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PubMed2004

Model reduction and analysis of robustness for the Wnt/beta-catenin signal transduction pathway.

We present a framework for model reduction of signal transduction networks. The methods are explained by considering a recent model for Wnt/beta-catenin signalling which plays an important regulatory role in cell development and oncogenesis. The procedure results in a reduction of system variables and parameters while maintaining the ability of the model to describe experimental data and to predict the in-vivo behaviour of the pathway. Using metabolic control analysis we quantified the response of the pathway towards random fluctuations of model parameters. This allows to characterise the robustness of the pathway against perturbations in stimulated and unstimulated states. We show that robustness depends on structural as well as kinetic properties of the pathway.

Animals↗
PubMed2001

Significance of cell-cycle delay, multiple initiation pathways, misrepair and replication errors in a model of radiobiological effects.

PURPOSE: To advance a biomathematical model of radiocarcinogenesis by describing multiple pathways for initiation, a radiologically induced cell-cycle delay, misrepair and spontaneous DNA damages caused by replication. It was investigated whether the incorporation of these biological features would improve the fit of the model to data showing plateaus in in vitro irradiations of different cell lines and whether the fit parameters were then more biologically realistic. MATERIALS AND METHODS: A biomathematical submodel was developed based on a previous State-Vector Model that mathematically described enhanced DNA repair and radical scavenging following irradiation. RESULTS: With the two initiation pathways and cell-cycle delay, the simulations better explained the mouse data but not the rat data, and for both data sets the fit parameters were biologically more realistic than previously assumed. Inclusion of misrepair and replicational errors did not significantly affect the fit. CONCLUSIONS: A plateau in the dose-effect relationship for in vitro irradiation of different cell lines can be explained by radioprotective mechanisms. The plateau-type dose-response relationships point to a non-linear dose- effect relationship at low doses and indicate that linear extrapolation from moderate (or high) to low doses may not be justified for in vitro studies of these cell lines.

Animals↗
PubMed2005

Colored Petri net modeling and simulation of signal transduction pathways.

Presented herein is a methodology for quantitatively analyzing the complex signaling network by resorting to colored Petri nets (CPN). The mathematical as well as Petri net models for two basic reaction types were established, followed by the extension to a large signal transduction system stimulated by epidermal growth factor (EGF) in an application study. The CPN models based on the Petri net representation and the conservation and kinetic equations were used to examine the dynamic behavior of the EGF signaling pathway. The usefulness of Petri nets is demonstrated for the quantitative analysis of the signal transduction pathway. Moreover, the trade-offs between modeling capability and simulation efficiency of this pathway are explored, suggesting that the Petri net model can be invaluable in the initial stage of building a dynamic model.

Algorithms↗
PubMed1983

Influx mechanisms for Na+ and Cl- across the brush border membrane of leaky epithelia: a model and microelectrode study.

This paper presents a numerical model for the movement of Na+, K+, Cl-, H+ and HCO3- in a leaky epithelium. The model describes the active transport of Na+ and K+ at the serosal membrane and electrodiffusive permeation across the mucosal, serosal and junctional pathways. The model accounts for H+ and HCO3- production in the cell. The influx of Na+ and Cl- is assumed to occur mainly via Na/H and Cl/HCO3 exchange. The behavior of the cell, with this influx mechanism, is compared to a cell with an obligatory neutral coupled influx of Na+ and Cl-. All parameters are obtained from the literature, primarily from studies utilizing the Necturus gallbladder. The analysis shows (i) that it is virtually impossible in steady-state experiments to distinguish between cells with Na/H - HCO3/Cl transport and cells with Na/Cl transport mechanisms. (ii) That nonsteady-state experiments can decide whether Na/H - HCO3/Cl or Na/Cl transport mechanisms mediate the influx of salt. A comparison between studies with ion-selective microelectrodes and the model predictions indicates that the influx of Na+ and Cl- is mediated by Na/H - HCO3/Cl transport when the external solutions contain CO2 and HCO3. (iii) The model also explains the diuretic effects of furosemide and carbonic anhydrase inhibitor, as well as the stimulatory effects on salt transport of elevated levels of HCO3- at a constant pH. (iv) The model fails to explain some experiments performed in HCO3/Co2-free media and some experiments using inhibitors.

Animals↗
PubMed1995

Tamoxifen enhances the chemosensitivity of bladder carcinoma cells.

PURPOSE: Chemosensitizers, which enhance cellular chemosensitivity and reduce chemoresistance, are expected to substantially improve response rates of systemic chemotherapy for patients with metastatic bladder cancer. Tamoxifen is a nonsteroidal antiestrogen that has been shown to reverse drug resistance in vitro in some cancer models through pathways not related to its antiestrogenic effect. In this study we tried to evaluate its possible effect on chemosensitization of bladder cancer cells. MATERIALS AND METHODS: In vitro chemosensitivity tests were done with 3 bladder cancer cell lines and 4 cytotoxic agents (methotrexate, vinblastine, doxorubicin and cisplatin) in the presence or absence of graded concentrations of tamoxifen. Verapamil was used in parallel experiments to compare the degrees of chemosensitization. The transcript and protein product [P-glycoprotein, (P-gp)] levels of the mdr-1 gene were also examined in the 3 cell lines by reverse-transcription polymerase chain reaction (RT-PCR) and flow cytometric assay, respectively. RESULTS: Tamoxifen at 5 and especially 10 microM. concentrations, which were minimally toxic to the 3 bladder cancer cell lines used, enhanced the chemosensitivity of bladder cancer cells in most drug combinations in a dose-dependent manner. In some combinations 10 microM. tamoxifen did better than 5 microM. in chemosensitization. The effect of chemosensitization was more evident in cells treated with 10 microM. tamoxifen plus methotrexate and vinblastine in which 12.9 to 95.4-fold and 12.4 to 21.3-fold IC50 reduction was observed, respectively. A less prominent, but still significant, effect could be seen in doxorubicin- and cisplatin-treated cells. Verapamil, although used at concentrations up to 10 microM. which are higher than systemically tolerable, was not able to enhance chemosensitivity of the 3 bladder cancer cell lines. By flow cytometric analysis of the P-gp level and by RT-PCR assay of the mdr-1 gene transcript level, it was shown that little if any mdr-1 gene expression could be detected in the 3 cell lines. This implies that the mdr-1 gene function may play a minimal role in drug resistance mechanisms of bladder cancer cells and that tamoxifen exerts its chemosensitization effect through pathways other than mdr-1 gene function modulation. CONCLUSIONS: Tamoxifen was shown to be a good chemosensitizer in a bladder cancer cell model and may well be tried in combination with systemic chemotherapy for metastatic human bladder cancers in the clinical setting.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1996

Hormones act downstream of TTG and GL2 to promote root hair outgrowth during epidermis development in the Arabidopsis root.

The Arabidopsis root produces a position-dependent pattern of hair-bearing and hairless cell types during epidermis development. Five loci (TRANSPARENT TESTA GLABRA [TTG], GLABRA2 [GL2], ROOT HAIR DEFECTIVE6 [RHD6], CONSTITUTIVE TRIPLE RESPONSE1 [CTR1], and AUXIN RESISTANT2 [AXR2]) and the plant hormones ethylene and auxin have been reported to affect the production of root hair and hairless cells in the Arabidopsis root. In this study, genetic, molecular, and physiological tests were employed to define the roles of these loci and hormones. Epistasis tests and reporter gene studies indicated that the hairless cell-promoting genes TTG and GL2 are likely to act early to negatively regulate the ethylene and auxin pathways. Studies of the developmental timing of the hormone effects indicated that ethylene and auxin pathways promote root hair outgrowth after cell-type differentiation has been initiated. The genetic analysis of ethylene-and auxin-related mutations showed that root hair formation is influenced by a network of hormone pathways, including a partially redundant ethylene signaling pathway. A model is proposed in which the patterning of root epidermal cells in Arabidopsis is regulated by the cell position-dependent action of the TTG/GL2 pathway, and the ethylene and auxin hormone pathways act to promote root hair outgrowth at a relatively late stage of differentiation.

Amino Acids↗
PubMed2002

Using structural equation model to explore occupational lead exposure pathways.

The aim of the present study was to demonstrate the use of a structural equation model to explore the complicated lead exposure pathways in a lead battery plant. A total of 96 out of 113 assembly workers were recruited in this study. Lead measurements included blood lead, respirable airborne lead, and body surface lead loadings. Latent variables of inadvertent contact of lead on fingers and ingested lead had indirect and direct effects on the blood lead levels, respectively, and so did the variables of respirable airborne lead, smoking, and the working-place clothes being washed. A model chi(22)2 value of 31.1 (P=0.094) for a goodness of fit test indicates that the derived structural equation model appropriately accounted for the variation of blood lead levels. It is concluded that lead loadings on fingers and lips had significant effects on occupational lead uptake, and, after-work hours and break times at work were the critical time periods for inadvertent lead exposure.

Activities of Daily Living↗
PubMed1995

Pathways, pathway tubes, pathway docking, and propagators in electron transfer proteins.

The simplest views of long-range electron transfer utilize flat one-dimensional barrier tunneling models, neglecting structural details of the protein medium. The pathway model of protein electron transfer reintroduces structure by distinguishing between covalent bonds, hydrogen bonds, and van der Waals contacts. These three kinds of interactions in a tunneling pathway each have distinctive decay factors associated with them. The distribution and arrangement of these bonded and nonbonded contacts in a folded protein varies tremendously between structures, adding a richness to the tunneling problem that is absent in simpler views. We review the pathway model and the predictions that it makes for protein electron transfer rates in small proteins, docked proteins, and the photosynthetic reactions center. We also review the formulation of the protein electron transfer problem as an effective two-level system. New multi-pathway approaches and improved electronic Hamiltonians are described briefly as well.

Electron Transport↗
PubMed2002

The developmental course of gender differentiation: conceptualizing, measuring, and evaluating constructs and pathways.

Gender differentiation is pervasive, and understanding how and why it develops is important for both theoretical and practical reasons. The work described here is rooted in constructivist accounts of gender differentiation. Past research provides considerable support for constructivist predictions concerning (a) developmental changes in gender attitudes and (b) the relation between gender attitudes and information processing. Little work, however, has addressed the more fundamental question of how children's developing gender attitudes about others are related to developing gender characterizations of self. The focus of the current Monograph is on this other-self relation during middle childhood. A brief review of past theory and empirical work on gender differentiation is provided. It is argued that a major explanation of the limitations and inconsistencies evident in earlier work may be traced to restrictions in the measures available to assess key constructs. A conceptual analysis of the specific limitations of past measures is presented. The Monograph then offers alternative models of the developmental relation between attitudes toward others and characterization of self (the attitudinal and the personal pathway models), and identifies conditions expected to influence the strength of the observed other-self relation. Four studies establish the reliability and validity of a suite of measures that provides comparable methods for assessing attitudes toward others (attitude measures, or AM) and sex typing of self (personal measures, or PM) in three domains: occupations, activities, and traits (or OAT). Parallel forms are provided for adults (the OAT-AM and OAT-PM) and for children of middle-school age, roughly 11-13 years old (the COAT-AM and COAT-PM). A fifth study provides longitudinal data from children tested at four times, beginning at the start of grade 6 (approximately age 11 years) and ending at the close of grade 7 (approximately age 13 years). These data are used to examine the developmental relation between children's sex typing of others and sex typing of the self, and to test the predictions concerning the factors hypothesized to affect the strength of the relation between the two types of sex typing. Overall, the data supported the conceptual distinctions among individuals' (a) gender attitudes toward others, (b) feminine self, and (c) masculine self, and, additionally, revealed some intriguing differences across domains. Interestingly, the data concerning the other-self relation differed by sex of participant. Among girls, analyses of concurrent relations showed that those girls who held fewer stereotypes of masculine activities for others showed greater endorsement of masculine items for self, a finding compatible with both the other-to-self attitudinal pathway model and the self-to-other personal pathway model. The prospective regression analyses, however, showed no effects. That is, preadolescent girls' gender attitudes about others did not predict their later self-endorsements, nor did self-endorsements predict later attitudes. Data from boys showed a strikingly different pattern, one consistent with the self-to-other personal pathway model: There was no evidence of concurrent other-self relations, but prospective analyses indicated that preadolescent boys who endorsed greater numbers of feminine traits as self-descriptive early in grade 6 developed increasingly egalitarian gender attitudes by the end of grade 7. The Monograph closes with discussions of additional implications of the empirical data, of preliminary work on developing parallel measures for younger children, and of the need to design research that illuminates the cognitive-developmental mechanisms underlying age-related changes in sex typing.

Adolescent↗
PubMed1995

Chloroethylene mixtures: pharmacokinetic modeling and in vitro metabolism of vinyl chloride, trichloroethylene, and trans-1,2-dichloroethylene in rat.

Environmental and occupational exposures are typically to mixtures of chemicals, although most toxicity information is for individual compounds. Interactions between chemicals may involve pharmacokinetic and/or pharmacodynamic effects resulting in modulation of toxicity. Therefore, physiologically based pharmacokinetic modeling has been used to analyze data describing the metabolism of vinyl chloride (VC) and trichloroethylene (TCE) mixtures in rats. A single saturable pathway was modeled, representing cytochrome P450 2E1. This was partially validated using preexposure to trans-1,2-dichloroethylene (tDCE) which virtually eliminated in vivo metabolism of both VC and TCE at low concentrations. Microsomes from tDCE-exposed animals showed inhibition of metabolism of P450 2E1 substrates (chlorzoxazone, p-nitrophenol, and TCE) and no effect on 7-ethoxycoumarin deethylation. Studies with liver microsomes from VC-exposed animals found that neither suicide inhibition nor induction occurred during 6-hr exposures to high concentrations. Therefore, these effects were not modeled. Modeling of mixtures of VC and TCE was successful only using competitive inhibition, as might be predicted for cytochrome P450 2E1 substrates, and not uncompetitive or noncompetitive inhibition. These results were further confirmed by determining the depletion of glutathione due to VC metabolism. The validation of a detailed model for the inhibition kinetics of metabolism of these two compounds permits better understanding of the implications of coexposures for toxicity. It is notable that competitive inhibition only becomes significant at relatively high concentrations (tens of ppm), while at typical low environmental concentrations (ppb), absorption is perfusion limited and enzyme is in excess so that the chemicals will be metabolized independently.

Administration, Inhalation↗
PubMed2001

Characterization of a p75(NTR) apoptotic signaling pathway using a novel cellular model.

The p75 neurotrophin receptor (p75(NTR)) belongs to the tumor necrosis factor receptor/nerve growth factor receptor superfamily. In some cells derived from neuronal tissues it causes cell death through a poorly characterized pathway. We developed a neuronal system using conditionally immortalized striatal neurons, in which the expression of p75(NTR) is inducibly controlled by the ecdysone receptor. In these cells p75(NTR) induces apoptosis through its death domain in a nerve growth factor-independent manner. Caspases 9, 6, and 3 are activated by receptor expression indicating the activation of the common effector pathway of apoptosis. Cell death is blocked by a dominant negative form of caspase 9 and Bcl-X(L) consistent with a pathway that involves mitochondria. Significantly, the viral flice inhibitory protein E8 protects from p75(NTR)-induced cell death indicating that death effector domains are involved. A p75(NTR) construct with a deleted death domain dominantly interferes with p75(NTR) signaling, implying that receptor multimerization is required. However, in contrast to the other receptors of the family, p75(NTR)-mediated apoptosis does not involve the adaptor proteins Fas-associated death domain protein or tumor necrosis factor-associated death domain protein, and the apical caspase 8 is not activated. We conclude that p75(NTR) signals apoptosis by similar mechanisms as other death receptors but uses different adaptors and apical caspases.

Apoptosis↗
PubMed2005

Developmental pesticide models of the Parkinson disease phenotype.

It has been hypothesized that developmental insults could contribute to Parkinson disease (PD), a neurodegenerative disorder resulting from the loss of the dopamine neurons of the nigrostriatal pathway. Two models of developmental pesticide exposures in mice are presented here that yield PD phenotypes consistent with this possibility. Combined exposures to the herbicide paraquat (PQ) and the fungicide maneb (MB), both of which adversely affect dopamine systems, administered from postnatal days 5-19, produced selective losses of dopamine and metabolites and reduced numbers of dopamine neurons in the substantia nigra. Effects were greater than those produced by adult-only exposures. Moreover, developmental PQ + MB exposures enhanced vulnerability to this pesticide regimen when administered subsequently in adulthood. In a second model, exposure to MB from gestational days 10-17 markedly increased vulnerability to PQ exposures during adulthood, with reductions in dopamine and metabolites and numbers of dopamine neurons in the substantia nigra. Females evidenced protection in both models. Collectively, these models demonstrate that developmental exposures can produce progressive, permanent, and cumulative neurotoxicity of the nigrostriatal dopamine system and enhance vulnerability to subsequent environmental insults. Finally, effects of PQ + MB were greater than those of either pesticide alone in the postnatal model. This is consistent with a multiple-hit hypothesis predicting that multiple concurrent insults occurring at different target sites within a system (here nigrostriatal dopamine) may constrict the range and flexibility of compensatory mechanisms, thereby compromising the integrity and viability of the system. As such, this hypothesis presents a biologic strategy for identifying potentially significant neurotoxic mixtures for hazard identification in future studies.

Age Factors↗
PubMed2001

Core formation in apomyoglobin: probing the upper reaches of the folding energy landscape.

An acid-destabilized form of apomyoglobin, the so-called E state, consists of a set of heterogeneous structures that are all characterized by a stable hydrophobic core composed of 30-40 residues at the intersection of the A, G, and H helices of the protein, with little other secondary structure and no other tertiary structure. Relaxation kinetics studies were carried out to characterize the dynamics of core melting and formation in this protein. The unfolding and/or refolding response is induced by a laser-induced temperature jump between the folded and unfolded forms of E, and structural changes are monitored using the infrared amide I' absorbance at 1648-1651 cm(-1) that reports on the formation of solvent-protected, native-like helix in the core and by fluorescence emission changes from apomyoglobin's Trp14, a measure of burial of the indole group of this residue. The fluorescence kinetics data are monoexponential with a relaxation time of 14 micros. However, infrared kinetics data are best fit to a biexponential function with relaxation times of 14 and 59 micros. These relaxation times are very fast, close to the limits placed on folding reactions by diffusion. The 14 micros relaxation time is weakly temperature dependent and thus represents a pathway that is energetically downhill. The appearance of this relaxation time in both the fluorescence and infrared measurements indicates that this folding event proceeds by a concomitant formation of compact secondary and tertiary structures. The 59 micros relaxation time is much more strongly temperature dependent and has no fluorescence counterpart, indicating an activated process with a large energy barrier wherein nonspecific hydrophobic interactions between helix A and the G and H helices cause some helix burial but Trp14 remains solvent exposed. These results are best fit by a multiple-pathway kinetic model when U collapses to form the various folded core structures of E. Thus, the results suggest very robust dynamics for core formation involving multiple folding pathways and provide significant insight into the primary processes of protein folding.

Animals↗
PubMed2026

Modeling meningioma in vitro in the omics era.

Meningioma biology has been substantially clarified by recent omics-based studies, which have identified recurrent mutations, copy-number alterations, and distinct molecular subgroups. However, although these approaches have provided a valuable framework, they are inherently limited in their ability to establish direct causal relationships. The mechanistic studies are therefore indispensable for translating these molecular observations into biological understanding. Nevertheless, the mechanistic literature has often evolved in a fragmented manner, with individual pathways and model systems studied in relative isolation from the broader multi-omic landscape. In this review, we synthesize these complementary bodies of work into an integrated framework and outline a clear roadmap for future studies. We first review the historical development of established meningioma cell lines, their current molecular characterization, and the recent emergence of 3D models and organoids. Intrinsic challenges in modeling meningioma in vitro are discussed, including the difficulty of establishing immortalized cell lines from predominantly benign tumors, genetic alterations introduced during immortalization, and drift under culture conditions that differ substantially from those of the parental tumors. Next, insights from functional studies centered on these models are integrated within the molecular framework established by large-scale omics analyses. To avoid fragmentation and overemphasis on isolated findings, prior studies are organized into six categories based on major signaling pathways: Hippo, PI3K/Akt/mTOR, MAPK, Wnt/β-catenin, FOXM1, and Notch. Finally, lessons from other cancer models, including experimental approaches to chromosome-scale genomic disturbances, are considered to provide a more integrated view of meningioma biology and to highlight directions for future research.

Meningioma↗
PubMed2001

Information transfer in metabolic pathways. Effects of irreversible steps in computer models.

Various metabolic models have been studied by computer simulation in an effort to understand why allowing for the reversibility of the reaction catalysed by pyruvate kinase, normally considered as irreversible for all practical purposes, significantly altered the behaviour of the model of glycolysis in Trypanosoma brucei [Eisenthal, R. & Cornish-Bowden, A. (1998) J. Biol. Chem. 273, 5500-5505]. Studies of several much simpler models indicate that the enzymes catalysing early steps in a pathway must receive information about the concentrations of the metabolites at the end of the pathway if a model is to be able to reach a steady state; treating all internal steps as reversible is just one way of ensuring this. Feedback inhibition provides a much better way, and as long as feedback loops are present in a model it makes almost no difference to the behaviour whether the intermediate steps with large equilibrium constants are treated as irreversible. In the absence of feedback loops, ordinary product inhibition of all the enzymes in the chain can also transfer information; this is efficient for regulating fluxes but very inefficient for regulating intermediate concentrations. More complicated patterns of regulation, such as activation of a competing branch or forcing flux through a parallel route, can also serve to some degree as ways of passing information around an irreversible step. However, they normally do so less efficiently than inhibition, because the extent to which an enzyme or a pathway can be activated always has an upper limit (which may be below what is required), whereas most enzymes are inhibited completely at saturating concentrations of inhibitor.

Animals↗
PubMed2006

Cell death pathways differ in several mouse models with motoneurone disease: analysis of pure motoneurone populations at a presymptomatic age.

To identify candidate genes that are responsible for motoneurone degeneration, we combined laser capture microdissection with microarray technology. We analysed gene expression in pure motoneurones from two mouse mutants that develop motoneurone degeneration, progressive motor neuronopathy and wobbler. At a presymptomatic age, there was a significant differential expression of a restricted number of genes (25 and 72 in progressive motor neuronopathy and wobbler respectively, of 22 600 transcripts screened). We compared these results to our previous analyses in the copper-zinc superoxide dismutase mutant mouse (SOD1(G93A)) in which we observed a de-regulation of 27 genes. Some of these genes were de-regulated uniquely in one mouse mutant and some have already been identified in cell death pathways implicated in amyotrophic lateral sclerosis and animal models of motoneurone degeneration (i.e. de-regulation of intermediate filaments, axonal transport, the ubiquitin-proteasome system and excitotoxicity). One gene, vimentin, was differentially up-regulated in all mouse mutants; this main candidate gene has been confirmed by in situ hybridization and immunohistochemistry to be expressed in motoneurones in all mouse mutants. Furthermore, vimentin expression correlated with the state of motoneurone degeneration. These results identify early molecular changes that may be involved in the pathogenesis of motoneurones leading to cell death and favour a complex multipathway induction of the disease; surprisingly, there was no important modification in cell death-associated genes. This is the first study to show a clear difference in the genes that are de-regulated at an early stage in three different mouse models of motoneurone disease.

Animals↗
PubMed2006

Bioenergetic abnormalities in discrete cerebral motor pathways presage spinal cord pathology in the G93A SOD1 mouse model of ALS.

Multiple cell death pathways are implicated in the etiology of amyotrophic lateral sclerosis (ALS), but the cause of the characteristic motor neuron degeneration remains unknown. To determine whether CNS metabolic defects are critical for ALS pathogenesis, we examined the temporal evolution of energetic defects in the G93A SOD1 mouse model of familial ALS. [14C]-2-deoxyglucose in vivo autoradiography in G93A mice showed that glucose utilization is impaired in components of the corticospinal and bulbospinal motor tracts prior to either pathologic or bioenergetic changes in the spinal cord. This was accompanied by significant depletions in cortical ATP content in presymptomatic mice, which was partially ameliorated by creatine administration. Findings suggest that bioenergetic defects are involved in the initial stages of mSOD1-induced toxicity in G93A mice and imply that the selective dysfunction and degeneration of spinal cord motor neurons in this model may be secondary to dysfunction within cerebral motor pathways.

Adenosine Triphosphate↗