Modelling metabolic

The values for metabolite concentrations are needed at different occasions for modeling metabolism (i) as an additional data source to validate kinetic models that are constructed in a bottom-up approach, (ii) as starting point for steady-state search algorithms, (iii) as additional experimental data for... 

P. J. Mulquiney and P. W. Kuchel, Modeling Metabolism with Mathematica, CRC Press, London, UK, 2003. 

Illius, A. W. and Jessop, N. S. (1995). Modeling metabolic costs of allelochemical ingestion by foraging hethivotes.JournalofChemicalEcologyZl, 693-719. 

This Accelrys provided database is based on the journals of the Royal Society of Chemistry (RSC) (308). It primarily contains information on the metabolic fate of chemicals (including pharmaceuticals, agrochemicals, food additives, and environmental and industrial chemicals) in vertebrates, invertebrates, and plants. New entries can be added, and the database may be searched graphically. This database can be combined with various computational tools from Accelrys for target-specific analysis and modeling. Metabolic pathways are organized alphanumerically, and future releases are scheduled to include a comprehensive survey of the metabolism literature (308,309). 

Buettner, R., Parhofer, K. G., Woenckhaus, M., Wrede, . E., Kunz-Schughart, L. A., Scholmerich, J., and Bollheimer, L. C. (2006). Defining high-fat-diet rat models Metabolic and molecular effects of different fat types. J. Mol. Endocrinol. 36, 485-501. 

Physiological toxicokinetic models have been presented describing the behaviour of inhaled butadiene in the human body. Partition coefficients for tissue air and tissue blood, respectively, had been measured directly using human tissue samples or were calculated based on theoretical considerations. Parameters of butadiene metabolism were obtained from in-vitro studies in human liver and lung cell constituents and by extrapolation of parameters from experiments with rats and mice in vivo (see above). In these models, metabolism of butadiene is assumed to follow Michaelis-Menten kinetics. 

Metabolic flux analysis Cellular metabolites and metabolic fluxes can be combined into a series of balance equations, not unlike a series of (bio)chemical reactions in a kinetic model. Metabolic flux analysis is the description of the components and their connections in a metabolic network. 

Levy, J., Zhu, Z., and Dunbar, J. C., 1998, The effect of glucose and calcium on Ca2+-adenosine triphosphatase in pancreatic islets isolated from a normal and a non-insulin-dependent diabetes mellitus rat model. Metabolism, 47 185-9. 

Martens, D. E. Hugenholtz, J. Kleere-bezem, M. et al. Metabolic engineering of lactic add bacteria, the combined approach kinetic modelling, metabolic control and experimental analysis. Microbiology 2002,148 1003-1013. 

Bonardi G, Vidi A (1973) Action of 4-phenyl-l,2-diphenyl-3,5-pyrazolidinedione (DA 2370) on an experimental hyper-uricosuria in the rat. Pharm Res Comm 5 125-129 Dan T, Yoneya T, Onoma M et al. (1994) Hypouricemic and uricosuric actions of AA-193 in a hyperuricemic rat model. Metabolism 43 123-128... 

These questions are amenable to various combinations of imaging, modelling, metabolic and gene expression studies and field observation to analyse the nutrient dynamics of the forest floor microbial decomposer subsystem, and to provide data for predictive models of forest floor responses to environmental change. 

R. Steudel and T. Gobel, unpublished results, T. Gobel, Synthesis and analysis of aliphatic (chain-forming) polysulfur compounds Modeling metabolism of sulfur bacteria. Doctoral Dissertation, Technical University of Berlin, Berlin, 1988. 

Metabolic pathways have been illustrated using simple diagrams since before the human genome project and related bioinformatics projects had begun. With the involvement of computer science techniques, however, systematic approaches to modeling metabolic pathways have progressed quickly, with various aims that range from metabolite analyses to pathway prediction and reconstruction (1-3). Systems analysis has come to incorporate... 

The analysis of network structure from the viewpoint of computer theory requires an introduction to some background information, which will be provided here. We will introduce the data involved for modeling metabolic pathways and the KEGG pathway database in particular. Furthermore, a basic introduction to graphs as used in computer science will be provided. 

LION Bioscience—providerof iDEA, a modular ADME predictive system. The absorption module predicts Caco-2 cell permeation, and performs dose-response modeling of the oral absorption. The metabolism module predicts first-pass effects and models metabolic parameters. Future modules are planned for distribution and elimination (124). 

Smith PA, Sorich MJ, Low LS, McKinnon RA, Miners JO. Towards integrated AD ME prediction Past, present and future directions for modelling metabolism by UDP-glucuronosyltransferases. J Mol Graph Model 2004 22 507-17. 

Under normal physiological conditions, the following heat transfer terms should be incorporated in a lumped or distributed parameter model metabolic heat generation conduction and convection within the body heat exchange with the environment by radiation, conduction and convection heat loss from the skin by evaporation of sweat and water diffused across the skin and respiratory heat loss. Expressions for each of these terms, along with the parameter values, are given elsewhere (Cooney, 1976). 

In the early stages of preclinical development, metabolite profiling is performed using in vitro systems from animal and human, mainly to identify potential species-dependent metabolism early in the development process and to support the selection of the animal species employed in safety assessment studies. As the compound moves further into development, in vivo animal ADME studies are performed. The compound is usually dosed into a rodent and nonrodent species along with an efficacy model. Metabolism data from the animal studies are then used in species selection for safety assessment to insure that all expected human metabolic transformations will be represented in the animal models used in the safety study. 

Genome-scale metabolic models Lactococcus lactis IL1403 First LAB genome-scale model metabolic engineering of central metabolism for diacetyl production Oliveira et al. (2005)... 

Mahadevan, R., SchiUing, C. H. (2003). The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metabolic Engineering, 5, 264—276. 

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