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PubMed1996

Activities of enzymes in platelet activating factor biosynthetic pathways in the gerbil model of cerebral ischemia.

The activities of enzymes in platelet activating factor (PAF) biosynthetic pathways were analyzed in hippocampal and cerebral cortical regions of normal and ischemic gerbil brain to assess changes in enzyme activities and potential modulators that could explain the accentuated production of PAF seen in ischemia. Global forebrain ischemia was produced by bilateral carotid artery ligation, and the effectiveness of the ligation was shown by free fatty acid release and ATP depletion. Specific activities of 1-alkyl-2-acetyl-sn-glycerol (AAG) choline phosphotransferase, 1-alkyl-sn-glycero-3-phosphate (AGP) acetyl transferase, and 1-alkyl-sn-glycero-3-phosphocholine (lyso PAF) acetyl transferase in tissue homogenates were in the ratio 4:1:0.1, respectively. Sham-operated and ischemic or ischemic-reperfused tissues showed similar activities for individual enzymes, indicating that enzyme levels or activation states did not change in ischemic or reperfused tissues. However, small metabolites (relevant to ischemia) added to the in vitro assays did modify enzyme activities. Physiological concentrations of MgATP severely inhibited AGP acetyl transferase activity, and this resulted in the ratio of AGP acyl transferase to AGP acetyl transferase activities changing from 48:1 in the presence of 2.5 mM MgATP to 6:1 in the absence of MgATP. This suggests that falling ATP levels in cerebral ischemia may promote the de novo pathway of PAF biosynthesis by releasing inhibition of AGP acetyl transferase. Lyso PAF acetyl transferase was much less active than AGP acetyl transferase and was also inhibited by MgATP. AAG choline phosphotransferase was not inhibited by MgATP but was inhibited by calcium. However the superior specific activity of the choline phosphotransferase in comparison with the AGP acetyl transferase suggested that the lowered choline phosphotransferase activity in the presence of rising intracellular calcium would not seriously compromise the synthesis of PAF by the de novo route. Both acetyl transferase enzymes were also inhibited by oleoyl CoA.

Acetyltransferases↗
PubMed2002

Modeling the energy transfer pathways. creatine kinase activities and heterogeneous distribution of ADP in the perfused heart.

The exchange scheme of high energy phosphate transport in a whole heart relies on a system of CK functioning in different ways. This suggests that the CKs are able to act both like a shuttle and like a buffer for the energy transfer. The challenge is to understand how these two functions are balanced in the CK system. One key of this balance is the knowledge of the local concentrations of the ADP nucleotide. These concentrations cannot be directly measured, but they may be derived by computation. In the present report we introduce the known properties of the enzymes catalyzing the exchange of high energy phosphate into the model of flux pathways derived from NMR experiments to compute both the maximum activity of each enzyme and the local concentrations of all the substrates. We show that the ADP distribution must be heterogeneous for the system to work. Its concentration is 50% higher in the vicinity of ATPase sites and 50% lower in the intermembrane space of the mitochondria than in the cytosol. Another result of this analysis is that the apparent large unbalance of the CKmito pathway is imposed by the adenosine nucleotide transferase fluxes. This analysis proves that it is possible to deduce biochemistry the local concentrations of a substrate by combining data originating from NMR, and enzymology into a common model.

Adenosine Diphosphate↗
PubMed1994

Structure identifiability in metabolic pathways: parameter estimation in models based on the power-law formalism.

An important step in understanding a metabolic pathway is to identify its structure, in terms of the flow of material and information. In pursuing this goal, the available information for a given system is usually obtained from experiments in vitro and comes from different sources. Frequently, the final set of regulatory signals acting in the system in vivo is unclear, and some kind of test is needed on the intact system. Besides defining an appropriate experimental approach, identification of the regulatory pattern needs a theoretical framework in which the different experimental measurements can be evaluated and a final picture can be agreed on. Mathematical approaches based on sensitivity coefficients provide a useful tool for addressing this problem. Within this framework, the appropriate parameters are related to both the structure of the reaction network and the signals that regulate the target system. Thus the identification of the regulatory structure can be related to the estimation of the appropriate set of parameters. In pursuing this goal, we will show the limitations of using steady-state measurements and the usefulness of using dynamic data. We suggest a way to test the regulatory pattern in a given metabolic pathway by combining both kinds of data, and we show, by using a reference system, the potential of the method suggested.

Metabolism↗
PubMed2006

Approximations and their consequences for dynamic modelling of signal transduction pathways.

Signal transduction is the process by which the cell converts one kind of signal or stimulus into another. This involves a sequence of biochemical reactions, carried out by proteins. The dynamic response of complex cell signalling networks can be modelled and simulated in the framework of chemical kinetics. The mathematical formulation of chemical kinetics results in a system of coupled differential equations. Simplifications can arise through assumptions and approximations. The paper provides a critical discussion of frequently employed approximations in dynamic modelling of signal transduction pathways. We discuss the requirements for conservation laws, steady state approximations, and the neglect of components. We show how these approximations simplify the mathematical treatment of biochemical networks but we also demonstrate differences between the complete system and its approximations with respect to the transient and steady state behavior.

Feedback, Physiological↗
PubMed2026

BioEMMA: Automated Generation of Model-Specific Escher-Compatible Maps from KEGG Pathways.

Genome-scale metabolic models are widely used to investigate cellular metabolism, but their interpretation and comparison are limited by the lack of reproducible pathway-level visualizations with a common spatial organization. This study presents BioEMMA, a Python-based tool for the automated generation of model-specific metabolic pathway maps in the Escher JSON format using coordinate information from curated KEGG pathway maps. BioEMMA parses KGML files, map reaction and metabolite identifiers to model database namespaces, filters pathway elements according to an input SBML model, adds non-primary metabolites, reconstructs Escher-compatible layouts, and supports flux visualization. The tool was integrated into a reproducible BioUML workflow for metabolic model reconstruction. BioEMMA was evaluated using the e_coli_core model and the KEGG glycolysis/gluconeogenesis pathway while generating a model-specific map with overlaid FBA fluxes. It was then applied to compare E. coli reconstructions generated by gapseq, ModelSEEDpy, and Reconstructor across three central carbon metabolism pathways. To broaden the evaluation, BioEMMA was applied using 87 prokaryotic BiGG models and three eukaryotic models. The analysis revealed pathway-specific differences in reaction coverage, shared and model-specific reactions, and predicted flux activity. BioEMMA therefore provides a reproducible framework for pathway-level visualization and comparison of genome-scale metabolic reconstructions within a common spatial coordinate system.

Escher maps↗
PubMed2006

A model of the ethylene signaling pathway and its gene response in Arabidopsis thaliana: pathway cross-talk and noise-filtering properties.

Dynamic models of molecular networks and pathways enable in silico evaluations of the consistency of proposed interactions and the outcomes of perturbations as well as of hypotheses on system-level structure and function. We postulate a continuous model of the activation dynamics of the ethylene response factor 1 (ERF1) gene in response to ethylene signaling. This activation elicits the response of the plant defensin 1 (PDF1) gene, which also responds to jasmonic acid, and the inhibition of the putative auxin responsive factor 2 (ARF2) gene, that also responds to auxin. Our model allows the effect of different ethylene concentrations in eliciting contrasting genetic and phenotypic responses to be evaluated allows the effect of different ethylene concentrations in eliciting contrasting genetic and phenotypic responses to be evaluated and seems to consider key components of the ethylene pathway because the ERF1 dose-response curve that we predict has the same qualitative form as the phenotypic dose-response curves obtained experimentally. Therefore, our model suggests that the phenotypic dose-response curves obtained experimentally could be due, at least in part, to ERF1 changes to different ethylene concentrations. Stability analyses show that the model's results are robust to parameter estimates. Of interest is that our model predicts that the ethylene pathway may filter stochastic and rapid chaotic fluctuations in ethylene availability. This novel approach may be applied to any cellular signaling and response pathway in plants and animals.

Arabidopsis↗
PubMed2006

Alternation of substance P-containing neural pathways in a rat model of irritable bowel syndrome with rectal distension.

OBJECTIVE: Irritable bowel syndrome (IBS) is a common disorder in clinical practice, but the pathophysiology of IBS has not been completely elucidated yet. Experiments have revealed that the concentrations of some kinds of brain-gut peptides, such as substance P, were abnormal in the plasma and/or the intestinal mucosa. In order to explore further the possible role of substance P containing nerve fibers in the enteric nervous system and central nervous system, the expression of c-fos, a well-established marker of activated neural pathway, was induced to show substance P containing a neural pathway in the rat model of constipation-predominant IBS by rectal distention. METHODS: The rat model was set up by intragastric instillation of 2.0 mL water at 0-4 degrees C in 20 male Wistar rats for two weeks. Both the model group and the controls underwent rectal distention under deep anesthesia. Sections containing the anatomical areas of interest were obtained and processed for c-fos protein and substance P immunohistochemistry using the strept avidin-biotin complex (SABC) method. The staining results were analyzed semi-quantitatively, using a computerized color image analyzer with two parameters: opacity density and immunoreactive areas. The statistical difference of the opacity density and immunoreactive areas between the two groups was analyzed by a t-test. Correlation analysis was used to investigate the relationship between the expression of substance P and c-fos protein of the same region in the model group. RESULTS: The opacity density of substance P immunoreactive tissues in the ileocecal junction, colon, the posterior horn of the spinal cord and the hypothalamus of the model group were all significantly higher compared with those in the control group (176.6 vs 155.5, 172.3 vs 152.0, 182.1 vs 160.2, 128.3 vs 117.9; P < 0.05, respectively). Meanwhile in the ileocecal junction, colon, the posterior horn of the spinal cord and the hypothalamus of the model group, the opacity density of c-fos protein-positive tissue were all significantly higher than those of the same region in the controls (120.9 vs 109.0, 101.3 vs 92.2, 125.4 vs 88.7, 115.5 vs 88.6; P < 0.05, respectively). The distribution of c-fos protein-positive tissue is similar to that of the substance P and the analysis shows that there is close correlation between the expression of substance P and c-fos protein of the same region in the model group (r = 0.594-0.721, P < 0.05). CONCLUSIONS: The expression of substance P and c-fos protein in both the enteric nervous system and the central nervous system of the constipation-predominant IBS rat model is abnormal, which suggests that an abnormal change in substance P may be involved in the pathogenesis of IBS and the substance P-containing neural pathway may be one of the neural pathways that play important role in the regulation of the gastrointestinal function.

Animals↗
PubMed2003

Bayesian modeling of complex metabolic pathways.

Many chronic diseases are the result of a complex sequence of biochemical reactions involving exposures to various environmental agents, metabolized by a number of different genes. Routine epidemiologic analyses of such associations have tended to rely on standard contingency table or logistic regression methods, typically focusing on one variable at a time or pairwise combinations. We consider two statistical alternatives to this approach, one based on Bayesian model averaging, one based on pharmacokinetic modeling of the biochemical pathways. These approaches are illustrated using data from a case-control study of colorectal polyps in relation to tobacco smoking and consumption of well done red meat, both viewed as sources of heterocyclic amines and polycyclic aromatic hydrocarbons. The new analyses are structured in a manner that attempts to take advantage of prior knowledge of the metabolism of these classes of compounds and the various genes that regulate these pathways.

Bayes Theorem↗
PubMed2006

Primary mouse hepatocytes for systems biology approaches: a standardized in vitro system for modelling of signal transduction pathways.

Complex cellular networks regulate regeneration, detoxification and differentiation of hepatocytes. By combining experimental data with mathematical modelling, systems biology holds great promises to elucidate the key regulatory mechanisms involved and predict targets for efficient intervention. For the generation of high-quality quantitative data suitable for mathematical modelling a standardised in vitro system is essential. Therefore the authors developed standard operating procedures for the preparation and cultivation of primary mouse hepatocytes. To reliably monitor the dynamic induction of signalling pathways, the authors established starvation conditions and evaluated the extent of starvation-associated stress by quantifying several metabolic functions of cultured primary hepatocytes, namely activities of glutathione-S-transferase, glutamine synthetase, CYP3A as well as secretion of lactate and urea into the culture medium. Establishment of constant metabolic activities after an initial decrease compared with freshly isolated hepatocytes showed that the cultured hepatocytes achieve a new equilibrium state that was not affected by our starving conditions. To verify the highly reproducible dynamic activation of signalling pathways in the in vitro system, the authors examined the JAK-STAT, SMAD, PI3 kinase, MAP kinase, NF-kappaB and Wnt/beta-catenin signalling pathways. For the induction of gp130, JAK1 and STAT3 phosphorylation IL6 was used, whereas TGFbeta was applied to activate the phosphorylation of SMAD1, SMAD2 and SMAD3. Both Akt/PKB and ERK1/2 phosphorylation were stimulated by the addition of hepatocyte growth factor. The time-dependent induction of a pool of signalling competent beta-catenin was monitored in response to the inhibition of GSK3beta. To analyse whether phosphorylation is actually leading to transcriptional responses, luciferase reporter gene constructs driven by multiple copies of TGFbeta-responsive motives were applied, demonstrating a dose-dependent increase in luciferase activity. Moreover, the induction of apoptosis by the TNF-like cytokine Fas ligand was studied in the in vitro system. Thus, the mouse hepatocyte in vitro system provides an important basis for the generation of high-quality quantitative data under standardised cell culture conditions that is essential to elucidate critical hepatocellular functions by the systems biology approach.

Animals↗
PubMed2004

Prediction of polychlorinated dibenzofuran congener distribution from gas-phase phenol condensation pathways.

A model for predicting the distribution of dibenzofuran and polychlorinated dibenzofuran (PCDF) congeners from a distribution of phenols was developed. The model is based on a simplified chemical mechanism. Relative rate constants and reaction order with respect to phenol precursors were derived from experimental results using single phenols and equal molar mixtures of up to four phenols. For validation, experiments were performed at three temperatures using a distribution of phenol and 19 chlorinated phenols as measured in municipal waste incinerator exhaust gas. Comparison of experimental measurements and model predictions for PCDF isomer distributions and homologue pattern shows agreement within measurement uncertainty. The R-squared correlation coefficient exceeds 0.9 for all PCDF isomer distributions and the distribution of PCDF homologues. These results demonstrate that the distribution of dibenzofuran and the 135 PCDF congeners from gas-phase condensation of phenol and chlorinated phenols can be predicted from measurement of the distribution of phenol and the 19 chlorinated phenol congeners.

Air Pollutants↗
PubMed2002

Comparative effects of unfractionated heparin and low molecular weight heparin on vascular endothelial cell tissue factor pathway inhibitor release: a model for assessing intrinsic thromboresistance.

OBJECTIVES: The purpose of our study was to characterize tissue factor pathway inhibitor (TFPI) release from human vascular endothelial cells following daily exposure to varying concentrations of unfractionated heparin (UFH) and low molecular weight heparin (LMWH). BACKGROUND: A "rebound" increase in ischemic/thrombotic events, including myocardial infarction and cardiovascular death, has been observed after the abrupt cessation of UFH. In a single center pilot study of patients with acute coronary syndromes (ACS) we reported that thrombin generation was evident within one (1) hour of UFH cessation, increased progressively over the subsequent 24 hours, correlated directly with factor VII activity and inversely with TFPI (concentration and activity). METHODS: Human umbilical vein endothelial cells were grown to confluence and incubated with varying concentrations of UFH or dalteparin, a low molecular weight haparin, for up to 144 hours. Daily samples of the cells supernatant were obtained and assayed for TFPI. Cellular reserve and responsiveness to recombinant endothelial cell growth factor (rEGF) stimulation were determined at 168 hours. RESULTS: In low concentrations (0.5 U/mL) UFH caused a progressive rise in TFPI concentration with a peak level of 6.36 +/- 0.5 ng/10(5) cells at 24 hours. By 72 hours of daily exposure, the levels declined to below control values and TFPI release following rEGF stimulation was reduced by approximately 60% compared to control (1.93 +/- 0.42 vs 4.3 +/- 0.78 ng/10(5) cells; p = 0.001). Initial endothelial cell release and rate of decline were more robust with high concentrations of UFH (5.0 U/ml). TFPI levels were above control values at each sampling time point up to 120 hours and cellular responsiveness to stimulation was preserved with dalteparin (compared to UFH) (p < 0.001). CONCLUSIONS: Thrombin generation and clinical events that occur during treatment with UFH and following its abrupt cessation may represent an acquired state of transiently impaired thromboresistance to the tissue factor-VIIa complex. The differing effects of UFH and LMWH on vascular endothelial cell TFPI synthesis, release and reserve with prolonged administration require further investigation.

Cells, Cultured↗
PubMed2005

Control of genomic instability and epithelial tumor development by the p53-Fbxw7/Cdc4 pathway.

Mouse models of cancer have provided novel insights into the timing of p53 loss during tumorigenesis. We have recently identified Fbxw7/Cdc4 as a downstream target of p53 loss that controls genomic instability and tumor development in epithelial tumors. Although p53-deficient mice primarily develop lymphomas and sarcomas, the additional loss of one copy of the Fbxw7 gene drives tumor development in a range of epithelial tissues. These data highlight the importance of genetic instability at the chromosome level in the development of common cancer types, and further illustrate the value of mouse models in identifying causal genetic events in epithelial tumor formation.

Animals↗
PubMed2006

Structural modeling and analysis of signaling pathways based on Petri nets.

The purpose of this paper is to discuss how to model and analyze signaling pathways by using Petri net. Firstly, we propose a modeling method based on Petri net by paying attention to the molecular interactions and mechanisms. Then, we introduce a new notion "activation transduction component" in order to describe an enzymic activation process of reactions in signaling pathways and shows its correspondence to a so-called elementary T-invariant in the Petri net models. Further, we design an algorithm to effectively find basic enzymic activation processes by obtaining a series of elementary T-invariants in the Petri net models. Finally, we demonstrate how our method is practically used in modeling and analyzing signaling pathway mediated by thrombopoietin as an example.

Algorithms↗
PubMed2005

Immunologic pathways in a quantitative model of immunosuppression based on rejection of an allogeneic or xenogeneic tumor graft.

BACKGROUND: A quantitative model of immunosuppression was previously developed based on the rejection of the allogeneic A/J murine tumor sarcoma 1 (Sa1) in immunocompetent mice. Here, the model is used to evaluate the immunologic mechanisms of graft rejection and to determine the potential of this model to detect synergistic effects of combined immunosuppressive therapies. METHODS: Wild-type, genetically-deficient, or drug-treated mice were used. Mice were challenged subcutaneously with the allogeneic murine tumor cell line, Sa1, or with the xenogenic human tumor, MDA435. Tumor growth was monitored with time, with increasing tumor size reflecting greater immunosuppression. In some cases, the mice were presensitized with either Sa1 or with A/J splenocytes. RESULTS: In naïve recipient mice, studies in major histocompatibility complex (MHC)-I-deficient mice and with depleting anti-CD8 monoclonal antibody (mAb) demonstrate that CD8 T cells are important for Sa1 rejection. A modest role for perforin but not for Fas/Fas ligand could be demonstrated. Blockade of CD4 T cells was more effective with decreasing histocompatibility barriers. In contrast, CD4 T cells were critical in second-set rejections, but CD8 T cells were not. Rejection of xenogeneic tumors was also T-cell dependent as demonstrated by anti-CD3 mAb, dependent on both CD4 and CD8 T cells as demonstrated using MHC-I- and MHC-II-deficient mice, but was more vigorous as demonstrated by the lack of effectiveness of immunosuppressive drugs in this model. CONCLUSIONS: This model can be used to define dominant and partial effects of immunologic pathways as well as synergistic interactions of agents to develop immunosuppressive strategies.

Animals↗
PubMed2006

Rofecoxib modulates multiple gene expression pathways in a clinical model of acute inflammatory pain.

New insights into the biological properties of cyclooxygenase-2 (COX-2) and its response pathway challenge the hypothesis that COX-2 is simply pro-inflammatory and inhibition of COX-2 solely prevents the development of inflammation and ameliorates inflammatory pain. The present study performed a comprehensive analysis of gene/protein expression induced by a selective inhibitor of COX-2, rofecoxib, compared with a non-selective COX inhibitor, ibuprofen, and placebo in a clinical model of acute inflammatory pain (the surgical extraction of impacted third molars) using microarray analysis followed by quantitative RT-PCR verification and Western blotting. Inhibition of COX-2 modulated gene expression related to inflammation and pain, the arachidonic acid pathway, apoptosis/angiogenesis, cell adhesion and signal transduction. Compared to placebo, rofecoxib treatment increased the gene expression of ANXA3 (annexin 3), SOD2 (superoxide dismutase 2), SOCS3 (suppressor of cytokine signaling 3) and IL1RN (IL1 receptor antagonist) which are associated with inhibition of phospholipase A(2) and suppression of cytokine signaling cascades, respectively. Both rofecoxib and ibuprofen treatment increased the gene expression of the pro-inflammatory mediators, IL6 and CCL2 (chemokine C-C motif ligand 2), following tissue injury compared to the placebo treatment. These results indicate a complex role for COX-2 in the inflammatory cascade in addition to the well-characterized COX-dependent pathway, as multiple pathways are also involved in rofecoxib-induced anti-inflammatory and analgesic effects at the gene expression level. These findings may also suggest an alternative hypothesis for the adverse effects attributed to selective inhibition of COX-2.

Acute Disease↗
PubMed1996

Constructing a new nigrostriatal pathway in the Parkinsonian model with bridged neural transplantation in substantia nigra.

The physical repair and restoration of a completely damaged pathway in the brain has not been achieved previously. In a previous study, using excitatory amino acid bridging and fetal neural transplantation, we demonstrated that a bridged mesencephalic transplant in the substantia nigra generated an artificial nerve pathway that reinnervated the striatum of 6-hydroxydopamine (6-OHDA)-lesioned rats. In the current study, we report that a bridged mesencephalic transplant can anatomically, neurochemically, and functionally reinstate the 6-OHDA-eradicated nigro-striatal pathway. An excitatory amino acid, kainic acid, laid down in a track during the transplant generated a trophic environment that effectively guided the robust growth of transplanted neuronal fibers in a bundle to innervate the distal striatum. Growth occurred at the remarkable speed of approximately 200 microm/d. Two separate and distinct types of dopamine (DA) innervation from the transplant have been achieved for the first time: (1) DA innervation of the striatum, and (2) DA innervation of the pars reticularis of the substantia nigra. In addition, neuronal tracing revealed that reciprocal connections were achieved. The grafted DA neurons in the SNr innervated the host's striatum, whereas the host's striatal neurons, in turn, innervated the graft within 3-8 weeks. Electrochemical volt- ammetry recording revealed the restoration of DA release and clearance in a broad striatal area associated with the DA reinnervation. Furthermore, the amphetamine-induced rotation was attenuated, which indicates that the artificial pathways were motor functional. This study provides additional evidences that our bridged transplantation technique is a potential means for the repair of a completely damaged neuronal pathway.

Animals↗
PubMed1995

Mathematical model of serine protease inhibition in the tissue factor pathway to thrombin.

A mathematical model has been developed to simulate the generation of thrombin by the tissue factor pathway. The model gives reasonable predictions of published experimental results without the adjustment of any parameter values. The model also accounts explicitly for the effects of serine protease inhibitors on thrombin generation. Simulations to define the optimum affinity profile of an inhibitor in this system indicate that for an inhibitor simultaneously potent against VIIa, IXa, and Xa, inhibition of thrombin generation decreases dramatically as the affinity for thrombin increases. Additional simulations show that the reason for this behavior is the sequestration of the inhibitor by small amounts of thrombin generated early in the reaction. This model is also useful for predicting the potency of compounds that inhibit thrombosis in rats. We believe that this is the first mathematical model of blood coagulation that considers the effects of exogenous inhibitors. Such a model, or extensions thereof, should be useful for evaluating targets for therapeutic intervention in the processes of blood coagulation.

Animals↗