Thomas W. Binsl

Measuring non-steady-state metabolic fluxes in starch-converting faecal microbiota in vitro

This paper explores human gut bacterial metabolism of starch using a combined analytical and computational modelling approach for metabolite and flux analysis. Non-steady-state isotopic labelling experiments were performed with human faecal microbiota in a well-established in vitro model of the human colon. After culture stabilisation, [U-13C] starch was added and samples were taken at regular intervals. Metabolite concentrations and 13C isotopomeric distributions were measured amongst other things for acetate, propionate and butyrate by mass spectrometry and NMR. The vast majority of metabolic flux analysis methods based on isotopomer analysis published to date are not applicable to metabolic non-steady-state experiments. We therefore developed a new ordinary differential equation-based representation of a metabolic model of human faecal microbiota to determine eleven metabolic parameters that characterised the metabolic flux distribution in the isotope labelling experiment. The feasibility of the model parameter quantification was demonstrated on noisy in silico data using a downhill simplex optimisation, matching simulated labelling patterns of isotopically labelled metabolites with measured metabolite and isotope labelling data. Using the experimental data, we determined an increasing net label influx from starch during the experiment from 94±1 µmol/l/min to 133±3 µmol/l/min. Only about 12% of the total carbon flux from starch reached propionate. Propionate production mainly proceeded via succinate with a small contribution via acrylate. The remaining flux from starch yielded acetate (35%) and butyrate (53%). Interpretation of 13C NMR multiplet signals further revealed that butyrate, valerate and caproate were mainly synthesised via cross-feeding, using acetate as a co-substrate. This study demonstrates for the first time that the experimental design and the analysis of the results by computational modelling allows the determination of time-resolved effects of nutrition on the flux distribution within human faecal microbiota in metabolic non-steady-state.

Endotoxemia decreases matching of regional blood flow and O2 delivery to O2 uptake in the porcine left ventricle

Heterogeneity of regional coronary blood flow is caused in part by heterogeneity in O(2) demand in the normal heart. We investigated whether myocardial O(2) supply/demand mismatching is associated with the myocardial depression of sepsis. Regional blood flow (microspheres) and O(2) uptake ([(13)C]acetate infusion and analysis of resultant NMR spectra) were measured in about nine contiguous tissue samples from the left ventricle (LV) in each heart. Endotoxemic pigs (n = 9) showed hypotension at unchanged cardiac output with a fall in LV stroke work and first derivative of LV pressure relative to controls (n = 4). Global coronary blood flow and O(2) delivery were maintained. Lactate accumulated in arterial blood, but net lactate extraction across the coronary bed was unchanged during endotoxemia. When LV O(2) uptake based on blood gas versus NMR data were compared, the correlation was 0.73 (P = 0.007). While stable over time in controls, regional blood flows were strongly redistributed during endotoxin shock, with overall flow heterogeneity unchanged. A stronger redistribution of blood flow with endotoxin was associated with a larger fall in LV function parameters. Moreover, the correlation of regional O(2) delivery to uptake fell from r = 0.73 (P < 0.001) in control to r = 0.18 (P = 0.25, P = 0.009 vs. control) in endotoxemic hearts. The results suggest a redistribution of LV regional coronary blood flow during endotoxin shock in pigs, with regional O(2) delivery mismatched to O(2) demand. Mismatching may underlie, at least in part, the myocardial depression of sepsis.

Electron Density Fingerprints (EDprints): Virtual Screening Using Assembled Information of Electron Density

We have designed a method to encode properties related to the electron densities of molecules (calculated (1)H and (13)C NMR shifts and atomic partial charges) in molecular fingerprints (EDprints). EDprints was evaluated in terms of their retrospective virtual screening accuracy against the Directory of Useful Decoys (DUD) and compared to the established ligand-based similarity search methods MOLPRINT 2D and FCFP-4. Although there are no significant differences in the overall virtual screening accuracies of the three methods, specific examples highlight interesting differences between the new EDprints fingerprint method and the atom-centered circular fingerprint methods of MOLPRINT 2D and FCFP-4. On one hand, EDprints similarity searches can be biased by the molecular protonation state, especially when reference ligands contain multiple ionizable groups. On the other hand, EDprints models are more robust toward subtle rearrangements of chemical groups and more suitable for screening against reference molecules with fused ring systems than MOLPRINT 2D and FCFP-4. EDprints is furthermore the fastest method under investigation in comparing fingerprints (average 56-233-fold increase in speed), which makes it highly suitable for all-against-all similarity searches and for repetitive virtual screening against large chemical databases of millions of compounds.

Computational estimation of tricarboxylic acid cycle fluxes using noisy NMR data from cardiac biopsies

BackgroundThe 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.ResultsHere 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.ConclusionsDespite 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.

CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs

SUMMARY CGHnormaliter is a package for normalization of array comparative genomic hybridization (aCGH) data. It uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs). CGHnormaliter is integrated in the Bioconductor environment allowing a smooth link to visualization tools and further data analysis. AVAILABILITY AND IMPLEMENTATION The CGHnormaliter package is implemented in R and under GPL 3.0 license available at Bioconductor: http://www.bioconductor.org CONTACT heringa@few.vu.nl

Robust modelling, measurement and analysis of human and animal metabolic systems

Modelling human and animal metabolism is impeded by the lack of accurate quantitative parameters and the large number of biochemical reactions. This problem may be tackled by: (i) study of modules of the network independently; (ii) ensemble simulations to explore many plausible parameter combinations; (iii) analysis of ‘sloppy’ parameter behaviour, revealing interdependent parameter combinations with little influence; (iv) multiscale analysis that combines molecular and whole network data; and (v) measuring metabolic flux (rate of flow) in vivo via stable isotope labelling. For the latter method, carbon transition networks were modelled with systems of ordinary differential equations, but we show that coloured Petri nets provide a more intuitive graphical approach. Analysis of parameter sensitivities shows that only a few parameter combinations have a large effect on predictions. Model analysis of high-energy phosphate transport indicates that membrane permeability, inaccurately known at the organellar level, can be well determined from whole-organ responses. Ensemble simulations that take into account the imprecision of measured molecular parameters contradict the popular hypothesis that high-energy phosphate transport in heart muscle is mostly by phosphocreatine. Combining modular, multiscale, ensemble and sloppy modelling approaches with in vivo flux measurements may prove indispensable for the modelling of the large human metabolic system.

Progressively heterogeneous mismatch of regional oxygen delivery to consumption during graded coronary stenosis in pig left ventricle

In normal hearts, myocardial perfusion is fairly well matched to regional metabolic demand, although both are distributed heterogeneously. Nonuniform regional metabolic vulnerability during coronary stenosis would help to explain nonuniform necrosis during myocardial infarction. In the present study, we investigated whether metabolism-perfusion correlation diminishes during coronary stenosis, indicating increasing mismatch of regional oxygen supply to demand. Thirty anesthetized male pigs were studied: controls without coronary stenosis (n = 11); group I, left anterior descending (LAD) coronary stenosis leading to coronary perfusion pressure reduction to 70 mmHg (n = 6); group II, stenosis with perfusion pressure of about 35 mmHg (n = 6); and group III, stenosis with perfusion pressure of 45 mmHg combined with adenosine infusion (n = 7). [2-(13)C]- and [1,2-(13)C]acetate infusion was used to calculate regional O2 consumption from glutamate NMR spectra measured for multiple tissue samples of about 100 mg dry mass in the LAD region. Blood flow was measured with microspheres in the same regions. In control hearts without stenosis, regional oxygen extraction did not correlate with basal blood flow. Average myocardial O2 delivery and consumption decreased during coronary stenosis, but vasodilation with adenosine counteracted this. Regional oxygen extraction was on average decreased during stenosis, suggesting adaptation of metabolism to lower oxygen supply after half an hour of ischemia. Whereas regional O2 delivery correlated with O2 consumption in controls, this relation was progressively lost with graded coronary hypotension but partially reestablished by adenosine infusion. Therefore, coronary stenosis leads to heterogeneous metabolic stress indicated by decreasing regional O2 supply to demand matching in myocardium during partial coronary obstruction.