PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Metabolic pathways”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7Linked to original sources

[Studies on bacterial metabolism pathway of 2-naphthoic acid].

The missing chemical Link (Phthalate) of bacterial metabolism pathway for 2-naphthoic acid has been identified to be existing. The genetic regulation mechanism of 2-NAT strain for 2-naphthoic acid metabolism is also investigated with plasmid curing, transposon Tn10 mutagenesis and mutation reversion experiments. It is discovered that 2-NAT strain carries at least one plasmid. The plasmid and the chromosomal DNA co-encode and control the bacterial metabolism pathway for 2-naphthoic acid.

DNA Transposable Elements↗

Metabolic pathways in the post-genome era.

Metabolic pathways are a central paradigm in biology. Historically, they have been defined on the basis of their step-by-step discovery. However, the genome-scale metabolic networks now being reconstructed from annotation of genome sequences demand new network-based definitions of pathways to facilitate analysis of their capabilities and functions, such as metabolic versatility and robustness, and optimal growth rates. This demand has led to the development of a new mathematically based analysis of complex, metabolic networks that enumerates all their unique pathways that take into account all requirements for cofactors and byproducts. Applications include the design of engineered biological systems, the generation of testable hypotheses regarding network structure and function, and the elucidation of properties that can not be described by simple descriptions of individual components (such as product yield, network robustness, correlated reactions and predictions of minimal media). Recently, these properties have also been studied in genome-scale networks. Thus, network-based pathways are emerging as an important paradigm for analysis of biological systems.

Biochemistry↗

The biodegradation of some anionic detergents in the rat. A common metabolic pathway.

1. The metabolism of the anionic detergents potassium decyl [35S]sulphate and potassium octadecyl [35S]sulphate was investigated in the rat. 2. The major route for elimination of radioactivity was urinary regardless of the route of administration. 3. Both surfactants were extensively degraded in vivo to yield a common metabolite, butyric acid 4-[35S]sulphate, the major urinary radioactive component. 4. Whole-body radioautography revealed the liver as the major site of cellular accumulation of radioactivity following administration of either compound indicating the liver as the major site of metabolism. 5. It is suggested that alkyl sulphates with even-numbered carbons are degraded by a common pathway involving omega-oxidation followed by beta-oxidation.

Administration, Oral↗

[Formation of an acetic-acid type microbial metabolism pathway and its stability during the course of sulfate-reduction].

Continuous-flow experiment was conducted in an acidogenic sulfate-reducing reactor supplied with molasses as sole carbon resource and sulfate sodium as electron acceptor. The composition of Volatile fat acid(VFA) in terminal liquid products, the distribution of acetic acid, the existence of microbial populations and the interspecific relationship between sulfate-reducing bacteria (SRB) and acidogenic bacteria (AB) were investigated in different experimental stages when sulfate removal rate and gas production maintained at a relatively stable status. The experimental results showed that an acetic-acid type microbial metabolism pathway was formed based on the fact that the proportion of acetic acid in terminal liquid products was as high as 50% to 82%. It was also explained the formation of acetic-acid type microbial metabolism pathway was resulted from acetic acid accumulation in the terminal liquid products, which was subjected to the bio-chain cooperation relationship between populations of SRB and AB, and the incomplete-oxidation of organic substance in acidogenic-phase reactor of two-phase anaerobic treatment process. It was also presented that the formation of acetic-acid type microbial metabolism pathway depended on the capability of acetic-acid utilized-SRB (ASRB) population competing against other populations and its ability of acetic acid consumption. Furthermore, this kind of metabolism pathway could offer suitable carbon resource for methane producing reactor in the two-phase anaerobic treatment process, and has significant effect on the sulfate removal rate of the whole treatment system and its running stability.

Acetic Acid↗

The mannitol cycle--a new metabolic pathway in the Coccidia.

A new metabolic pathway, known as the mannitol cycle, has been identified in the coccidian parasite Eimeria tenella. It appears that this pathway may be important for the production and utilization of energy reserves for the parasite. This pathway has not been found in any other animal system and was previously thought to be unique to fungi.

Journal Article↗

Metabolic pathways of apolipoprotein B in heterozygous familial hypercholesterolemia: studies with a [3H]leucine tracer.

The kinetics of apolipoprotein B (apoB) were measured in seven studies in heterozygous, familial hypercholesterolemic subjects (FH) and in five studies in normal subjects, using in vivo tracer kinetic methodology with a [3H]leucine tracer. Very low density (VLDL) and low density lipoproteins (LDL) were isolated ultracentrifugally and LDL was fractionated into high and low molecular weight subspecies. ApoB was isolated, its specific radioactivity was measured, and the kinetic data were analyzed by compartmental modeling using the SAAM computer program. The pathways of apoB metabolism differ in FH and normal subjects in two major respects. Normals secrete greater than 90% of apoB as VLDL, while one-third of apoB is secreted as intermediate density lipoprotein IDL/LDL in FH. Normals lose 40-50% of apoB from plasma as VLDL/IDL, while FH subjects lose none, metabolizing all of apoB to LDL. In FH, there is also the known prolongation of LDL residence time. The leucine tracer, biosynthetically incorporated into plasma apoB, permits distinguishing the separate pathways by which the metabolism of apoB is channeled. ApoB synthesis and secretion require 1.3 h. ApoB is secreted by three routes: 1) as large VLDL where it is metabolized by a delipidation chain; 2) as a rapidly metabolized VLDL fraction converted to LDL; and 3) as IDL or LDL. ApoB is metabolized along two pathways. The delipidation chain processes large VLDL to small VLDL, IDL, and LDL. The IDL pathway channels nascent, rapidly metabolized VLDL and IDL particles into LDL. It thus provides a fast pathway for the entrance of apoB tracer into LDL, while the delipidation pathway is a slower route for channeling apoB through VLDL into LDL. LDL apoB is derived in almost equal amounts from both pathways, which feed predominantly into large LDL. Small LDL is a product of large LDL, and the major loss of LDL-apoB is from small LDL. Two features of apoB metabolism in FH, the major secretory pathway through IDL and the absence of a catabolic loss of apoB from VLDL/IDL, greatly facilitate measuring the metabolic channeling of apoB into LDL.

Adult↗

Biochemical networking contributes more to genetic buffering in human and mouse metabolic pathways than does gene duplication.

During evolution different genes evolve at unequal rates, reflecting the varying functional constraints on phenotype. An important contributor to this variation is genetic buffering, which reduces the potential detrimental effects of mutations. We studied whether gene duplication and redundant metabolic networks affect genetic buffering by comparing the evolutionary rate of 242 human and mouse orthologous genes involved in metabolic pathways. A gene with a redundant network is defined as one for which the structural layout of metabolic pathways provides an alternative metabolic route that can, in principle, compensate for the loss of a protein function encoded by the gene. We found that genes with redundant networks evolve at similar rates as did genes without redundant networks, [corrected] but no significant difference was detected between single-copy genes and gene families. This implies that redundancy in metabolic networks provides significantly more genetic buffering than do gene families. We also found that genes encoding proteins involved in glycolysis and gluconeogenesis showed as a group a distinct pattern of variation, in contrast to genes involved in other pathways. These results suggest that redundant networks provide genetic buffering and contribute to the functional diversification of metabolic pathways.

Animals↗

Metabolic pathways and pharmacokinetics of BOF-4272, a sulfoxide-containing drug, in the dog: in vivo and in vitro studies.

BOF-4272, (+/-)-8-(3-methoxy-4- phenylsulfinylphenyl)pyrazolo[1,5-a]-1,3,5-triazine-4(1H)-one, is a new drug intended for the treatment of hyperuricemia. This report describes the detailed metabolic pathways of BOF-4272 in the dog. The metabolic pathways were investigated using the metabolites found in plasma, urine, and feces after intravenous or oral administration of BOF-4272, as well as the metabolites found in the liver S9 incubation mixture after the addition of BOF-4272 or BOF-4269. BOF-4269 (the sulfide metabolite of BOF-4272) was the only metabolite detected in plasma and feces after the intravenous or oral administration of BOF-4272. BOF-4269 was detected in dog plasma after a lag time following the oral administration of BOF-4272, and the Cmax and AUC0-t of BOF-4269 were higher in fed dogs than in fasted dogs after the oral administration of BOF-4272. A small amount of BOF-4269 was detected in dog plasma immediately after the intravenous administration of BOF-4272. Only BOF-4276 (the sulfone metabolite of BOF-4272) was detected in the S9 incubation mixture after the addition of BOF-4272. Mainly BOF-4272 was detected and small amounts of BOF-4276 and M-1 (the hydroxy metabolite of BOF-4269) were detected in the S9 incubation mixture after the addition of BOF-4269. These findings suggest that BOF-4272 is mainly metabolized to BOF-4269 by the intestinal flora in dogs, whereas little of this drug is metabolized to BOF-4269 in the dog liver. In conclusion, this work has allowed us to formulate the proposed metabolic pathways of BOF-4272 in the dog.

Animals↗

Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era.

This article reviews the relatively short history of metabolic pathway analysis. Computer-aided algorithms for the synthesis of metabolic pathways are discussed. Important algebraic concepts used in pathway analysis, such as null space and convex cone, are explained. It is demonstrated how these concepts can be translated into meaningful metabolic concepts. For example, it is shown that the simplest vectors spanning the region of all admissible fluxes in stationary states, for which the term elementary flux modes was coined, correspond to fundamental pathways in the system. The concepts are illustrated with the help of a reaction scheme representing the glyoxylate cycle and adjacent reactions of aspartate and glutamate synthesis. The interrelations between pathway analysis and metabolic control theory are outlined. Promising applications for genome annotation and for biotechnological purposes are discussed. Armed with a better understanding of the architecture of cellular metabolism and the enormous amount of genomic data available today, biochemists and biotechnologists will be able to draw the entire metabolic map of a cell and redesign it by rational and directed metabolic engineering.

Biotechnology↗

The puzzle of the Krebs citric acid cycle: assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution.

The evolutionary origin of the Krebs citric acid cycle has been for a long time a model case in the understanding of the origin and evolution of metabolic pathways: How can the emergence of such a complex pathway be explained? A number of speculative studies have been carried out that have reached the conclusion that the Krebs cycle evolved from pathways for amino acid biosynthesis, but many important questions remain open: Why and how did the full pathway emerge from there? Are other alternative routes for the same purpose possible? Are they better or worse? Have they had any opportunity to be developed in cellular metabolism evolution? We have analyzed the Krebs cycle as a problem of chemical design to oxidize acetate yielding reduction equivalents to the respiratory chain to make ATP. Our analysis demonstrates that although there are several different chemical solutions to this problem, the design of this metabolic pathway as it occurs in living cells is the best chemical solution: It has the least possible number of steps and it also has the greatest ATP yielding. Study of the evolutionary possibilities of each one-taking the available material to build new pathways-demonstrates that the emergence of the Krebs cycle has been a typical case of opportunism in molecular evolution. Our analysis proves, therefore, that the role of opportunism in evolution has converted a problem of several possible chemical solutions into a single-solution problem, with the actual Krebs cycle demonstrated to be the best possible chemical design. Our results also allow us to derive the rules under which metabolic pathways emerged during the origin of life.

Acetates↗

Measles virus-induced mononuclear leukocyte adherence inhibition: effect of some drugs influencing arachidonic acid metabolic pathways.

Effect of some drugs influencing arachidonic acid metabolic pathways upon the measles virus-induced leukocyte adherence inhibition was investigated in multiple sclerosis patients and in the control group. The drugs used were natrium salicylate, ethanol, and phenidon(1-phenyl-3-pyrazolidon). Statistically significant differences were proved between multiple sclerosis patients and controls using phenidon, a drug inhibiting both cyclooxygenase and lipoxygenase pathways of the arachidonic acid metabolism. The results obtained provide suggestion on participation of arachidonic acid metabolism in the measles virus-induced leukocyte adherence inhibition phenomenon and in its alterations in multiple sclerosis.

Adult↗

Metabolic formation of ceramide-1-phosphate in cerebellar granule cells: evidence for the phosphorylation of ceramide by different metabolic pathways.

Aiming to investigate the possible production of ceramide-1-phosphate from complex sphingolipid metabolism in neurons, we administered radiolabeled sphingolipids to cerebellar granule cells and inspected the formation of labeled ceramide-1-phosphate in different experimental conditions. We report that differentiated granule cells are capable to form Cer-1-P via ceramide derived from SM degradation at the plasma membrane level. Moreover we observed that ceramide-1-phosphate can be also produced from a metabolic pathway not involving SM degradation. In particular, we obtained evidence that ceramide, synthesized via the recycling of sphingosine produced from ganglioside catabolism, can also be the precursor of ceramide-1-phosphate. We also found that undifferentiated and differentiated granule cells display different capacities to phosphorylate Cer produced by the two different metabolic pathways. The results here obtained demonstrate that cerebellar neurons are able to metabolically produce ceramide-1-phosphate and support that this molecule may serve a potential role in sphingoid-mediated signaling in the nervous system.

Animals↗

Analysis of in vitro skin permeation of 22-oxacalcitriol having a complicated metabolic pathway.

PURPOSE: The purpose of this study is to analyze simultaneous skin permeation and metabolism of 22-oxacalcitriol (OCT) having several metabolites in skin by observing skin permeation of only unchanged OCT through excised rat skin. METHODS: A diffusion model including metabolic processes was employed to express simultaneous skin permeation and metabolism of OCT. In vitro permeation experiments of OCT from Oxarol ointment through full-thickness and stripped rat skin were carried out using Franz-type diffusion cells. Time courses of unchanged OCT amounts in ointment, skin, and receptor fluid were determined and fitted to diffusion equations to obtain permeation parameters and a metabolic rate. RESULTS: Fitting curves of the skin permeation profile obtained by the model were sufficiently close to observed data of unchanged OCT amounts in ointment, skin, and receptor fluid. The following parameters were obtained: metabolic rate of 1.37 x 10(-1) h(-1), and diffusion constants of OCT in stratum corneum (SC) (D(SC)) and viable epidermis and dermis (VED) (D(VED)) of 1.50 x 10(-7) and 2.96 x 10(-4) cm2/h, respectively. The partition coefficient of OCT for SC/ointment (K(SC/D)) was 7 times greater than that of VED/ointment (K(VED/D)). CONCLUSIONS: The present analysis made it possible to calculate skin permeation parameters (partitioning, diffusivity, and metabolic rate) of OCT without requiring metabolic information, e.g., quantification of metabolites or identification of metabolic pathways. This would be widely applicable for drugs that are not suitable for conventional methods due to complicated metabolic pathways.

Algorithms↗

Evaluation of computational metabolic-pathway predictions for Helicobacter pylori.

MOTIVATION: We seek to determine the accuracy of computational methods for predicting metabolic pathways in sequenced genomes, and to understand the contributions of both the prediction algorithms, and the reference pathway databases used by those algorithms, to the prediction accuracy. RESULTS: The comparisons we performed were as follows. (1) We compared two predictions of the pathway complements of Helicobacter pylori that were computed by an early version of our pathway-prediction algorithm: prediction A used the EcoCyc E. coli pathway DB as the reference database (DB) for prediction, and prediction B used the MetaCyc pathway DB (a superset of EcoCyc) as the reference pathway DB. The MetaCyc-based prediction contained 75% more pathway predictions, but we believe a significant number of those predictions were false positives. (2) We compared two predictions of the pathway complement of H. pylori that used MetaCyc as the reference pathway DB, but that used different algorithms: the original PathoLogic algorithm, and an enhanced version of the algorithm designed to eliminate false-positive pathway predictions. The improved algorithm predicted 30\% fewer metabolic pathways than the original algorithm; all of the eliminated pathways are believed to be false-positive predictions. (3) We compared the 98 pathways predicted by the enhanced algorithm with the results of a manual analysis of the pathways of H. pylori. Results: 40 of the computationally predicted pathways were consistent with the manual analysis, 13 pathways are considered false-positive predictions, and four pathways had partially overlapping topologies. Twenty-six predicted pathways were not mentioned in the manual analysis; we believe these are correct predictions by PathoLogic that were not found by the manual analysis. Five pathways from the manual analysis were not found computationally. Agreement between the computational and manual predictions was good overall, with the computational analysis inferring many pathways that the manual analysis did not identify. Ultimately the manual analysis is also partially speculative, and therefore is not an absolute measure of correctness. The algorithm is designed to err on the side of more false positives to bring more potential pathways to the user's attention. The resulting H. pylori pathway DB is freely available at http://ecocyc.org:1555/HPY/organism-summary?object=HPY. AVAILABILITY: The Pathway Tools software is freely available to academic users, and is available to commercial users for a fee. Contact pkarp@ai.sri.com for information on obtaining the software.

Algorithms↗

Localization of the human tyrosine hydroxylase gene to 11p15: gene duplication and evolution of metabolic pathways.

Phenylalanine hydroxylase (PAH) and tyrosine hydroxylase (TH) are consecutive enzymes in the metabolic pathway leading to the production of catecholamine neurotransmitters. A comparison of recently available sequence data of these enzymes in the rat indicates about 70% homology in the 3' coding regions. We have localized TH by in situ hybridization to human chromosome region 11p15. Consideration of this assignment and that of PAH to chromosome 12, together with the known distribution of other pairs of related genes on these two chromosomes, provides convincing evidence of their ancestral relationship and suggests a role for gene duplication in the diversification of metabolic pathways in the vertebrate ancestors of mammals.

Animals↗

In vivo measurement of fluxes through metabolic pathways: the missing link in functional genomics and pharmaceutical research.

In the postgenomic era of biology, much attention has been given to functional genomics, or the relation between genes and higher levels of organization in the cell. The latter are typically represented as mRNA, protein, or organic metabolite complements. The theme of this review is that the operational unit of function in complex biological systems is more properly seen as the fully assembled metabolic pathway in the whole organism. Due to the connectivity, interactions, and complexity of metabolic pathways, the measurement of components is an inadequate method for predicting phenotype. Measurement of the outputs of pathways (molecular fluxes) involves different tools than static measures of components, however. Here, we review recently developed stable isotope-mass spectrometric tools for measuring fluxes through metabolic pathways in vivo, focusing on the response to dietary macronutrients (carbohydrates and fats). Methods discussed include measurement of lipid dynamics, DNA replication, hepatic assembly of lipoproteins, and long-lived protein synthesis. Measuring fluxes through multiple pathways concurrently allows regulatory themes to emerge. Use of 2H2O-labeling is emerging as a particularly powerful approach for multiple concurrent biosynthetic flux measurements. Several examples demonstrate that pathway flux results are often unexpected and not predicted by classic biochemistry or the expression of genes and proteins.

Animals↗

Arachidonic acid metabolic pathways regulating activity of renal Na(+)-K(+)-ATPase are age dependent.

Locally formed arachidonic acid (AA) metabolites are important as modulators of many aspects of renal tubular function, including regulation of the activity of tubular Na(+)-K(+)-ATPase. Here we examined the ontogeny of the AA metabolic pathways regulating proximal convoluted tubular (PCT) Na(+)-K(+)-ATPase activity in infant and adult rats. Eicosatetraynoic acid, an inhibitor of all AA-metabolizing pathways, abolished this effect. AA inhibition of PCT Na(+)-K(+)-ATPase was blocked by the 12-lipoxygenase inhibitor baicalein in infant but not in adult rats and by the specific cytochrome P-450 fatty acid omega-hydroxylase inhibitor 17-octadecynoic acid in adult but not in infant rats. The lipoxygenase metabolite 12(S)-hydroxyeicosatetraenoic acid (HETE) and the cytochrome P-450 metabolite 20-HETE both inhibited PCT Na(+)-K(+)-ATPase in a protein kinase C-dependent manner, but the effect was significantly more pronounced in infant PCT. Lipoxygenase mRNA was only detected in infant cortex. Expression of renal isoforms of cytochrome P-450 mRNA was more prominent in adult cortex. In summary, the AA metabolic pathways that modulated the activity of rat renal proximal tubular Na(+)-K(+)-ATPase are age dependent.

5,8,11,14-Eicosatetraynoic Acid↗

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↗