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PubMed2005

Synuclein, dopamine and oxidative stress: co-conspirators in Parkinson's disease?

The etiology of Parkinson's disease (PD) is presently unknown. The unifying hallmark of disease is depletion of dopamine and loss of nigrostriatal dopamine neurons. Familial and sporadic forms of the disease are described. The familial mutations occur within alpha-synuclein and molecules involved in protein degradation and mitochondrial function. Sporadic PD is thought to involve the interplay of genetic and environmental factors. Despite disparate initiating triggers, a convergent pathobiologic model for this common neurodegenerative disease has been proposed. Likely players have emerged that may form the basis for this common pathway model of disease. In this review, we examine the role of three most implicated PD pathogenic conspirators: synuclein, dopamine and oxidative stress.

Animals↗

PubMed2006

Shewanella oneidensis MR-1 fluxome under various oxygen conditions.

The central metabolic fluxes of Shewanella oneidensis MR-1 were examined under carbon-limited (aerobic) and oxygen-limited (microaerobic) chemostat conditions, using 13C-labeled lactate as the sole carbon source. The carbon labeling patterns of key amino acids in biomass were probed using both gas chromatography-mass spectrometry (GC-MS) and 13C nuclear magnetic resonance (NMR). Based on the genome annotation, a metabolic pathway model was constructed to quantify the central metabolic flux distributions. The model showed that the tricarboxylic acid (TCA) cycle is the major carbon metabolism route under both conditions. The Entner-Doudoroff and pentose phosphate pathways were utilized primarily for biomass synthesis (with a flux below 5% of the lactate uptake rate). The anaplerotic reactions (pyruvate to malate and oxaloacetate to phosphoenolpyruvate) and the glyoxylate shunt were active. Under carbon-limited conditions, a substantial amount (9% of the lactate uptake rate) of carbon entered the highly reversible serine metabolic pathway. Under microaerobic conditions, fluxes through the TCA cycle decreased and acetate production increased compared to what was found for carbon-limited conditions, and the flux from glyoxylate to glycine (serine-glyoxylate aminotransferase) became measurable. Although the flux distributions under aerobic, microaerobic, and shake flask culture conditions were different, the relative flux ratios for some central metabolic reactions did not differ significantly (in particular, between the shake flask and aerobic-chemostat groups). Hence, the central metabolism of S. oneidensis appears to be robust to environmental changes. Our study also demonstrates the merit of coupling GC-MS with 13C NMR for metabolic flux analysis to reduce the use of 13C-labeled substrates and to obtain more-accurate flux values.

Algorithms↗

PubMed2007

Dynamics of tyrosine hydroxylase mediated regulation of dopamine synthesis.

Tyrosine hydroxylase's catalysis of tyrosine to dihydroxyphenylalanine (DOPA) is the highly regulated, rate-limiting step catalyzing the synthesis of the catecholamine neurotransmitter dopamine. Phosphorylation, cofactor-mediated regulation, and the cell's redox status, have been shown to regulate the enzyme's activity. This paper incorporates these regulatory mechanisms into an integrated dynamic model that is capable of demonstrating relative rates of dopamine synthesis under various physiological conditions. Most of the kinetic equations and substrate parameters used in the model correspond with published experimental data, while a few which were not available in literature have been optimized based on explicit assumptions. This kinetic pathway model permits a comparison of the relative regulatory contributions made by variations in substrate, phosphorylation, and redox status on enzymatic activity and permits predictions of potential disease states. For example, the model correctly predicts the recent observation that individuals with haemochromatosis and having excessive iron accumulation are at increased risk for acquiring Parkinsonism, a defect in neuronal dopamine synthesis (Bartzokis et al., 2004; Costello et al., 2004). Alpha synuclein mediated regulation of tyrosine hydroxylase has also been incorporated in the model, allowing an insight into the overexpression and aggregation of alpha synuclein in Parkinson's disease.

Dopamine↗

PubMed1972

A mechanism of action for carboxypeptidase A.

In an attempt to gain a better understanding of the mechanism of action of carboxypeptidase A (EC 3.4.2.1), many kinetic studies have been undertaken using numerous substrates-both esters and peptides-that have exhibited substrate linearity, inhibition, activation, and sigmoid-shaped rate plots. Numerous interpretations of the kinetic data have been proposed, none of which are fully in accord both with kinetic data and x-ray crystallographic studies. Much of the kinetic data has been interpreted using multisite binding while the x-ray information seems to severely restrict these possibilities. We have examined the feasibility of a simple model with a single active site, without modifier sites, that allows only one substrate molecule to bind the enzyme at a time. A random-pathway model was identified that simultaneously accounts for the nonlinear kinetic data and meets the restrictions imposed by the x-ray crystallographic studies.

Binding Sites↗

PubMed2000

Genetic and environmental influences on behavioral disinhibition.

Comorbidity among childhood disruptive behavioral disorders is commonly reported in both epidemiologic and clinical studies. These problems are also associated with early substance use and other markers of behavioral disinhibition. Previous twin research has suggested that much of the covariation between antisocial behavior and alcohol dependence is due to common genetic influences. Similar results have been reported for conduct problems and hyperactivity. For the present study, an adolescent sample consisting of 172 MZ and 162 DZ twin pairs, recruited through the Colorado Twin Registry and the Colorado Longitudinal Twin Study were assessed using standardized psychiatric interviews and personality assessments. DSM-IV symptom counts for conduct disorder and attention deficit hyperactivity disorder, along with a measure of substance experimentation and novelty seeking, were used as indices of a latent behavioral disinhibition trait. A confirmatory factor model fit to individual-level data showed a strong common factor accounting for 16-42% of the observed variance in each measure. A common pathway model evaluating the genetic and environmental architecture of the latent phenotype suggested that behavioral disinhibition is highly heritable (a(2) = 0.84), and is not influenced significantly by shared environmental factors. A residual correlation between conduct disorder and substance experimentation was explained by shared environmental effects, and a residual correlation between attention deficit hyperactivity disorder and novelty seeking was accounted for by genetic dominance. These results suggest that a variety of adolescent problem behaviors may share a common underlying genetic risk.

Adolescent↗

PubMed1995

Drug-related morbidity and mortality. A cost-of-illness model.

BACKGROUND: Preventable drug-related morbidity and mortality represent a serious medical problem that urgently requires expert attention. The costs to society of the misuse of prescription medications, in terms of morbidity, mortality, and treatment, can be immense. To date, research has primarily documented increased rates of hospitalization secondary to medication noncompliance and/or adverse drug effects. OBJECTIVES: To develop a conceptual model of drug-related morbidity and mortality, and to estimate the associated costs in the ambulatory setting in the United States. METHODS: A probability pathway model was developed to estimate the cost of drug-related morbidity and mortality in the United States. Pharmacist practitioners were surveyed to determine conditional probabilities of therapeutic outcomes owing to drug therapy. Health care utilization and associated costs owing to negative therapeutic outcomes were estimated. RESULTS: Drug-related morbidity and mortality was estimated to cost $76.6 billion in the ambulatory setting in the United States. The largest component of this total cost was associated with drug-related hospitalizations. When assumptions of the model were varied, the estimated cost ranged from a conservative estimate of $30.1 to $136.8 billion in a worst-case scenario. CONCLUSIONS: The cost of drug-related morbidity and mortality in the ambulatory setting in the United States is considerable and should be considered in health policy decisions with regard to pharmaceutical benefits. Policies and services should be developed to reduce and prevent drug-related morbidity and mortality.

Cost of Illness↗

PubMed2004

Oxidative DNA damage background estimated by a system model of base excision repair.

Human DNA can be damaged by natural metabolism through free radical production. It has been suggested that the equilibrium between innate damage and cellular DNA repair results in an oxidative DNA damage background that potentially contributes to disease and aging. Efforts to quantitatively characterize the human oxidative DNA damage background level, based on measuring 8-oxoguanine lesions as a biomarker, have led to estimates that vary over three to four orders of magnitude, depending on the method of measurement. We applied a previously developed and validated quantitative pathway model of human DNA base excision repair, integrating experimentally determined endogenous damage rates and model parameters from multiple sources. Our estimates of at most 100 8-oxoguanine lesions per cell are consistent with the low end of data from biochemical and cell biology experiments, a result robust to model limitations and parameter variation. Our findings show the power of quantitative system modeling to interpret composite experimental data and make biologically and physiologically relevant predictions for complex human DNA repair pathway mechanisms and capacity.

DNA Damage↗

PubMed2006

Automated sensitivity analysis of stiff biochemical systems using a fourth-order adaptive step size Rosenbrock integration method.

Sensitivity analysis is one of the most effective approaches for studying mathematical models of biochemical systems. A stiff Rosenbrock integrator has been developed for sensitivity analysis using a direct sensitivity approach. Automated sparse Jacobian and Hessian calculations of the coupled system (the original model equations and the sensitivity equations) have been implemented in the freely available software package CellSim. The accuracy and efficiency of the integrator are tested extensively on the complex mitogen-activated protein kinase (MAPK) pathway model of Bhalla and Iyengar. Both time-dependent concentration and parameter-based sensitivity coefficients are measured using several integration schemes. The method is shown to perform sensitivity analysis in a manner that is cost effective with moderate accuracy. The error control strategy between the decoupled direct method and the Rosenbrock with direct method is discussed and their computational accuracies are compared. The method is used to analyse the positive feedback loop within the MAPK signal transduction pathway.

Algorithms↗

PubMed2004

Modeling and simulation of biological systems with stochasticity.

Mathematical modeling is a powerful approach for understanding the complexity of biological systems. Recently, several successful attempts have been made for simulating complex biological processes like metabolic pathways, gene regulatory networks and cell signaling pathways. The pathway models have not only generated experimentally verifiable hypothesis but have also provided valuable insights into the behavior of complex biological systems. Many recent studies have confirmed the phenotypic variability of organisms to an inherent stochasticity that operates at a basal level of gene expression. Due to this reason, development of novel mathematical representations and simulations algorithms are critical for successful modeling efforts in biological systems. The key is to find a biologically relevant representation for each representation. Although mathematically rigorous and physically consistent, stochastic algorithms are computationally expensive, they have been successfully used to model probabilistic events in the cell. This paper offers an overview of various mathematical and computational approaches for modeling stochastic phenomena in cellular systems.

Algorithms↗

PubMed2003

Structural modeling analysis of prospective risk factors for eating disorder.

Many variables have been suggested as possible risk factors for eating disorders (ED), although the validity of these suggestions has seldom been tested causally. The current study tested a pathway model for the development of ED using prospective data from a randomly selected sample of 807 women, aged 18-32 years, from the general population of Sweden. Data was collected using self-report questionnaires with well-established psychometric properties. The cardinal symptoms of binge eating, purging, and fear of weight gain according to the DSM-IV characterized ED. Data supported the hypothesized model suggesting that low self-esteem, low perceived social support from the family, high levels of body concern, and high relative use of escape avoidance coping constitute a risk profile for later development of ED. Given the results and the fact that these risk factors can be modified, their practical utility and clinical significance should be examined in prevention studies.

Journal Article↗

PubMed2005

Water clusters on graphite: methodology for quantum chemical a priori prediction of reaction rate constants.

The properties, interactions, and reactions of cyclic water clusters (H(2)O)(n=1-5) on model systems for a graphite surface have been studied using pure B3LYP, dispersion-augmented density functional tight binding (DFTB-D), and integrated ONIOM(B3LYP:DFTB-D) methods. Coronene C(24)H(12) as well as polycircumcoronenes C(96)H(24) and C(216)H(36) in monolayer, bilayer, and trilayer arrangements were used as model systems to simulate ABA bulk graphite. Structures, binding energies, and vibrational frequencies of water clusters on mono- and bilayer graphite models have been calculated, and structural changes and frequency shifts due to the water cluster-graphite interactions are discussed. ONIOM(B3LYP:DFTB-D) with coronene and water in the high level and C(96)H(24) in the low level mimics the effect of extended graphite pi-conjugation on the water-graphite interaction very reasonably and suggests that water clusters only weakly interact with graphite surfaces, as suggested by the fact that water is an excellent graphite lubricant. We use the ONIOM(B3LYP:DFTB-D) method to predict rate constants for model pathways of water dissociative adsorption on graphite. Quantum chemical molecular dynamics (QM/MD) simulations of water clusters and water addition products on the C(96)H(24) graphite model are presented using the DFTB-D method. A three-stage strategy is devised for a priori investigations of high temperature corrosion processes of graphite surfaces due to interaction with water molecules and fragments.

Journal Article↗

PubMed2000

The MAPK kinase kinase TAK1 plays a central role in coupling the interleukin-1 receptor to both transcriptional and RNA-targeted mechanisms of gene regulation.

Mechanisms of fulminant gene induction during an inflammatory response were investigated using expression of the chemoattractant cytokine interleukin-8 (IL-8) as a model. Recently we found that coordinate activation of NF-kappaB and c-Jun N-terminal protein kinase (JNK) is required for strong IL-8 transcription, whereas the p38 MAP kinase (MAPK) pathway stabilizes the IL-8 mRNA. It is unclear how these pathways are coupled to the receptor for IL-1, an important physiological inducer of IL-8. Expression of the MAP kinase kinase kinase (MAPKKK) TAK1 together with its coactivator TAB1 in HeLa cells activated all three pathways and was sufficient to induce IL-8 formation, NF-kappaB + JNK2-mediated transcription from a minimal IL-8 promoter, and p38 MAPK-mediated stabilization of a reporter mRNA containing IL-8-derived regulatory mRNA sequences. Expression of a kinase-inactive mutant of TAK1 largely blocked IL-1-induced transcription and mRNA stabilization, as well as formation of endogenous IL-8. Truncated TAB1, lacking the TAK1 binding domain, or a TAK1-derived peptide containing a TAK1 autoinhibitory domain were also efficient in inhibition. These data indicate that the previously described three-pathway model of IL-8 induction is operative in response to a physiological stimulus, IL-1, and that the MAPKKK TAK1 couples the IL-1 receptor to both transcriptional and RNA-targeted mechanisms mediated by the three pathways.

Adaptor Proteins, Signal Transducing↗

PubMed1986

Significance of contaminated food in collective dose after a severe reactor accident.

The importance of the ingestion dose pathways in collective effective dose due to severe reactor accidents is evaluated by studying two different radioactive accidental releases. A short description of the ingestion dose pathway model is also given. Typically, exposure via contaminated food without countermeasures causes considerably more than half of the collective effective dose in the long term, and milk consumption is the most important pathway. Also the season when the release occurs has a major effect on the doses and on the areas where food products should be interdicted.

Accidents↗

PubMed2003

Direction of causation modeling between cross-sectional measures of parenting and psychological distress in female twins.

Under certain conditions, cross-sectional analysis of cross-twin intertrait correlations can provide important information about the direction of causation (DOC) between two variables. A community-based sample of Australian female twins aged 18 to 45 years was mailed an extensive Health and Lifestyle Questionnaire (HLQ) that covered a wide range of personality and behavioral measures. Included were self-report measures of recent psychological distress and perceived childhood environment (PBI). Factor analysis of the PBI yielded three interpretable dimensions: Coldness, Overprotection, and Autonomy. Univariate analysis revealed that parental Overprotection and Autonomy were best explained by additive genetic, shared, and nonshared environmental effects (ACE), whereas the best-fitting model for PBI Coldness and the three measures of psychological distress (Depression, Phobic Anxiety, and Somatic Distress) included only additive genetic and nonshared environmental effects (AE). A common pathway model best explained the covariation between (1) the three PBI dimensions and (2) the three measures of psychological distress. DOC modeling between latent constructs of parenting and psychological distress revealed that a model which specified recollected parental behavior as the cause of psychological distress provided a better fit than a model which specified psychological distress as the cause of recollected parental behavior. Power analyses and limitations of the findings are discussed.

Adolescent↗

PubMed2004

Decoupling dynamical systems for pathway identification from metabolic profiles.

RATIONALE: Modern molecular biology is generating data of unprecedented quantity and quality. Particularly exciting for biochemical pathway modeling and proteomics are comprehensive, time-dense profiles of metabolites or proteins that are measurable, for instance, with mass spectrometry, nuclear magnetic resonance or protein kinase phosphorylation. These profiles contain a wealth of information about the structure and dynamics of the pathway or network from which the data were obtained. The retrieval of this information requires a combination of computational methods and mathematical models, which are typically represented as systems of ordinary differential equations. RESULTS: We show that, for the purpose of structure identification, the substitution of differentials with estimated slopes in non-linear network models reduces the coupled system of differential equations to several sets of decoupled algebraic equations, which can be processed efficiently in parallel or sequentially. The estimation of slopes for each time series of the metabolic or proteomic profile is accomplished with a 'universal function' that is computed directly from the data by cross-validated training of an artificial neural network (ANN). CONCLUSIONS: Without preprocessing, the inverse problem of determining structure from metabolic or proteomic profile data is challenging and computationally expensive. The combination of system decoupling and data fitting with universal functions simplifies this inverse problem very significantly. Examples show successful estimations and current limitations of the method. AVAILABILITY: A preliminary Web-based application for ANN smoothing is accessible at http://bioinformatics.musc.edu/webmetabol/. S-systems can be interactively analyzed with the user-friendly freeware PLAS (http://correio.cc.fc.ul.pt/~aenf/plas.html) or with the MATLAB module BSTLab (http://bioinformatics.musc.edu/bstlab/), which is currently being beta-tested.

Algorithms↗

PubMed1994

COMIDA: a radionuclide food chain model for acute fallout deposition.

A dynamic food chain model and computer code, named "COMIDA," has been developed to estimate radionuclide concentrations in agricultural food products following an acute fallout event. COMIDA estimates yearly harvest concentrations for five human crop types (Bq kg-1 crop per Bq m-2 deposited) and integrated concentrations for four animal products (Bq d kg-1 animal product per Bq m-2) for a unit deposition that occurs on any user-specified day of the year. COMIDA is structurally very similar to the PATHWAY model and includes the same seasonal transport processes and discrete events for soil and vegetation compartments. Animal product assimilation is modeled using simpler equilibrium models. Differential transport and ingrowth of up to three radioactive progeny are also evaluated. Benchmark results between COMIDA and PATHWAY for monthly fallout events show very similar seasonal agreement for integrated concentrations in milk and beef. Benchmark results between COMIDA and four international steady-state models show good agreement for deposition events that occur during the middle of the growing season. COMIDA will be implemented in the new Department of Energy version of the MELCOR Accident Consequence Code System for evaluation of accidental releases from nuclear power plants.

Computer Simulation↗

PubMed2001

Memory-driven movements in limb apraxia: is there evidence for impaired communication between the dorsal and the ventral streams?

Memory-driven reaching and grasping movements were analysed in patients with left cerebral hemispheric damage and impaired gesture imitation. The dorsal and ventral streams of the visual pathway model of Milner and Goodale (Milner and Goodale, The Visual Brain in Action, 1995) are thought to operate relatively independently. However, cross-connections between the areas of each pathway are likely to enable interactions essential for higher-level praxis. Apraxic errors such as seen in gesture imitation can possibly be understood as arising from a disconnection of the two visual pathways. If the integrated action of the perceptual and visuomotor systems in patients with apraxia is compromised, then we would expect to find indications of impaired motor programming and misreaching in these patients when making movements driven by stored representations. Such a pattern, however, was not found in our sample of apraxic patients. Patients with limb apraxia produced normal movement kinematics and normal end-point accuracy when making memory-driven reaching movements with or without visual guidance of movement. Furthermore, perceptual information about object size and object distance were incorporated as normal in memory-driven grasping movements of these patients.

Aged↗

PubMed1994

In vitro-in vivo correlation of percutaneous absorption: isosorbide dinitrate and morphine hydrochloride.

The potential of an in vitro skin preparation as a model for predicting in vivo percutaneous absorption of drugs was examined. In vitro and in vivo skin permeation data for two model drugs with different lipophilicity, isosorbide dinitrate (ISDN) and morphine hydrochloride (MPH), were compared using pharmacokinetic techniques. In vitro permeation data published previously were analyzed based on a single pathway model, and permeation parameters were obtained. The disposition parameters were estimated from the plasma concentration profiles after i.v. administration. The plasma concentrations after topical application were then simulated using the obtained permeation and disposition parameters, and the values were compared with the corresponding observed ones. Although the simulated plasma concentration curves were not greatly different from those observed, there were some differences in the time course-pattern. Causes for these in vitro-in vivo differences were discussed.

Animals↗