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A flux model of glycolysis and the oxidative pentosephosphate pathway in developing Brassica napus embryos.

Developing oilseeds synthesize large quantities of triacylglycerol from sucrose and hexose. To understand the fluxes involved in this conversion, a quantitative metabolic flux model was developed and tested for the reaction network of glycolysis and the oxidative pentose phosphate pathway (OPPP). Developing Brassica napus embryos were cultured with [U-13C6]glucose, [1-13C]glucose, [6-13C]glucose, [U-13C12]sucrose, and/or [1,2-13C2]glucose and the labeling patterns in amino acids, lipids, sucrose, and starch were measured by gas chromatography/mass spectrometry and NMR. Data were used to verify a reaction network of central carbon metabolism distributed between the cytosol and plastid. Computer simulation of the steady state distribution of isotopomers in intermediates of the glycolysis/OPPP network was used to fit metabolic flux parameters to the experimental data. The observed distribution of label in cytosolic and plastidic metabolites indicated that key intermediates of glycolysis and OPPP have similar labeling in these two compartments, suggesting rapid exchange of metabolites between these compartments compared with net fluxes into end products. Cycling between hexose phosphate and triose phosphate and reversible transketolase velocity were similar to net glycolytic flux, whereas reversible transaldolase velocity was minimal. Flux parameters were overdetermined by analyzing labeling in different metabolites and by using data from different labeling experiments, which increased the reliability of the findings. Net flux of glucose through the OPPP accounts for close to 10% of the total hexose influx into the embryo. Therefore, the reductant produced by the OPPP accounts for at most 44% of the NADPH and 22% of total reductant needed for fatty acid synthesis.

Amino Acids↗

Low grade B cell lymphoma of gut-associated lymphoid tissue (GALT): a model of the structure and migration pathways of the B cell component of normal human GALT.

The histology, microenvironment and migratory pathways of low grade B cell lymphomas (LGBL) are thought to reflect those of normal lymphoid tissue of similar lineage. Striking clinical differences between LGBL of peripheral lymph nodes and those of the gastrointestinal tract serve to emphasize the lineage differences between mucosal and non-mucosal B cells and suggest that LGBL of gut-associated lymphoid tissue (GALT) could serve as a natural experimental model for the investigation of the properties of normal human GALT. The histology of LGBL of GALT parallels that of normal GALT and draws particular attention to the previously undescribed GALT marginal zone B cells which show close lineage homology with LGBL of GALT. These cells known as centrocyte-like (CCL) cells surround follicles, infiltrate the epithelium and frequently show plasma cell differentiation possibly in response to stimulation from the gut lumen. In LGBL of GALT the CCL cells have an intimate relationship with reactive follicles similar to that described for rat splenic marginal zone cells. LGBL of GALT are slow to disseminate to the periphery and can often be cured by local eradication. This suggests CCL cells do not enter the peripheral blood. However, the gastrointestinal tract remote from the primary tumour is occasionally selectively involved, a finding which supports circulation and homing as described in animals. Using a murine monoclonal anti-idiotypic antibody in one case of LGBL of GALT we have shown that CCL cells appear to enter the circulation and, in the absence of evident tumour, can be identified in the mucosae as well as the marginal zone of the spleen where they undergo plasma cell differentiation.(ABSTRACT TRUNCATED AT 250 WORDS)

B-Lymphocytes↗

Rapid development of nitric oxide-induced hyperalgesia depends on an alternate to the cGMP-mediated pathway in the rat neuropathic pain model.

Intrathecal injection of a nitric oxide releasing compound, NOC-18, was used to define the role of nitric oxide (NO) in the spinal mechanism of neuropathic pain caused by unilateral chronic constriction injury to rat sciatic nerves. Paw withdrawal latency was used to evaluate nociception induced by thermal stimuli before surgery and afterwards at 1, 3, and 6 h, and on days 1, 2, 3, 4, 5, 8, and 12 after the nerve ligature. In the sham-surgery control groups, intrathecal injection of 10 or 100 microg of NOC-18 did not produce any change in withdrawal latencies. In rats with unilateral nerve ligation, however, administration of 1 or 10 microg, but not 0.1 microg, of NOC-18 significantly shortened the time in which thermal hyperalgesia developed after nerve injury. Injection of 1 microg of NOC-18 decreased the onset time of thermal hyperalgesia from 2 days to 3 h and with 10 microg hyperalgesia developed within 1 h after the nerve injury. The effects of intrathecal injection of MK-801, a N-methyl-D-aspartate (NMDA) receptor antagonist, N-nitro-L-arginine methyl ester (L-NAME), a NO synthase inhibitor, methylene blue (MB), a soluble guanylate cyclase inhibitor, and hemoglobin (Hb), a NO scavenger, on the development of thermal hyperalgesia after the sciatic nerve ligature were examined in the presence and absence of 1 and 10 microg of NOC-18. Acceleration of the development of thermal hyperalgesia induced by 1 and 10 microg NOC-18 was completely inhibited by Hb, but was not affected by either MK-801, L-NAME or MB. These findings indicate that NO plays an important role in the rapid development of thermal hyperalgesia after the nerve injury, but that facilitation of nociceptive processing in the spinal cord may entail an alternate to the NO-cyclic guanosine 3',5'-monophosphate (cGMP) pathway.

Animals↗

A cooperation and competition based simple cell receptive field model and study of feed-forward linear and nonlinear contributions to orientation selectivity.

We present a model for development of orientation selectivity in layer IV simple cells. Receptive field (RF) development in the model, is determined by diffusive cooperation and resource limited competition guided axonal growth and retraction in geniculocortical pathway. The simulated cortical RFs resemble experimental RFs. The receptive field model is incorporated in a three-layer visual pathway model consisting of retina, LGN and cortex. We have studied the effect of activity dependent synaptic scaling on orientation tuning of cortical cells. The mean value of hwhh (half width at half the height of maximum response) in simulated cortical cells is 58 degrees when we consider only the linear excitatory contribution from LGN. We observe a mean improvement of 22.8 degrees in tuning response due to the non-linear spiking mechanisms that include effects of threshold voltage and synaptic scaling factor.

Animals↗

A mathematical model for the spatio-temporal dynamics of intrinsic pathway of blood coagulation. II. Results.

This paper continues our study (see Part I) where we modeled the spatio-temporal dynamics of the intrinsic pathway of blood coagulation. Here, we analyzed this model and showed that it describes the threshold behavior of coagulation. When activation is subthreshold (which produces not more than 0.07 nM factor XIa at saturating free calcium concentrations of 2 mM or higher), the concentration of generated thrombin remains below 0.01 nM. At the abovethreshold activation corresponding to factor XIa exceeding 0.07 nM, the concentration of thrombin explosively increases and then abruptly decreases. The peak concentration of thrombin reaches hundreds nM. With respect to free calcium concentration, the system also behaves in a threshold manner. For activation corresponding to 0.3 nM factor XIa, the threshold concentration of free calcium where the outburst of explosive thrombin generation occur is equal to 0.21 mM. The model simulations are in a good agreement with the experimentally recorded kinetics of thrombin generation at different concentrations of free calcium (1). Analysis of the spatial dynamics of coagulation showed that if activation exceeded the threshold level at a certain point, the concentration wave of thrombin arises and propagates at a high speed from the activation zone. The parameters of this wave depends mainly on the efficiency of the feedback loops. The feedback loops through the backbone factors of the intrinsic pathway (autoactivation of factor X or activation of factor XI by thrombin) has a potential for the unlimited propagation of the thrombin wave. With increasing activity of activated protein C (the effect equivalent to that of thrombomodulin), oscillating regimes arise in the model. The first thrombin wave is followed by several secondary running waves. The amplitudes of secondary waves increases to the periphery of the clot consolidating its surface layer.

Blood Coagulation↗

Building a framework to transform health care.

Advances in information technology are helping clinicians to realize the promise of evidence-based medicine, which includes benchmarking, outcomes monitoring, predictive modeling, and clinical pathways. By integrating individual clinical expertise and the best available research, physicians can apply the disciplines and techniques of clinical research to their practice of medicine, one patient at a time. Evidence-based medicine also allows organizations to move forward with continuous clinical quality improvement programs. Standards, open systems, data warehouses, and evidence-based medicine help a health care delivery system obtain the technical infrastructure, decision-making processes, analytical skills, clinical databases, predictive models, and clinical pathways. With this information technology (1) physicians can practice evidence-based medicine and (2) the delivery system can profile clinicians' practice habits for managed care contracting and continuous clinical quality improvement.

Decision Making↗

A substrate switch: a new mode of regulation in the methionine metabolic pathway.

We propose a simple mathematical model of liver S -adenosylmethionine (AdoMet) metabolism. Analysis of the model has shown that AdoMet metabolism can operate under two different modes. The first, with low metabolic rate and low AdoMet concentration, serves predominantly to supply the cell with AdoMet, the substrate for various cellular methylation reactions. The second, with high metabolic rate and high AdoMet concentration, provides an avenue for cleavage of excess methionine and can serve as a source of cysteine when its increased synthesis is necessary. The switch that triggers interconversion between the "low" and "high" modes is methionine concentration. Under a certain set of parameters both modes may coexist. This behavior results from the kinetic properties of (i) the two isoenzymes of AdoMet synthetase, MATI and MATIII, that catalyse AdoMet production; one is inhibited by AdoMet, whereas the other is activated by it, and (ii) glycine- N -methyltransferase that displays highly cooperative kinetics that is different from that of other AdoMet-dependent methyltransferases. Thus, the model provides an explanation for how different cellular needs are met by regulation of this pathway. The model also correctly identifies a critical role for glycine N -methyltransferase in depleting excess methionine in the high mode, thus avoiding the toxicity associated with elevated levels of this essential amino acid.

Animals↗

Secretory pathways and processing of human proopiomelanocortin (POMC) using transformed mouse cultured fibroblasts (L cells) and AtT20 cells by human POMC gene--preembedding immunoelectron microscopic studies.

In order to elucidate the relationship between secretory pathway and processing for precursor molecule of peptide hormones, we performed immunoelectron microscopic studies to localize POMC-derived peptides in mouse cultured L cells (fibroblasts without secretory granules) and in mouse AtT20 cells (ACTH secreting pituitary tumor cells with secretory granules) which had been transformed with human POMC gene. From the electron microscopic localization patterns, L42 cells were considered to serve as a model of constitutive pathway without processing of POMC, and A53 cells were considered to serve as a model of transgranular (regulated) pathway with processing of POMC. Immunoblotting supported these interpretations.

Adrenocorticotropic Hormone↗

Bone anabolic effects of sonic/indian hedgehog are mediated by bmp-2/4-dependent pathways in the neonatal rat metatarsal model.

A neonatal rat metatarsal organ culture model has been employed to study the anabolic effects of Sonic/Indian hedgehog and BMP-4. In this culture system, a significant increase in endochondral ossification is measured by an increase in length of mineralized bone, after daily treatment for 7 days with Sonic hedgehog protein (Shh-N). Previous evidence indicated that PTH related protein (PTHrP) is a critical target of hedgehog function in endochondral ossification. Using a PTHrP blocking antibody, it is shown that hedgehog mediates this activity via pathways other than through PTHrP. A dose-related increase in endochondral ossification is observed when metatarsals are treated with 25 ng/ml recombinant human bone morphogenetic protein 4 (BMP-4). However, this activity is not evident at higher doses of BMP-4 (200 ng/ml). High doses of BMP-4 resulted in increased expression of noggin messenger RNA and cotreatment of noggin and Shh-N resulted in reversal of the anabolic action of Shh-N. This observation suggests that BMP-4 signaling can influence the Shh-N mediated increase in endochondral ossification. Finally, we show that the Shh-N and BMP-4 mediated increase in endochondral ossification is reversed by treatment with antisense oligonucleotides targeted against Cbfa1. Thus, this report identifies Shh-N as an inducer of endochondral ossification that mediates its effect via BMP-4 and Cbfa1-dependent pathways.

Animals↗

Gene expression analysis in a murine model of allergic asthma reveals overlapping disease and therapy dependent pathways in the lung.

Accumulating evidence in animal models and human asthma support a central role for IL-13 signaling in disease pathogenesis. In order to identify asthma and therapy associated genes, global transcriptional changes were monitored in mouse lung following antigen challenge (ovalbumin (OVA)), either alone or in the presence of a soluble IL-13 antagonist. Changes in whole lung gene expression after instillation of mIL-13 were also measured both in wild type and STAT6 deficient mice. A striking overlap in the gene expression profiles induced by either OVA challenge or mIL-13 was observed, further strengthening the relationship of IL-13 signaling to asthma. Consistent with results from functional studies, a subset of the OVA-induced gene expression was significantly inhibited by a soluble IL-13 antagonist while IL-13-modulated gene expression was completely attenuated in the absence of STAT6-mediated signaling. Results from these experiments greatly expand our understanding of asthma and provide novel molecular targets for therapy and potential biomarkers of IL-13 antagonism.

Animals↗

A mathematical model of the inner medullary collecting duct of the rat: pathways for Na and K transport.

A mathematical model of the inner medullary collecting duct (IMCD) of the rat has been developed representing Na+, K+, Cl-, HCO3-, CO2, H2CO3, phosphate, ammonia, and urea. Novel model features include: finite rates of hydration of CO2, a kinetic representation of the H-K-ATPase within the luminal cell membrane, cellular osmolytes that are regulated in defense of cell volume, and the repeated coalescing of IMCD tubule segments to yield the ducts of Bellini. Model transport is such that when entering Na+ is 4% of filtered Na+, approximately 75% of this load is reabsorbed. This requirement renders the area-specific transport rate for Na+ comparable to that for proximal tubule. With respect to the luminal membrane, there is experimental evidence for both NaCl cotransport and an Na+ channel in parallel. The experimental constraints that transepithelial potential difference is small and that the fractional apical resistance is greater than 85% mandate that more than 75% of luminal Na+ entry be electrically silent. When Na+ delivery is limited, an NaCl cotransporter can be effective at reducing luminal Na+ concentration to the observed low urinary values. Given the rate of transcellular Na+ reabsorption, there is necessarily a high rate of peritubular K+ recycling; also, given the lower bound on luminal membrane Cl- reabsorption, substantial peritubular Cl- flux must be present. Thus, if realistic limits on cell membrane electrical resistance are observed, then this model predicts a requirement for peritubular electroneutral KCl exit.

Animals↗

[Functional analysis of calcineurin-mediated signalling pathway using fission yeast as a model system].

Calcineurin (CN), a highly conserved Ca2+/calmodulin-regulated phosphatase, is a critical component of many calcium-regulated processes in mammalian cells, including T cell activation, cardiac hypertrophy, learning and memory. CN is specifically inhibited by the immunosuppressant drugs cyclosporin A and tacrolimus (FK506), and these drugs have served as valuable reagents in identifying the role of CN in a wide variety of cell types. CN may have additional functions in other cell types, and the loss of these functions may contribute to the side effects of these drugs, which include nephrotoxicity and neurotoxicity. A better understanding of the biological roles of CN in different cell types may promote the development of improved strategies for immunosuppression. We have been studying the CN signal transduction pathway in fission yeast because this system is amenable to genetics and has many advantages in terms of relevance to higher systems. Fission yeast has a single gene encoding the catalytic subunit of CN, ppb1+, that is essential for cytokinesis. We have shown that in fission yeast CN plays an essential role in maintaining chloride ion homeostasis and acts antagonistically with the Pmk1 MAP kinase pathway. We also carried out an isolation and a screening for several FK506-sensitive mutants in order to identify genes that share an essential function for viability with CN. Possible roles of these gene products in cellular functions in relation to calcineurin are discussed.

Calcineurin↗

Model analysis of difference between EGF pathway and FGF pathway.

The difference in time course of Ras and mitogen activated protein kinase (MAPK) cascade by different growth factors is considered to be the cause of different cellular responses. We have developed the computer simulation of Ras-MAPK signal transduction pathway containing newly identified negative feedback system, Sprouty, and adaptor molecules. Unexpectedly, negative feedback system did not profoundly affect time course of MAPK activation. We propose the key role of fibroblast growth factor receptor substrate 2 (FRS2) in NGF/FGF pathway for sustained MAPK activation. More Grb2-SOS complexes were recruited to the plasma membrane by binding to membrane-bound FRS2 in FGF pathway than in EGF pathway and caused sustained activation of ERK. The EGF pathway with high concentration of EGF receptor also induced sustained MAPK activation, which is consistent with the results in the PC12 cell overexpressing the EGF receptors. The simulated time courses of FRS2 knock-out cells were consistent with those of the reported experimental results.

Epidermal Growth Factor↗

Effect of gas density variations on respiratory input impedance in humans.

The forced oscillation technique is a widely-used non-invasive method of characterizing the dynamic behaviour of the respiratory system. We used the forced oscillation technique to investigate respiratory mechanics in healthy subjects during simulated dives in dry hyperbaric chambers. We observed frequency dependence of input impedance, which was mainly density-dependent. To explain this result, we propose a model of the respiratory system, based on flow redistribution in a two-pathway circuit. This model, using the electrical analogue, is composed of two Resistance-Self Inductance-Capacitance (R-I-C) pathways set up in parallel. It allowed us to explain the dynamic behaviour of respiratory impedance under hyperbaric conditions in healthy subjects. Changes in respiratory impedance according to frequency vary with the relative importance of the inequalities of the two time constants RC and I/R between the two pathways. With low values of density, RC inequality predominates, whereas I/R inequality tends to predominate with high values of density.

Air Pressure↗

Impairment of PI3-K/Akt pathway underlies attenuated endothelial function in aorta of type 2 diabetic mouse model.

The phosphatidylinositol 3-kinase (PI3-K) pathway, which activates serine/threonine protein kinase Akt, enhances endothelial nitric oxide synthase (eNOS) phosphorylation and nitric oxide (NO) production. We investigated the involvement of the PI3-K/Akt pathway in the relaxation responses to acetylcholine (ACh) and clonidine in a new type 2 diabetic model (streptozotocin plus nicotinamide-induced diabetic mice). Plasma glucose and insulin levels were significantly elevated in our model, and intravenous glucose tolerance tests revealed clear abnormalities in glucose tolerance and insulin responsiveness. Although in our model the ACh-induced relaxation and NOx- (NO2-+NO3-)/cGMP production were unchanged, the clonidine-induced and insulin-induced relaxations and NOx-/cGMP production were all greatly attenuated. In control mice, the clonidine-induced and insulin-induced relaxations were each abolished by LY294002 and by Wortmannin (inhibitors of PI3-K), and also by Akt-inhibitor treatment. The ACh-induced relaxation was unaffected by such treatments in either group of mice. The expression level of total Akt protein was significantly decreased in the diabetic mice aorta, but those for the p85 and p110gamma subunits of PI3-K were not. The clonidine-induced Ser-473 phosphorylation of Akt through PI3-K was significantly decreased in our model; however, that induced by ACh was not. These results suggest that relaxation responses and NO production mediated via the PI3-K/Akt pathway are decreased in this type 2 diabetic model. This may be a major cause of endothelial dysfunction (and the resulting hypertension) in type 2 diabetes.

Acetylcholine↗

Regeneration of the mammalian central vestibular pathway using the rat as animal model.

Regeneration of the mammalian central vestibular system was examined in rat. The lateral vestibulospinal tract (LVST) of infant rat was transected unilaterally at the level of C1-3. After a postoperative interval of several weeks, the LVST was examined by injecting an anterograde tracer (wheat germ agglutinin-conjugated horseradish peroxidase) into the lateral vestibular nucleus (LVN) and a retrograde tracer (Fast Blue) into the lumbar enlargement. More than half of the rats showed successful regeneration, indicating definite plasticity in the mammalian central vestibular system.

Animals↗

Framework for the uncertainty assessment in the impact pathway analysis with an application on a local scale in Spain.

The estimation of damage estimates due to air emissions gives important basic knowledge for decision-making on the level of environmental politics and business strategies. Nowadays, a frequently applied method to estimate environmental damages is the Impact Pathway Analysis (IPA), which can be easily carried out using models such as EcoSense or PathWays. These models produce results in a relatively short term. However, there is a lack of reliability in the results. As in many other environmental software tools, the uncertainty is the key problem that makes it difficult to convince decision-makers by the outcomes of a study. Therefore, a framework that allows assessing the uncertainties within studies in which the IPA is applied on a local scale has been developed. In this assessment framework, the uncertainties of the used parameters, including their spatial and temporal variability, are taken into account. As the model is processing a huge quantity of data, one step of the assessment consists of a screening procedure to determine the parameters that are supposed to be fixed. For the other data, probability distributions have to be selected and classified into two groups: extensively available data for which average and standard deviation can be calculated and data based on little information. A quantification of the uncertainty can be completed by a stochastic model in the form of Monte Carlo (MC) simulation on the basis of the framework. As an illustration of the framework, we have applied it to a study on the installation of an advanced gas treatment in the municipal waste incinerator of Tarragona. It can be shown that the presented stochastic approach gives a lower geometric deviation than the analytical one and that the new gas treatment reduces the environmental damages without any doubt.

Costs and Cost Analysis↗