Quantitative flux coupling analysis

Journal of Mathematical Biology - Flux coupling analysis (FCA) aims to describe the functional dependencies among reactions in a metabolic network. Currently studied coupling relations are...     

Quantitative analysis of the microtubule system in isolated fish melanophores

Isolated melanophores of the angelfish, Pterophyllum scalare, have been used in a morphometric analysis and a quantitative study of their microtubule system. Using transverse sections spaced at regular intervals, the changes associated with the process of pigment aggregation have been determined. Upon the concentration of pigment granules in the central cell region, almost half of the cytoplasmic portion is also withdrawn from the peripheral cell regions. Counts of microtubules within a cell sector in cells with pigment aggregated and dispersed, respectively, reveal (a) a constancy of the number of microtubules in this sector regardless of the distance from the cell center, and (b) a reduction of microtubule number in cells with pigment aggregated by about 58%. On the basis of these counts, the total number of microtubules has been calculated. In the dispersed state, about 2,400 microtubules extend between the center and the periphery of the cell, while their number is about 1,000 in the aggregated state. Using a 13-protofilament model of a microtubule and relevant data on size and molecular weight of microtubule subunits, the amount of tubulin present as microtubules is calculated. In the average, the cells contain 1.95·10⁸ monomers corresponding to 1.78·10^?8 mg tubulin. A tentative estimation of the concentration of tubulin inside a melanophore yields values of 6.1 mg/ml for the whole cell and 16.5 mg/ml for the cytoplasm alone (excluding membrane-bound organelles). Based on this estimation, a comparison, with microtubule assembly in vitro is made.     

Quantitative analysis of flux along the gluconeogenic, glycolytic and pentose phosphate pathways under reducing conditions in hepatocytes isolated from fed rats.

Hepatocytes were isolated from the livers of fed rats and incubated with a mixture of glucose (10 mM), ribose (1 mM), mannose (4 mM), glycerol (3 mM), acetate (1.25 mM), and ethanol (5 mM) with one substrate labelled with 14C in any given incubation. Incorporation of label into CO2, glucose, glycogen, lipid glycerol and fatty acids, acetate and C-1 of glucose was measured at 20 and 40 min after the start of the incubation. The data (about 48 measurements for each interval) were used in conjunction with a single-compartment model of the reactions of the gluconeogenic, glycolytic and pentose phosphate pathways and a simplified model of the relevant mitochondrial reactions. An improved method of computer analysis of the equations describing the flow of label through each carbon atom of each metabolite under steady-state conditions was used to compute values for the 34 independent flux parameters in this model. A good fit to the data was obtained, thereby permitting good estimates of most of the fluxes in the pathways under consideration. The data show that: net flux above the level of the triose phosphates is gluconeogenic; label in the hexose phosphates is fully equilibrated by the second 20 min interval; the triose phosphate isomerase step does not equilibrate label between the triose phosphates; substrate cycles are operating at the glucose-glucose 6-phosphate, fructose 6-phosphate-fructose 1,6-bisphosphate and phosphoenolpyruvate-pyruvate-oxaloacetate cycles; and, although net flux through the enzymes catalysing the non-oxidative steps of the pentose phosphate pathway is small, bidirectional fluxes are large.     

Quantitative analysis of autophagic flux by confocal pH-imaging of autophagic intermediates

Although numerous techniques have been developed to monitor autophagy and to probe its cellular functions, these methods cannot evaluate in sufficient detail the autophagy process, and suffer limitations from complex experimental setups and/or systematic errors. Here we developed a method to image, contextually, the number and pH of autophagic intermediates by using the probe mRFP-GFP-LC3B as a ratiometric pH sensor. This information is expressed functionally by AIPD, the pH distribution of the number of autophagic intermediates per cell. AIPD analysis reveals how intermediates are characterized by a continuous pH distribution, in the range 4.5–6.5, and therefore can be described by a more complex set of states rather than the usual biphasic one (autophagosomes and autolysosomes). AIPD shape and amplitude are sensitive to alterations in the autophagy pathway induced by drugs or environmental states, and allow a quantitative estimation of autophagic flux by retrieving the concentrations of autophagic intermediates.     

Role of the adenylate system and glycolytic flux in the control of protein synthesis in isolated rat lung cells

(1) Glucose stimulates the incorporation of amino acids into protein in lung cells isolated by digestion of the lung stroma with collagenase. This effect reflects mainly an increase in protein synthesis since no effect of glucose had been found to the uptake of amino acid precursors and, although glucose decreases the rate of intracellular proteolysis by 15%, this effect cannot account for the increased incorporation of radioactivity into proteins. Furthermore, glucose did not induce any significant change in the intracellular content of valine. (2) For glucose to act on protein synthesis, it must be glycolyzed since its stereoisomer, L-glucose, which is not metabolized by lung cells, has no effect. (3) The mechanism of glucose action does not seem to be related simply to variations of cellular ATP content or energy charge. The following arguments seem to support this conclusion: (i) glucose does not bring about significant variations in the concentration of reactants of the adenylate system; (ii) the increase in protein synthesis induced by glucose in energy-depleted cells correlates with a rise in ATP content and energy charge; however, adenosine, which increases ATP levels in a form quantitatively similar to glucose, is unable to affect protein synthesis: (iii) glucose also accelerates the incorporation of amino acids into proteins in adenosine-treated lung cells in which the ATP concentration was almost double that of the control and the energy charge was considerably elevated, ruling out the possibility that a rise in the steady-state concentration of ATP and/or energy charge alone could be responsible for the acceleration of protein synthesis. (4) It can be concluded that the effect of glucose in increasing protein synthesis in lung cells is dependent on some signal arising from its breakdown and not to variations in the concentration of reactants or energy charge of the adenylate system.     

Quantitative analysis of internalization of glucagon by isolated hepatocytes

Biochemical methods have been used to quantitate total, acid-stable and acid-labile association of (mono[125I]iodoTyr10) glucagon with rat hepatocytes in suspension to evaluate internalization of glucagon and its receptors. Internalization is inhibited by low temperature, phenylarsine oxide, and by blocking receptor binding, consistent with receptor-mediated endocytosis. Approximately 30% of the total cell-associated hormone is internalized at 30 min of incubation. The rate declines until 90 min when the internalization of glucagon ceases, although the cells remain competent to internalize asialofetuin. From 90 min to 4 h, 27% of the maximum label internalized at 30 min remains within cells. The number of cell surface receptors decreases but the affinity of those remaining is unchanged. However, 1.7-2.7 surface receptors are lost to binding for each molecule of radiolabeled glucagon internalized. Uptake occurs according to a rate constant of 0.183 min-1 (t1/2 = 3.8 min). We conclude that (i) hepatocytes internalize a finite quantity of glucagon, implying the existence of undefined regulatory mechanisms; (ii) hormone is retained for greater than 2 h within cells and may play a physiological role within cells; and (iii) both occupied and unoccupied receptors become inaccessible to extracellular hormone as internalization proceeds; rapid recycling of receptors does not occur.     

Quantitative analysis of tubulin and microtubule compartments in isolated rat hepatocytes

A combined morphometric and biochemical approach has been used to identify and quantitate microtubules and tubulin in isolated hepatocytes. The total soluble pool of microtubule protein was estimated by specific high affinity binding to radiolabeled colchicine. Scatchard analysis of the data identified two populations of binding sites: high affinity-low capacity sites resembling tubulin and low affinity-high capacity sites believed to represent nonspecific colchicine-binding sites. Data from these studies indicate that tubulin represents 1% of the soluble protein of the cell, that 9.0 X 10(-14) dimers of tubulin are present per microgram soluble hepatocyte protein, and that the average hepatocyte contains 3.1 X 10(7) tubulin dimers. Our calculations suggest that this amount of tubulin would form a microtubule 1.9 cm in length if totally assembled. However, stereological measurements indicate that the actual length of microtubules in the cytosolic compartment of the average hepatocyte is only 0.28 cm. Thus, these experiments suggest that only 15% of the available tubulin in hepatocytes of postabsorptive rats is assembled in the form of microtubules.     

Quantitative pathologic analysis of first and second primary cancers in double tumors of the lung

In spite of the frequent occurrence of double tumors of the lung, pathologic reports on these tumors are rare. In this study, 34 patients with double tumors (10 metachronous and 24 synchronous) were quantitatively analyzed; in all cases, both the first and second tumors had been completely resected and had adequate archival material. One aim of the study was to investigate whether there was a difference in the malignancy of the first and second tumors, as evaluated from their pathologic features. A second question was whether the length of the disease-free interval between the first and second tumors or the survival could be predicted on the basis of any of the investigated features. It was found that the first and second tumors, whether synchronous or metachronous, were strikingly similar: there was no difference in any of the quantitative pathologic features studied (epithelial percentage, DNA index, mean nuclear area and standard deviation of the nuclear area). It was not possible to predict by either univariate or multivariate analysis from any of the parameters either the length of the disease-free interval between the first and second tumors or the survival. These quantitative pathologic similarities suggest that the malignancy of the second tumor (synchronous as well as metachronous) is not higher than that of the first tumor. Thus, in the case of metachronous tumors, the fact that most of the second tumors (60%) are detected at a higher (inoperable) stage is probably caused by inadequate follow-up and not by increased malignancy.(ABSTRACT TRUNCATED AT 250 WORDS)     

Quantitative RT-PCR analysis and immunohistochemical localization of the kallikrein-related peptidases 13 and 14 in lung

Expression of the KLK13 and KLK14 genes was examined at the mRNA and protein levels in a cohort of 57 patients with non-small-cell lung cancer (NSCLC). The mRNA levels, assessed by real-time RT-PCR, were significantly different in malignant tissues compared to adjacent non-malignant tissues (KLK13, p=0.006; KLK14, p=0.022). KLK13 and KLK14 mRNA overexpression in tumors (1/3 of the patients) was associated with a positive nodal status in multivariate analysis (p=0.018 and p=0.069, respectively). KLK13 and KLK14 were localized in the cytoplasm of epithelial cells of normal bronchus and NSCLC, as determined by immunohistochemistry. Moreover, positive staining was significantly associated with adenocarcinoma histotype (KLK13, p=0.014) and tumor size (KLK14, p=0.048). Although the results are marginally significant, patients with high KLK13 expression at the mRNA or protein level had lower overall survival.     

Finding elementary flux modes in metabolic networks based on flux balance analysis and flux coupling analysis: application to the analysis of Escherichia coli metabolism

Elementary modes (EMs) are steady-state metabolic flux vectors with minimal set of active reactions. Each EM corresponds to a metabolic pathway. Therefore, studying EMs is helpful for analyzing the production of biotechnologically important metabolites. However, memory requirements for computing EMs may hamper their applicability as, in most genome-scale metabolic models, no EM can be computed due to running out of memory. In this study, we present a method for computing randomly sampled EMs. In this approach, a network reduction algorithm is used for EM computation, which is based on flux balance-based methods. We show that this approach can be used to recover the EMs in the medium- and genome-scale metabolic network models, while the EMs are sampled in an unbiased way. The applicability of such results is shown by computing “estimated” control-effective flux values in Escherichia coli metabolic network.     

Quantitative analysis of transpiration stream dynamics in an intact cucumber stem by a heat flux control method

Water flux of transpiration stream in an intact stem of the 10 leaf stage cucumber plant (Cucumis sativus L. cv. Chojitsu-Ochiai) was measured by a novel system of heat flux control method with a resolution of 1 × 10⁻³ grams per second and a time constant of 1 minute; two heat flux control sensors were attached to the seventh internode and the stem base. The transpiration stream responded clearly to leaf transpiration and root water absorption when the plant was exposed to light, and the water flux at the stem base corresponded to the transpiration rate per plant in steady state. Root water absorption lagged about 10 minutes behind leaf transpiration. Dynamics of water fluxes were affected by the lag of water absorption in roots, and temporary water loss caused by rapid increase in leaf transpiration was buffered by about 5% of the water content in the stem.