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Biomedical subjects

D Garfinkel

Publications and source records attributed to D Garfinkel.

At least 73 records · Page 4Linked to original sources
PubMed1980

Computer modeling, complex biological systems, and their simplifications.

The amount of information defining a biological system, as specified in its genome, is vastly larger than the amount of information the human mind can handle simultaneously in its short-term memory (7 +/- 2 items at most). In such a situation the mind tends to simplify, linearize, and consider only a few of many variables that may be involved. This may be limiting when an experimenter interprets his own experiments without help from theory or modeling as is common in biology. The Michaelis-Menten model, which is very useful although not necessarily valid, and its linearizations are described as an example of this. The social processes and obligations involved in simplifying complex situations are discussed. Computer simulation provides a method for investigating complex nonlinear systems that does not require excessive simplification of the biological system being studied and whose economics are becoming steadily more favorable.

Computers↗
PubMed1979

Computer simulation of the fructose bisphosphatase/phosphofructokinase couple in rat liver.

Recycling of fructose 6-phosphate and fructose 1,6-bisphosphate in the rat liver under gluconeogenic and glycolytic conditions was investigated with a computer model containing representations of the kinetic properties of phosphofructokinase and fructose 1,6-bisphosphatase under realistic physiological conditions. The two enzyme submodels were constructed from data for the isolated enzymes in vitro by formal optimization. Tissue metabolite concentrations were corrected for cytosolic/mitochondrial compartmentation and effects of chelation and protonation equilibria. This model, which mostly considers the behavior of livers from starved rats, predicts negligible recycling under physiologically realistic conditions. Metabolic regulation of fructose 6-phosphate, the magnesium ion concentration and the distribution of adenine nucleotides appear to prevent operation of a 'futile cycle' in vivo. Rate-limiting chemical species were identified by sensitivity analysis.

Animals↗
PubMed1979

Metabolism of the acutely ischemic dog heart. I. Construction of a computer model.

Construction of a computer model of glycolysis, the Krebs cycle, and related metabolism in acutely ischemic dog heart, involving 122 metabolites, 65 enzymes, and 406 chemical reactions, is described. A previous model of the same metabolism in normal-flow rat heart was modified to fit ischemic dog heart experimental data to within experimental error. The result resembles other models of ischemic heart preparations, implying common underlying mechanisms. The principal change made was reduction of enzyme amounts, consistent with the generally slower metabolism of large animals, suggesting that differing enzyme amounts are a major component of interspecies metabolic difference. Glycolytic intermediates oscillate, asynchronously and with large changes in level; pyridine nucleotides become highly reduced; pH falls, but mitochondria stay alkaline relative to cytoplasm even after oxidative phosphorylation stops.

Animals↗
PubMed1979

Metabolism of the acutely ischemic dog heart. II. Interpretation of a model.

The glycolytic oscillations occurring in an acutely ischemic dog heart are analyzed with a computer model. The major regulations of the glycolytic pathway flux occur at phosphohexose isomerase, which is inhibited by accumulated pentose shunt intermediates; at phosphorylase, which shapes the first cycle of the oscillation; and at aldolase, which shapes the last two cycles. Aldolase is not under normal substrate control. Its activity, and that of some subsequent glycolytic enzymes, appears to be regulated by known interactions with the muscle proteins. The mitochondria become reduced as a result of anoxia, and their metabolism reorganizes to export rather than import reducing equivalents. It is in general feasible to account for the behavior of this preparation in terms of the known metabolism of less severely perturbed hearts, especially (but not completely) in terms of effects of anoxia. The reasons for the inapplicability of the crossover theorem previously used to analyze this preparation are described.

Animals↗
PubMed1979

Computer simulation of metabolism in pyruvate-perfused rat heart. I. Model construction.

A computer model of energy metabolism was constructed for the pyruvate-perfused rat heart subjected to a sudden increase in work load. The model construction techniques are explained and justified. Hypotheses defining a plausible sequence of physiological events resulting in the observed behavior of the organ were arrived at from the measured metabolite time profiles. There is a lag in increasing pyruvate utilization following the work-jump. A transient increase in fatty acid oxidation is required to account for the observed respiration rate. The observed increase in lactate production of this preparation is due to a transient "burst" of glycogenolysis after which the remaining lactate is imported from the interstitium and oxidized, reversing lactate dehydrogenase and hence the alpha-ketoglutarate-malate portion of the malate-aspartate shuttle.

Animals↗
PubMed1979

Computer simulation of metabolism in pyruvate-perfused rat heart. II. Krebs cycle.

A realistic metabolic model of the tricarboxylic acid cycle in the perfused rat heart was constructed to help explain the sequence of biochemical events regulating the metabolism of exogenous pyruvate following a large increase in work load. The unchelated Mg2+ level was the most important controlling factor. The resulting mixture of chelated and unchelated nucleotides and tribasic acids effected coordinated control of citrate synthase, aconitase, isocitrate dehydrogenase, succinyl CoA synthetase, fumarase, and nucleoside diphosphokinase, because Mg2+-chelates are generally substrates whereas unchelated species are inhibitors. Succinate dehydrogenase is largely controlled by the ubiquinone redox potential. The fluxes through alpha-ketoglutarate and malate dehydrogenases are largely dependent on thepyridine nucleotide redox potential, but the succinyl CoA-to-CoASH ratio strongly affects the former enzyme as well. The model predicts an accumulation of succinate during the transition to higher work output.

Animals↗
PubMed1979

Computer simulation of metabolism in pyruvate-perfused rat heart. III. Pyruvate dehydrogenase.

A physiologically and biochemically realistic model of the regulation of pyruvate dehydrogenase complex (PDH) was constructed for the perfused rat heart. It includes conversion between inactive (phospho) and active (dephospho) forms by a specific protein kinase (PDHK) and phosphoprotein phosphatase (PDHP). The activity of the tightly bound PDHK is influenced by synergistic activation/inhibition by acetyl CoA/CoASH and NADH/NAD. PDHK in this simulation was more sensitive to the fraction of ADP that was Mg2+-chelated than to the ATP-to-ADP ratio. Ca2+ stimulates binding of Mg2+-dependent PDHP to the complex; the bound enzyme was considered to be the active species. The fraction of PDH in the active form, rather than substrate and inhibitor levels, determines PDH activity under these conditions. This fraction depends on the present value and recent history of the difference between PDHK and PDHP activities. Both of these are active continuously and continuously control PDH.

Animals↗
PubMed1979

Computer simulation of metabolism in pyruvate-perfused rat heart. IV. Model behavior.

The behavior of a computer model of energy metabolism was determined for perfused rat hearts utilizing pyruvate as sole exogenous fuel and subjected to a rapid increase in work load. Computer-generated metabolite profiles, which are solutions of the differential equations for 1 min elapsed time, closely match 12 experimental curves (involving 120 concentration measurements) and exhibit the following properties. The computed cytosolic pyruvate level oscillates due to large changes in the rates of the processes that produce and consume this metabolite. Cytosolic Mg2+ seems to act as a coordinated controller of glycolytic enzymes; its transient increase permits a transient increase of glycolysis without an accumulation of glucose 6-phosphate. Lactate is exported to the interstitium by a lactate permease and then reimported and oxidized. As a result, the malate-aspartate shuttle reverses direction, and the Krebs cycle is "unspanned."

Animals↗