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Kinetic and binding studies of Mn (II) and fructose 1,6-bisphosphate with rabbit liver hexosebisphosphatase.

The separate interaction of the substrate fructose 1,6-bisphosphate and a metal ion cofactor Mn2+ with neutral hexosebisphosphatase has been studied under equilibrium conditions at pH 7.5 with gel filtration and electron paramagnetic resonance measurements, respectively. Binding data for both ligands to the enzyme yielded nonlinear Scatchard plots that analyze in terms of four negatively cooperative binding sites per enzyme tetramer. Graphical estimates of the binding constants were refined by a computer searching procedure and nonlinear least squares analysis. These results are qualitatively similar to those obtained from binding studies involving teh alkaline enzyme, a modified form of hexosebisphosphatase whose pH optimum is in the alkaline pH region. Both forms of the enzyme enhance the proton relaxation rate of water protons by a factor of approximately 7 to 8 at 24 MHz, demonstrating similar metal ion environments. Teh activator Co(III)-EDTA did not affect Mn2+ binding to the neutral enzyme. In the presence of (alpha + beta)methyl-D-fructofuranoside 1,6-bisphosphate, however, two sets--each containing four Mn2+ binding sites--were observed per enzyme tetramer with loss of the negatively cooperative interaction. These results are viewed in terms of four noncatalytic and four catalytic Mn2+ binding sites. Parallel kinetic investigations were conducted on the neutral enzyme to determine specific activity as a function of Mn2+ and fructose 1,6-bisphosphate concentration. A pro-equilibrium sequential pathway model involving Mn2+-enzyme and the Mn2+-fructose 1,6-bisphosphate complex both as substrate and as an allosteric inhibitor satisfactorily fit the kinetic observations. All possible enzyme species were computed from the determined binding constants and grouped according to the number of moles of Mn2+-fructose 1,6-bisphosphate complex bound to the Mn2+-enzyme, and individual rate constants were calculated. The testing of other models and their failure to describe the kinetic observations are discussed.

Animals↗

Nonparametric pathway-based regression models for analysis of genomic data.

High-throughout genomic data provide an opportunity for identifying pathways and genes that are related to various clinical phenotypes. Besides these genomic data, another valuable source of data is the biological knowledge about genes and pathways that might be related to the phenotypes of many complex diseases. Databases of such knowledge are often called the metadata. In microarray data analysis, such metadata are currently explored in post hoc ways by gene set enrichment analysis but have hardly been utilized in the modeling step. We propose to develop and evaluate a pathway-based gradient descent boosting procedure for nonparametric pathways-based regression (NPR) analysis to efficiently integrate genomic data and metadata. Such NPR models consider multiple pathways simultaneously and allow complex interactions among genes within the pathways and can be applied to identify pathways and genes that are related to variations of the phenotypes. These methods also provide an alternative to mediating the problem of a large number of potential interactions by limiting analysis to biologically plausible interactions between genes in related pathways. Our simulation studies indicate that the proposed boosting procedure can indeed identify relevant pathways. Application to a gene expression data set on breast cancer distant metastasis identified that Wnt, apoptosis, and cell cycle-regulated pathways are more likely related to the risk of distant metastasis among lymph-node-negative breast cancer patients. Results from analysis of other two breast cancer gene expression data sets indicate that the pathways of Metalloendopeptidases (MMPs) and MMP inhibitors, as well as cell proliferation, cell growth, and maintenance are important to breast cancer relapse and survival. We also observed that by incorporating the pathway information, we achieved better prediction for cancer recurrence.

Adult↗

Application of cybernetic models to metabolic engineering: investigation of storage pathways

A cybernetic model is proposed to examine generic features of storage pathways. This model is capable of describing synthesis of carbon and non-carbon storage polymers. The effect of environmental conditions is evaluated using storage polymer level as a fraction of total biomass as a gauge of pathway performance. The base wild-type pathway is then analyzed to determine the effect of genetic alterations upon system performance. Proposed modifications are tested using the cybernetic model as a diagnostic tool to ascertain the ramifications of potential genetic alterations. A methodology is developed within the cybernetic framework to describe alterations of enzyme activity and over-expression of pathway enzymes. Copyright 1998 John Wiley & Sons, Inc.

Journal Article↗

Ontology based standardization of Petri net modeling for signaling pathways.

Taking account of the great availability of Petri nets in modeling and analyzing large complicated signaling networks, semantics of Petri nets is in need of systematization for the purpose of consistency and reusability of the models. This paper reports on standardization of units of Petri nets on the basis of an ontology that gives an intrinsic definition to the process of signaling in signaling pathways.

Computer Simulation↗

Molecular models for shikimate pathway enzymes of Xylella fastidiosa.

The Xylella fastidiosa is a bacterium that is the cause of citrus variegated chlorosis (CVC). The shikimate pathway is of pivotal importance for production of a plethora of aromatic compounds in plants, bacteria, and fungi. Putative structural differences in the enzymes from the shikimate pathway, between the proteins of bacterial origin and those of plants, could be used for the development of a drug for the control of CVC. However, inhibitors for shikimate pathway enzymes should have high specificity for X. fastidiosa enzymes, since they are also present in plants. In order to pave the way for structural and functional efforts towards antimicrobial agent development, here we describe the molecular modeling of seven enzymes of the shikimate pathway of X. fastidiosa. The structural models of shikimate pathway enzymes, complexed with inhibitors, strongly indicate that the previously identified inhibitors may also inhibit the X. fastidiosa enzymes.

Amino Acid Sequence↗

[Mathematical model of two pathways of light perception by the photoreceptor cell].

On the basis of the concept postulating polyfunctional role of rhodopsin in the photoreceptor cell excitation a mathematical model of two pathways of excitation was formulated. One pathway involves the appearance of Ca2+ ions in the cell, which block the sodium channels. The second one results in cGMP splitting which also brings about the blocking of sodium channels. A change in the concentration of acting agents and development of cell excitation under illumination was calculated. The calcium branch is shown to be rapid and direct, but of a low sensitivity. The cGMP branch is a slow one but has a high intensification coefficient. The action time of the calcium branch does not depend on illumination, while the time of cGMP branch decreases with the illumination rise and is in an inverse proportion to the square root of the flash intensity. Under repeated illumination the amplitude of calcium response decreases, and its time remains constant. In cGMP branch the time of the response to the second flash decreases. The amplitude of the second response depends on the intensity of the first flash, it can be smaller or larger than the amplitude of the first response.

Cyclic GMP↗

Analysis and prediction of the effect of uncertain boundary values in modeling a metabolic pathway.

The integration of large quantities of biological information into mathematical models of cell metabolism provides a way for quantitatively evaluating the effect of parameter changes on simultaneous, coupled, and, often, counteracting processes. From a practical point of view, the validity of the model's predictions would critically depend on its quality. Among others, one of the critical steps that may compromise this quality is to decide which are the boundaries of the model. That is, we must decide which metabolites are assumed to be constants, and which fluxes are considered to be the inputs and outputs of the system. In this article, we analyze the effect of the experimental uncertainty on these variables on the system's characterization. Using a previously defined model of glucose fermentation in Saccharomyces cerevisiae, we characterize the effect of the uncertainty on some key variables commonly considered to be constants in many models of glucose metabolism, i.e., the intracellular pH and the pool of nucleotides. Without considering if this variability corresponds to a possible true physiological phenomenon, the goal of this article is to illustrate how this uncertainty may result in an important variability in the systemic responses predicted by the model. To characterize this variability, we analyze the utility and limitations of computing the sensitivities of logarithmic-gains (control coefficients) to the boundary parameters. With the exception of some special cases, our analysis shows that these sensitivities are good indicators of the dependence of the model systemic behavior on the parameters of interest.

Anaerobiosis↗

The peripheral unconditioned stimulus pathway in a model learning system involving defensively conditioned heart rate change in the pigeon.

The peripheral pathway transmitting the unconditioned stimulus information is described in a vertebrate model system for studying learning-visually conditioned heart rate change in the pigeon. In this system footshock serves as the unconditioned stimulus, and it is shown that the effective stimulation field of this stimulus, defined with respect to the unconditioned cardioacceleratory response, includes cutaneous dermatomes 21-25 (L1-Sl). The stimulus information is then transmitted by Group III and IV fibers in portions of the femoral and sciatic nerves which enter the spinal cord over segments 21-25. Further, it is shown that interrupting this pathway by section of dorsal roots 21-25 precludes establishing conditioned heart rate change with footshock as the unconditioned stimulus.

Action Potentials↗

Construction of a model demonstrating neural pathways and reflex arcs.

Employment opportunities in the future will require higher skills and an understanding of mathematics and science. As a result of the growing number of careers that require solid science and mathematics training, the methods of science education are undergoing major reform. To adequately equip students for technologically advanced positions, new teaching methods must be developed that prepare tomorrow's workforce for the challenges of the 21st century. One such method is the use of models. By actively building and manipulating concrete models that represent scientific concepts, students are involved in the most basic level of Piaget's learning scheme: the sensorimotor stage. Models are useful in reaching all students at the foundational levels of learning, and further learning experiences are rapidly moved through higher learning levels. This success ensures greater comprehension and understanding compared with the traditional methods of rote memorization. We developed an exercise for the construction of an inexpensive, easy-to-build model demonstrating neural pathways and reflex arcs. Our exercise also includes many supplemental teaching tools. The exercise is designed to fulfill the need of sound physiological teaching materials for high school students.

Animals↗

Testing the importance of p27 degradation by the SCFskp2 pathway in murine models of lung and colon cancer.

Decreased expression of the CDK inhibitor p27kip1 in human tumors directly correlates with increased resistance to chemotherapies, increased rates of metastasis, and an overall increased rate of patient mortality. It is thought that decreased p27 expression in tumors is caused by increased proteasomal turnover, in particular activation of the pathway governed by the SCFskp2 E3 ubiquitin protein ligase. We have directly tested the importance of the SCFskp-mediated degradation of p27 in tumorigenesis by analyzing the tumor susceptibility of mice that express a form of p27 that cannot be ubiquitinated and degraded by this pathway (p27T187A). In mouse models of both lung and colon cancer down-regulation of p27 promotes tumorigenesis. However, we found that preventing p27 degradation by the SCFskp2 pathway had no impact on tumor incidence or overall survival in either tumor model. Our study unveiled a previously unrecognized role for the control of p27 mRNA abundance in the development of non-small cell lung cancers. In the colon cancer model, the frequency of intestinal adenomas was similarly unaffected by the p27T187A mutation, but, unexpectedly, we found that it inhibited progression of intestinal adenomas to carcinomas. These studies may guide the choice of clinical settings in which pharmacologic inhibitors of the Skp2 pathway might be of therapeutic value.

Animals↗

Chloroquine-induced endocytic pathway abnormalities: Cellular model of GM1 ganglioside-induced Abeta fibrillogenesis in Alzheimer's disease.

Endocytic pathway abnormalities were previously observed in brains affected with Alzheimer's disease (AD). To clarify the pathological relevance of these abnormalities to assembly of amyloid beta-protein (Abeta), we treated PC12 cells with chloroquine, which potently perturbs membrane trafficking from endosomes to lysosomes. Chloroquine treatment induced accumulation of GM1 ganglioside (GM1) in Rab5-positive enlarged early endosomes and on the cell surface. Notably, an increase in GM1 level on the cell surface was sufficient to induce Abeta assembly. Our results suggest that endocytic pathway abnormalities in AD brain induce GM1 accumulation on the cell surface, leading to amyloid fibril formation in brain.

Alzheimer Disease↗

Pathway: a dynamic food-chain model to predict radionuclide ingestion after fallout deposition.

This manuscript describes the structure and basis for parameter values of a computerized food-chain transport model for radionuclides. The model, called "PATHWAY," estimates the time-integrated ingestion intake by humans of 20 radionuclides after a single deposition from the atmosphere to the landscape. The model solves a set of linear, coupled differential equations to estimate the inventories and concentrations of radionuclides in soil, vegetation, animal tissues and animal products as a function of time following deposition. Dynamic processes in the model include foliar interception, weathering and absorption; plant growth, uptake, harvest and senescence; soil resuspension, percolation, leaching and tillage; radioactive decay; and livestock ingestion, absorption and excretion. Human dietary data are included to permit calculation of time-dependent radionuclide ingestion rates, which are then numerically integrated. The model considers seasonal changes in the biomass of vegetation and animal diets, as well as specific plowing and crop-harvest dates; thus the integrated radionuclide intakes by humans are dependent on the seasonal timing of deposition. The agricultural data base represents the arid and semi-arid regions of the western United States. The foliar deposition parameters apply to regional fallout out to a few hundred miles from nuclear detonations at the Nevada Test Site. With modification, the model could be applied to chronic or other acute releases, providing the ground deposition in Bq m-2 could be estimated. The output of PATHWAY (Bq ingested per Bq m-2 deposited) may be multiplied by the deposition and a dose conversion factor (Gy Bq-1) to yield an organ-specific dose estimate. The model may be run deterministically to yield single estimates or stochastically ("Monte-Carlo" mode) to provide distributional output that reflects uncertainty in the output due to uncertainty in parameters. Tests of the predictive accuracy are briefly described and work published to date on validation trials is cited.

Animals↗

Mathematical modelling of metabolic pathways affected by an enzyme deficiency. Energy and redox metabolism of glucose-6-phosphate-dehydrogenase-deficient erythrocytes.

The effects of various forms of glucose-6-phosphate dehydrogenase deficiency on erythrocyte metabolism have been studied on the basis of a complex mathematical model which comprises the main pathways of this cell: glycolysis, pentose pathway, reactions of the glutathione and adenine nucleotide metabolism. The calculated flux rates through the oxidative pentose pathway with and without methylene blue are in good accord with experimental results. The degree of deficiency as predicted by the model on the basis of calculated upper oxidative load boundaries, as well as of maximal methylene blue stimulation, correlates with the individual clinical manifestation of the metabolic disease. Therefore, the model allows one to judge the degree of metabolic disorder in the presence of glucose-6-phosphate dehydrogenase enzymopathies if the kinetic properties of the defect enzyme are known. Experimentally accessible parameters for an assessment of the oxidative load capacity of cells in vivo are proposed. It is pointed out that the threshold of tolerance as to energetic load is drastically reduced in the case of severe glucose-6-phosphate dehydrogenase deficiency.

Catalysis↗

A model of the pathways of inhaled medicaments to their receptor sites.

From controlled inhalation experiments with bronchotropic substances, it becomes clear that the 'dust model of the lungs' is inadequate in explaining the 'facts and findings' of drug inhalation. Two pathway flow charts are worked out, permitting a more specific description of the transport processes involved, in order to meet the need for a more appropriate model.

Bronchodilator Agents↗

The Pathways study: a model for lowering the fat in school meals.

We describe the development and implementation of the Pathways school food service intervention during the feasibility phase of the Pathways study. The purpose of the intervention was to lower the amount of fat in school meals to 30% of energy to promote obesity prevention in third- through fifth-grade students. The Pathways nutrition staff and the food service intervention staff worked together to develop 5 interrelated components to implement the intervention. These components were nutrient guidelines, 8 skill-building behavioral guidelines, hands-on materials, twice yearly trainings, and monthly visits to the kitchens by the Pathways nutrition staff. The components were developed and implemented over 18 mo in a pilot intervention in 4 schools. The results of an initial process evaluation showed that 3 of the 4 schools had implemented 6 of the 8 behavioral guidelines. In an analysis of 5 d of school menus from 3 control schools, the lunch menus averaged from 34% to 40% of energy from fat; when the menus were analyzed by using the food preparation and serving methods in the behavioral guidelines, they averaged 31% of energy from total fat. This unique approach of 5 interrelated food service intervention components was accepted in the schools and is now being implemented in the full-scale phase of the Pathways study in 40 schools for 5 y.

Asian People↗

Insights into the behaviour of systems biology models from dynamic sensitivity and identifiability analysis: a case study of an NF-kappaB signalling pathway.

Mathematical modelling offers a variety of useful techniques to help in understanding the intrinsic behaviour of complex signal transduction networks. From the system engineering point of view, the dynamics of metabolic and signal transduction models can always be described by nonlinear ordinary differential equations (ODEs) following mass balance principles. Based on the state-space formulation, many methods from the area of automatic control can conveniently be applied to the modelling, analysis and design of cell networks. In the present study, dynamic sensitivity analysis is performed on a model of the IkappaB-NF-kappaB signal pathway system. Univariate analysis of the Euclidean-form overall sensitivities shows that only 8 out of the 64 parameters in the model have major influence on the nuclear NF-kappaB oscillations. The sensitivity matrix is then used to address correlation analysis, identifiability assessment and measurement set selection within the framework of least squares estimation and multivariate analysis. It is shown that certain pairs of parameters are exactly or highly correlated to each other in terms of their effects on the measured variables. The experimental design strategy provides guidance on which proteins should best be considered for measurement such that the unknown parameters can be estimated with the best statistical precision. The whole analysis scheme we describe provides efficient parameter estimation techniques for complex cell networks.

I-kappa B Kinase↗

Modelling computerised clinical pathways.

Since the mid 1980s, paper clinical pathways have been used in defining the road map of patient care. They have been used with varying degree of success for providing more cost-effective healthcare and helped to establish quality improvement models for healthcare delivery. Many attempts have been made to produce electronic versions of the paper clinical pathways in order to maximise benefits of the paper based systems. However, all paper systems are designed based on linear sequential model with little decision support capability. Current electronic versions of the paper systems produce only minimal improvements on the functionality of their paper counterparts. A state-transition information model (STIM) grounded in the Object Oriented system design paradigm is used to reconceptualise a computerised clinical pathways design. A computerised clinical pathways prototype is currently being developed based on this STIM model. The prototype will demonstrate improved functionality: better information management and decision support capabilities.

Computer Simulation↗