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Results for “Pathway modelling”

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At least 433 records · Page 24Linked to original sources

PubMed2004

Increased excitability in cortico-striatal synaptic pathway in a model of paroxysmal dystonia.

Dystonias are movement disorders whose pathomechanism is largely unknown. Dystonic dt(sz) hamsters represent a model of primary dystonias, where alterations of striatal interneuron density and sodium channel function in projection neurones were described. Here, using cortico-striatal slices, we explore whether also the communication between neocortex and striatum is altered in dt(sz) hamsters. Field and intracellular recordings were done in dorsomedial striatum. Electrical stimulation was used to mimic neocortical afferents. Neuronal characteristics, synaptic connections, input-output relations and short- and long-term plasticity were analysed. Regarding cellular properties, striatal neurons of affected animals showed no alterations. Concerning network properties, evoked responses at threshold stimulation were mediated by (+/-)-alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA)/kainate receptors. In dt(sz) slices, field responses, paired-pulse accentuation and LTP were larger than in control, possibly by an increase in presynaptic release probability at glutamatergic synapses. In summary, the study indicates that a change of cortico-striatal communication is involved in the manifestation of paroxysmal dystonia in the dt(sz) mutant.

6-Cyano-7-nitroquinoxaline-2,3-dione↗

PubMed2000

Modeling of signaling pathways for endocrine disruptors.

The so called endocrine disruptors have become an important working hypothesis for a wide range of toxicology researchers. This hypothesis has also attracted those who have worked on designer estrogens or selective estrogen receptor modulators. Already numbers of substances have been identified as such chemicals, but there remain a large number of chemicals waiting to be tested for their endocrine modulating capabilities. Because of the time and costs required for wet lab tests, it is unrealistic to apply these kinds of tests to all such suspicious or probable chemicals. Thus some theoretical methods must be developed for this purpose. However the conventional QSAR (quantitative structure activity relationships) approach is of limited relevance to this problem, because these methods do not take detailed mechanisms of molecular interactions in biological systems into account. Thus we have developed a database complex system that enables one to trace molecular interactions triggered by interaction of receptors with xenobiotic chemicals. The main components of this database complex are a potential endocrine disruptor database, a receptor database, a cell signaling networks database, a transcription factor database, and an affinity binding database based on modes of actions.

Database Management Systems↗

PubMed2026

Small-Molecule Degradation of the MicroRNA-21 Precursor Rescues Pathogenic Pathways in Cellular Models of Fibrosis.

MicroRNAs (miRNAs) are short RNA molecules that bind to target mRNAs, resulting in translational repression and gene silencing. Overexpression of microRNA-21 (miR-21) is associated with various human diseases, including autosomal dominant polycystic kidney disease (ADPKD) and pulmonary fibrosis. In this study, a previously described heterobifunctional molecule, TGP-21-RiboTAC, that degrades the miR-21 precursor (pre-miR-21) in triple-negative breast cancer cells was investigated in polycystic kidney cell lines and a lung fibroblast cell line. In the former, TGP-21-RiboTAC degraded pre-miR-21 and derepressed miR-21's downstream targets, programmed cell death 4 (PDCD4) and peroxisome proliferator-activated receptor alpha (PPARα), known drivers of ADPKD. The heterobifunctional molecule also inhibited cyst growth and rescued the metabolic alterations that occur in ADPKD. In the lung fibroblast cell line, MRC-5, TGP-21-RiboTAC also reduced pre- and mature miR-21 levels, rescued transforming growth factor β (TGF-β)-induced repression of SMAD family member 7 (SMAD7), and inhibited cell invasion. Collectively, these studies demonstrate the potential of targeted RNA degradation as therapeutic agents that retard the development of organ fibrosis.

MicroRNAs↗

PubMed2006

Degradation of chlorpyrifos in aqueous chlorine solutions: pathways, kinetics, and modeling.

Chlorpyrifos (CP) was used as a model compound to develop experimental methods and prototype modeling tools to forecast the fate of organophosphate (OP) pesticides under drinking water treatment conditions. CP was found to rapidly oxidize to chlorpyrifos oxon (CPO) in the presence of free chlorine. The primary oxidant is hypochlorous acid (HOCl), kr = 1.72 (+/-0.68) x 10(6) M(-1)h(-1). Thus, oxidation is more rapid at lower pH (i.e., below the pKa of HOCl at 7.5). At elevated pH, both CP and CPO are susceptible to alkaline hydrolysis and degrade to 3,5,6-trichloro-2-pyridinol (TCP), a stable end product. Furthermore, hydrolysis of both CP and CPO to TCP was shown to be accelerated in the presence of free chlorine by OCl-, kOCl,CP = 990 (+/-200) M(-1)h(-1) and kOCl,CPO = 1340 (+/-110) M(-1)h(-1). These observations regarding oxidation and hydrolysis are relevant to common drinking water disinfection processes. In this work, intrinsic rate coefficients for these processes were determined, and a simple mechanistic model was developed that accurately predicts the temporal concentrations of CP, CPO, and TCP as a function of pH, chlorine dose, and CP concentration.

Chlorine↗

PubMed2000

Of genes and phenotypes: the immunological and molecular spectrum of combined immune deficiency. Defects of the gamma(c)-JAK3 signaling pathway as a model.

Cytokines play a major role in lymphoid development. Defects of the common gamma chain (gamma(c)) or of the JAK3 protein in humans have been shown to result in a severe combined immune deficiency (SCID), with a profound defect in T and natural killer (NK)-cell development, whereas B-cell generation is apparently unaffected (T-B+NK-SCID). While extensive molecular and biochemical analysis of these patients has been instrumental in understanding better the biological properties of the gamma(c) and JAK3 protein, an unexpected phenotypic heterogeneity of gamma(c) and JAK3 deficiency has emerged, indicating the need for appropriate and extensive investigations even in patients with atypical presentations. At the same time, characterization of the defects has been instrumental in the development of novel therapeutic approaches, from in utero hematopoietic stem cell transplantation to gene therapy.

Cytokines↗

PubMed2001

Paired human fibrosarcoma cell lines that possess or lack endogenous mutant N-ras alleles as experimental model for Ras signaling pathways.

We present here a human cell model for examination of mutant N-ras function. The HT1080 human fibrosarcoma cell line is pseudodiploid and contains a single endogenous mutant N-ras allele. MCH603c8 cells are a variant of HT1080 cells, in which the mutant allele has been deleted. The two cell lines differ dramatically in the constitutive levels of activation of downstream members of the Ras signaling pathways, and in biological features of transformation and tumorigenicity. Downregulation or activation of individual Ras-dependent pathways can be accomplished via transfection of dominant negatives or activated mutant cDNAs into HT1080 and MCH603c8 cells, respectively. The biochemical and biological consequences of expression of these mutant cDNAs can be assessed. There are dramatic effects on both the transformed and tumorigenic phenotype, depending on the cell line and mutant cDNA that is transfected.

Actins↗

PubMed1991

Structural modeling of functional neural pathways mapped with 2-deoxyglucose: effects of acoustic startle habituation on the auditory system.

This paper describes the first application of structural modeling to neuroscience. Structural modeling (also known as path analysis) is a method to assess the relative impact of directional links in a system and how these interrelations may change under different conditions. The objective was to demonstrate how structural modeling can be used to determine the functional interrelationships between brain structures that form the auditory system. Using structural modeling, changes in auditory system 2-DG uptake were examined during long- and short-term habituation of the acoustic startle reflex. Models were based on the anatomical connections between central auditory system structures. Using functional 2-DG data, the correlations between these structures were calculated and numerical weights were computed for each anatomical link. The analysis revealed that the lemniscal path was dominant during short-term habituation, while during long-term habituation this influence was modified through extra-lemniscal pathways. The models are discussed in the context of previous findings to demonstrate how structural modeling can not only complement, but also extract more information from 2-DG mapping experiments.

Acoustic Stimulation↗

PubMed1989

Kinetic model of bacteriorhodopsin photocycle: pathway from M state to bR.

A model of the last parts of the bacteriorhodopsin (bR) photocycle is proposed on the basis of experimental data for the kinetic behavior of the 'O' intermediate during a temperature pulse in distilled water suspension. The model includes the previously proposed (but not well characterized) intermediate 'N' between the 'M' and 'O' states of bR. This intermediate exists in fast temperature-dependent quasi-stationary equilibrium with the red-shifted intermediate 'O' and has a maximum of absorption close to the bR spectrum.

Bacteriorhodopsins↗

PubMed2005

FEDMA--a simple algorithm for theoretical modeling of linear metabolic pathways: from fuzzy data sets to prediction and experiment.

A theoretical model of a chain of irreversible Michaelis-Menten reactions proceeding inside a living cell, taking cell growth, division and subcellular compartmentation into account, was proposed. It became a basis for the construction of a "fuzzy" enzymatic data-modeling algorithm (FEDMA) - a procedure allowing the estimation of missing parameter values for the modeled system, in accordance both with the derived theoretical rules and the available experimental data. The obtained tool was tested to model the heme biosynthesis pathway in Saccharomyces cerevisiae, where about 40% of parameters remain unknown. The missing parameters estimated by means of FEDMA fall in the range of expected values.

Algorithms↗

PubMed2004

Model validation of biological pathways using Petri nets--demonstrated for apoptosis.

This paper demonstrates the first steps of a new integrating methodology to develop and analyse models of biological pathways in a systematic manner using well established Petri net technologies. The whole approach comprises step-wise modelling, animation, model validation as well as qualitative and quantitative analysis for behaviour prediction. In this paper, the first phase is addressed how to develop and validate a qualitative model, which might be extended afterwards to a quantitative model. The example used in this paper is devoted to apoptosis, the genetically programmed cell death. Apoptosis is an essential part of normal physiology for most metazoan species. Disturbances in the apoptotic process could lead to several diseases. The signal transduction pathway of apoptosis includes highly complex mechanisms to control and execute programmed cell death. This paper explains how to model and validate this pathway using qualitative Petri nets. The results provide a mathematically unique and valid model enabling the confirmation of known properties as well as new insights in this pathway.

Apoptosis↗

PubMed1996

Tiagabine prevents seizures, neuronal damage and memory impairment in experimental status epilepticus.

A novel antiepileptic drug, tiagabine ((R)-N-[4,4-di-(3-methylthien-2-yl) but-3-enyl] nipecotic acid hydrochloride), was studied in rats in order to determine its efficacy in preventing seizures, seizure-induced neuronal damage and impairment of spatial memory in the perforant pathway stimulation model of status epilepticus. In pilot experiments, administration of tiagabine (50, 100 or 200 mg/kg/day) with subcutaneously implanted Alzet osmotic pumps led to a dose-dependent increase in tiagabine concentrations in the serum and brain. Two days of tiagabine treatment at a dose range of 50-200 mg/kg/day did not change the levels of gamma-aminobutyric acid (GABA), glutamate or aspartate in cisternal cerebrospinal fluid (CSF) compared to the controls. In the pentylenetetrazol test, the maximal anticonvulsive effect of tiagabine administered via osmotic pumps was achieved already with a dose of 50 mg/kg/day. In the perforant pathway model of status epilepticus, subchronic treatment with tiagabine (Alzet pumps, 50 mg/kg/day) completely prevented the appearance of generalized clonic seizures during stimulation (P < 0.001). In the same rats, tiagabine treatment reduced the loss of pyramidal cells in the CA3c and CA1 fields of the hippocampus (P < 0.05) but not the loss of somatostatin immunoreactive neurons in the hilus. Two weeks after perforant pathway stimulation, the tiagabine-treated rats performed better in the Morris water-maze test than the vehicle-treated rats did (P < 0.001). Our results show that tiagabine treatment reduces the severity of seizures in the perforant pathway stimulation model of status epilepticus. Possibly associated with the reduction in seizure number and severity, tiagabine treatment also reduced seizure-induced damage to pyramidal cells in the hippocampus as well as the impairment of the spatial memory associated with hippocampal damage.

Animals↗

PubMed2003

Importance of sequence specificity for predicting protein folding pathways: perturbed Gaussian chain model.

Recent experimental and theoretical studies suggest that rates and pathways of protein folding are largely decided by topology of the native structures, at least for small proteins. However, some exceptions are known; for example, protein L and protein G have the same topology, but exhibit different characteristics of the TSE. Thus, folding pathways of some proteins are critically affected by detailed information on amino acid sequences. To investigate the sequence specificity, we calculate folding pathways of 20 small proteins using the perturbed Gaussian chain model developed by Portman et al. (Phys Rev Lett 1998;81:5237-5240; J Chem Phys 2001;114:5069-5081). Characteristics of the TSE predicted by the model are in good agreement with experimental phi-value data for many proteins at coarse-grained level. Especially, estimation of folding TSE for protein G and protein L based on both topology and additional sequence information are consistent with experimental phi-value data. With only topology information, however, the model predicts the TSE of protein G incorrectly. Moreover, the model that uses topology and sequence information describes free energy profiles of two-state and three-state folders consistently with experiment, whereas the topology only model predicts free energy profiles of some proteins incorrectly. This indicates that sequence specificity also has critical roles in determining the folding pathways for some proteins.

Bacterial Proteins↗

PubMed1997

Steady state approximation in the minimal model of the alternative pathway of complement.

Complement is a response mechanism of the immune system. Two initiation pathways have been characterized for complement. The classical pathway is antibody mediated while the alternative pathway is not. Since the alternative pathway is independent of antibodies, it is always active. For the alternative pathway we have previously developed a minimal model. Using parameters within physiological bounds, the model showed complex behavior also within physiological bounds. Thus the model seems to be an appropriate representation of the alternative pathway response. By applying a steady state assumption to the Michaelis Menten step of the minimal model, we reduce the number of variables from six to five. A comparison between the dynamics of the minimal and contracted models reveals that the two descriptions may not be compatible. Although both systems show chaotic behavior it occurs in different regions of parameter space.

Journal Article↗

PubMed1997

Chaos in a minimal model of the alternative pathway of the complement system.

In previous work, we introduced a minimal model of the alternative pathway of the complement. We also limited our analysis to a reduced set of parameter values because, for some parameters, experimentally supported estimates were not found. On the other hand, changes in value of some parameters may be a result of a pathological condition. Therefore, here we extend our analysis and include a wider range of values of five of the physiologically relevant parameters. For all the parameters considered, we observe chaotic oscillations, and we construct bifurcation diagrams using Poincaré sections of local maxima.

Journal Article↗

PubMed1989

Models of quantitative variation of flux in metabolic pathways.

As a model of variation in a quantitative character, enzyme activity variation segregating in a population is assumed to affect the flux in simple metabolic pathways. The genetic variation of flux is partitioned into additive and nonadditive components. An interaction component of flux variance is present because the effect of an allelic substitution is modified by other substitutions which change the concentrations of shared metabolites. In a haploid population, the the proportion of interaction variance is a function of the gene frequencies at the loci contributing to the flux variation, enzyme activities of mutant and wild type at variable loci and activities at nonvariable loci. The proportion of interaction variance is inversely related to the ratio of mutant to wild-type activities at the loci controlling the enzyme activities. The interaction component as a function of gene frequencies is at a maximum with high mutant allele frequencies. In contrast, the dominance component which would apply to a diploid population is maximal as a proportion of the total when mutant alleles are at low frequencies. Unless there are many loci with large differences in activity between the alleles, the interaction component is a small proportion of the total variance. Data on enzyme activity variation from natural and artificial populations suggest that such variation generates little nonadditive variance despite the highly interactive nature of the underlying biochemical system.

Alleles↗

PubMed2003

Transient and progressive electrophysiological alterations in the corticostriatal pathway in a mouse model of Huntington's disease.

Alterations in the corticostriatal pathway may precede symptomatology and striatal cell death in Huntington's disease (HD) patients. Here we examined spontaneous EPSCs in striatal medium-sized spiny neurons in slices from a mouse model of HD (R6/2). Spontaneous EPSC frequency was similar in young (3-4 weeks) transgenics and controls but decreased significantly in transgenics when overt behavioral symptoms began (5-7 weeks) and was most pronounced in severely impaired transgenics (11-15 weeks). These differences were maintained after bicuculline or tetrodotoxin, indicating they were specific to glutamatergic input and likely presynaptic in origin. Decreases in presynaptic and postsynaptic protein markers, synaptophysin and postsynaptic density-95, occurred in 11-15 week R6/2 mice, supporting the electrophysiological results. Furthermore, isolated, large-amplitude synaptic events (>100 pA) occurred more frequently in transgenic animals, particularly at 5-7 weeks, suggesting additional dysregulation of cortical inputs. Large events were blocked by tetrodotoxin, indicating a possible cortical origin. Addition of bicuculline and 4-aminopyridine facilitated the occurrence of large events. Riluzole, a compound that decreases glutamate release, reduced these events. Together, these observations indicate that both progressive and transient alterations occur along the corticostriatal pathway in experimental HD. These alterations are likely to contribute to the selective vulnerability of striatal medium-sized spiny neurons.

Animals↗

PubMed2002

Schema design and implementation of the grasp-related mirror neuron system.

Mirror neurons within a monkey's premotor area F5 fire not only when the monkey performs a certain class of actions but also when the monkey observes another monkey (or the experimenter) perform a similar action. It has thus been argued that these neurons are crucial for understanding of actions by others. We offer the hand-state hypothesis as a new explanation of the evolution of this capability: the basic functionality of the F5 mirror system is to elaborate the appropriate feedback - what we call the hand state - for opposition-space based control of manual grasping of an object. Given this functionality, the social role of the F5 mirror system in understanding the actions of others may be seen as an exaptation gained by generalizing from one's own hand to an other's hand. In other words, mirror neurons first evolved to augment the "canonical" F5 neurons (active during self-movement based on observation of an object) by providing visual feedback on "hand state," relating the shape of the hand to the shape of the object. We then introduce the MNS1 (mirror neuron system 1) model of F5 and related brain regions. The existing Fagg-Arbib-Rizzolatti-Sakata model represents circuitry for visually guided grasping of objects, linking the anterior intraparietal area (AIP) with F5 canonical neurons. The MNS1 model extends the AIP visual pathway by also modeling pathways, directed toward F5 mirror neurons, which match arm-hand trajectories to the affordances and location of a potential target object. We present the basic schemas for the MNS1 model, then aggregate them into three "grand schemas" - visual analysis of hand state, reach and grasp, and the core mirror circuit - for each of which we present a useful implementation (a non-neural visual processing system, a multijoint 3-D kinematics simulator, and a learning neural network, respectively). With this implementation we show how the mirror system may learn to recognize actions already in the repertoire of the F5 canonical neurons. We show that the connectivity pattern of mirror neuron circuitry can be established through training, and that the resultant network can exhibit a range of novel, physiologically interesting behaviors during the process of action recognition. We train the system on the basis of final grasp but then observe the whole time course of mirror neuron activity, yielding predictions for neurophysiological experiments under conditions of spatial perturbation, altered kinematics, and ambiguous grasp execution which highlight the importance of the timing of mirror neuron activity.

Animals↗

PubMed2003

KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data.

UNLABELLED: KnowledgeEditor is a graphical workbench for biological experts to model biomolecular network graphs. The modeled network data are represented by SRML, and can be published via the internet with the help of plug-in module 'GSCope'. KnowledgeEditor helps us to model and analyze biological pathways based on microarray data. It is possible to analyze the drawn networks by simulating up-down regulatory cascade in molecular interactions. AVAILABILITY: KnowledgeEditor is available at http://gscope.gsc.riken.go.jp/.

Cluster Analysis↗