Intracellular sodium elevation reprograms cardiac metabolism

doi: 10.1038/s41467-020-18160-x

Figure Lengend Snippet: a representative Sham control and banded hypertrophy (dry hearts). b Myocardial 13 C MRS assessment of oxidative metabolism—% contribution of 13 C-U palmitate, 13 C 1,6 glucose and the remnant unlabelled 12 C substrate pool (triglycerides, glycogen, pyruvate, lactate, ketone bodies). Impact of the mitochondrial Na/Ca exchange inhibition with CGP37157 on metabolic fluxes: myocardial 13 C NMR assessment of oxidative metabolism after 30 min administration of CGP37157 in 13 C-KH metab buffer—% contribution of 13 C-U palmitate, 13 C 1,6 glucose and the remnant unlabelled 12 C substrate pool to oxidative phosphorylation Banded vs Sham hearts ( n = 5/group). Banded vs Sham palmitate oxidation P < 0.05, glucose oxidation P < 0.005, unlabelled P < 0.03 by t -test (two-tailed); Banded + CGP37157 vs banded P < 0.05, by one-way ANOVA and Bonferroni multiple comparisons post-test. c 1 H NMR metabolite profile - fold change normalized to control concentration (Sham levels = 1) with propagated error (SEM) ( n = 6/group). * P < 0.05 vs control by t -test (two tailed, df = 9). d Impact of 30 min perfusion with 1 μM CGP37157 in KH metab buffer on 1 H NMR metabolomic profile of Banded ( n = 4) versus Sham ( n = 5) hearts. * P < 0.05 vs Sham, by t-test (two tailed) ♯♯ P < 0.01 PCr vs. Sham + CGP37157, P < 0.01 Aspartate Banded CGP37157 vs Sham by one-way ANOVA and Bonferroni multiple comparisons post-test. Data are mean ± SEM. Source data are provided as a Source Data file.

Article Snippet: Flux distributions were calculated by Flux balance analysis (FBA) using the mammalian network of cardiac metabolism, CardioNet.

Techniques: Control, Inhibition, Phospho-proteomics, Two Tailed Test, Concentration Assay

Journal: Nature Communications

Article Title: Intracellular sodium elevation reprograms cardiac metabolism

doi: 10.1038/s41467-020-18160-x

Figure Lengend Snippet: a Myocardial 13 C NMR assessment of oxidative metabolism—% contribution of 13 C-U palmitate, 13 C 1,6 glucose and the remnant unlabelled 13 C substrate pool (pyruvate, lactate, amino acids, triglycerides, glycogen). 13 C glucose + unlabelled = 100%- 13 C palmitate oxidation) ( n = 5/group) *** P < 0.005 vs control by unpaired t-test (two-tailed, t = 3.74 df = 8). b Metabolic profile plotted as metabolite fold change normalized to control concentration (control levels = 1) with propagated error (SEM). 1 H NMR metabolite analysis: NAD, ATP + ADP, PCr, creatine, carnitine, phosphocholine, choline, acetyl carnitine, acetate, aspartate, glutamine, glutamate, glycine, alanine. GC and LC-MS/MS analysis: pyruvate, lactate, citrate, isocitrate, α ketoglutarate, succinate, fumarate, malate. C57/BL6 hearts perfused for 30 min with Control = Krebs Henseleit buffer + vehicle (DMSO); Ouab = 75 μmol/l ouabain; Blebbi = 100 nmol/l blebbistatin; Ouab + Blebbi = 75 μmol/l ouabain + 100 nmol/l ouabain. P < 0.005 vs control by unpaired t -test (two-tailed, df = 2.2). c Energetic reserve PCr/ATP (Control n = 8, n = 4/treatment group, * P < 0.001 vs control by one-way ANOVA F = 8.6). d Impact of the mitochondrial Na/Ca exchange inhibition with CGP37157 on GC-MS/MS metabolic profile. CGP37157 + Ouab + Blebbi = 1 μmol/l CGP37157 + 75 μmol/l ouabain + 100 nmol/l blebbistatin; CGP37157 = 1 μmol/l CGP37157; Control = KH buffer + vehicle (DMSO); Blebbi = 100 nmol/l blebbistatin ( n = 5/group)* P < 0.05 lactate, P < 0.0002 citrate, succinate, fumarate, malate vs control by one-way ANOVA. Data are mean ± SEM ( a , c ) and fold change versus control (control = 1) with propagated error of mean ( b , d ). Comparisons by one-way ANOVA were subject to Bonferroni multiple comparisons post-test. Source data are provided as a Source Data file.

Article Snippet: Flux distributions were calculated by Flux balance analysis (FBA) using the mammalian network of cardiac metabolism, CardioNet.

Techniques: Control, Two Tailed Test, Concentration Assay, Liquid Chromatography with Mass Spectroscopy, Inhibition, Gas Chromatography-Mass Spectrometry

Journal: Nature Communications

Article Title: Intracellular sodium elevation reprograms cardiac metabolism

doi: 10.1038/s41467-020-18160-x

Figure Lengend Snippet: Unsupervised hierarchical clustering of estimated z-scored flux rate changes reveals metabolic adaptation in response to [Na] i elevation. Heat maps summarize results for reactions in the Krebs cycle, OXPHOS, and glucose metabolism. Flux distributions were calculated by Flux balance analysis (FBA) using the mammalian network of cardiac metabolism, CardioNet. Z-scores were calculated to visualize how many standard deviations an estimated flux rate is away from the mean across all experimental groups. The z-score describes the distance from the mean for a given flux rate as a function of the standard deviation. For example, a z-score equal to 1 represents a flux for a given experimental group that is 1 standard deviation greater than the mean across all experimental groups. The colour scale indicates the degree to which estimated flux rate changes are predicted to be respectively lower or higher in response to Na i elevation. Source data are provided in Supplementary Data .

Article Snippet: Flux distributions were calculated by Flux balance analysis (FBA) using the mammalian network of cardiac metabolism, CardioNet.

Techniques: Standard Deviation