H. Westerhoff - Academia.edu (original) (raw)
Papers by H. Westerhoff
Calculations required to assess the difference between correlation coefficients at significance l... more Calculations required to assess the difference between correlation coefficients at significance level α = 0.05 for a minimum sample size of 27 and a minimum absolute correlation coefficient of ± 0.7 in at least one of the experimental groups compared. (a) is the Fishers z-transformation where C i is the Pearsons rank correlation coefficient (in this case chosen to be 0.7) and (b) is the permutation test for comparing correlations between metabolites, where Ẑ T is a value that corresponds to the confidence of a correlation, z 1 and z 2 are the values calculated through equation 3a and N 1 and N 2 are the minimum sample sizes for each metabolite.
Frontiers in Physiology, 2012
Non-alcoholic fatty liver disease comprises a broad spectrum of disease states ranging from simpl... more Non-alcoholic fatty liver disease comprises a broad spectrum of disease states ranging from simple steatosis to non-alcoholic steatohepatitis. As a result of increases in the prevalences of obesity, insulin resistance, and hyperlipidemia, the number of people with hepatic steatosis continues to increase. Differences in susceptibility to steatohepatitis and its progression to cirrhosis have been attributed to a complex interplay of genetic and external factors all addressing the intracellular network. Increase in sugar or refined carbohydrate consumption results in an increase of insulin and insulin resistance that can lead to the accumulation of fat in the liver. Here we demonstrate how a multidisciplinary approach encompassing cellular reprogramming, transcriptomics, proteomics, metabolomics, modeling, network reconstruction, and data management can be employed to unveil the mechanisms underlying the progression of steatosis. Proteomics revealed reduced AKT/mTOR signaling in fibroblasts derived from steatosis patients and further establishes that the insulin-resistant phenotype is present not only in insulin-metabolizing central organs, e.g., the liver, but is also manifested in skin fibroblasts. Transcriptome data enabled the generation of a regulatory network based on the transcription factor SREBF1, linked to a metabolic network of glycerolipid, and fatty acid biosynthesis including the downstream transcriptional targets of SREBF1 which include LIPIN1 (LPIN) and low density lipoprotein receptor. Glutathione metabolism was among the pathways enriched in steatosis patients in comparison to healthy controls. By using a model of the glutathione pathway we predict a significant increase in the flux through glutathione synthesis as both gamma-glutamylcysteine synthetase and glutathione synthetase have an increased flux. We anticipate that a larger cohort of patients and matched controls will confirm our preliminary findings presented here.
Scientific data, Jan 8, 2015
Non-alcoholic fatty liver disease (NAFLD) is a consequence of sedentary life style and high fat d... more Non-alcoholic fatty liver disease (NAFLD) is a consequence of sedentary life style and high fat diets with an estimated prevalence of about 30% in western countries. It is associated with insulin resistance, obesity, glucose intolerance and drug toxicity. Additionally, polymorphisms within, e.g., APOC3, PNPLA3, NCAN, TM6SF2 and PPP1R3B, correlate with NAFLD. Several studies have already investigated later stages of the disease. This study explores the early steatosis stage of NAFLD with the aim of identifying molecular mechanisms underlying the etiology of NAFLD. We analyzed liver biopsies and serum samples from patients with high- and low-grade steatosis (also pre-disease states) employing transcriptomics, ELISA-based serum protein analyses and metabolomics. Here, we provide a detailed description of the various related datasets produced in the course of this study. These datasets may help other researchers find new clues for the etiology of NAFLD and the mechanisms underlying its ...
Trends in Biochemical Sciences, 1995
Trends in Biochemical Sciences, 1984
New Biotechnology, 2012
Robustness is a fundamental and essential property of evolvable biological systems. It provides s... more Robustness is a fundamental and essential property of evolvable biological systems. It provides system to conserve its functionalities against internal/external perturbations and uncertainties. Product inhibition, feed-forward and feed-back inhibition and stimulation, and regulatory loops within signal transduction networks are a few of the approaches generated by biological systems to maintain both their robustness and adaptability. In this study, we are able to show the interaction of the stress hormone cortisol with its two nuclear receptors, the high affinity glucocorticoid receptor (GR) and the low affinity pregnane X-receptor (PXR) by using a mathematical model based on realistic kinetic parameters. We checked the importance of regulatory loops, within this network, in terms of pharmacodynamic and pharmacokinetic responses. Then, we demonstrate the alterations in the system response with respect to variable cortisol perturbations, such as initial single peak in cortisol, and repeated stimuli of cortisol with differing frequencies and time frames. As a conclusion, we reveal that the network is robust towards low frequency perturbations, shows adaptation at moderate stress frequencies, but transitions to an altered steady state at high frequency stimulation, which we believe is a predisposing factor towards stress-induced pathologies
Faraday Discussions, 2001
The mechanism of active phase synchronization in a suspension of oscillatory yeast cells has rema... more The mechanism of active phase synchronization in a suspension of oscillatory yeast cells has remained a puzzle for almost half a century. The difficulty of the problem stems from the fact that the synchronization phenomenon involves the entire metabolic network of glycolysis and fermentation, and consequently it cannot be addressed at the level of a single enzyme or a single chemical species. In this paper it is shown how this system in a CSTR (continuous flow stirred tank reactor) can be modelled quantitatively as a population of Stuart-Landau oscillators interacting by exchange of metabolites through the extracellular medium, thus reducing the complexity of the problem without sacrificing the biochemical realism. The parameters of the model can be derived by a systematic expansion from any full-scale model of the yeast cell kinetics with a supercritical Hopf bifurcation. Some parameter values can also be obtained directly from analysis of perturbation experiments. In the mean-field limit, equations for the study of populations having a distribution of frequencies are used to simulate the effect of the inherent variations between cells.
Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1979
Molecular BioSystems, 2012
Dupuytren's disease (DD) is an ill-defined fibroproliferative disorder affecting the palm of the ... more Dupuytren's disease (DD) is an ill-defined fibroproliferative disorder affecting the palm of the hand, resulting in progressive and irreversible digital contracture. In view of the abnormal gene dysregulation found in DD, and its potential effect on metabolites at a functional level, we chose to examine the metabolic profile involved in DD. Using Fourier transform infrared (FT-IR) spectroscopy to generate metabolic fingerprints of cultured cells, we compared the profiles of DD cords and nodules (1) against the unaffected transverse palmar fascia (internal control), (2) against carpal ligamentous fascia (external control), and (3) against fibroblasts from fat surrounding the nodule and skin overlying the nodule (environmental control). We also determined the effects of serial passaging of the cells on DD fingerprints. Subsequently, gas chromatographymass spectrometry (GC-MS) was employed for metabolic profiling in order to identify metabolites characteristic of the DD tissue phenotypes. We developed a robust metabolomic analysis procedure of DD using cultured fibroblasts derived from DD tissues. Our carefully controlled culture conditions, combined with assessment of metabolic phenotypes by FT-IR and GC-MS, enabled us to demonstrate metabolic differences between DD and unaffected transverse palmar fascia and between DD and healthy control tissue. In early passage (0-3) the metabolic differences were clear, but cells from subsequent passages (4-6) started to lose this distinction between diseased and non-diseased origin. The dysregulated metabolites we identified were leucine, phenylalanine, lysine, cysteine, aspartic acid, glycerol-3-phosphate and the vitamin precursor to coenzyme A. Early passage DD cells exhibit a clear metabolic profile, in which central metabolic pathways appear to be involved. Experimental conditions have been identified in which these DD data are reproducible. The experimental reproducibility will be useful in DD diagnostics and for DD systems biology.
Nature biotechnology, Jan 7, 2015
Figure 1 The DREAM5 challenge performances of the Barzel & Barabási 'silencer' method (dark blue)... more Figure 1 The DREAM5 challenge performances of the Barzel & Barabási 'silencer' method (dark blue) and the raw statistical similarity measures, the Pearson (red) and Spearman (light blue) correlations and mutual information (MI, green). As in the original DREAM5 challenge, the performance was estimated using two scores: (a-c) AUROC. (d-f) AUPR. TPR, true-positive rate; FPR, false-positive rate; 'Precision' indicates the fraction of correctly inferred true interactions; 'Recall' equals TPR. Insets show the AUROC and AUPR scores for the Barzel & Barabási algorithm, the Pearson and Spearman correlations, and mutual information. In all three cases, the performance of the Barzel & Barabási algorithm was lower than the performance of the raw similarity measures alone (note that in Fig. 3 of the original publication 1 , the Barzel & Barabási algorithm was inappropriately applied and scored).
Biochimica Et Biophysica Acta, 1984
Experimental data are reviewed that are not in keeping with the scheme of 'delocalized' protonic ... more Experimental data are reviewed that are not in keeping with the scheme of 'delocalized' protonic coupling in membrane-linked free-energy transduction. It turns out that there are three main types of anomalies: (i) rates of electron transfer and of ATP synthesis do not solely depend on their own driving force and on A/2 H, (ii) the ('static head') ratio of AGp to A/2 H varies with A/2 H and (iii) inhibition of either some of the electron-transfer chains or some of the ~I +-ATPases, does not cause an overcapacity in the other, non-inhibited proton pumps. None of the earlier free-energy coupling schemes, alternative to delocalized protonic coupling, can account for these three anomalies. We propose to add a fifth postulate, namely that of the coupling unit, to the four existing postulates of 'delocalized protonic coupling' and show that, with this postulate, protonic coupling can again account for most experimental observations. We also discuss: (i) how experimental data that might seem to be at odds with the 'coupling unit' hypothesis can be accounted for and (ii) the problem of the spatial arrangement of the electrical field in the different free-energy coupling schemes.
Molecular Biology Reports, 2002
Nature Biotechnology, 2008
Calculations required to assess the difference between correlation coefficients at significance l... more Calculations required to assess the difference between correlation coefficients at significance level α = 0.05 for a minimum sample size of 27 and a minimum absolute correlation coefficient of ± 0.7 in at least one of the experimental groups compared. (a) is the Fishers z-transformation where C i is the Pearsons rank correlation coefficient (in this case chosen to be 0.7) and (b) is the permutation test for comparing correlations between metabolites, where Ẑ T is a value that corresponds to the confidence of a correlation, z 1 and z 2 are the values calculated through equation 3a and N 1 and N 2 are the minimum sample sizes for each metabolite.
Frontiers in Physiology, 2012
Non-alcoholic fatty liver disease comprises a broad spectrum of disease states ranging from simpl... more Non-alcoholic fatty liver disease comprises a broad spectrum of disease states ranging from simple steatosis to non-alcoholic steatohepatitis. As a result of increases in the prevalences of obesity, insulin resistance, and hyperlipidemia, the number of people with hepatic steatosis continues to increase. Differences in susceptibility to steatohepatitis and its progression to cirrhosis have been attributed to a complex interplay of genetic and external factors all addressing the intracellular network. Increase in sugar or refined carbohydrate consumption results in an increase of insulin and insulin resistance that can lead to the accumulation of fat in the liver. Here we demonstrate how a multidisciplinary approach encompassing cellular reprogramming, transcriptomics, proteomics, metabolomics, modeling, network reconstruction, and data management can be employed to unveil the mechanisms underlying the progression of steatosis. Proteomics revealed reduced AKT/mTOR signaling in fibroblasts derived from steatosis patients and further establishes that the insulin-resistant phenotype is present not only in insulin-metabolizing central organs, e.g., the liver, but is also manifested in skin fibroblasts. Transcriptome data enabled the generation of a regulatory network based on the transcription factor SREBF1, linked to a metabolic network of glycerolipid, and fatty acid biosynthesis including the downstream transcriptional targets of SREBF1 which include LIPIN1 (LPIN) and low density lipoprotein receptor. Glutathione metabolism was among the pathways enriched in steatosis patients in comparison to healthy controls. By using a model of the glutathione pathway we predict a significant increase in the flux through glutathione synthesis as both gamma-glutamylcysteine synthetase and glutathione synthetase have an increased flux. We anticipate that a larger cohort of patients and matched controls will confirm our preliminary findings presented here.
Scientific data, Jan 8, 2015
Non-alcoholic fatty liver disease (NAFLD) is a consequence of sedentary life style and high fat d... more Non-alcoholic fatty liver disease (NAFLD) is a consequence of sedentary life style and high fat diets with an estimated prevalence of about 30% in western countries. It is associated with insulin resistance, obesity, glucose intolerance and drug toxicity. Additionally, polymorphisms within, e.g., APOC3, PNPLA3, NCAN, TM6SF2 and PPP1R3B, correlate with NAFLD. Several studies have already investigated later stages of the disease. This study explores the early steatosis stage of NAFLD with the aim of identifying molecular mechanisms underlying the etiology of NAFLD. We analyzed liver biopsies and serum samples from patients with high- and low-grade steatosis (also pre-disease states) employing transcriptomics, ELISA-based serum protein analyses and metabolomics. Here, we provide a detailed description of the various related datasets produced in the course of this study. These datasets may help other researchers find new clues for the etiology of NAFLD and the mechanisms underlying its ...
Trends in Biochemical Sciences, 1995
Trends in Biochemical Sciences, 1984
New Biotechnology, 2012
Robustness is a fundamental and essential property of evolvable biological systems. It provides s... more Robustness is a fundamental and essential property of evolvable biological systems. It provides system to conserve its functionalities against internal/external perturbations and uncertainties. Product inhibition, feed-forward and feed-back inhibition and stimulation, and regulatory loops within signal transduction networks are a few of the approaches generated by biological systems to maintain both their robustness and adaptability. In this study, we are able to show the interaction of the stress hormone cortisol with its two nuclear receptors, the high affinity glucocorticoid receptor (GR) and the low affinity pregnane X-receptor (PXR) by using a mathematical model based on realistic kinetic parameters. We checked the importance of regulatory loops, within this network, in terms of pharmacodynamic and pharmacokinetic responses. Then, we demonstrate the alterations in the system response with respect to variable cortisol perturbations, such as initial single peak in cortisol, and repeated stimuli of cortisol with differing frequencies and time frames. As a conclusion, we reveal that the network is robust towards low frequency perturbations, shows adaptation at moderate stress frequencies, but transitions to an altered steady state at high frequency stimulation, which we believe is a predisposing factor towards stress-induced pathologies
Faraday Discussions, 2001
The mechanism of active phase synchronization in a suspension of oscillatory yeast cells has rema... more The mechanism of active phase synchronization in a suspension of oscillatory yeast cells has remained a puzzle for almost half a century. The difficulty of the problem stems from the fact that the synchronization phenomenon involves the entire metabolic network of glycolysis and fermentation, and consequently it cannot be addressed at the level of a single enzyme or a single chemical species. In this paper it is shown how this system in a CSTR (continuous flow stirred tank reactor) can be modelled quantitatively as a population of Stuart-Landau oscillators interacting by exchange of metabolites through the extracellular medium, thus reducing the complexity of the problem without sacrificing the biochemical realism. The parameters of the model can be derived by a systematic expansion from any full-scale model of the yeast cell kinetics with a supercritical Hopf bifurcation. Some parameter values can also be obtained directly from analysis of perturbation experiments. In the mean-field limit, equations for the study of populations having a distribution of frequencies are used to simulate the effect of the inherent variations between cells.
Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1979
Molecular BioSystems, 2012
Dupuytren's disease (DD) is an ill-defined fibroproliferative disorder affecting the palm of the ... more Dupuytren's disease (DD) is an ill-defined fibroproliferative disorder affecting the palm of the hand, resulting in progressive and irreversible digital contracture. In view of the abnormal gene dysregulation found in DD, and its potential effect on metabolites at a functional level, we chose to examine the metabolic profile involved in DD. Using Fourier transform infrared (FT-IR) spectroscopy to generate metabolic fingerprints of cultured cells, we compared the profiles of DD cords and nodules (1) against the unaffected transverse palmar fascia (internal control), (2) against carpal ligamentous fascia (external control), and (3) against fibroblasts from fat surrounding the nodule and skin overlying the nodule (environmental control). We also determined the effects of serial passaging of the cells on DD fingerprints. Subsequently, gas chromatographymass spectrometry (GC-MS) was employed for metabolic profiling in order to identify metabolites characteristic of the DD tissue phenotypes. We developed a robust metabolomic analysis procedure of DD using cultured fibroblasts derived from DD tissues. Our carefully controlled culture conditions, combined with assessment of metabolic phenotypes by FT-IR and GC-MS, enabled us to demonstrate metabolic differences between DD and unaffected transverse palmar fascia and between DD and healthy control tissue. In early passage (0-3) the metabolic differences were clear, but cells from subsequent passages (4-6) started to lose this distinction between diseased and non-diseased origin. The dysregulated metabolites we identified were leucine, phenylalanine, lysine, cysteine, aspartic acid, glycerol-3-phosphate and the vitamin precursor to coenzyme A. Early passage DD cells exhibit a clear metabolic profile, in which central metabolic pathways appear to be involved. Experimental conditions have been identified in which these DD data are reproducible. The experimental reproducibility will be useful in DD diagnostics and for DD systems biology.
Nature biotechnology, Jan 7, 2015
Figure 1 The DREAM5 challenge performances of the Barzel & Barabási 'silencer' method (dark blue)... more Figure 1 The DREAM5 challenge performances of the Barzel & Barabási 'silencer' method (dark blue) and the raw statistical similarity measures, the Pearson (red) and Spearman (light blue) correlations and mutual information (MI, green). As in the original DREAM5 challenge, the performance was estimated using two scores: (a-c) AUROC. (d-f) AUPR. TPR, true-positive rate; FPR, false-positive rate; 'Precision' indicates the fraction of correctly inferred true interactions; 'Recall' equals TPR. Insets show the AUROC and AUPR scores for the Barzel & Barabási algorithm, the Pearson and Spearman correlations, and mutual information. In all three cases, the performance of the Barzel & Barabási algorithm was lower than the performance of the raw similarity measures alone (note that in Fig. 3 of the original publication 1 , the Barzel & Barabási algorithm was inappropriately applied and scored).
Biochimica Et Biophysica Acta, 1984
Experimental data are reviewed that are not in keeping with the scheme of 'delocalized' protonic ... more Experimental data are reviewed that are not in keeping with the scheme of 'delocalized' protonic coupling in membrane-linked free-energy transduction. It turns out that there are three main types of anomalies: (i) rates of electron transfer and of ATP synthesis do not solely depend on their own driving force and on A/2 H, (ii) the ('static head') ratio of AGp to A/2 H varies with A/2 H and (iii) inhibition of either some of the electron-transfer chains or some of the ~I +-ATPases, does not cause an overcapacity in the other, non-inhibited proton pumps. None of the earlier free-energy coupling schemes, alternative to delocalized protonic coupling, can account for these three anomalies. We propose to add a fifth postulate, namely that of the coupling unit, to the four existing postulates of 'delocalized protonic coupling' and show that, with this postulate, protonic coupling can again account for most experimental observations. We also discuss: (i) how experimental data that might seem to be at odds with the 'coupling unit' hypothesis can be accounted for and (ii) the problem of the spatial arrangement of the electrical field in the different free-energy coupling schemes.
Molecular Biology Reports, 2002
Nature Biotechnology, 2008