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PubMed1997

Raf-1/bcl-2 phosphorylation: a step from microtubule damage to cell death.

Recent studies have shown that paclitaxel leads to activation of Raf-1 kinase and have suggested that this activation is essential for bcl-2 phosphorylation and apoptosis. In the present study, we demonstrate that, in addition to paclitaxel, other agents that interact with tubulin and microtubules also induce Raf-1/bcl-2 phosphorylation, whereas DNA-damaging drugs, antimetabolites, and alkylating agents do not. Activation of Raf-1 kinase by paclitaxel is linked to tubulin polymerization; the effect is blunted in paclitaxel-resistant cells, the tubulin of which does not polymerize following the addition of paclitaxel. In contrast, vincristine and vinblastine, drugs to which the paclitaxel-resistant cells retain sensitivity were able to bring about Raf-1 phosphorylation. The requirement for disruption of microtubules in this signaling cascade was strengthened further using paclitaxel analogues by demonstrating a correlation between tubulin polymerization, Raf-1/bcl-2 phosphorylation, and cytotoxicity. Inhibition of RNA or protein synthesis prevents Raf-1 activation and bcl-2 phosphorylation, suggesting that an intermediate protein(s) acts upstream of Raf-1 in this microtubule damage-activating pathway. A model is proposed that envisions a pathway of Raf-1 activation and bcl-2 phosphorylation following disruption of microtubular architecture, serving a role similar to p53 induction following DNA damage.

Antineoplastic Agents↗

PubMed1990

A new rat brain tumor model: glioma disseminated via the cerebral spinal fluid pathways.

A rat brain tumor model has been developed with the clinical and pathological features of dissemination via the cerebral spinal fluid (CSF) pathways. A precise number of 9L gliosarcoma cells (5 x 10(2) to 5 x 10(5)) is stereotactically injected into the CSF of the lateral ventricle. The interval until the onset of neurological symptoms and then death is reproducible and dependent upon the number of cells injected. The median survival of three groups of rats receiving 5 x 10(5) cells in three different experiments was 17, 18 and 19 days respectively. For three groups receiving 5 x 10(4) cells, the median survival was 23, 24 and 25.5 days respectively and for two groups receiving 5 x 10(3) cells the median survival was 28 and 30 days respectively. The animals developed multiple tumor implants along the CSF pathways usually resulting in hydrocephalus. This tumor model was developed to simulate dissemination via CSF pathways as seen with medulloblastoma and other primitive neuroectodermal tumors of the central nervous system. It will be used to evaluate the therapeutic efficacy of intraventricularly administered anti-neoplastic drugs against small implants and malignant cells in the CSF pathways.

Animals↗

PubMed2004

Models of cell signaling pathways.

Cellular signaling circuits handle an enormous range of computations. Beyond the housekeeping, replicating and other functions of individual cells, signaling circuits must implement the immensely complex logic of development and function of multicellular organisms. Computer models are useful tools to understand this complexity. Recent studies have extended such models to include electrical, mechanical and spatial details of signaling, and to address the stochastic effects that arise when small numbers of molecules interact. Increasing numbers of models have been developed in close conjunction with experiments, and this interplay gives a deeper and more reliable insight into signaling function.

Cell Cycle↗

PubMed1996

Effects of recombinant human tissue factor pathway inhibitor on thrombus formation and its in vivo distribution in a rat DIC model.

Tissue factor pathway inhibitor (TFPI) plays a key role in modulating tissue factor-dependent blood coagulation. This study was done to determine not only the inhibitory effects of recombinant human TFPI (rTFPI) on thrombus formation in rat models with disseminated intravascular coagulation (DIC), but also to identify the distribution of exogenous TFPI in vivo. Disseminated intravascular coagulation was induced by administering a priming dose of carrageenan 10 mg/kg body weight and was followed 24 hours later by a provocative dose of lipopolysaccharide (LPS) 500 mg/kg body weight. The rTFPI was administered intravenously at a dose of either 1 or 4 mg/kg body weight immediately after LPS treatment. Exogenous rTFPI at a dose of 4 mg/kg significantly inhibited the consumption of fibrinogen, platelets and factor VIIa (P < .05) and also reduced the number of fibrin thrombi formed in the liver, lungs, kidneys, and spleen (P < .05), whereas rTFPI at a dose of 1 mg/kg had no significant inhibitory effect on these DIC parameters. Recombinant human rTFPI activity was rapidly cleared from the plasma; however, a significant amount of the inhibitor was still present in tissues even 3 to 6 hours after intravenous administration. Exogenous TFPI was mainly identified in Kupffer cells, macrophages, and on the microvascular endothelial lining of different organs. In the kidney, rTFPI was identified on both the abluminal surface of the renal tubules and the luminal surface of the proximal convoluted tubules. No rTFPI, however, was detected in the hepatocytes. Tissue factor was mainly expressed by monocytes/macrophages. These findings suggest that TFPI plays an important role in modulating TF-dependent thrombogenesis. The elucidation of the rTFPI distribution and interactions in vivo might thus provide valuable insight into its inhibitory mechanisms as well as its therapeutic implications in DIC.

Animals↗

PubMed2005

Lipopolysaccharide-induced inflammation exacerbates tau pathology by a cyclin-dependent kinase 5-mediated pathway in a transgenic model of Alzheimer's disease.

Inflammation is a critical component of the pathogenesis of Alzheimer's disease (AD). Although not an initiator of this disorder, inflammation nonetheless plays a pivotal role as a driving force that can modulate the neuropathology. Here, we characterized the time course of microglia activation in the brains of a transgenic model of AD (3xTg-AD) and discerned its relationship to the plaque and tangle pathology. We find that microglia became activated in a progressive and age-dependent manner, and this activation correlated with the onset of fibrillar amyloidbeta-peptide plaque accumulation and tau hyperphosphorylation. To determine whether microglial activation can exacerbate the pathology, we exposed young 3xTg-AD mice to lipopolysaccharide (LPS), a known inducer of CNS inflammation. Although amyloid precursor protein processing appeared unaffected, we find that LPS significantly induced tau hyperphosphorylation at specific sites that were mediated by the activation of cyclin-dependent kinase 5 (cdk5) through increased formation of the p25 fragment. We further show that administration of roscovitine, a selective and potent inhibitor of cdk5, markedly blocked the LPS-induced tau phosphorylation in the hippocampus. Therefore, this study clearly demonstrates that microglial activation exacerbates key neuropathological features such as tangle formation.

Aging↗

PubMedDate not supplied

[Dynamics of orotic acid metabolism in chick tissues].

The processes of pyrimidine nucleotides metabolism were analyzed in cells of chicken small intestine mucosa using the kinetic series-parallel model of the first order equations. The rate constants are calculated for absorption of [2-14C]orotic acid by mucosa cells, its accumulation in blood anc conversion to uridine nucleotides. Stages of uridine nucleotides conversion to cytidine ones and their incorporation into RNA are not described by the system of the first order equations based on the series-parallel model with the single-channel utilization of orotic acid through the pyrimidine pathway. The model into two pathways of free nucleotides metabolism and two individual flows of precursors into RNA corresponds qualitatively to the obtained experimental data. Metabolism of orotic acid along two separate channels might be typical of the chicken liver.

Animals↗

PubMed2004

Modeling threshold phenomena, metabolic pathways switches and signals in chemostat-cultivated cells: the Crabtree effect in Saccharomyces cerevisiae.

The long-term Crabtree effect in Saccharomyces cerevisiae cultivated in aerobic chemostat at steady state has been studied for three different substrate concentrations in the feed of the bioreactor (data: J. Gen. Microbiol., 129 (1983) 653). We have shown that a model using two ways of transport/metabolization (T/M) of hyperbolic form, with high and low affinity for the substrate, allowed to represent correctly the main characteristics of the phenomenon. The model is based on an explicit form of the T/M kinetics when the bioreactor is considered as a polyphasic dispersed system (PDS). Mass balances analysis also allows to quantify the critical dilution rate value (threshold), Dc, of the transition between respiratory and respirofermentative mode, for which ethanol is produced. A good approximation for the threshold is Dc = V(S)0 Y(Xc, S) where Y(Xc,S) is the average yield coefficient before transition and V(S)0, the maximum specific rate of high affinity T/M pathway. The theoretical value is 0.3 h(-1), and is equal to the experimental value. We thus show in a quantitative way that the transition depends both on culture conditions (global characteristic of the system) and on strain properties (intrinsic characteristic of the microorganism as well). Using two different methods to calculate the residual substrate has carried out the comparison between the simulations end the experimental data. This allowed showing that the latter is not well represented by Monod's model and has confirmed that the affinity for the substrate varies according to the biomass. We have then shown how to calculate the most important specific rates (or metabolic flux) related to biomass, ethanol, oxygen, hydrogen, respiratory and fermentative CO(2) and H(2)O within the cellular phase. It has appeared that the oxygen uptake rate directly depends on high-affinity T/M pathway. This let us think that the regulation of the Crabtree effect in S. cerevisiae depends on the saturation of some glucose metabolization and transport pathways rather than on saturation of the respiratory chains. The specific rates analysis has also allowed us to show, at least in this case, that the metabolization rate (biosynthesis+fueling) had its maximum value on the whole dilution rates interval; metabolites excretion (ethanol and fermentative CO(2)) only intervenes to drain a "surplus" glucose flux. As a consequence, the transport capacity must be higher than the one of metabolization. Maximization of the metabolization specific rate could then be used as an optimization criterion in the stoichiometric calculation of metabolic flux (and not the specific growth rate maximization because growth is limited in a chemostat (mu = D)). We have also shown that the mass balances based on the T/M processes are in agreement with molar and elementary balances of the general stoichiometric equation for glucose respiration and fermentation under aerobic conditions. Thanks to the specific rates calculating the stoichiometric coefficients has done this. The total mass balance difference does not exceed 4%, which is compatible with the experimental carbon balance. Finally, we have emphasized that the ratio of biosynthesis flux and metabolization flux is constant before and after transition. This observation could be applied as soon as the free substrate concentration in the cellular phase is low. The paper succinctly describes the former theoretical results on which the model is built and sufficiently explains the algorithm for straightforward implementation.

Algorithms↗

PubMed1983

A model for the reaction pathways of the K+-dependent phosphatase activity of the (Na+ + K+)-dependent ATPase.

(Na+ + K+)-dependent ATPase preparations from rat brain, dog kidney, and human red blood cells also catalyze a K+ -dependent phosphatase reaction. K+ activation and Na+ inhibition of this reaction are described quantitatively by a model featuring isomerization between E1 and E2 enzyme conformations with activity proportional to E2K concentration: (formula; see text) Differences between the three preparations in K0.5 for K+ activation can then be accounted for by differences in equilibria between E1K and E2K with dissociation constants identical. Similarly, reductions in K0.5 produced by dimethyl sulfoxide are attributable to shifts in equilibria toward E2 conformations. Na+ stimulation of K+ -dependent phosphatase activity of brain and red blood cell preparations, demonstrable with KCl under 1 mM, can be accounted for by including a supplementary pathway proportional to E1Na but dependent also on K+ activation through high-affinity sites. With inside-out red blood cell vesicles, K+ activation in the absence of Na+ is mediated through sites oriented toward the cytoplasm, while in the presence of Na+ high-affinity K+ -sites are oriented extracellularly, as are those of the (Na+ + K+)-dependent ATPase reaction. Dimethyl sulfoxide accentuated Na+ -stimulated K+ -dependent phosphatase activity in all three preparations, attributable to shifts from the E1P to E2P conformation, with the latter bearing the high-affinity, extracellularly oriented K+ -sites of the Na+ -stimulated pathway.

Animals↗

PubMed2006

Interactions between leukotriene C4 and interleukin 13 signaling pathways in a mouse model of airway disease.

CONTEXT: During an asthmatic episode, leukotriene C4 (LTC4) and interleukin 13 (IL-13) are released into the airways and are thought to be central mediators of the asthmatic response. However, little is known about how these molecules interact or affect each other's signaling pathway. OBJECTIVE: To determine if the LTC4 and IL-13 signaling pathways interact with each other's pathways. DESIGN: We examined airway responsiveness, cysteinyl LTs (Cys-LTs), and Cys-LT and IL-13 receptor transcript levels in wild-type mice and in mice that were deficient in gamma-glutamyl leukotrienase (an enzyme that converts LTC4 to LTD4), STAT6 (signal transducer and activator of transcription 6 [a critical molecule in IL-13 signaling]), and IL-4Ralpha (a subunit of the IL-13 receptor). RESULTS: Wild-type (C57BL/129SvEv) and gamma-glutamyl leukotrienase-deficient mice showed increased airway responsiveness after intranasal instillation of IL-13; similar results were observed after intranasal instillation of IL-13 or LTC4 in a second wild-type strain (BALB/c). Interleukin 13 treatment reduced levels of Cys-LTs in bronchoalveolar lavage fluid. This change was unaccompanied by changes in other arachidonic acid metabolites or in RNA transcript levels of enzymes associated with Cys-LT synthesis. Interleukin 13 treatment also increased transcript levels of the Cys-LT 1 and Cys-LT 2 receptors, while LTC4 increased transcript levels of the alpha1 chain of the IL-13 receptor. Furthermore, IL-4Ralpha-deficient mice had increased airway responsiveness to LTC4 but not to IL-13, whereas STAT6-deficient mice failed to respond to either agonist. CONCLUSIONS: These findings indicate that LTC4 and IL-13 are dependent on or signal through STAT6 to increase airway responsiveness and that both agonists regulate expression of each other's receptors.

Airway Resistance↗

PubMed2005

Repair of double-strand DNA breaks by the human nonhomologous DNA end joining pathway: the iterative processing model.

Naturally-occurring ionizing radiation and reactive oxygen species (ROS) from oxidative metabolism are factors that have challenged all life forms during the course of evolution. Ionizing radiation (IR) and reactive oxygen species cause a diverse set of double-strand DNA end configurations. Non-homologous DNA end joining (NHEJ) is an optimal DNA repair pathway for dealing with such a diverse set of DNA lesions. NHEJ can carry out nucleolytic, polymerization, and ligation operations on each strand independently. This iterative processing nature of NHEJ is ideal for repair of pathologic and physiologic double-strand breaks because it permits sequential action of the NHEJ enzymes on each DNA end and on each strand. The versatility of the Artemis:DNA-PKcs endonuclease in cleaving 5' and 3' overhangs, hairpins, gaps, flaps, and various loop conformations makes it well-suited for DNA end modifications on oxidized overhangs. In addition, the ability to cleave stem-loop and hairpin structures permits it to open terminal fold-back configurations that may arise at DNA ends after IR damage. The ability of the XRCC4:DNA ligase IV complex to ligate one strand without ligation of the other permits additional end joining flexibility in NHEJ and raises the possibility of optional involvement of repair proteins from other pathways.

Animals↗

PubMed2003

Catalytic mechanism of the inverting N-acetylglucosaminyltransferase I: DFT quantum mechanical model of the reaction pathway and determination of the transition state structure.

The complex N-glycan structures on glycoproteins play important roles in cell adhesion and recognition events in metazoan organisms. A critical step in the biosynthetic pathway leading from high mannose to these complex structures includes the transfer of N-acetylglucosamine (GlcNAc) to a mannose residue by the inverting N-acetylglucosaminyltransferase I (GnT-I). The catalytic mechanism of this enzymatic reaction is explored herein using DFT quantum chemical methods. The computational model used to follow the reaction is based on the X-ray crystallographic structure of GnT-I and contains 127 atoms that represent fragments of residues critical for the substrate binding and catalysis. The mechanism of the catalytic reaction was monitored by means of a 2D potential energy map calculated as a function of predefined reaction coordinates at the B3LYP/6-31G** level. This potential energy surface revealed one transition state associated with a reaction pathway following a concerted mechanism. The reaction barrier was estimated, and the structure of the transition state was characterized at the B3LYP/6-311++G**// B3LYP/6-31G** level.

Binding Sites↗

PubMed2001

[Quality management: internal guidelines and critical pathways for patients].

BACKGROUND: The construction and implementation of "Practice Guidelines" was one of the most important developments in American medicine of the last 15 years. There is ongoing controversy about the effectiveness of these guidelines to get introduced into practice. It has been proved, however, that guidelines developed by care organizations themselves, will show a higher effectiveness and acceptance and will achieve more positive results (Internal Guidelines, "Locally Owned" Standards). "Mipp": Internal Guidelines are also the starting point for the patient pathways of the model of integrated patient pathways "mipp", developed at the Kantonsspital Aarau in the last 7 years. The model is presented with its main features: Construction and Implementation of Pathways, Path-Controlling, Path-Benchmarking and Path-Visualization. "Mipp" Pathways share with Clinical Pathways the interdisciplinary perspectives for an efficient quality management. The description of processes is combined with an integrated calculation of costs, which is the basis of standard cost accounting and even activity based-costing. CONCLUSION: In the field of upcoming prospective payment systems (PPS) like ARDRG, APDRG etc. it is of utmost importance for care organizations to have a clear view regarding the treatment processes and the possibilities of their improvement.

Benchmarking↗

PubMed1993

The torso pathway in Drosophila: a model system to study receptor tyrosine kinase signal transduction.

In the Drosophila embryo, specification of terminal cell fates that result in the formation of both the head (acron) and tail (telson) regions is under the control of the torso (tor) receptor tyrosine kinase. The current knowledge suggests that activation of tor at the egg pole initiates a signal transduction pathway that is mediated sequentially by the guanine nucleotide releasing factor son of sevenless (Sos), the p21Ras1 GTPase, the serine/threonine kinase D-raf and the tyrosine/threonine kinase MAPKK (Dsor1). Subsequently, it is postulated that activation, possibly by phosphorylation, of a transcription factor at the egg poles activates the transcription of the terminal gap genes tailless and huckebein. These gap genes, which encode putative transcription factors, then control the expression of more downstream factors that ultimately result in head and tail differentiation. Also involved in tor signaling is the non-receptor protein tyrosine phosphatase corkscrew (csw). Here, we review the current model and discuss future research directions in this field.

Animals↗

PubMed2002

Mathematical modeling of plant metabolic pathways.

The understanding of the control of metabolic flux in plants requires integrated mathematical formulations of gene and protein expression, enzyme kinetics, and developmental biology. Plants have a large number of metabolically active compartments, and non-steady-state conditions are frequently encountered. Consequently steady-state metabolic flux balance and isotopic flux balance modeling approaches have limited utility in probing plant metabolic systems. Transient isotopic flux analysis and kinetic modeling are powerful proven techniques for the quantification of metabolic fluxes in compartmentalized, dynamic metabolic systems. These tools are now widely used to address metabolic flux responses to environmental and genetic perturbations in plant metabolism. Continued developments in isotopic and kinetic modeling, quantifying metabolite exchange between compartments, and transcriptional and posttranscriptional regulatory mechanisms governing enzyme level and activity will enable simulation of large sections of plant metabolism under non-steady-state conditions. Metabolic control analysis will continue to make substantial contributions to the understanding of quantitative distribution of control of flux. From the synergy between mathematical models and experiments, creative methods for controlling the distribution of flux by genetic or environmental means will be discovered and rationally implemented.

Forecasting↗

PubMed1999

Folding pathway of a lattice model for proteins.

The folding of a protein-like heteropolymer is studied by using direct simulation of a lattice model that folds rapidly to a well-defined "native" structure. The details of each molecular folding event depend on the random initial conformation as well as the random thermal fluctuations of the polymer. By analyzing the statistical properties of hundreds of folding events, a classical folding "pathway" for such a polymer is found that includes partially folded, on-pathway intermediates that are shown to be metastable equilibrium states of the polymer. These results are discussed in the context of the "classical" and "new" views of folding.

Models, Chemical↗

PubMed2005

The relationship between sexual abuse during childhood and parenting outcomes: modeling direct and indirect pathways.

OBJECTIVE: This study examined the association between childhood sexual abuse (CSA) and parenting outcomes including parenting stress, feelings of competence and discipline strategies. Maternal depression and current partner violence were hypothesized to be mediators of the association between CSA and parenting. METHOD: This study is based on secondary data analysis of archived data. The participants were 263 primiparous mothers (107 with a history of CSA and 156 comparison mothers recruited from a prenatal clinic prior to the birth of their first child. Mothers were interviewed twice: once when they were between 28 and 32 weeks gestation and again when their child was between 2 and 4 years of age. During the first interview, women were asked about childhood experiences of sexual abuse. During their second interview, they were asked about current symptoms of pathology and experiences with partner violence and parenting beliefs and practices. RESULTS: Structural Equation Modeling indicated that the relationship between CSA and punitive discipline was mediated by maternal depression and current partner violence. CSA was associated with higher maternal depression and higher partner violence. CSA, maternal depression, and current partner violence were associated with more negative parental perceptions and higher punitive discipline. Once maternal depression and current partner violence were in the model, the relationship between CSA and parenting outcomes was no different from zero. CONCLUSION: These results highlight the risks associated with CSA for parenting outcomes and suggest two potential pathways for this increased risk.

Adult↗

PubMed2003

Invade or proliferate? Two contrasting events in malignant behavior governed by p16(INK4a) and an intact Rb pathway illustrated by a model system of basal cell carcinoma.

Using a highly infiltrative tumor type as basal cell carcinoma as the model system, we have examined the relation between invasive behavior and proliferation. Our results studying alterations in G(1)-S cell cycle regulatory proteins and proliferation in infiltrative cells were surprising and clearly indicated that invasion in tumors with an intact p16(INK4a)-cyclin D-retinoblastoma protein (Rb) pathway was equivalent to ceased proliferation. Using immunohistochemistry and Western blotting of microdissected parts of basal cell carcinomas, we showed that p16(INK4a) was up-regulated at the invasive front of the majority of basal cell carcinomas with infiltrative growth patterns, followed by ceased proliferation, as well as decreased phosphorylation of Rb. Besides supporting the fact that basal cell carcinomas have an intact Rb pathway, our results clearly indicate that invasive tumor cells change phenotype from a proliferative state to an invasive phenotype. Thus, invasion is not necessarily analogous with proliferation, implicating a paradigm shift in the understanding of two central processes in malignant behavior.

Blotting, Western↗

PubMed2005

Morphological impairments in retinal neurons of the scotopic visual pathway in a monkey model of Parkinson's disease.

Physiological abnormalities resulting from death of dopaminergic neurons of the central nervous system in Parkinson's disease also extend to the retina, resulting in impaired visual functions. In both parkinsonian patients and animal models, low levels of dopamine and loss of dopaminergic cells in the retina have been reported. However, the morphology and connectivity of their postsynaptic neurons, the amacrine cells, have not been analyzed. Here we report, with macaques chronically treated with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) as a model of Parkinson's disease, that morphological impairments in dopaminergic retinal neurons and their plexus in the inner retina are accompanied by an immunoreactivity decrease in gamma-aminobutyric acidergic and glycinergic amacrine cells. Especially deteriorated were AII amacrine cells, the main neuronal subtype postsynaptic to dopaminergic cells, which exhibited a marked loss of lobular appendages and dendritic processes. Concomitantly, electrical synapses among AII cells, as well as chemical synapses between these and rod bipolar cells, were highly deteriorated in parkinsonian monkeys. These results highlight that the scotopic visual pathway is severely impaired in the parkinsonian condition and provide a morphological basis for a number of abnormalities found in electrophysiological and psychophysical trials in Parkinson's disease patients and animal models.

Amacrine Cells↗