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PubMed1994

A model for the tissue factor pathway to thrombin. I. An empirical study.

The activation of prothrombin, factor V, factor VIII, factor IX, and factor X by the tissue factor-factor VIIa complex, in vitro, in a system in which each precursor protein was present at plasma concentration, was evaluated using a combination of activity assays, immunoblots, active-site blots, and autoradiography. The thrombin generation curves observed were distinctly nonlinear and typically displayed a time lag in which little or no thrombin was observed. This was followed by an almost linear propagation phase of thrombin formation. The lag was a function of tissue factor/factor VIIa concentration and represented primarily the interval of factor V and factor VIII activation. The postlag propagation phase of thrombin generation was nearly independent of the initial activator (factor VIIa or tissue factor) concentration over a 10(3)-fold range in factor VIIa-tissue factor concentration. Maximum thrombin generation rates were observed when less than 1% of the factor IX and X present was activated but when nearly 100% activation of the cofactors, factor V and factor VIII, was achieved. Analyses of the activation pattern of factor V indicated that the cofactor is activated by both factor Xa and thrombin which are formed at low levels during the lag phase of the reaction. When the initial reaction mixture contained factor Va instead of factor V, the lag was substantially reduced. When factor V was deleted from the reaction mixture, no thrombin formation was observed. When either factor VII or factor IX was deleted from the reaction system, the propagation phase of thrombin formation (at 5 pM tissue factor-factor VIIa complex) was only one-third that observed for reactions which contained factor VIII and factor IX. The addition of factor XI to the experimental system increased the rate of thrombin formation by 15% during the propagation phase but had no effect upon the lag phase of the reaction. Our data suggest that normal hemostasis may be initiated by the factor VIIa-tissue factor complex and support the concept of multiple feedback reactions which amplify and propagate the hemostatic response.

Blood Coagulation Factors↗
PubMed2006

Parameter estimation in models combining signal transduction and metabolic pathways: the dependent input approach.

Biological complexity and limited quantitative measurements pose severe challenges to standard engineering methodologies for modelling and simulation of genes and gene products integrated in a functional network. In particular, parameter quantification is a bottleneck, and therefore parameter estimation, identifiability, and optimal experiment design are important research topics in systems biology. An approach is presented in which unmodelled dynamics are replaced by fictitious 'dependent inputs'. The dependent input approach is particularly useful in validation experiments, because it allows one to fit model parameters to experimental data generated by a reference cell type ('wild-type') and then test this model on data generated by a variation ('mutant'), so long as the mutations only affect the unmodelled dynamics that produce the dependent inputs. Another novel feature of the approach is in the inclusion of a priori information in a multi-objective identification criterion, making it possible to obtain estimates of parameter values and their variances from a relatively limited experimental data set. The pathways that control the nitrogen uptake fluxes in baker's yeast (Saccharomyces cerevisiae) have been studied. Well-defined perturbation experiments were performed on cells growing in steady-state. Time-series data of extracellular and intracellular metabolites were obtained, as well as mRNA levels. A nonlinear model was proposed and was shown to be structurally identifiable given data of its inputs and outputs. The identified model is a reliable representation of the metabolic system, as it could correctly describe the responses of mutant cells and different perturbations.

Algorithms↗
PubMed1996

Nitric oxide and the rectoanal inhibitory reflex: retrograde neuronal tracing reveals a descending nitrergic rectoanal pathway in a guinea-pig model.

Nitric oxide has been implicated as the neurotransmitter mediating internal anal sphincter (IAS) relaxation during the rectoanal inhibitory reflex. However, there has been no direct demonstration of a nitrergic rectoanal neuronal pathway appropriate to mediating the reflex. This study combined retrograde neuronal tracing techniques with enzyme histochemistry in a guinea-pig model. Wheatgerm agglutinin conjugated to horseradish peroxidase was injected into the IAS. Transported tracer was demonstrated in neurones of the myenteric ganglia of the distal rectum and all labelled neurones showed co-localization with nitric oxide synthase as revealed by reduced nicotinamide adenine dinucleotide phosphate diaphorase histochemistry. In vivo anal canal manometry showed that the mean maximal resting pressure was 16 (8-20) cmH2O and confirmed the presence of the rectoanal inhibitory reflex. In vitro organ bath studies showed that strips of IAS developed spontaneous myogenic tone and relaxed in response to intrinsic nerve stimulation. Addition of N omega-nitro-L-arginine (L-NOArg) reduced the relaxant response in a dose-dependent fashion; the relaxant response was maximally reduced by a mean(s.e.m.) 35.2(3.8) per cent (P < 0.001) at a concentration of 3 x 10(-5) mol/l L-NOArg. This study provides direct anatomical evidence of a descending nitrergic rectoanal neuronal pathway in a guinea-pig model. In vivo anal manometry and in vitro organ bath studies provide additional evidence that this pathway is responsible for the inhibitory motor innervation of the rectoanal inhibitory reflex.

Anal Canal↗
PubMed2002

Pharmacogenetics of lithium prophylaxis in mood disorders: analysis of COMT, MAO-A, and Gbeta3 variants.

We studied the possible association between the prophylactic efficacy of lithium in mood disorders and the following gene variants: catechol-O-methyltransferase (COMT) G158A, monoamine oxydase A (MAO-A) 30-bp repeat, G-protein beta 3-subunit (Gbeta3) C825T. A total of 201 subjects affected by bipolar (n = 160) and major depressive (n = 41) disorder were followed prospectively for an average of 59.8 months and were typed for their gene variants using PCR techniques. COMT, MAO-A, and Gbeta3 variants were not associated with lithium outcome, even when possible stratification effects such as sex, polarity, age at onset, duration of lithium treatment, and previous episodes were included in the model. The pathways influenced by those variants are not therefore involved with long-term lithium outcome in our sample.

Adult↗
PubMed2005

Metabolic pathways reconstruction by frequency and amplitude response to forced glycolytic oscillations in yeast.

The hypothesis that frequency and amplitude response can be used in a complicated metabolic pathway kinetics model for optimal parameter estimation, as speculated by its successful prior usage for a mechanical oscillator and a heterogeneous chemical system, is tested here. Given the complexity of the glycolysis model of yeast chosen, this question is limited to three kinetics parameters of the 87 in the in vitro model developed in the literature. The direct application of the approach, used with the uninformed selection of operating conditions for the oscillation of external glucose concentration, led to miring the data assimilation process in local minima. Application of linear systems theory, however, identified two natural resonant frequencies that, when excited by external forced oscillations of the same frequency, result in the expression of many harmonics in the Fourier spectra, that is, information-rich experiments. A single such information-rich experiment at one of the resonant frequencies was sufficient to break away from the local minima to find the optimum kinetics parameter estimates. The resonant frequencies themselves represent oscillation modes in glycolysis akin to those previously observed. Furthermore, operation of the bioreactor with large amplitude oscillations of glucose feed (25%) leads to enhanced ethanol average yield by 1.6% at the resonant frequency.

Bioreactors↗
PubMed2003

Novel mutations of the growth hormone 1 (GH1) gene disclosed by modulation of the clinical selection criteria for individuals with short stature.

Subtle mutations in the growth hormone 1 (GH1) gene have been regarded as a comparatively rare cause of short stature. Such lesions were sought in a group of 41 individuals selected for short stature, reduced height velocity, and bone age delay; a group of 11 individuals with short stature and idiopathic growth hormone deficiency (IGHD); and a group of 154 controls. Heterozygous mutations were identified in all three groups but disproportionately in the individuals with short stature, both with (odds ratio 25.2; 95% CI, 5.1-132.2) and without (odds ratio 3.6; 95% CI, 1.0-12.9) IGHD. Twenty-four novel GH1 gene lesions were found. Thirteen novel missense mutations were characterized by assaying the signal transduction activity of in vitro expressed variants; six (T27I, K41R, N47D, S71F, S108R, and T175A) exhibited a reduced ability to activate the JAK/STAT pathway. Molecular modeling suggested that both K41R and T175A might compromise GH receptor binding. Seven GH variants (R16C, K41R, S71F, E74K, Q91L, S108C, and a functional polymorphism, V110I) manifested reduced secretion in rat pituitary cells after allowance had been made for the level of expression attributable to the associated GH1 proximal promoter haplotype. A further leader peptide variant (L-11P) was not secreted. Eleven novel mutations in the GH1 gene promoter were assessed by reporter gene assay but only two, including a GH2 gene-templated gene conversion, were found to be associated with a significantly reduced level of expression. Finally, a novel intron 2 acceptor splice-site mutation, detected in a family with autosomal dominant type II IGHD, was shown to lead to the skipping of exon 3 from the GH1 transcript. A total of 15 novel GH1 gene mutations were thus considered to be of probable phenotypic significance. Such lesions are more prevalent than previously recognized and although most may be insufficient on their own to account for the observed clinical phenotype, they are nevertheless likely to play a contributory role in the etiology of short stature.

Adolescent↗
PubMed1998

Angiogenic stimuli are essential for survival of vascular endothelial cells in three-dimensional collagen lattice.

Cultured vascular endothelial cells derived from bovine aorta (BAECs) can survive and proliferate in the condition of two-dimensional monolayer culture in the presence of serum without any specific growth factors. When BAECs were embedded in collagen lattice, they underwent apoptotic death within 2 days unless the cultures were repeatedly supplied with angiogenic growth factor such as fibroblast growth factor-2 (FGF-2). Supplementation with FGF-2 induced endothelial cell differentiation, resulting in capillary-like tube formation inside collagen lattice. Following tube formation, withdrawal of FGF-2 induced disruption of the tube structures associated with the characteristic apoptotic cell death. These effects of FGF-2 were regulated by tyrosine phosphorylation, but not mediated through protein kinase C pathway. This model of endothelial cell apoptosis inside collagen lattice may represent in vivo endothelial cell-matrix interaction during angiogenesis process, indicating that apoptotic death of endothelial cells may regulate angiogenesis and the regression of vessels.

Animals↗
PubMed2005

An automated approach to connectivity-based partitioning of brain structures.

We present an automated approach to the problem of connectivity-based partitioning of brain structures using diffusion imaging. White-matter fibres connect different areas of the brain, allowing them to interact with each other. Diffusion-tensor MRI measures the orientation of white-matter fibres in vivo, allowing us to perform connectivity-based partitioning non-invasively. Our new approach leverages atlas-based segmentation to automate anatomical labeling of the cortex. White-matter connectivities are inferred using a probabilistic tractography algorithm that models crossing pathways explicitly. The method is demonstrated with the partitioning of the corpus callosum of eight healthy subjects.

Algorithms↗
PubMed1996

The kynurenine pathway and neurologic disease. Therapeutic strategies.

The neurotoxic effects of QUIN have been well established. Clinical conditions have been identified where substantial elevations in CNS QUIN levels occur. There is a relationship between the severity of neurologic impairments and macrophage activation, with the magnitude of the increases in QUIN. The magnitude of QUIN increases in experimental immune activation, and macrophages in vitro, are highest in non-human primates, intermediate in gerbils and guinea pigs, and lowest in mice and rats. Macrophages in vitro are a useful screening system to evaluate potential inhibitors of the kynurenine pathway. Several models of CNS inflammation are available, including brain injury in post-ischemic gerbils and spinal cord injury in guinea pigs. 4-Chloro-3-hydroxyanthranilate is a potent inhibitor of QUIN production by macrophages and reduces QUIN accumulations in spinal cord injury. Such reductions are associated with significant neurologic improvements in the early post-injury period. The results support further investigation of QUIN as a mediator of neurologic dysfunction and damage in neurologic diseases.

3-Hydroxyanthranilic Acid↗
PubMed1987

Relationships between cell-cell interactions, cAMP, and gene expression in a developmental mutant of Dictyostelium discoideum.

Previous work has led us to propose that close cell-cell associations during D. discoideum development serve as a signal to deactivate expression of discoidin I mRNA, and that intracellular cAMP serves as a mediator of this regulatory pathway. This model is based in part on the failure of a morphogenetic mutant, EB-21, to deactivate discoidin I expression under conditions where these cells fail to acquire cell-cell cohesiveness and hence remain as single cells, unlike the wild type strain which forms multicellular aggregates. Here we show that the failure of EB-21 to express specific cohesiveness depends on developmental conditions, and that under conditions where close cell-cell associations are allowed to form, discoidin I mRNA expression is deactivated normally. Furthermore, in both wild type and EB-21 there is a close correlation between formation close cell-cell associations and elevation of intracellular cAMP under different developmental conditions. Additional analyses of the biological behavior of EB-21 indicate that it acquires a normal cAMP chemotactic signal-response system, and that the morphogenetic defect cannot be corrected by co-development with wild type cells. The results are discussed in terms of possible relationships between cell-cell interactions, cAMP metabolism, and developmental gene expression in this organism.

Chemotaxis↗
PubMed2006

Genetic and biochemical characterization of the dioxygenase involved in lateral dioxygenation of dibenzofuran from Rhodococcus opacus strain SAO101.

Rhodococcus opacus strain SAO101 was shown to degrade on various polycyclic aromatic hydrocarbons such as naphthalene, dibenzofuran (DF), and dibenzo-p-dioxin (DD). One of the unique traits of the strain SAO101 is its ability to oxidize DF compounds by lateral dioxygenation. To clone the lateral dioxygenase gene involved in compound degradation in strain SAO101, we identified a cosmid clone that oxidizes aromatic compounds by using SAO101 genomic DNA. Sequencing analysis revealed that isolated cosmid clone contained ring-hydroxylating dioxygenase genes (narAaAb) with homologies to indene dioxygenase genes of Rhodococcus strain I24 and naphthalene dioxygenase genes of Rhodococcus strain NCIMB12038. The NarAaAb-expressing Rhodococcus cells exhibited broad substrate specificity for bicyclic aromatic compounds and had high ability to degrade dibenzofuran and naphthalene. Metabolite analysis revealed that dihydrodiol compounds were detected as metabolites from dibenzofuran by the NarAaAb-expressing Rhodococcus strain, indicating that dibenzofuran was converted by lateral dioxygenase activity of NarA dioxygenase. Based on reverse transcriptase-polymerase chain reaction analysis, it was found that the narAaAb genes were cotranscribed and that their expression was induced in the presence of aromatic hydrocarbon compounds. It is likely that these genes are involved in the degradation pathways of a wide range of aromatic hydrocarbons by this strain. Strain SAO101 harbors three huge linear plasmids, pWK301 (1,100 kbp), pWK302 (1,000 kbp), and pWK303 (700 kbp), and the nar genes were found to be located on the pWK301 plasmid.

Benzofurans↗
PubMed2006

Redirection electron flow to high coupling efficiency of terminal oxidase to enhance riboflavin biosynthesis.

The metabolic impact of redirection electron flow to high coupling efficiency of terminal oxidases on riboflavin biosynthetic ability was quantitatively assessed during batch culture in this paper. While disruption of the low coupling bd oxidase of the riboflavin overproducing B. subtilis PK, the apparent phenotype with more rapid specific growth rate and higher biomass yield was achieved. Compared to by-products formation, a discernible shift to less acetate and more acetoin in cyd mutant was observed. As the overflow metabolism was decreased in B. subtilis PK cyd, more carbon source was directed to biomass and riboflavin biosynthetic pathway, which resulted in higher biomass and about 30% improvement of riboflavin biosynthetic ability. The higher product-corrected biomass yield in mutant showed that the efficient energy generation is an important factor for exponential growth of riboflavin overproducing B. subtilis strain in batch culture.

Bacillus subtilis↗
PubMed2006

Profiles of purine biosynthesis, salvage and degradation in disks of potato (Solanum tuberosum L.) tubers.

To find general metabolic profiles of purine ribo- and deoxyribonucleotides in potato (Solanum tuberosum L.) plants, we looked at the in situ metabolic fate of various (14)C-labelled precursors in disks from growing potato tubers. The activities of key enzymes in potato tuber extracts were also studied. Of the precursors for the intermediates in de novo purine biosynthesis, [(14)C]formate, [2-(14)C]glycine and [2-(14)C]5-aminoimidazole-4-carboxyamide ribonucleoside were metabolised to purine nucleotides and were incorporated into nucleic acids. The rates of uptake of purine ribo- and deoxyribonucleosides by the disks were in the following order: deoxyadenosine > adenosine > adenine > guanine > guanosine > deoxyguanosine > inosine > hypoxanthine > xanthine > xanthosine. The purine ribonucleosides, adenosine and guanosine, were salvaged exclusively to nucleotides, by adenosine kinase (EC 2.7.1.20) and inosine/guanosine kinase (EC 2.7.1.73) and non-specific nucleoside phosphotransferase (EC 2.7.1.77). Inosine was also salvaged by inosine/guanosine kinase, but to a lesser extent. In contrast, no xanthosine was salvaged. Deoxyadenosine and deoxyguanosine, was efficiently salvaged by deoxyadenosine kinase (EC 2.7.1.76) and deoxyguanosine kinase (EC 2.7.1.113) and/or non-specific nucleoside phosphotransferase (EC 2.7.1.77). Of the purine bases, adenine, guanine and hypoxanthine but not xanthine were salvaged for nucleotide synthesis. Since purine nucleoside phosphorylase (EC 2.4.2.1) activity was not detected, adenine phosphoribosyltransferase (EC 2.4.2.7) and hypoxanthine/guanine phosphoribosyltransferase (EC 2.4.2.8) seem to play the major role in salvage of adenine, guanine and hypoxanthine. Xanthine was catabolised by the oxidative purine degradation pathway via allantoin. Activity of the purine-metabolising enzymes observed in other organisms, such as purine nucleoside phosphorylase (EC 2.4.2.1), xanthine phosphoribosyltransferase (EC 2.4.2.22), adenine deaminase (EC 3.5.4.2), adenosine deaminase (EC 3.5.4.4) and guanine deaminase (EC 3.5.4.3), were not detected in potato tuber extracts. These results suggest that the major catabolic pathways of adenine and guanine nucleotides are AMP --> IMP --> inosine --> hypoxanthine --> xanthine and GMP --> guanosine --> xanthosine --> xanthine pathways, respectively. Catabolites before xanthosine and xanthine can be utilised in salvage pathways for nucleotide biosynthesis.

Adenine↗
PubMed2006

Genetic and transgenic perturbations of carbon reserve production in Arabidopsis seeds reveal metabolic interactions of biochemical pathways.

The biosynthesis of seed oil and starch both depend on the supply of carbon from the maternal plant. The biochemical interactions between these two pathways are not fully understood. In the Arabidopsis mutant shrunken seed 1 (sse1)/pex16, a reduced rate of fatty acid synthesis leads to starch accumulation. To further understand the metabolic impact of the decrease in oil synthesis, we compared soluble metabolites in sse1 and wild type (WT) seeds. Sugars, sugar phosphates, alcohols, pyruvate, and many other organic acids accumulated in sse1 seeds as a likely consequence of the reduced carbon demand for lipid synthesis. The enlarged pool size of hexose-P, the metabolites at the crossroad of sugar metabolism, glycolysis, and starch synthesis, was likely a direct cause of the increased flow into starch. Downstream of glycolysis, more carbon entered the TCA cycle as an alternative to the fatty acid pathway, causing the total amount of TCA cycle intermediates to rise while moving the steady state of the cycle away from fumarate. To convert the excess carbon metabolites into starch, we introduced the Escherichia coli starch synthetic enzyme ADP-glucose pyrophosphorylase (AGPase) into sse1 seeds. Expression of AGPase enhanced net starch biosynthesis in the mutant, resulting in starch levels that reached 37% of seed weight. However, further increases above this level were not achieved and most of the carbon intermediates remained high in comparison with the WT, indicating that additional mechanisms limit starch deposition in Arabidopsis seeds.

Amino Acids↗
PubMed2006

Prediction of clinical outcome of fluoropyrimidine-based chemotherapy for gastric cancer patients, in terms of the 5-fluorouracil metabolic pathway.

Fluoropyrimidines are widely used in chemotherapy regimens for metastatic gastric cancer. Interindividual variation in the enzyme activity of the 5-fluorouracil (FU) metabolic pathway can affect the extent of 5-FU metabolism and affect the efficacy of 5-FU based chemotherapy. In this review, the role of the genetic factors affecting the therapeutic efficacy of fluoropyrimidines is discussed, with a special emphasis on enzymes involved in the 5-FU metabolic pathway. The gene expressions of thymidylate synthase, dihydropyrimidine dehydrogenase, thymidine phosphorylase, and orotate phosphoribosyltransferase are discussed in relation to the efficacy of fluoropyrimidine treatment for metastatic gastric cancer. These candidate genes, along with others yet to be identified, could allow accurate prediction of the clinical outcome in patients receiving fluoropyrimidine-based chemotherapy in the future. Well-designed and large prospective studies, which include relevant pharmacogenetic parameters, are needed to confirm the values required to predict clinical outcome.

Antimetabolites, Antineoplastic↗
PubMed2006

Protease pathways in peptide neurotransmission and neurodegenerative diseases.

1. Recent research demonstrates the critical importance of neuroproteases for the production of peptide neurotransmitters, and for the production of toxic peptides in major neurodegenerative diseases that include Alzheimer's (AD) and Huntington's diseases. This review describes the strategies utilized to identify the appropriate proteases responsible for producing active peptides for neurotransmission, with application of such approaches for defining protease mechanisms in neurodegenerative diseases. 2. Integration of multidisciplinary approaches in neurobiology, biochemistry, chemistry, proteomics, molecular biology, and genetics has been utilized for neuroprotease studies. These investigations have identified secretory vesicle cathepsin L for the production of the enkephalin opioid peptide neurotransmitter and other neuropeptides. Furthermore, new results using these strategies have identified secretory vesicle cathepsin B for the production of beta-amyloid (Abeta) in the major regulated secretory pathway that provides activity-dependent secretion of Abeta peptides, which accumulate in AD. 3. CNS neuroproteases that participate in peptide neurotransmission and in neurodegenerative diseases represent new candidate drug targets that may be explored in future research for the development of novel therapeutic agents for neurological conditions.

Animals↗
PubMed2006

Adiponectin and leptin: potential tools in the differential diagnosis of pediatric diabetes?

The incidence of type 1 and type 2 diabetes mellitus in the pediatric population has increased over the past decade. The practitioner is often faced with the challenge of differentiating between type 1 and type 2 diabetes at the time of initial diagnosis because of the overlap of clinical and laboratory characteristics between these two entities. Adipokines are proteins secreted by the adipose tissue. Leptin and adiponectin are two adipokines that have been extensively studied in vitro, in animal studies, and in human subjects with type 1 and type 2 diabetes. Leptin and adiponectin play a significant role in the regulation of lipid and carbohydrate metabolism. Adiponectin increases insulin sensitivity in both the liver and skeletal muscle. Leptin decreases appetite, increases energy expenditure, suppresses insulin synthesis and secretion and increases insulin sensitivity. Changes in the secretion or sensitivity to leptin and adiponectin may contribute to the development of type 1 and type 2 diabetes. Adiponectin is higher in adult and pediatric patients with type 1 diabetes compared to those with type 2 diabetes. Data regarding leptin levels are contradictory. Most studies report decreased serum leptin at the time of diagnosis in type 1 diabetes compared to type 2 diabetes subjects and non-diabetic controls. This paper will review basic research and clinical evidence supporting the role of adiponectin and leptin in the development of type 1 and type 2 diabetes and discuss their potential use as tools in the differential diagnosis of pediatric diabetes.

Adiponectin↗