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PubMed2001

Knowledge representation of signal transduction pathways.

MOTIVATIONS: Signal transduction is the common term used to define a diverse topic that encompasses a large body of knowledge about the biochemical mechanisms. Since most of the knowledge of signal transduction resides in scientific articles and is represented by texts in natural language or by diagrams, there is the need of a knowledge representation model for signal transduction pathways that can be as readily processed by a computer as it is easily understood by humans. RESULTS: A signal transduction pathway representation model is presented. It is based on a compound graph structure and is designed to handle the diversity and hierarchical structure of pathways. A prototype knowledge base was implemented on a deductive database and a number of biological queries are demonstrated on it.

Amino Acid Motifs↗

PubMed1996

Kinetic and thermodynamic studies of the folding/unfolding of a tryptophan-containing mutant of ribonuclease A.

Tryptophan was substituted for Tyr92 to create a sensitive and unique optical probe in order to study the unfolding and refolding kinetics of disulfide-intact bovine pancreatic ribonuclease A by fluorescence-detected stopped-flow techniques. The stability of the Trp mutant was found to be similar to that of wild-type RNase A when denatured by heat or GdnHCl, and the mutant was found to have 85% of the activity of the wild-type protein. Single-jump unfolding experiments showed that the unfolding pathway of the Trp mutant contains a fast and a slow phase similar to those seen previously for the wild-type protein, indicating that the mutation did not alter the unfolding pathway significantly. The activation energy of the slow-unfolding phase suggested that proline isomerization is involved, with the Trp residue presumably reporting on changes in its local environment. Single-jump refolding experiments revealed the presence of GdnHCl-independent burst phase and a native-like intermediate, most likely IN, on the folding pathway. Single-jump refolding data at various final GdnHCl concentrations were fit to a kinetic folding model involving two pathways to the native state; one pathway involves the intermediate IN, and the other is a direct one to the native state. This model provides site-specific information, since Trp92 monitors the formation of local structure only in the neighborhood of that residue. Double-jump refolding experiments permitted the detection of a previously reported, hydrophobically collapsed intermediate, I phi. The refolding data support the hypothesis that the region around position 92 is a chain-folding initiation site in the folding pathway.

Animals↗

PubMed1992

Patterns of spatiotemporal organization in an "ambiquitous" enzyme model.

Many enzymes in pathways such as glycolysis associate reversibly with cellular substructures. The spatiotemporal behavior of a "limit-cycle" oscillation model is studied under the condition that the "ambiquitous" oscillophor, phosphofructokinase, is partitioned between "bulk-phase" and "bound" forms in a heterogeneous system. Computer simulation demonstrates the occurrence of sustained, wave-like spatiotemporal patterns of chemical concentration in the bulk medium. Kinetic dissimilarity among the localized populations of bound enzyme leads to a "polarity" effect in the wave phenomenon. It is suggested that a key physiological role of the limit-cycle regime is to engender a rapid, site-to-site, signal-transmission modality in large eukaryotic (e.g., mammalian) cells.

Adenine Nucleotides↗

PubMed2002

The role of the ubiquitination-proteasome pathway in breast cancer: use of mouse models for analyzing ubiquitination processes.

Turnover of several regulatory proteins results from targeted destruction via ubiquitination and subsequent degradation through the proteosome. The timely and irreversible degradation of critical regulators is essential for normal cellular function. The precise biochemical mechanisms that are involved in protein turnover by ubiquitin-mediated degradation have been elucidated using in vitro assays and cell culture systems. However, pathways that lead to ubiquitination of critical regulatory proteins in vivo are more complex, and have both temporal and tissue-specific differences. In vivo models will allow identification of substrates and enzymes of the ubiquitin-proteosome pathway that play important roles in selected tissues and diseases. In addition, assessment of the therapeutic efficacy of drugs designed to inhibit or enhance protein turnover by ubiquitination requires in vivo models. In the present review we describe selected examples of transgenic and knockout models of proteins that are known either to be regulated by ubiquitin-mediated degradation or to have a catalytic function in this process, and to play an important role in breast cancer. We outline the functions of these proteins in vivo and focus on knowledge gained in the comparison of in vivo behavior predicted from cell-free in vitro data or from experiments conducted in cell culture systems.

Animals↗

PubMed2000

Dynamic biochemical reaction process analysis and pathway modification predictions.

Recently, the area of model predictive modification of biochemical pathways has received attention with the aim to increase the productivity of microbial systems. In this study, we present a generalization of previous work, where, using a sensitivity study over the fermentation as a dynamic system, the optimal selection of reaction steps for modification (amplification or attenuation) is determined. The influence of metabolites in the activity of enzymes has also been considered (through activation or inhibition). We further introduce a new concept in the dynamic modeling of biochemical reaction systems including a generalized continuous superstructure in which two artificial multiplicative terms are included to account for: (a) enzyme overexpression or underexpression (attenuation or amplification) for the whole enzyme pool; and (b) modification of the apparent order of a kinetic expression with respect to the concentration of a metabolite or any subset of metabolites participating in the pathway. This new formulation allows the prediction of the sensitivity of the pathway performance index (objective function) with respect to the concentration of the enzyme, as well as the interaction of the enzyme with other metabolites. Using this framework, a case study for the production of penicillin V is analyzed, obtaining the most sensitive reaction steps (or bottlenecks) and the most significant regulations of the system, due to the effect of concentration of intracellular metabolites on the activity of each enzyme.

Biochemistry↗

PubMed2001

Physiological tremor of the upper limb segments.

The acceleration signal produced by physiological tremor from four different upper limb segments (the finger, hand, forearm and upper limb) was measured by an acceleration sensor during holding posture and was analyzed by power spectrum analysis. Two prominent peaks appeared in the power spectrum, suggesting that the tremor in the four different limb segments was composed of two frequency components. The frequency of one peak at 8-12 Hz did not change between the different limb segments, while the frequency of the other peak decreased with the increase in the mass of the limb segment. A model with two reflex pathways was developed for the tremor in the four limb segments. The model includes two reflex pathways, a spinal pathway and a supraspinal pathway. The theoretical values of the frequency and the amplitude of the tremor predicted by the model were in good agreement with the experimental results. Analysis of the model revealed that one of the two frequency components of the tremor was of spinal origin and was dependent upon the mass of the limb segment, and the second was of supraspinal origin, corresponding to the frequency at 8-12 Hz. In the normal subject, it is possible that the tremor could be used to evaluate the change in neuromuscular function produced by prolonged work involving just part of a limb segments (e.g., typing). It may also be used to evaluate the neuromuscular function of patients suffering from neurological diseases such as muscular dystrophy and Parkinson's disease.

Adult↗

PubMed2005

Differential regulation of proteasome activity in the nucleus and the synaptic terminals.

Proteasome is a multi-subunit proteolytic complex that degrades proteins covalently linked to multiple molecules of ubiquitin. Earlier studies showed a role for the ubiquitin-proteasome pathway in several models of long-term memory and other forms of synaptic plasticity. In Aplysia, the ubiquitin-proteasome pathway has been shown to contribute to the induction of long-term facilitation. In other model systems, ubiquitin-proteasome-mediated proteolysis has also been shown to play a role in synapse development. Previous studies of synaptic plasticity focused on changes in components or the substrates of the ubiquitin-proteasome pathway in whole neurons. Modification of specific synapses would require precise spatial and temporal regulation of the components of the ubiquitin-proteasome pathway within the subcellular compartments of neurons during learning. As a first step towards testing the idea of local regulation of the ubiquitin-proteasome pathway in neurons, we investigated proteasome activity in nuclear and synaptosomal fractions. Here we show that proteasome activity in the synaptic terminals is higher compared to the activity in the nucleus in the Aplysia nervous system as well as in the mouse brain. Furthermore, the proteasome activity in the two neuronal compartments is differentially modulated by protein kinases. Differential regulation of proteasome activity in neuronal compartments such as the synaptic terminals is likely to be a key mechanism underlying synapse-specific plasticity.

Animals↗

PubMed2005

Inhibition of TGF-beta signaling by an ALK5 inhibitor protects rats from dimethylnitrosamine-induced liver fibrosis.

1 Chronic liver disease is characterized by an exacerbated accumulation of matrix, causing progressive fibrosis, which may lead to cirrhosis. Transforming growth factor beta (TGF-beta), a well-known profibrotic cytokine, transduces its signal through the ALK5 ser/thr kinase receptor, and increases transcription of different genes including PAI-1 and collagens. The identification of GW6604 (2-phenyl-4-(3-pyridin-2-yl-1H-pyrazol-4-yl)pyridine), an ALK5 inhibitor, allowed us to evaluate the therapeutic potential of inhibiting TGF-beta pathway in different models of liver disease. 2 A cellular assay was used to identify GW6604 as a TGF-beta signaling pathway inhibitor. This ALK5 inhibitor was then tested in a model of liver hepatectomy in TGF-beta-overexpressing transgenic mice, in an acute model of liver disease and in a chronic model of dimethylnitrosamine (DMN)-induced liver fibrosis. 3 In vitro, GW6604 inhibited autophosphorylation of ALK5 with an IC(50) of 140 nM and in a cellular assay inhibited TGF-beta-induced transcription of PAI-1 (IC(50): 500 nM). In vivo, GW6604 (40 mg kg(-1) p.o.) increased liver regeneration in TGF-beta-overexpressing mice, which had undergone partial hepatectomy. In an acute model of liver disease, GW6604 reduced by 80% the expression of collagen IA1. In a chronic model of DMN-induced fibrosis where DMN was administered for 6 weeks and GW6604 dosed for the last 3 weeks (80 mg kg(-1) p.o., b.i.d.), mortality was prevented and DMN-induced elevations of mRNA encoding for collagen IA1, IA2, III, TIMP-1 and TGF-beta were reduced by 50-75%. Inhibition of matrix genes overexpression was accompanied by reduced matrix deposition and reduction in liver function deterioration, as assessed by bilirubin and liver enzyme levels. 4 Our results suggest that inhibition of ALK5 could be an attractive new approach to treatment of liver fibrotic diseases by both preventing matrix deposition and promoting hepatocyte regeneration.

Activin Receptors, Type I↗

PubMed2003

Cholinergic pathways modulate experimental dinitrobenzene sulfonic acid colitis in rats.

Recent studies have suggested that neuroimmune interactions modulate intestinal mucosal immune responses. In the current study, we examined the role of cholinergic pathways in modulating the severity of acute dinitrobenzene sulfonic acid colitis, using pharmacological agents to suppress acetylcholinesterase in Sprague-Dawley rats, and evaluating the colitis in the cholinergic hyperresponsive Flinder's sensitive line rats and their control counterparts, the Flinder's resistant line. Colitis was induced by intrarectal dinitrobenzene sulfonic acid (80 mg x ml(-1) in 50% ethanol); controls received intrarectal saline. Sprague-Dawley rats received an acetylcholinesterase inhibitor, physostigmine (50 microg x kg(-1) s.c.) or neostigmine (50 microg x kg(-1) s.c.), 30 min prior to intrarectal dinitrobenzene sulfonic acid; controls received saline vehicle. On day 5, the macroscopic damage score, myeloperoxidase activity (an estimate of granulocyte infiltration) and smooth muscle thickness were evaluated in the inflamed colonic segment. Significant increases in macroscopic damage score and colonic smooth muscle thickness were observed in Sprague-Dawley and Flinder's Resistant Line rats on day 5 following intrarectal dinitrobenzene sulfonic acid compared to saline controls. Increased myeloperoxidase activity was also observed in dinitrobenzene sulfonic acid-treated Sprague-Dawley rats and Flinder's Resistant Line rats. In contrast, Flinder's Sensitive Line rats failed to demonstrate a significant rise in macroscopic damage, smooth muscle layer thickness, or myeloperoxidase activity on day 5 following intrarectal dinitrobenzene sulfonic acid when compared to saline-treated Flinder's Sensitive Line controls. Neostigmine and physostigmine treatment prior to intrarectal dinitrobenzene sulfonic acid significantly attenuated macroscopic damage score, myeloperoxidase activity and smooth muscle thickness on day 5 compared to colitic Sprague-Dawley controls. Significantly greater reductions in myeloperoxidase activity were observed with physostigmine vs. neostigmine pretreatment. These data suggest that cholinergic pathways modulate the acute colonic inflammatory response associated with the dinitrobenzene sulfonic acid model, with central pathways exerting a greater protective effect relative to peripheral pathways. Further studies are required to determine the contributions of sites in the nervous system and neuro-effector junctions.

Animals↗

PubMed1996

A life course perspective on retirement, gender, and well-being.

The existing research literature on the links between retirement and physical and psychological health is examined. This synthesis characterizes the complexity of the relationship between retirement and health; points out potential gender differences in the nature, experience, and implications of retirement; and develops a life course model of the pathways through occupational career and retirement leading to health. Such a life course model suggests a research agenda that can produce important insights on the dynamics and consequences of the retirement transition, including the mechanisms and conditions linking withdrawal from employment to changes in health and well-being.

Aged↗

PubMed2001

The use of indoor air measurements to evaluate intrusion of subsurface VOC vapors into buildings.

The implementation of a risk-based corrective action approach often requires consideration of soil vapor migration into buildings and potential inhalation exposure and risk to human health. Due to the uncertainty associated with models for this pathway, there may be a desire to analyze indoor air samples to validate model predictions, and this approach is followed on a somewhat frequent basis at sites where risks are considered potentially significant. Indoor air testing can be problematic for a number of reasons. Soil vapor intrusion into buildings is complex, highly dependent on site-specific conditions, and may vary over time, complicating the interpretation of indoor air measurements when the goal is to deduce the subsurface-derived component. An extensive survey of indoor air quality data sets highlights the variability in indoor volatile organic compound (VOC) concentrations and numerous sources that can lead to elevated VOC levels. The contribution from soil vapor is likely to be small relative to VOCs from other sources for most sites. In light of these challenges, we discuss how studies that use indoor air testing to assess subsurface risks could be improved. To provide added perspective, we conclude by comparing indoor air concentrations and risks arising from subsurface VOCs, predicted using standard model equations for soil vapor fate and intrusion into buildings, to those associated with indoor sources.

Air Pollution, Indoor↗

PubMed2002

Chloride channels in the kidney: lessons learned from knockout animals.

Cl- channels are involved in a range of functions, including regulation of cell volume and/or intracellular pH, acidification of intracellular vesicles, and vectorial transport of NaCl across many epithelia. Numerous Cl- channels have been identified in the kidney, based on single-channel properties such as conductance, anion selectivity, gating, and response to inhibitors. The molecular counterpart of many of these Cl- channels is still not known. This review will focus on gene-targeted mouse models disrupting two structural classes of Cl- channels that are relevant for the kidney: the CLC family of voltage-gated Cl- channels and the CFTR. Disruption of several members of the CLC family in the mouse provided useful models for various inherited diseases of the kidney, including Dent's disease and diabetes insipidus. Mice with disrupted CFTR are valuable models for cystic fibrosis (CF), the most common autosomal recessive, lethal disease in Caucasians. Although CFTR is expressed in various nephron segments, there is no overt renal phenotype in CF. Analysis of CF mice has been useful to identify the role and potential interactions of CFTR in the kidney. Furthermore, observations made in CF mice are potentially relevant to all other models of Cl- channel knockouts because they emphasize the importance of alternative Cl- pathways in such models.

Animals↗

PubMed2003

A kinetic model of the branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana.

This work proposes a model of the metabolic branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana which involves kinetic competition for phosphohomoserine between the allosteric enzyme threonine synthase and the two-substrate enzyme cystathionine gamma-synthase. Threonine synthase is activated by S-adenosylmethionine and inhibited by AMP. Cystathionine gamma-synthase condenses phosphohomoserine to cysteine via a ping-pong mechanism. Reactions are irreversible and inhibited by inorganic phosphate. The modelling procedure included an examination of the kinetic links, the determination of the operating conditions in chloroplasts and the establishment of a computer model using the enzyme rate equations. To test the model, the branch-point was reconstituted with purified enzymes. The computer model showed a partial agreement with the in vitro results. The model was subsequently improved and was then found consistent with flux partition in vitro and in vivo. Under near physiological conditions, S-adenosylmethionine, but not AMP, modulates the partition of a steady-state flux of phosphohomoserine. The computer model indicates a high sensitivity of cystathionine flux to enzyme and S-adenosylmethionine concentrations. Cystathionine flux is sensitive to modulation of threonine flux whereas the reverse is not true. The cystathionine gamma-synthase kinetic mechanism favours a low sensitivity of the fluxes to cysteine. Though sensitivity to inorganic phosphate is low, its concentration conditions the dynamics of the system. Threonine synthase and cystathionine gamma-synthase display similar kinetic efficiencies in the metabolic context considered and are first-order for the phosphohomoserine substrate. Under these conditions outflows are coordinated.

Adenosine Monophosphate↗

PubMed2001

Nitrogen cycling in a Norway spruce plantation in Denmark--a SOILN model application including organic N uptake.

A dynamic carbon (C) and nitrogen (N) circulation model, SOILN, was applied and tested on 7 years of control data and 3 years of manipulation data from an experiment involving monthly N addition in a Norway spruce ( Picea abies, L. Karst) forest in Denmark. The model includes two pathways for N uptake: (1) as mineral N after mineralisation of organic N, or (2) directly from soil organic matter as amino acids proposed to mimic N uptake by mycorrhiza. The model was parameterised and applied to the data from the control plot both with and without the organic N uptake included. After calibration, the models performance was tested against data from the N-addition experiment by comparing model output with measurements. The model reproduced well the overall trends in C and N pools and the N concentrations in soil solutions in the top soil layers whereas discrepancies in soil-solution concentrations in the deeper soil layers are seen. In the control data, the needle-N concentration was well reproduced except for small underestimations in some years because of drought effects not included in the model. In the N-addition experiment, SOILN reproduces the observed changes; in particular, the changes in needle-N concentrations and the overall distribution within the ecosystem of the extra added 3.5 g N m(-2) year(-1) parallel the observations. When organic N uptake is included, the simulations indicate that in the control plot receiving c. 1.9 g N m(-2) year(-1), the organic N uptake in average supplies 35% of the total plant N uptake. By addition of an extra 35 kg N ha(-1) year(-1), the organic N uptake is reduced to 16% of the total N uptake. Generally, inclusion of the pathway for organic N uptake improves model performance compared with observations for both C and N. This is because mineral N uptake alone implies a larger mineralisation rate, leading to bigger concentrations of N in the soil and soil water, bigger N losses, and net loss of c. 100 kg C ha(-1) year(-1), thereby causing depletion of the organic soil layer.

Biomass↗

PubMed1997

An in vitro analysis of the combination of hemophilia A and factor V(LEIDEN).

The classification of factor VIII deficiency, generally used based on plasma levels of factor VIII, consists of severe (<1% normal factor VIII activity), moderate (1% to 4% factor VIII activity), or mild (5% to 25% factor VIII activity). A recent communication described four individuals bearing identical factor VIII mutations. This resulted in a severe bleeding disorder in two patients who carried a normal factor V gene, whereas the two patients who did not display severe hemophilia were heterozygous for the factor V(LEIDEN) mutation, which leads to the substitution of Arg506 --> Gln mutation in the factor V molecule. Based on the factor VIII level measured using factor VIII-deficient plasma, these two patients were classified as mild/moderate hemophiliacs. We studied the condition of moderate to severe hemophilia A combined with the factor V(LEIDEN) mutation in vitro in a reconstituted model of the tissue factor pathway to thrombin. In the model, thrombin generation was initiated by relipidated tissue factor and factor VIIa in the presence of the coagulation factors X, IX, II, V, and VIII and the inhibitors tissue factor pathway inhibitor, antithrombin-III, and protein C. At 5 pmol/L initiating factor VIIa x tissue factor, a 10-fold higher peak level of thrombin formation (350 nmol/L), was observed in the system in the presence of plasma levels of factor VIII compared with reactions without factor VIII. Significant increase in thrombin formation was observed at factor VIII concentrations less than 42 pmol/L (approximately 6% of the normal factor VIII plasma concentration). In reactions without factor VIII, in which thrombin generation was downregulated by the addition of protein C and thrombomodulin, an increase of thrombin formation was observed with the factor V(LEIDEN) mutation. The level of increase in thrombin generation in the hemophilia A situation was found to be dependent on the factor V(LEIDEN) concentration. When the factor V(LEIDEN) concentration was varied from 50% to 150% of the normal plasma concentration, the increase in thrombin generation ranged from threefold to sevenfold. The data suggested that the analysis of the factor V genotype should be accompanied by a quantitative analysis of the plasma factor V(LEIDEN) level to understand the effect of factor V(LEIDEN) in hemophilia A patients. The presented data support the hypothesis that the factor V(LEIDEN) mutation can increase thrombin formation in severe hemophilia A.

Factor V↗

PubMed1998

A model for early events in the assembly pathway of cyanobacterial phycobilisomes.

Biological self-assembly is remarkable in its fidelity and in the efficient production of intricate molecular machines and functional materials from a heterogeneous mixture of macromolecules. The phycobilisome, a light-harvesting structure of cyanobacteria, presents the opportunity to study an in vivo assembly process in detail. The phycobilisome molecular architecture is defined, and crystal structures are available for all major proteins, as are a large sequence database (including a genome sequence) and effective genetic systems exist for some cyanobacteria. Recent studies on subunit interaction, covalent modification, and protein stability suggest a model for the earliest events in the phycobilisome assembly pathway. Partitioning of phycobilisome proteins between degradation and assembly is proposed to be controlled by the interaction equilibria between phycobilisome assembly partners, processing enzymes and chaperones. The model provides plausible explanations for existing observations and makes predictions that are amenable to direct experimental investigation.

Bacterial Proteins↗

PubMed2001

Carbohydrate and amino acid degradation pathways in L-methionine/D-[13C] glucose model systems.

Maillard model systems consisting of labeled D-[(13)C]glucoses, L-[(15)N]methionine, and L-[methyl-(13)C]methionine, have been utilized to identify the amino acid and carbohydrate fragmentation pathways occurring in the model system through Py-GC/MS analysis. The label incorporation analyses have indicated that the carbohydrate moiety produces 1-deoxy- and 3-deoxyglucosones and undergoes C(2)/C(4) and C(3)/C(3) cleavages to produce glycolaldehyde, tetrose, and C(3)-reactive sugar derivatives such as acetol, glyceraldehyde, and pyruvaldehyde. Glycolaldehyde was found to incorporate C-1, C-2 (70%) and C-5, C-6 (30%) glucose carbon fragments, whereas the tetrose moiety incorporates only C-3, C-4, C-5, C-6 glucose carbon atoms. In addition, the major source of reactive C(3) fragments was found to contain C-4, C-5, C-6 sugar moiety. On the other hand, methionine alone also generated Strecker aldehyde as detected by its condensation product with 3-(methylthio)propylamine. Plausible mechanisms were proposed for the formation of the interaction products between sugar and amino acid degradation products on the basis of the label incorporation patterns.

Amino Acids↗

PubMed1999

Investigating the role of alienation in a multicomponent model of juvenile delinquency.

Research findings indicate that there are multiple causal pathways to delinquency. A multicomponent model of delinquency was developed to explore systematically the interrelationships of psychosocial variables and their relationships to delinquent behaviour. Most importantly, alienation was tested for its ability to act as a core mediating predictor variable. One hundred and fifty-two adolescents, 78 females and 74 males, completed a battery of questionnaires designed to assess each of the variables in the proposed model. Several salient pathways to delinquency were identified. They include environmental and person-centred factors. Alienation, when operationalized as a general construct, was not found to be a necessary mediating predictor variable. "Societal" alienation, on the other hand, was shown to have important explanatory power. Re-examining the model within a large-scale, time-extended study could inform programmes for the prevention and early intervention of delinquent behaviour.

Adolescent↗