Pyruvate Metabolism Pathways Research Articles

Coexistence of obesity and asthma determines a distinct respiratory metabolic phenotype

Epidemiologic and clinical evidence supports the existence of an obesity-related asthma phenotype. No distinct pathophysiologic elements or specific biomarkers have been identified thus far, but increased oxidative stress has been reported. We aimed at verifying whether metabolomics of exhaled breath condensate from obese asthmatic (OA) patients, lean asthmatic (LA) patients, and obese nonasthmatic (ONA) subjects could recognize specific and statistically validated biomarkers for a separate "asthma-obesity" respiratory metabolic phenotype, here defined as "metabotype." Twenty-five OA patients, 30 ONA subjects, and 30 mild-to-moderate LA age-matched patients participated in a cross-sectional study. Nuclear magnetic resonance (NMR) profiles were analyzed by using partial least-squares discriminant analysis, and the results were validated with an independent patient set. From NMR profiles, we obtained strong regression models that distinguished OA patients from ONA subjects (quality parameters: goodness-of-fit parameter [R2]=0.81 and goodness-of-prediction parameter [Q2]=0.79), as well as OA patients from LA patients (R2=0.91 and Q2=0.89). The all-classes comparison (R2=0.86 and Q2=0.83) indicated that OA patients possess a respiratory metabolic profile fully divergent from those obtained in the other patient groups. We also identified specific biomarkers for between-class separation, which are independent from clinical bias. They are involved in the methane, pyruvate, and glyoxylate and dicarboxylate metabolic pathways. NMR-based metabolomics indicates that OA patients are characterized by a respiratory metabolic fingerprint fully different from that of patients independently affected by asthma or obesity. Such a phenotypic difference strongly suggests unique pathophysiologic pathways involved in the pathogenesis of asthma in adult obese subjects. Furthermore, the OA metabotype could define a strategy for patient stratification based on unbiased biomarkers, with important diagnostic and therapeutic implications.

Qishen Yiqi Drop Pill improves cardiac function after myocardial ischemia.

Myocardial ischemia (MI) is one of the leading causes of death, while Qishen Yiqi Drop Pill (QYDP) is a representative traditional Chinese medicine to treat this disease. Unveiling the pharmacological mechanism of QYDP will provide a great opportunity to promote the development of novel drugs to treat MI. 64 male Sprague-Dawley (SD) rats were divided into four groups: MI model group, sham operation group, QYDP treatment group and Fosinopril treatment group. Echocardiography results showed that QYDP exhibited significantly larger LV end-diastolic dimension (LVEDd) and LV end-systolic dimension (LVEDs), compared with the MI model group, indicating the improved cardiac function by QYDP. 1H-NMR based metabonomics further identify 9 significantly changed metabolites in the QYDP treatment group, and the QYDP-related proteins based on the protein-metabolite interaction networks and the corresponding pathways were explored, involving the pyruvate metabolism pathway, the retinol metabolism pathway, the tyrosine metabolism pathway and the purine metabolism pathway, suggesting that QYDP was closely associated with blood circulation. ELISA tests were further employed to identify NO synthase (iNOS) and cathepsin K (CTSK) in the networks. For the first time, our work combined experimental and computational methods to study the mechanism of the formula of traditional Chinese medicine.

Bacterial cellulose synthesis mechanism of facultative anaerobe Enterobacter sp. FY-07.

Enterobacter sp. FY-07 can produce bacterial cellulose (BC) under aerobic and anaerobic conditions. Three potential BC synthesis gene clusters (bcsI, bcsII and bcsIII) of Enterobacter sp. FY-07 have been predicted using genome sequencing and comparative genome analysis, in which bcsIII was confirmed as the main contributor to BC synthesis by gene knockout and functional reconstitution methods. Protein homology, gene arrangement and gene constitution analysis indicated that bcsIII had high identity to the bcsI operon of Enterobacter sp. 638; however, its arrangement and composition were same as those of BC synthesizing operon of G. xylinum ATCC53582 except for the flanking sequences. According to the BC biosynthesizing process, oxygen is not directly involved in the reactions of BC synthesis, however, energy is required to activate intermediate metabolites and synthesize the activator, c-di-GMP. Comparative transcriptome and metabolite quantitative analysis demonstrated that under anaerobic conditions genes involved in the TCA cycle were downregulated, however, genes in the nitrate reduction and gluconeogenesis pathways were upregulated, especially, genes in three pyruvate metabolism pathways. These results suggested that Enterobacter sp. FY-07 could produce energy efficiently under anaerobic conditions to meet the requirement of BC biosynthesis.

Identification of low potassium stress-responsive proteins in tobacco (Nicotiana tabacum) seedling roots using an iTRAQ-based analysis.

Potassium is one of the three main mineral nutrients, and is vital for leaf growth and the quality of tobacco (Nicotiana tabacum) plants. In recent years, the isobaric tags for relative and absolute quantitation (iTRAQ) method has been one of the most popular techniques for quantitative proteomic analysis. In this study, we used iTRAQ to compare protein abundances in the roots of control and low potassium-treated tobacco seedlings, and found that 108 proteins were differentially expressed between the two treatments. Of these, 34 were upregulated and 74 were downregulated, and 39 (36%) were in the chloroplasts. Kyoto Encyclopedia of Genes and Genomes pathway enrichment results suggested that metabolic pathways were the dominant pathways (10 upregulated and 14 downregulated proteins). Ten proteins involved in the pyruvate metabolism pathway increased their expression levels, and 17 upregulated proteins were enriched in the ribosomes category. To evaluate correlations between protein and gene transcript abundances, the expression patterns of 12 randomly chosen genes were examined. A quantitative real-time polymerase chain reaction revealed that the 12 genes were induced after low potassium treatment for 3, 6, 12, and 24 h. Our results demonstrate that low potassium levels affect protein profiles in tobacco roots.

1H-NMR and HPLC–MS/MS-based global/targeted metabolomic evaluation of Hypericum perforatum L. intervention for menopause

Hypericum perforatum L., which includes a wide range of bioactive substances and is sold as a functional food formulation, has been used as an alternative to estrogen replacement treatment to relieve menopausal syndromes. However, methods to track HPL mechanisms and link them to metabolism disorder regulation during menopause periods have been lacking. To investigate HPL function in endocrine-related metabolic recognition, we applied both global and targeted metabolomic methods on ovariectomised rat serum and urine metabolites for treatment-specific metabolic profiling and to explore biomarkers and deduce their mechanisms via1H-NMR and HPLC–MS/MS techniques. Results from the comparison of metabolite levels of rats that underwent an ovariectomy (OVX) before and after the administration of different doses of HPL showed that HPL can reverse the disordered changes induced in multiple biomarkers by menopausal syndromes. Through screening, identification, and quantification of the differential regulatory metabolites, 23 metabolites involved in 4 major metabolic pathways, including the arginine, taurine, pyruvate and tryptophan metabolic pathways, were highlighted as important for explaining the mechanisms of HPL. These pathways may be applicable for explanations of other menopausal syndrome symptoms, such as depression and hot flashes, and the effects of other herbs rich in flavonoids with menopause remission potential.

Roles of Pyruvate, NADH, and Mitochondrial Complex I in Redox Balance and Imbalance in β Cell Function and Dysfunction.

Pancreatic β cells not only use glucose as an energy source, but also sense blood glucose levels for insulin secretion. While pyruvate and NADH metabolic pathways are known to be involved in regulating insulin secretion in response to glucose stimulation, the roles of many other components along the metabolic pathways remain poorly understood. Such is the case for mitochondrial complex I (NADH/ubiquinone oxidoreductase). It is known that normal complex I function is absolutely required for episodic insulin secretion after a meal, but the role of complex I in β cells in the diabetic pancreas remains to be investigated. In this paper, we review the roles of pyruvate, NADH, and complex I in insulin secretion and hypothesize that complex I plays a crucial role in the pathogenesis of β cell dysfunction in the diabetic pancreas. This hypothesis is based on the establishment that chronic hyperglycemia overloads complex I with NADH leading to enhanced complex I production of reactive oxygen species. As nearly all metabolic pathways are impaired in diabetes, understanding how complex I in the β cells copes with elevated levels of NADH in the diabetic pancreas may provide potential therapeutic strategies for diabetes.

α-Acetolactate overexpression from glucose in the diacetyl producer Lactococcus lactis ssp. lactis bv. diacetylactis B2103, a natural mutant lacking α-acetolactate decarboxylase

We investigated the effects of the oxygen supply rate on the activity of pyruvate metabolic pathways and their end products, the lactatedehydrogenase (LDH), pyruvateformiatelyase (PFL), pyruvatedehydrogenase (PDH) and acetolactatesynthase (ALS) pathways, in the Lactococcus lactis ssp. lactis bv. diacetylactis strain B2103/74. We found that this culture, apart from inactivated α-acetyldecarboxylase, also possesses a unique natural capacity to overexpress α-acetolactate (AL) up to 25–28 mM. Our search for similar properties among the diacetilicus bv. strains showed that this ability is quite rare. We identified a single additional strain, 7590 from the National Russian Collection of Industrial Microorganisms (NRCIM-7590), which displayed a similar capacity. However, unlike B2103/74, NRCIM-7590 has an active α-acetolactate decarboxylase and therefore can only produce acetoin. AL overexpression took place under conditions of intense aeration (KLa ≥ 90–120 h−1), and the composition of the medium played a decisive role in AL productivity. We found that AL overproduction is determined by a diversion of a portion of pyruvate flow from the LDH to the PDH and ALS pathways. We further found that all additional pyruvate, supplied from LDH, is utilized exclusively by the ALS pathway because of the restricted capacity of the PDH pathway. This shift in pyruvate metabolism in the B2103/74 strain, from LDH to PDH and ALS pathways, is associated with the initiation of an oxidation reaction that reduces oxygen to H2O and sequesters NADH from the LDH pathway in the process. A specific manifestation of this reaction in B2103/74 and NRCIM-7590 cultures, which results in a profound shift of the pyruvate metabolism towards the production of α-acetolactate, is due to the function of a potent oxidative system that shifts 75–80% of NADH flow from LDH to the oxidative pathway, resulting in the regeneration of NAD+. The nature of this oxidative system is not known. Based on our studies, we propose that the structure of the newly discovered oxidative system is similar to a simple transmembrane electron transport chain.

Comparative transcriptional study on the hydrogen evolution of marine microalga Tetraselmis subcordiformis

It's the first comparative transcriptome study of Tetraselmis subcordiformis' H2 production with carbonyl cyanide m-chlorophenylhydrazone (CCCP) by de novo RNA-seq. The global analysis of the annotated genes and pathways unveiled it a good candidate for biofuels. Focusing on H2 production, the genes coding active center subunit (HydA) and assembly subunits (HydEF and HydG) of hydrogenase proportionally expressed during the induction but stopped after illuminated; on contrast, the gene of the active centre stabilization subunit (Hyd3) highly expressed during the H2 evolution, indicating its key role in the prolonged H2 production. The results also showed genes of HCP4, ppGpp phosphohydrolase and RpoD relating to the hydrogenase expression regulation. On the energy aspect, genes of CF-ATPases and ferredoxin-NADP reductase in chloroplast down-regulated while Mito-ATPase in mitochondria and pyruvate metabolism pathway up-regulated during the H2 production, consisting with our previous reports on physiological level.

Heterogeneity research in muscle-invasive bladder cancer based on differential protein expression analysis.

The aim of this study was to study the expression profiles of muscle-invasive bladder cancer (MIBC) cells of different risk groups and to explore the crucial role of biological pathway change in heterogeneity of MIBC cells. Thirty individual samples (cancer and non-cancerous specimens) were obtained from patients with MIBC. Laser capture microdissection was employed to harvest the homogeneous MIBC cells and normal urothelial cells. iTRAQ and 2D-LC-MS/MS were used to quantify and identify the differently expressed proteins. Then, the significantly changed proteins were further analyzed using Arraytrack ™ software. The interested proteins were compared with the published literatures to discuss the exact functions. A total of 3,073 non-redundant proteins were identified in this research; therefore, 855/2,210/633 (fold change >1.5 relative to normal group) presented in high-/median-/low-risk groups, respectively. 617/1,620/463 proteins with SWISS-ACC number output from Arraytrack ™ software and presented in high-/median-/low-risk groups, respectively. Pathway analysis revealed that the mainly changed pathways (top-10, p < 0.05) in Genetic information processing category were similar in high- and median-risk groups, including Kyoto Encyclopedia of Genes and Genomes (KEGG) spliceosome, protein export, ribosome pathways. The mainly altered pathways in Metabolism category included glycolysis/gluconeogenesis, pentose phosphate, pyruvate metabolism pathway for high-risk group, and glutathione metabolism, citrate cycle, oxidative phosphorylation pathways for median-risk group. The major changed pathways for low-risk group included focal adhesion pathway and ECM-receptor interaction pathway. The changed biological pathways are closely related to the regulation of heterogeneity for MIBC. The KEGG pathways of Genetic information processing category and Metabolism (anaerobic or aerobic) category play a crucial role in determining the malignant phenotype of MIBC cells. The quantification analysis of proteins combining with the KEGG pathway analysis contributes to screening candidate biomarkers and guides the biological molecular therapy of MIBC.

Fatty acid synthesis and pyruvate metabolism pathways remain active in dihydroartemisinin-induced dormant ring stages of Plasmodium falciparum.

Artemisinin (ART)-based combination therapy (ACT) is used as the first-line treatment of uncomplicated falciparum malaria worldwide. However, despite high potency and rapid action, there is a high rate of recrudescence associated with ART monotherapy or ACT long before the recent emergence of ART resistance. ART-induced ring-stage dormancy and recovery have been implicated as possible causes of recrudescence; however, little is known about the characteristics of dormant parasites, including whether dormant parasites are metabolically active. We investigated the transcription of 12 genes encoding key enzymes in various metabolic pathways in P. falciparum during dihydroartemisinin (DHA)-induced dormancy and recovery. Transcription analysis showed an immediate downregulation for 10 genes following exposure to DHA but continued transcription of 2 genes encoding apicoplast and mitochondrial proteins. Transcription of several additional genes encoding apicoplast and mitochondrial proteins, particularly of genes encoding enzymes in pyruvate metabolism and fatty acid synthesis pathways, was also maintained. Additions of inhibitors for biotin acetyl-coenzyme A (CoA) carboxylase and enoyl-acyl carrier reductase of the fatty acid synthesis pathways delayed the recovery of dormant parasites by 6 and 4 days, respectively, following DHA treatment. Our results demonstrate that most metabolic pathways are downregulated in DHA-induced dormant parasites. In contrast, fatty acid and pyruvate metabolic pathways remain active. These findings highlight new targets to interrupt recovery of parasites from ART-induced dormancy and to reduce the rate of recrudescence following ART treatment.

Adaptive response of Amphibacillus xylanus to normal aerobic and forced oxidative stress conditions

Amphibacillus xylanus grows at the same rate and with the same cell yield under aerobic and anaerobic conditions. Under aerobic conditions, it exhibits vigorous oxygen consumption in spite of lacking a respiratory system and haem catalase. To understand the adaptive response of A. xylanus to oxidative stresses, a genomic analysis of A. xylanus was conducted. The analysis showed that A. xylanus has the genes of four metabolic systems: two pyruvate metabolic pathways, a glycolytic metabolic pathway and an NADH oxidase (Nox)-AhpC (Prx) system. A transcriptional study confirmed that A. xylanus has these metabolic systems. Moreover, genomic analysis revealed the presence of two genes for NADH oxidase (nox1 and nox2), both of which were identified in the transcriptional analysis. The nox1 gene in A. xylanus was highly expressed under normal aerobic conditions but that of nox2 was not. A purification study of NADH oxidases indicated that the gene product of nox1 is a primary metabolic enzyme responsible for metabolism of both oxygen and reactive oxygen species. A. xylanus was successfully grown under forced oxidative stress conditions such as 0.1 mM H2O2, 0.3 mM paraquat and 80 % oxygen. Proteomic analysis revealed that manganese SOD, Prx, pyruvate dehydrogenase complex E1 and E3 components, and riboflavin synthase β-chain are induced under normal aerobic conditions, and the other proteins except the five aerobically induced proteins were not induced under forced oxidative stress conditions. Taken together, the present findings indicate that A. xylanus has a unique defence system against forced oxidative stress.

Linking genome content to biofuel production yields: a meta-analysis of major catabolic pathways among select H2and ethanol-producing bacteria

BackgroundFermentative bacteria offer the potential to convert lignocellulosic waste-streams into biofuels such as hydrogen (H2) and ethanol. Current fermentative H2 and ethanol yields, however, are below theoretical maxima, vary greatly among organisms, and depend on the extent of metabolic pathways utilized. For fermentative H2 and/or ethanol production to become practical, biofuel yields must be increased. We performed a comparative meta-analysis of (i) reported end-product yields, and (ii) genes encoding pyruvate metabolism and end-product synthesis pathways to identify suitable biomarkers for screening a microorganism’s potential of H2 and/or ethanol production, and to identify targets for metabolic engineering to improve biofuel yields. Our interest in H2 and/or ethanol optimization restricted our meta-analysis to organisms with sequenced genomes and limited branched end-product pathways. These included members of the Firmicutes, Euryarchaeota, and Thermotogae.ResultsBioinformatic analysis revealed that the absence of genes encoding acetaldehyde dehydrogenase and bifunctional acetaldehyde/alcohol dehydrogenase (AdhE) in Caldicellulosiruptor, Thermococcus, Pyrococcus, and Thermotoga species coincide with high H2 yields and low ethanol production. Organisms containing genes (or activities) for both ethanol and H2 synthesis pathways (i.e. Caldanaerobacter subterraneus subsp. tengcongensis, Ethanoligenens harbinense, and Clostridium species) had relatively uniform mixed product patterns. The absence of hydrogenases in Geobacillus and Bacillus species did not confer high ethanol production, but rather high lactate production. Only Thermoanaerobacter pseudethanolicus produced relatively high ethanol and low H2 yields. This may be attributed to the presence of genes encoding proteins that promote NADH production. Lactate dehydrogenase and pyruvate:formate lyase are not conducive for ethanol and/or H2 production. While the type(s) of encoded hydrogenases appear to have little impact on H2 production in organisms that do not encode ethanol producing pathways, they do influence reduced end-product yields in those that do.ConclusionsHere we show that composition of genes encoding pathways involved in pyruvate catabolism and end-product synthesis pathways can be used to approximate potential end-product distribution patterns. We have identified a number of genetic biomarkers for streamlining ethanol and H2 producing capabilities. By linking genome content, reaction thermodynamics, and end-product yields, we offer potential targets for optimization of either ethanol or H2 yields through metabolic engineering.

Abstract 19466: Metabolomic and Gene Expression Changes in End-Stage Heart Failure are Reversed by Left Ventricular Assist Device

Introduction: Heart muscle tissue in advanced heart failure (HF) is reported to be ‘energy-depleted’ and inflexible to metabolic changes. Left ventricular assist devices (LVAD) and ventricular unloading with LVAD is known to regress cardiac hypertrophy, reduce fibrosis and partially improve function. The metabolic alterations with HF and LVAD support are not fully understood. We hypothesize that HF is associated with metabolic changes that are reversible with LVAD placement. Methods: We analyzed gene and protein expression and performed metabolomics analyses in failing left ventricular (LV) tissue obtained at the time of heart explant or LVAD placement (HF, n = 13) and removal (post-LVAD, n = 7). Control LV tissue was procured from patients undergoing heart-lung transplantation for severe right HF (control, n = 4). P&lt;0.05 was considered significant. Results: In HF samples, expression levels of mitochondrial transcription factors and coactivators were decreased, while LVAD increased expression of PGC1α, PGC1β, ERRγ and TFAM to levels of control samples. Gene and protein expression of mitochondrial complex subunits NDUFS6, SDHA, UQCRC1, Cox5a, ATP5a1 were reduced in HF, but increased after LVAD. LVAD rescued reduced expression of fatty acid oxidation genes CPT2, ACADvl, ACADm, HADHA and PPARα, as well as pyruvate and glucose metabolism genes ME3, MCT1, PDHB, GPT and PFK. Targeted metabolomics analysis showed a reduction in short- and medium-chain acylcarnitines (C2-C10) in failing LV indicating decreased substrate catabolism, with these analytes universally restored to normal post-LVAD. Pyruvate levels tended to increase (P=0.07), whereas all measured Krebs cycle intermediates including citrate, α-ketoglutarate, succinate, fumarate and malate were reduced in the HF samples compared to normal controls. LVAD normalized pyruvate levels, and normalized the levels of all Krebs cycle intermediates. Conclusion: Both the gene expression and metabolomics profiles for mitochondrial, fatty acid, pyruvate and glucose metabolism pathways indicate that HF is associated with a global defect in substrate utilization. Complete reversal by ventricular unloading demonstrates the reversibility of metabolic defects.

Transcriptional profiling analysis of HMP-treated rats with experimentally induced myocardial infarction

Heart-protecting musk pill (HMP), a traditional Chinese medicine prescription, has extensive cardioprotective effects against angina pectoris and myocardial infarction (MI), but the molecular mechanism behind such cardio protective effects still remains unclear. In this article, we aim to investigate the effect of HMP on mRNA expression in MI rat. A rat model of coronary artery ligation was used to assess the cardioprotective effects of HMP. Microarray technology was applied to detect the gene expression in the heart of MI rats treated with HMP. Besides, quantitative real-time PCR was performed to verify the microarray results. Our results showed that HMP could ameliorate heart function, and diminish infarct size in MI rats. Compared with sham-operated rats, 500 genes' expression changed, with 234 genes down-regulated and 266 genes up-regulated. And the expression of 129 genes was different between HMP administrated rats and MI rats, with 22 genes down-regulated and 107 genes up-regulated. Citrate cycle (TCA cycle), Valine, leucine and isoleucine degradation, Glycolysis/Gluconeogenesis and Pyruvate metabolism pathway are probably involved in the cardioprotective effects of HMP.

Optimizing ethanol production selectivity

Lactococcus lactis metabolizes glucose homofermentatively to lactate. However, after disruption of the gene coding for lactate dehydrogenase, L D H , a key enzyme in NAD + regeneration, the glycolytic flux shifts from homolactic to mixed-acid fermentation with the redirection of pyruvate towards production of formate, acetate, ethanol and CO 2. A mathematical model of the pyruvate metabolism pathway that enhances ethanol production was developed from in vivo Nuclear Magnetic Resonance (NMR) time-series measurements that describe the dynamics of the metabolites in L. lactis. Both Michaelis–Menten and S-system models capture the observed in vivo dynamics of the glycolysis pathway in L. lactis, while prior models describe only the in vitro dynamics. The models provide insight into the maximization of selectivity of ethanol with respect to acetate and CO 2 as undesired products in multiple reactions. High concentrations of NADH and acetyl-CoA and low concentrations of pyruvate and NAD appear to maximize ethanol selectivity.

Proteomic comparative analysis of pathogenic strain 232 and avirulent strain J of Mycoplasma hyopneumoniae

Mycoplasma hyopneumoniae is an important pathogen of pigs causing enzootic pneumonia of swine. The pathogen remains largely enigmatic as far as the host-pathogen interactions are concerned. In the present study, the protein profiles of two strains of M. hyopneumoniae were compared by two-dimensional gel electrophoresis and mass spectrometry. The results indicate that the major adhesin P97, the 50-kDa protein derived from P159 adhesin, and the 43-kDa cleavage product of P102 are expressed at much higher levels in the pathogenic strain 232. In contrast, the avirulent strain J switches its focus to metabolism and expresses more glyceraldehyde 3-phosphate dehydrogenase in gluconeogenesis and lactate dehydrogenase, pyruvate dehydrogenase, and phosphate acetyltransferase in the pyruvate metabolism pathway. We speculate that the avirulent strain may have developed better capabilities to cope with the rich environment during repeated inoculations. Simultaneously, the capability to infect host cells may become less important so that the adhesion-related protein genes are down-regulated.

Taxonomical and physiological comparisons of the three species of the genus Amphibacillus

Amphibacillus is a genus for Gram-positive, spore-forming, rod-shaped, facultatively anaerobic bacteria with low-G+C content of DNA, established by Niimura et al. in 1990. Amphibacillus xylanus, the type species of the genus, grows well under both strictly anaerobic and aerobic conditions in spite of lacking any isoprenoid quinones, cytochromes, and catalase. Amphibacillus fermentum and Amphibacillus tropicus were later proposed by Zhilina et al. in 2001 for the isolates from a soda lake. In this paper, we revealed the latter two species also lacked isoprenoid quinones, cytochrome and catalase, and that they grew well under strictly anaerobic and aerobic conditions. The consistent growth of A. xylanus under both conditions is due to the presence of anaerobic and aerobic pathways for glucose metabolism in the organism. Although A. fermentum and A. tropicus are supposed to have a side enzymatic pyruvate pathway to produce lactate under both conditions, the two species have two major pyruvate metabolic pathways as observed in A. xylanus. Analysis data indicated that NADH formed both by the aerobic pyruvate pathway and by the glycolytic pathway was re-oxidized by the NADH oxidase in A. fermentum and A. tropicus as well as A. xylanus, and furthermore that the NADH oxidase-Prx (AhpC) system, i.e., NADH oxidase scavenging hydrogen peroxide with Prx, also functions in A. tropicus as observed with A. xylanus. Not only the taxonomical character of the genus Amphibacillus but also the growth characterization based on the two metabolic pathways and unique oxygen metabolism are distinctive in those traits from other facultative anaerobes.

Metabolic cycling in control of glucose-stimulated insulin secretion

Glucose-stimulated insulin secretion (GSIS) is central to normal control of metabolic fuel homeostasis, and its impairment is a key element of beta-cell failure in type 2 diabetes. Glucose exerts its effects on insulin secretion via its metabolism in beta-cells to generate stimulus/secretion coupling factors, including a rise in the ATP/ADP ratio, which serves to suppress ATP-sensitive K(+) (K(ATP)) channels and activate voltage-gated Ca(2+) channels, leading to stimulation of insulin granule exocytosis. Whereas this K(ATP) channel-dependent mechanism of GSIS has been broadly accepted for more than 30 years, it has become increasingly apparent that it does not fully describe the effects of glucose on insulin secretion. More recent studies have demonstrated an important role for cyclic pathways of pyruvate metabolism in control of insulin secretion. Three cycles occur in islet beta-cells: the pyruvate/malate, pyruvate/citrate, and pyruvate/isocitrate cycles. This review discusses recent work on the role of each of these pathways in control of insulin secretion and builds a case for the particular relevance of byproducts of the pyruvate/isocitrate cycle, NADPH and alpha-ketoglutarate, in control of GSIS.

Bayesian inference of the sites of perturbations in metabolic pathways via Markov chain Monte Carlo

Genetic modifications or pharmaceutical interventions can influence multiple sites in metabolic pathways, and often these are 'distant' from the primary effect. In this regard, the ability to identify target and off-target effects of a specific compound or gene therapy is both a major challenge and critical in drug discovery. We applied Markov Chain Monte Carlo (MCMC) for parameter estimation and perturbation identification in the kinetic modeling of metabolic pathways. Variability in the steady-state measurements in cells taken from a population can be caused by differences in initial conditions within the population, by variation of parameters among individuals and by possible measurement noise. MCMC-based parameter estimation is proposed as a method to help in inferring parameter distributions, taking into account uncertainties in the initial conditions and in the measurement data. The inferred parameter distributions are then used to predict changes in the network via a simple classification method. The proposed technique is applied to analyze changes in the pathways of pyruvate metabolism of mutants of Lactococcus lactis, based on previously published experimental data. MATLAB code used in the simulations is available from ftp://anonymous@dbkweb.mib.man.ac.uk/pub/Bioinformatics_BJ.zip

Proteomic Analyses of Zebra Finch Optic Tectum and Comparative Histochemistry

Proteomic analyses of zebra finch (Taeniopygia guttata) optic tectum resulted in identification of 176 proteins. In the Swissprot database, only 52 proteins were identified as bird homologs and only 71 proteins were identified in songbird transcriptome databases, reflecting a lack of completeness in the T. guttata genomic sequence. Analysis in Kyoto encyclopedia of genes and genome (KEGG) pathway database found that identified proteins most frequently belong to glucose, pyruvate, glyoxylate, dicarboxylate, alanine, and aspartate metabolism pathways. A number of identified proteins have been previously reported to exist in the avian optic tectum. The immunohistochemical localization of selected proteins showed their distribution in similar laminae of the owl (Tyto alba) and chicken (Gallus gallus) tectum. Immunohistochemical analysis of identified proteins can provide clues about cell types and circuit layout of the avian optic tectum in general. As the optic tectum of nonmammals is homologous to the superior colliculus of mammals, the analysis of the tectal and collicular proteome may provide clues about conserved cell and circuit layout, circuit function, and evolution.