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Topic: Metabolic pathway

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	Chapter Abstracts: Metabolic Engineering in the Post Genomic Era
		The control of the enzymes in the main pathway on the branch flux is dependent on the relative magnitude of the elasticity of the main pathway enzymes for the branching metabolite compared to the sensitivity of the enzymes in the branch.
		Metabolic engineering of glycine betaine synthesis to increase plant resistance to osmotic stresses (drought and salinity) has initially focused on manipulation of genes encoding enzymes of choline and betaine aldehyde oxidation, including expression of choline monooxygenase and betaine aldehyde dehydrogenase in the chloroplast of tobacco leaves.
		Metabolic flux analysis using transient radiolabeling has shown that limitations reside at the level of choline import from the cytosol to the chloroplast, and endogenous synthesis of choline moieties in tobacco.
	www.horizonpress.com /hsp/abs/absmet.html (2817 words)

	Shroomery - The Metabolic Pathway of Psilocybin Production
		Metabolic pathways are important to understand when you are trying to produce a certain chemical from a living organism.
		The Shikimate pathway is present in many different plants, fungi and bacteria, but is not present in animals, and is important for producing many different aromatic compounds, including many antibiotics and the tryptamine-based psychedelic drugs, like DMT, the ergot alkaloids and psilocybin.
		The pathway for the conversion of tryptamine to psilocybin and psilocin is still unclear, but it is proposed that there are many different steps, since the phosphorylated intermediates baeocystin and norbaeocystin are produced, in addition to psilocybin, which is most likely produced via one phosphorylase enzyme from psilocin.
	www.shroomery.org /6227/The-Metabolic-Pathway-of-Psilocybin-Production (579 words)

	Heredity - Ecological genetics: The decline and fall of a metabolic pathway in yeast
		Simple evolutionary principles suggest that the metabolic capabilities of a microbe should evolve in response to the availability of different resources in the environment: new pathways are expected to evolve when novel resources are encountered and existing pathways are expected to degrade in environments that lack the substrate the pathway degrades (Kassen, 2002).
		In this scenario, unused metabolic pathways degenerate as an indirect consequence of adaptation to a new niche.
		Both theoretical (Horowitz, 1945) and empirical (Mortlock, 1984) studies of metabolic pathway evolution have tended to concentrate on the mechanisms that give rise to new metabolic pathways with novel functions, and not on the degradation of existing pathways.
	www.nature.com /hdy/journal/v94/n3/full/6800632a.html (1067 words)

	MetaCyc: A multiorganism database of metabolic pathways and enzymes
		MetaCyc is the reference database of pathways and enzymes that is used in conjunction with SRI's metabolic pathway prediction program to predict the metabolic network of an organism from its annotated genome.
		The MetaCyc database (see URL http://MetaCyc.org/) is a collection of metabolic pathways and enzymes from a wide variety of organisms, primarily microorganisms and plants.
		In addition, MetaCyc is the reference database of pathways and enzymes that is used in conjunction with SRI's metabolic pathway prediction program to predict the metabolic network of an organism from its annotated genome.
	www.metabolicengineering.gov /pkarp.htm (394 words)

	An algorithm for linear metabolic pathway alignment
		The presence and absence of metabolic pathways in organisms was presented as a Boolean vector.
		A prevailing definition is that a metabolic pathway is a special case of a metabolic network with distinct start and end points, initial and terminal vertices, respectively, and a unique path between them, i.
		Typical metabolic pathways are given by the wall chart of Boehringer Mannheim [Michal, 1999] and KEGG [Kanehisa and Goto, 2000] (http://www.genome.ad.jp/kegg/metabolism.html), which have been verified with a number of printed and on-line sources.
	www.bioinfo.de /isb/2004/05/0013/main.html (4530 words)

	Biopharmaceutical Metabolic profiling
		Since each step of a metabolic pathway is catalyzed by an enzyme, it is these enzymes that are of most interest with respect to the genomics of metabolic pathways.
		Although the structures of metabolic pathways and protein interaction maps are similar, there are a number of significant differences: While metabolic pathways focus on the conversion of small molecules and the enzymes responsible for these conversions, protein interaction maps concentrate mainly on physical contacts without obvious chemical conversions.
		The term biochemical pathways has principally referred to metabolic pathways, which are the pathways by which a cell converts compounds that enter it into cellular components (e.g., small molecules and macromolecules including proteins, nucleic acids, storage carbohydrates, and fatty acids) and by which the cell derives energy.
	www.genomicglossaries.com /content/metabolic_engineering.asp (3804 words)

	BioMed Central \| Full text \| Phylophenetic properties of metabolic pathway topologies as revealed by global analysis
		As metabolic pathways are essential to the survival of organisms, and their evolution has been under debate for more than half a century [1], a combined phylogenetic and phenetic analysis of pathway topology might expand the understanding of the evolutionary processes molding their form and structure.
		As single pathways only provided topological information of "branches" to reconstruct the pathway set based tree, the higher similarity value for the pathway set based tree might indicate the existence of global constraints working on the global metabolic networks topology, which are reflected by the individual metabolic pathways.
		We compare the diameter of an organism-specific pathway graph to the average path length of the reference pathway graph, which is one of the most important topological parameters of a graph and also taken as the characteristic path length of the graph [25].
	www.biomedcentral.com /1471-2105/7/252 (5728 words)

	Metabolic Pathway Data in MaizeGDB
		A metabolic pathway is a series of chemical reactions inside of a living organism that results in the transformation of a particular molecule into a different molecule.
		Metabolic pathways include food digestion, energy storage, and other such biochemical tasks.
		Metabolic pathways are the methods that organisms use to achieve the basic acts of life.
	www.maizegdb.org /metabolic_pathway.php (302 words)

	Case Pathways Database System: PathCase Desktop Client
		Metabolic pathways, processes, and molecular entities can be browsed in different orders (Figure 2-a), and a set of useful queries can be specified about pathways, processes and molecular entities, from predefined simple queries to parameterized path selection and neighborhood queries.
		Similarly, for signaling pathways, signaling steps, and signaling and signaled molecules and their components can be browsed; a set of useful queries for signaling pathways are presently being developed (Figure 2-b).
		The Pathway Viewer presently visualizes a single metabolic pathway (Figure 3) or multiple metabolic pathways in an organism-specific or organism-independent manner, provides a large number of functionalities including collapsing-zooming, hiding-expanding, editing, and node property-setting.
	nashua.cwru.edu /PathwaysWeb/Desktop/Components2.aspx (293 words)

	BioCarta - Charting Pathways of Life
		Glycolysis was one of the first metabolic pathways studied and is one of the best understood, in terms of the enzymes involved, their mechanisms of action, and the regulation of the pathway to meet the needs of the organism and the cell.
		While the main route of fatty acid metabolism is through beta-oxidation, some minor metabolic pathways such as omega oxidation also contribute to the metabolism of fatty acids and other molecules.
		Catabolic pathways for alanine, glycine, serine, cysteine, tryptophan, and threonine
	www.biocarta.com /genes/catMetabolism.asp (853 words)

	Metabolic network modelling - Wikipedia, the free encyclopedia
		Metabolic network reconstruction and simulation allows for an in depth insight into comprehending the molecular mechanisms of a particular organism, especially correlating the genome with molecular physiology (Francke, Siezen, and Teusink 2005).
		Examples of various metabolic pathways include glycolysis, Krebs cycle, pentose phosphate pathway, etc. In simplified terms, a reconstruction involves collecting all of the relevant metabolic information of an organism and then compiling it in a way that makes sense for various types of analyses to be performed.
		During a metabolic network reconstruction of Lactobacillus plantarum, the model showed that succinyl-CoA was one of the reactants for a reaction that was a part of the biosynthesis of methionine.
	en.wikipedia.org /wiki/Metabolic_network_reconstruction_and_simulation (2121 words)

	Metabolic pathways databases
		It is one of several databases nested within the metabolic pathway database set of the SRS5 sequence retreival system at EBI.
		KEGG Metabolic Pathways include graphical pathway maps for all known metabolic pathways from various organisms.
		Ortholog group tables, containing conserved, functional units in a molecular pathway or assembly as well comparative lists of genes for a given functional unit in different organisms, are also available.
	www.wisdom.weizmann.ac.il /~biopsi/metDB_links.htm (226 words)

	eMedicine - Inherited Metabolic Disorders : Article by Pieter R Kark, MD, MA, FAAN, FACP
		Metabolism is the physiological and biochemical mechanisms by which foodstuffs are taken in by the body and converted from one form to another to provide energy for all the activities of the body.
		A defect of a certain severity in a specific pathway might be associated with a specific disease entity with a well-defined clinical picture, whereas defects of lesser severity in the same pathway or even in the same enzyme could sometimes be associated with different, less severe clinical entities.
		With a sudden demand on this metabolic pathway and up-regulation of enzymes to synthesize porphyrins combined with the inherited partial deficiency of uroporphyrinogen I synthetase, the toxic metabolites accumulate and cause damage to neural tissues, resulting in clinical symptoms.
	www.emedicine.com /NEURO/topic680.htm (6140 words)

	Metabolic Engineering (Solazyme)
		Metabolic engineering includes not only manipulation of endogenous metabolic pathways, but also the transplantation of metabolic pathways into new host organisms.
		In some instances the genes in a metabolic pathway are unknown, while in other cases some or all of the genes necessary and sufficient to produce a molecule are known.
		Solazyme’s technology is directed to increasing the productivity of selected metabolic pathways at levels that are commercially profitable and cheaper than fermentation-based methods.
	www.solazyme.com /metabolic-engineering.shtml (257 words)

	ISMB 2001 Poster Abstracts: Complex Biological Networks
		We illustrate the use of minimal pathway distances by calculating them for Escherichia coli small molecule metabolism pathways and considering their correlations with genomic distance (distance separating two genes on a chromosome) and enzyme function (as characterised by EC number).
		Pathways were predicted for 69 of these compounds; 91% of them were reasonably similar to known pathways.
		Several pathways have been identified to be responsible for cancer development by over- / underexpression of genes or by functional modification of signal proteins caused by alterations of their sequence.
	ismb01.cbs.dtu.dk /ComplexBiologicalNetworks.html (6322 words)

	Genome Biology \| Full text \| Genomic analysis of metabolic pathway gene expression in mice
		We show that this approach allows identification of specific pathways whose gene expression is coordinately regulated in association with obesity, defined genomic regulatory loci controlling the expression of these genes, and novel genes that are functionally associated with the identified pathways.
		In this work, we identified metabolic pathway gene sets with altered gene expression in association with the subcutaneous fat-pad mass trait, but the concept is applicable to other phenotypic traits where the target organ examined would be expected to show changes in relevant pathway gene expression.
		Within any given pathway, only about half of the genes showed a correlation between transcript levels and fat mass, consistent with the concept that regulation of a metabolic pathway requires the control of only selected elements rather than all constituents.
	genomebiology.com /2005/6/7/R59 (6175 words)

	Pathway Studio (formerly PathwayAssist), software for pathway analysis and visualization. (Site not responding. Last check: 2007-09-11)
		Pathway Studio® (formerly known as PathwayAssist) pathway analysis software helps you to interpret your experimental results in the context of pathways, gene regulation networks and protein interaction maps.
		Pathway Studio comes with proprietary ResNet database of 1,000,000+ functional relationships automatically extracted from scientific literature, and works with leading public and commercial databases of signaling and biochemical pathways, including KEGG, BIND, GO, PathArt, STKE Connections Maps and Prolexys HyNet.
		The information can be presented as a pathway diagram or a table of entities and relations, and is regularly updated once the new papers are published.
	www.ariadnegenomics.com /products/pathway/index.php?cmp=GPS (704 words)

	SRI International to Expand MetaCyc Metabolic Pathway Database
		The grant allows SRI and Carnegie to expand MetaCyc's size and scope, address the wealth of metabolic pathway information available in scientific literature, and continue to serve the growing audience for this information.
		One of MetaCyc's primary applications is as a reference database for computationally predicting the metabolic network of an organism from its annotated genome using algorithms pioneered by an SRI team led by Peter Karp, Ph.D., director of SRI's Bioinformatics Program.
		Metabolic engineers use MetaCyc as an encyclopedia of metabolic pathways and enzymes that may be genetically engineered into an organism to alter its metabolism.
	www.sri.com /news/releases/05-17-04.html (792 words)

	Insulin resistance: A metabolic pathway to chronic liver disease
		Metabolic abnormalities are common in liver disease, hence the term hepatogenous diabetes, which is used to describe the hyperglycemia that develops in advanced cirrhosis.
		IR may be defined as a condition in which (1) higher-than-normal insulin concentrations are needed to achieve normal metabolic responses or (2) normal insulin concentrations fail to achieve a normal metabolic response.
		Adiponectin activity strongly depends upon the metabolic milieu and the inflammatory pattern, and adiponectin concentrations in the plasma and liver are not always correlated.
	www.natap.org /2005/HIV/110705_02.htm (2683 words)

	Metabolic Pathway (Site not responding. Last check: 2007-09-11)
		The Metabolic Pathway is key to understanding the complexity of research.
		Having knowledge about research empowers parents and takes the edge off of the frustration many parents experience while waiting for the next discovery and hopefully a cure.
		Pathway Any sequence of chemical reactions leading from one compound to another.
	www.ziplink.net /users/mykids/scott/pathway.htm (518 words)

	Analysis of Metabolic Capabilities Using Singular Value Decomposition of Extreme Pathway Matrices -- Price et al. 84 ...
		The extreme pathways are represented by gray circles on the edges of the cone.
		Metabolic pathway analysis of a recombinant yeast for rational strain development.
		Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective.
	www.biophysj.org /cgi/content/full/84/2/794 (5380 words)

	Pathway Studio, software for pathway analysis and visualization.
		PathwaySolver pathway dynamics analysis module of Pathway Studio 4.0 emulates the dynamics of biological pathways by calculating concentrations of proteins and biochemical compounds during different times and conditions.
		You can start pathway simulation in Pathway Studio by importing the kinetic model of a pathway from an SBML file, or by adding kinetic data to a well-known or newly generated pathway.
		You can view concentrations of selected pathway entities at a specified time, as well as graphical curves of changes in a synchronized table or directly on a pathway diagram.
	www.ariadnegenomics.com /products/pathway/solver (291 words)

	Metabolic pathway
		In biochemistry, a metabolic pathway is a series of chemical reactions occurring within a cell, catalyzed by enzymes, to achieve in either the formation of a metabolic product to be used or stored by the cell, or the initiation of another metabolic pathway (then called a flux generating step).
		Many of these pathways are elaborate, and involve a step by step modification of the initial substance to shape it into the product with the exact chemical structure desired.
		The pathways are regulated, usually by feedback inhibition, or may be a cycle where the end product starts the reaction again, such as the Krebs Cycle (see below).
	www.mrsci.com /Metabolism/Metabolic_pathway.php (706 words)

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