text:
Metabolomics/Metabolites/Amino Acids

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=Glutamate=

Interconverting between glutamate and 2-oxoglutarate is known to play a significant role in plant carbon (C) and nitrogen (N) metabolism, and can be catalyzed by glutamate dehydrogenase (GDH). However, GDH maintains trivial functionality, in plants. In an attempt to expound upon the role of GDH, researchers analyzed GDH expression in Arabidopsis thaliana tissues. Results indicated that Arabidopsis GDH gene expression regulation was dependent upon the type of organ or tissue analyzed and the cellular C concentration. In addition, gdh1-2 and gdh2-1 were identified as Arabidopsis mutants that were defective in GDH genes. These mutants were isolated, crossed to make a double knockout mutant, characterized as gdh1-2/gdh2-1, containing negligible levels of NAD(H)-dependent GDH activity. Phenotypic analysis of these mutants revealed that gdh1-2/gdh2-1 plants are more susceptible to C-deficient conditions, which indicated that the double-knockout mutant supports the catabolic role of GDH, and contributes to fuelling the TCA cycle during C starvation. When glutamate was provided as an alternative N source, there was a determined reduced rate of glutamate catabolism in gdh2-1 and gdh1-2/gdh2-1 plants that was indicated by the consequential growth retardation, of these mutants. There were significant differences among amino acid profiles obtained from WT and the gdh mutant plants, during prolonged dark conditions. These differences were evident when glutamate levels were discovered to increase in WT plants and decrease in gdh1-2/gdh2-1. In addition, identified contributing factors to GDH regulation were cellular carbohydrate, and ATP levels. Further evidence was provided by the abnormal accumulation of several amino acids that was observed in gdh1-2/gdh2-1 plants. These results conclude that GDH has a significant role in the breakdown of amino acids, during C-starvation.

GDH participation in amino acid breakdown is apparently significant to all organisms, during C deficiency. Although, plants are capable of sacrificing tissues and cells in order to support other tissues and cells that are more metabolically significant, for survival. This behavior was exemplified when the observed damage to rosette leaves was more severe than the damage that stems or shoot apical meristems incurred, during C deficient conditions. Mitochondrial localization of GDH was determined to directly affect GDH involvement in carbon skeleton funneling of amino acids into the TCA cycle, during C deficiency. In addition, the ability of GDH to bind to RNA, inhibiting in vitro RNA editing, was attenuated by increased levels of NADH, NADPH, and ATP. This provided further insight into the capability of GDH to bind to these molecules.

References:

http://jxb.oxfordjournals.org/cgi/content/full/59/3/667#SEC4

Review Article: Arginine deprivation and metabolomics: Important aspects of intermediary metabolism in relation to the differential sensitivity of normal and tumour cells http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WWY-4G4N5TG-1&_user=47004&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000005018&_version=1&_urlVersion=0&_userid=47004&md5=0a03a14d1acfa0f568a0b83046a6d5ab Arginine deprivation is known to cause a wide range of tumor cell types to die due to the inability to convert urea cycle intermediates to arginine. In rapidly multiplying and growing organisms arginine is often the rate-limiting amino acid or "semi-essential" amino acid. Tumors have a high requirement for arginine and causes increase mitotic activity in animal tumors. Therefore, low arginine, slows proliferation and in malignant tumor cells low, but not completely deficient arginine concentrations cause cell death, however the pathway to death is not clear and apoptosis has been considered. Cell culture in vivo experiments were performed and it was demonstrated that homeostatic mechanisms existing in vivo to restore arginine levels were not present in vitro where there is no available citrulline. Arginine elimination was also assessed for cells where arginine was directly eliminated and for cells where elimination of arginine occurred via arginine degrading enzymes. In normal cell cultures made arginine deficient with arginine catabolizing enzymes, cell growth was recovered by citrulline, which was converted to arginine by the urea cycle, but none were resucued with the addition of argininge due to the catabolizing enzymes. In vivo the elimination of arginine without catabolic enzymes is not successful unless citrulline synthesis has been compromised such as in renal failure. Nevertheless, in vitro studies seem more promising. Under normal conditions the conversion rate of citrulline to arginine is too low to sustain tumor growth. The prospect of developing arginine anticancer drugs is very likely, although there is quite sometime before this can occur. Different enzymes will produce different products and these may impact cell metabolism differently. Metabolomics is relevant and could be useful in characterizing tumors and patients in the future. In addition metabolomics could be used to facilitate certain protocols in cancer therapy.

1. semi-essential amino acid- amino acids are ones that can sometimes be made internally if conditions are right. Arginine and histidine can be converted from other amino acids if needed. 2. citrulline- is an alpha amino acid and a key intermediate in the urea cycle. Citrulline is a substituted urea that is produced from ornithine and carbamoyl phosphate and also is produced from argininge as a byproduct catalyzed by nitric oxide synthase. When starved for arginine, organisms will convert ornithine to citrulline to yield arginine. 3. in vitro- is an experiment in a controlled environment outside living systems. 4. in vivo- experiments taking place inside an organism. 5. catabolism- metabolic process where molecules are broken down into smaller units and yield energy. 6. cell culture- the process by which prokaryotic, eukaryotic or plant cells are grown under controlled conditions. 7.. hepatocellular carcinoma- is a primary malignancy (cancer) of the liver. Most cases of HCC are secondary to either a viral hepatitides infection (hepatitis B or C) or cirrhosis (alcoholism being the most common cause of hepatic cirrhosis). 8. stroma- is a nonfunctional connective framework found in cells, tissues, or organs. 9.. Argininosuccinate- Some cells produce argininosuccinic acid from citrulline and aspartic acid and use it as a precursor for arginine in the urea cycle. Argininosuccinic acid is a precursor to fumarate in the citric acid cycle via argininosuccinate lyase.

This article is related to our biochemistry metabolism class in that citrulline can be converted to arginine in the urea cycle. In the urea cycle, two amino groups enter the cycle as carbamoyl phosphate, which is formed in the mitochondrial matrix and as aspartate also formed in the mitochondrial matrix by transamination of oxolacetate and glutamate. Subsequently, the fist step is formation of citrulline from ornithine and carbomyl phosphpate. Citrulline is generated in the mitochondria then passes into the cytosol. Argininosuccinate is formed through citrullyl-AMP, an intermediate. Arginine is generated from argininosuccinate and fumarate is released, which can enter the citric acid cycle. From arginine, urea is produced and ornithine is regenerated.

Arginine- An essential Amino acid (pubchem) KEGG links:

Metacyc links: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=ARGSYN-PWY http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=ARGASEDEG-PWY

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCN-4DVBVM9-1&_user=47004&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000005018&_version=1&_urlVersion=0&_userid=47004&md5=867c1849aa7bbf8b41bb218f2d1cd367 Peer Reviewed article: d-Serine-induced nephrotoxicity: a HPLC–TOF/MS-based metabonomics approach

The role in of D-serine as an endogenous modulator of the glycine site on the N-methyl-D- aspartate receptor in the brain of humans and experimental animals has recently been demonstrated. D-serine levels in the brain are analogous to glycine, however D-serine levels in some areas such as the stratium is 2.6 times higher than that of glycine. D- serine is known to cause selective damage to the renal proximal tubule cells and leads to proteinuria, glucosuria, and aminoaciduria. Aminoaciduria is the important product that cause onset of necrosis. The mechanism that D-serine produces renal injury in the rat is still unclear. D-serine is metabolized once it enters the pars recta region of the proximal tubule and alpha keto acid, ammonia and hydrogen peroxide are produced. Investigators of this paper used HPLC-MS metabonomics to study the characteristics of urinary metabolites related to D-serine induced nephrotoxicity. By HPLC-MS it was shown that D-serine caused a change in the urinary metabolic report. Metabolites such as proline, methionine, leucine, tyrosine and valine were observed in addition to an increase in acetyl carnitine. This information provided information of D-serine metabolism and its performed function in the kidney.

1. nephrotoxicity- is the poisonous effect on the kidney that may be caused by medications or toxins. 2. aminoaciduria- amino acids in the urine 3. proteinuria- protein in the urine 4. glucosuria- glucose in the urine 5. proximal tubule- is the portion of the duct system of the nephron leading from Bowman's capsule to the loop of Henle. 6. Perturbations- alteration of function induced by external or internal mechanisms. 7. halothane- is an anaesthetic that triggers malignant hyperthermia in susceptible animals or individuals. In this paper it was used to kill experimental rats. 8. exsanguinations- "bleeding to death"- fatal process of blood loss, after halothane treatment, exsnaguinations followed.

One way that this article is related to class is through the production of ammonia and hydrogen peroxide from D-serine as it enters the kidney. Catabolic production of ammonia is a threat to biochemical processes because of ammonia’s toxicity. The end stages of ammonia in humans includes a comatose state with cerebral edema and increased cranial pressure. To eliminate the cytosol of unwanted ammonia, reductive amination of alpha-ketogulturate to glutamate by glutamate dehydrogenase and conversion of glutamate to glutamine by glutamine synthetase is required. Both of these enzymes are available in the brain, however glutamine synthetase is more prominent for the pathway of ammonia removal.

D-serine- A nonessential Amino Acid (pubchem) KEGG links:

Metacyc links: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=SERSYN-PWY http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=SERDEG-PWY

Peer Review Article: Combined Metabolomic and Genetic Approaches Reveal a Link between the Polyamine pathway and Albumin 2 in Developing Pea Seeds http://www.plantphysiol.org/cgi/content/full/146/1/74 Pea (Pisum sativum) albumin 2 (PA2) is a protein from a seed that is not a classical storage protein, lacks a signal peptide, is not degraded on germination, and is poorly digested by farm animals and shows to be a potential allergen. Metabolomic approaches have been applied to investigate the biological function of the albumin protein PA2. The PA2 protein has four copies of a hemopexin repeat, which is related structurally to a group of mammalian regulatory proteins such as vitronectin. Due to this it has been thought that PA2 may function as a regulator of metabolic processes. In mammals, hemopexins act as scavengers and transporters of plasma heme that is toxic and may contribute in the homeostasis of nitric oxide. Investigators identified and characterized a mutant with a reduced PA2 in seeds that could provide ways of improving seed quality characteristics, including digestibility and reduced allergic reaction. Seeds lacking PA2 had more N content and higher levels of total seed protein and starch levels remained the same. Metabolites demonstrated a dramatic different in amino acid composition and polyamine content.. A lack of PA2 led to decreased amounts of the polyamine. Examining polyamine synthesis showed that the different spermidine amounts were due to changes in spermidine synthase and arginine decarboxylase. Researcher concluded that PA2 regulates polyamine metabolism. Polyamine- are organic compounds having two or more primary amino groups - such as putrescine, cadaverine, spermidine, and spermine - that are growth factors in both eucaryotic and procaryotic cells. Spermidine synthase- is an enzyme that catalyzes the transfer of the propylamine group from 5'-deoxy-5'-S-(3-methylthiopropylamine)sulfonium adenosine to putrescine in the biosynthesis of spermidine. Arginine decarboxylase- is an enzyme that catalyzes the chemical reaction of L-arginine and producing agmatine and carbon dioxide. Lyophilization- also called freeze-drying, is a method of drying that significantly reduces such damage. Dansylation- the process of using dansyl chloride- is a reagent that reacts with primary amino groups in both aliphatic and aromatic amines to produce stable blue- or blue-green–fluorescent sulfonamide adducts. Dansyl chloride is widely used in protein sequencing and amino acid analysis This article is related to biosynthesis of nucleotides. Polyamines such as spermine and spermidine are involved in DNA packaging. They are derived from methionine and ornithine by a pathway starting out with the decarboxylation of ornithine, a precursor of arginine. Ornithine decarboxylase is a PLP requiring enzyme and that converts ornithine to putrescine. Propylaminotransferase I converts putrescine the spermidine and in a second propylaminotransferase recation spermidine is converted to spermine. S-adenosylmethioine provides propylamino groups for the propylamontransferase reactions.

Spermine- A biogenic polyamine formed from spermidine. It is found in a wide variety of organisms and tissues and is an essential growth factor in some bacteria. It is found as a polycation at all pH values. Spermine is associated with nucleic acids, particularly in viruses, and is thought to stabilize the helical structure. (pubchem)

Spermidine KEGG links:

Metacyc links: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=BSUBPOLYAMSYN-PWY

Peer Review Article: Transcriptomics and Metabolomics of Dietary Leucine Excess http://jn.nutrition.org/cgi/reprint/135/6/1571S Previous studies has shown that leucine given to animals in diets with adequate protein levels had no problem with large doses of leucine. In this paper researchers analyzed rats that were fed for two weeks on a basal dies or with diets containing varying leucine concentractions including 1.5,5,10,15, and 30%. Also, the changes in gene expression in livers of the rats that were fed the basal diet or diets with 5% and 15% had leucine added and were analyzed by DNA microarrays. Data showed that there was little change in the expression of enzymes of leucine catabolic pathways but there were changes in enzymes associated with nitrogen metabolism and other downstream pathways of leucine catabolism. CAMC revealed that excess nitrogen clustered together with leucine and alpha-ketoisocaproate. In conclusion, excess leucine may be overloading nitrogen metabolism and urea or alpha-ketoisocaproate may be early markers for excessive leucine intake.

alpha-ketoisocaproate- Alpha-ketoisocaproate (KIC) is a keto acid of leucine (branched chain amino acid). Branched-chain keto acids (BCKAs) are very similar to branched-chain amino acids (BCAAs), the only difference being the presence of a keto group instead of an amino group. Thus, BCKAs can be viewed as ammonia-free sources of BCAAs. CAMC- Cluster analysis of multivariate correlations- is the classification of objects into different groups, or more precisely, the partitioning of a data set into subsets, so that the data in each subset share some common trait - often proximity according to some defined distance measure. SDH- succinate dehydrogenase is an enzyme complex bound to the inner mitochondrial membrane. It is the only enzyme that participates in both the citric acid cycle and the mitochondrial electron transport chain (Complex II). Ketoacids- are organic acids containing a ketone functional group and a carboxylic acid group DNA microarrays- is a collection of microscopic DNA spots, commonly representing single genes, arrayed on a solid surface by covalent attachment to a chemical matrix. DNA arrays are different from other types of microarray only in that they either measure DNA or use DNA as part of its detection system. Qualitative or quantitative measurements with DNA microarrays utilize the selective nature of DNA-DNA or DNA-RNA hybridization under high-stringency conditions and fluorophore-based detection BUN- The blood urea nitrogen (BUN) test is a measure of the amount of nitrogen in the blood that comes from urea This article is related to nitrogen metabolism that we learned in class. The biosynthetic pathways of amino acids and nucleotides share a requirement for nitrogen. The molecular nitrogen in the atmosphere is unavailable to most organisms until it is reduced. Fixation takes place in certain bacteria. The nitrogen cycle includes the formation of ammonia by the bacterial fixation previously noted of N2. The fixation of N2 as NH3 is done by the nitrogenase complex, which requires ATP. The reduced nitrogen is incorporated first into amino acids and then in other biomolecules including nucleotides. Glutamate and glutamine are the nitrogen donors. This article is also related to pathways of amino acid degradation. Leucine catabolism yields acetyl CoA and acetoacetyl Co-A.

Leucine- an essential amino acid (pubmed) KEGG links:

Metacyc links: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=LEUSYN-PWY http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=LEU-DEG2-PWY http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-5075 http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-5076 Review Article: Biomarkers, Metabonomics, and Drug Development: Can Inborn Errors of Metabolism Help Understanding Drug Toxicity? http://www.aapsj.org/articles/aapsj0903/aapsj0903031/aapsj0903031.pdf Drug discovery and development has been rapidly expanding due to new technologies and advancements. This review article talks primarily about the role of metabonomics and its use in the drug development process and to facilitate the transition from preclinical to clinical applications. Investigators analyzed the knowledge gap between pharmaceutical companies and pediatric hospitals since there has been metabonomic applications already applied to screen and treat new born neonates who are born with inborn errors of metabolism. Inborn errors of metabolism disorders in humans have been linked to defects in enzymes catalyzing amino acids (other enzymes are also discussed catalyzing carbohydrates, fatty acids, nucleic acid, and urea cycle.) Amino acid metabolism disorders include phenylketonuria where phenylalanine hydroxylase is the defective enzyme, Tyrosinemia 1 where Fumarylacetoacetate hydrolase is the defective enzyme, Tyrosinemia 2 (Tyrosine aminotransferase), Urea cycle disorder (Arginosuccinate lysate), Maple syrup urine disease (Branched chain alpha- ketoacid dehydrogenase), homocystinuria (Cystathionine synthase), and alkaptonuria (homogentisic oxidase.) The available metabonomics biomarkers from the inborn errors of metabolism diseases should facilitate toxicologists characterize the mechanisms of drug induced toxicities and it is predicted in the review that clinical chemistry will be replaced by metabonomics. Hypoglycemia- lower than normal level of glucose (sugar) in the blood. Bilirubin- is a yellow breakdown product of normal heme catabolism. Its levels are elevated in certain diseases and it is responsible for the yellow colour of bruises and the brown colour of feces. Metabolic acidosis- is a process which if unchecked leads to acidemia (i.e. blood pH is low (less than 7.35) due to increased production of H+ by the body or the inability of the body to form bicarbonate (HCO3-) in the kidney. Sitosterolemia- is a rare autosomal recessively inherited lipid metabolic disorder. It is characterized by hyperabsorption and decreased biliary excretion of dietary sterols leading to hypercholesterolemia, tendon and tuberous xanthomas, premature development of atherosclerosis, and abnormal hematologic and liver function test results. Glaucoma- is a group of diseases of the optic nerve involving loss of retinal ganglion cells in a characteristic pattern of optic neuropathy. Staphyloma- A protrusion of any part of the globe of the eye; as, a staphyloma of the cornea. One way this article is related to our class discussions is through the of pathways of amino acid degradation. Many amino acids are neurotransmitters or precursors or antagonists of neurotransmitters. Genetic defects of amino acid metabolism can cause defective neural development and mental retardation and in most cases a specific intermediate accumulates. Both phenylketonuria and alkaptonuria were highlighted in our class discussions. Phenylketonuria is caused by the accumulation of phenylalanine hydroxylase, which is the first enzyme involved in the phenylalanine pathway. Phenylketonuria was one of the first inheritable metabolic defects discovered. Alkaptonuria is caused by the defective enzyme homogentistate dioxygenase. This is less severe than phenylketonuria but large amounts of homogentisate are excreted and black urine results upon oxidation. Arthritis is a concern with people who suffer from alkaptonuria.

homogentistate dioxygenase

Phenylalanine KEGG links:

Metacyc links: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=TYRFUMCAT-PWY http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PHENYLALANINE-DEG1-PWY

Peer Reviewed Article: Flexibility in energy metabolism supports hypoxia tolerance in Drosophila flight muscle: metabolomic and computational systems analysis

http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1865581&blobtype=pdf

The fruitfly is potential genetic model for studying hypoxia adaptation; however the metabolic source for intense hypoxia tolerance is not well understood in flies. Understanding cellular hypoxia adaptation is important in designing treatments for injuries caused by ischemia-repulsion, stroke, and myocardial infarction. Cell damage during hypoxia is generally caused by decreased pH, altered calcium concentrations, an increasing osmotic pressure, and damage to the mitochondrian which all influence decreased ATP. Metabolic characteristics were generated and it was shown that accumulation of lactate, alanine, and acetate may be major products of anaerobic fly metabolism. A model was built to show ATP producing pathways and then adaptation to hypoxia was analyzed in silico. Investigators concluded that the ability to convert pyruvate to acetate, alanine, and acetate might provide some hypoxia tolerance by improving the ATP/proton ratia and its glucose use.

Hypoxia- is a pathological condition in which the body as a whole (generalised hypoxia) or region of the body (tissue hypoxia) is deprived of adequate oxygen supply.

ischemia-reperfusion- Functional, metabolic, or structural changes, including necrosis, in ischemic tissues thought to result from reperfusion to ischemic areas of the tissue. Ischemia - A decrease in the blood supply to a bodily organ, tissue, or part caused by constriction or obstruction of the blood vessels.

in silico- is an expression used to mean "performed on computer or via computer simulation."

ANOVA- one way analysis of variance- is a collection of statistical models, and their associated procedures, in which the observed variance is partitioned into components due to different explanatory variables.

TCA cycle- this stands for the citric acid cycle.

Alanine is produced during hypoxia by transamination to pyruvate from another amino acid. In class we talked about alanine aminotransferase. In muscle and some other tissues that degrade amino acids for fuel, amino groups are collected in the form of glutamate by transamination. Glutamate is then converted to glutamine and transported to the liver or alternatively, it can be transferred to pyruvate by using alanin amino transferase. Alanine travels to the liver and in the cytosol of hepatocytes, alanine aminotransferase carries the amino group from alanine to alpha ketogluturate to form pyruvate and glutamate. This process is used to transport ammonia from the skeletal muscles to the liver.

Alanine- a non-essential amino acid

KEGG links:

Metacyc links: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=ALANINE-VALINESYN-PWY

http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=ALANINE-SYN2-PWY

http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY0-1021

http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=ALADEG-PWY

http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=ALACAT2-PWY

http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=ALANINE-DEG3-PWY http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY1-2 Retrieved from "http://en.wikibooks.org/wiki/Talk:Metabolomics/Metabolites/Amino_Acids" Views

AMINO ACIDS Metabolic engineering of a genetic selection system with tunable stringency. (http://www.pnas.org/cgi/reprint/104/35/13907)

Summary: The main focus of this paper is the fine-tuning of the biosynthesis of small molecules by engineering metabolic flux within cells. In this case, it was achieved through provision of a regulable enzyme leading it down another parallel biopathway. Using this approach, the optimization of an in vivo selection system for the conversion of prephenate to phenylpyruvate (a step in the synthesis of phenylalanine) was achieved.

Terms: Metabolic Flux – the rate at which a certain metabolite is produced during a bioprocess.

Auxotrophy – the inability of an organism to synthesize a particular organic compound required for its growth.

Prototrophy - not requiring specific nutritional substances for normal metabolism and reproduction and not differing from the wild type in nutritional requirements.

Prephenate Dehydrogatase – catalyzes the conversion of prephenate to phenylpyruvate.

Site-directed Mutagenesis – The development of a mutation at a specific site that was targeted for the mutation.

Relevance: We have been studying how glycolysis and gluconeogenesis can be regulated in the cell, and this provides an alternate way to regulate a metabolic process and its flux by redirecting a specific metabolite down a parallel pathway.

Articles and Web Pages for Review and Inclusion
Peer-Reviewed Article #1:

Predicting metabolic biomarkers of human inborn errors of metabolism

Molecular Systems Biology 5 Article number: 263 Published online: 28 April 2009

Reviewer: Joseph B.

Main Focus
Using a computational model to predict biomarkers from gene knockouts.

New Terms

 * boundary metabolite: a metabolite that is known to be taken up or secreted between the intracellular and extracellular compartments. (source: http://)
 * exchange interval: a possible range of uptake and secretion flukes of a given boundary exchange interval (source: http://)
 * flux variable analysis: CBM method that computes the exchange interval. (source: http://)
 * biomarker: boundary metabolite concentration in biofluid. (source: http://)
 * precision: fraction of the predicted biomarkers that are correct when comparing the predicted accuracy with a random model. (source: http://)
 * recall: fraction of the biomarkers that are correctly predicted when comparing the predicted accuracy with a random model. (source: http://)
 * mass-balance: an application of conservation of mass; accounts for material entering and leaving a system. (source: http://)
 * Constraint Based Modeling: the computational model used by the authors to predict the metabolic phenotypes of gene knockouts in microorganisms. (source: http://)
 * regulatory constraint: accounting for gene regulation (in the constraing based model). (source: http://)
 * Metabolic network: a database for metabolic pathways and diseases. (source: http://)

Summary
The authors describe the accuracy and potential usefulness of using a computational model to predict biomarkers of diseases caused by gene knockouts. In order to evaluate the model, they compared their predicted biomarkers with the known biomarkers published on the OMIM and HMDB databases. When the constraint based model was used for red blood cell metabolism, the authors found that the model predictions were accurate with a precision of .73 and a recall of .40. However, in some cases the CBM leads to false predictions. Such is true for argeninemia. The model fails to predict the elevated extracellular concentrations of arginine because of alternative arginine catabolic pathways. The alternative pathways cannot compensate for the main catabolic pathway due to low expression of certain enzymes involved in those reactions. Hence the CBM lacks a regulatory constraint. Some other reasons why this computational model gives false predictions is because of the simplifying assumptions in the model and the incompleteness of the metabolic network. Overall, the authors site that the probability of the model to predict correct biomarkers ranges from 6-15.8 times higher than a random model. These results are encouraging and the authors hope to use this model to predict biomarkers for gene knockouts that have not yet been documented to cause disease. Some needed improvements are integrating the model with larger human metabolic networks and integrating metabolic regulation with the model to improve the predictions.

Relevance to a Traditional Metabolism Course
This article discusses an analytic approach to predicting differing concentrations of metabolites resulting from gene mutations that lead to protein malfunction in pathways such as amino acid catabolism, glycolysis and the pentose phosphate pathway. A constraint based model was employed along with the OMIM and HMDB databases to measure the accuracy of predicted biomarkers. The future of the computational model described can possibly add a new dimension to the human genome project by predicting biomarkers of gene disruptions before the mutation has been identified.

title: Metabolomics/Metabolites/Amino Acids


text: User talk:71.165.21.213

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

title: User talk:71.165.21.213


text: User talk:24.131.216.39

title: User talk:24.131.216.39


text:
Metabolomics/Metabolites/Nucleotides

Back to Previous Chapter: Introduction to Metabolomics Next chapter: Hormones Go to first page: Carbohydrates Go back to: Amino Acids

Guanosine Monophosphate (GMP)
Researchers have utilized chemical proteomics in order to identify the novel target molecules of cyclic guanosine monophosphate (cGMP), with the intention of obtaining a better understanding of the cGMP pathway. Experiments were conducted on cGMP that had been immobilized onto agarose beads with linkers directed at three different cGMP positions. The employment of agarose beads allowed for maximum accessibility of cGMP to its binding partners. Using a pull-down assay with the beads as bait on tissue lysates, nine proteins were identified via Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) mass spectrometry. A portion of these proteins consisted of previously identified cGMP targets, which included cGMP-dependent protein kinase and cGMP-stimulated phosphodiesterase. Evidence from competition binding assays determined that protein interactions occurred by specific binding of cGMP into the binding pockets of its target proteins, and were also highly stereo-specific to cGMP against other nucleotides. MAPK1 was confirmed as one of the identified target proteins via immunoblotting with an anti-MAPK1 antibody. Further evidence was provided by observing the stimulation of mitogen-activated protein kinase 1 signaling by membrane-permeable cGMP, in the treated cells. Further research in the field of proteomics is expected to yield more efficient tools and techniques applicable to the identification and analysis of bioactive molecules and their target proteins.

cGMP binding protein isolation revealed that the brain tissue samples had a higher concentration of cGMP binding proteins than did the heart or liver tissue samples. This observation implied that there is a more diverse cGMP signal transduction role in the brain than in the heart or liver. In addition, an increase of MAPK phosphorylation was discovered via immunoblotting with an anti-phospho MAPK antibody. Researchers have determined that direct interactions occur between cGMP binding proteins and cGMP. The binding proteins are also strongly believed to be regulated by the concentration of cellular cGMP. Further research in the field of proteomics is expected to yield more efficient tools and techniques applicable to the identification and analysis of bioactive molecules and their target proteins.

References:

http://www.jbmb.or.kr/fulltext/jbmb/view.php?vol=36&page=299

Web Resources:

Resource #1: Nucleotide Metabolism

http://www.med.unibs.it/~marchesi/nucmetab.html

Main Focus: This resource provides a very comprehensive overview of multiple aspects of nucleotide metabolism. These include biosynthesis, catabolism, salvage pathways, and regulation as well as clinical significance of both purine and pyrimidine nucleotides. Regulation of deoxyribonucleotides (dNTP’s) and interconversion of nucleotides are also discussed. An advantage to this website is that mechanisms are displayed pictorially to make it easier to follow and understand the movement of electrons, bonds, charge, molecules and substituents in these complicated pathways.

New Terms: Endonucleases = degrade DNA and RNA at internal sites producing oligonucleotides Phosphodiesterases = digest oligonucleotides from the ends inward yielding free nucleosides Nucleoside phosphorylases = hydrolyze bases from nucleosides yielding ribose 1- phosphate and free bases PRPP synthetase = requires energy in the form of ATP to generate PRPP (5-phospho--D-ribosyl-1-pyrophosphate), an activated sugar PRPP = 5-phospho--D-ribosyl-1-pyrophosphate, activated sugar Inosine 5’-monophosphate (IMP) = first fully formed purine nucleotide Hypoxanthine = purine base Feedback inhibition = inhibition of an allosteric enzyme at the beginning of a metabolic sequence by the end product of the sequence Purine nucleotide cycle = synthesis of AMP from IMP and salvage of IMP via AMP catabolism causes deamination of aspartate to fumarate Tetrahydrofolate (THF) = carries formyl moieties in the form of N10-formyl-THF Uric acid = product of catabolism of purine nucleotides, insolube substance, excreted in urine as sodium urate crystals Salvage pathway = series of steps in which nucleotides are synthesized from purine bases and nucleosides Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) = enzyme involved in purine metabolism, more specifically the salvage pathway for hypoxanthine and guanine Ribonucleotide reductase = catalyzes conversion of ribonucleotides to deoxyribonucleotides (dNTP’s) von Gierke’s disease = glycogen storage disease I, basic defect in glucose 6-phosphatase, excessive uric acid production Carbamoyl phosphate = rids body of excess nitrogen in pyrimidine synthesis and urea cycle CTP synthase = aminates UTP to form CTP Aspartate transcarbamoylase (ATCase) = rate limiting enzyme of pyrimidine nucleotide biosynthesis Suicide substrates = class of molecules used to inhibit thymidylate synthase, irreversibly inhibit the enzyme(includes 5-fluorouracil and 5-fluorodeoxyuridine) 5-fluorodeoxyuridylate (FdUMP) = drug metabolite, which inhibits thymidylate synthase Anaplerotic reaction = an enzyme-catalyzed reaction that can replenish the supply of intermediates in the citric acid cycle Thioredoxin reductase = enzyme which reduces thioredoxin Glutathione reductase = enzyme which reduces glutathione disulfide (GSSG) to the sulfhydryl form (GSH)

Connections: When analyzing the mechanism for purine nucleotide biosynthesis, there are many common metabolic features present, which we’ve discussed throughout the quarter. Purine nucleotides are built upon a sugar. In the first step, catalyzed by glutamine-PRPP amidotransferase, glutamine acts as a source of ammonia and PPi (inorganic pyrophosphate) is released. The release of this PPi can lead to its cleavage to form two inorganic phosphates. The cleavage of this phosphoanhydride bond provides energy to drive reactions forward. In the steps two, four and five, ATP, an activated molecule is used for energy. In the third and ninth step, tetrahydrofolate, a cofactor, acts to perform 1-carbon transfers at intermediate oxidation levels. Glutamine is used again in the fourth step as a source of ammonia. Step six is a carboxylation reaction, and it’s very unusual that the cofactor biotin is not utilized. Most other carboxylation reactions are biotin dependent. The fumarate produced in step eight can be used to replenish citric acid cycle intermediates, meaning that purine nucleotide synthesis acts as an anaplerotic reaction.

Resource #2: Targets of Natural Compounds Vs. Targets of Chemotherapy Drugs

http://www.e-articles.info/e/a/title/Targets-of-Natural-Compounds-VS-Targets-of-Chemotherapy-Drugs/

Main Focus: Cancer cells that receive a high throughput of proliferation signals keep dividing uncontrollably, but if not bombarded with these signals will enter apoptosis. This resource discusses the differences between what natural compounds target and what chemotherapy drugs target in order to reduce the flow of information to a cell leading to cell proliferation, in order to prevent cancer. For the most part, chemotherapy drugs target DNA and more specifically the structure of nucleotides and the integrity of them within DNA as well as enzymes that participate in the synthesis phase such as DNA polymerase and topoisomerase in order to prevent completion of the cell cycle. One way of inhibiting cancer cell proliferation is to inhibit the production of nucleotides. This is done by chemotherapy drugs. For example, methotrexate is a drug that inhibits folate activity, while folate is required for the synthesis of some bases. Another drug is called cytarabine and it inhibits DNA polymerase by substituting the sugar arabinose for ribose during DNA synthesis. This is effective because nucleotides are only functional if they contain ribose. Other chemotherapy drugs such as cyclophosphamide and mitomycin alter the nucleotides within DNA, damaging the DNA and inhibiting its replication and transcription. Intercalating drugs such as bleomycin insert themselves into the DNA between adjacent base pairs causing free radical damage.

New Terms: Proliferation = rapid growth or production of cells through multiplication of parts Apoptosis = form of programmed cell death Cancer = disease in which cells grow and divide aggressively without limits Chemotherapy = treatment of disease by chemicals that kill cells Antimetabolites = chemicals with a similar structure to the chemical required to carry out normal biochemical reactions, interferes with DNA production and cell division, chemotherapy drugs Folate = B vitamin, required for synthesis of some bases Methotrexate = chemotherapy drug which inhibits folate activity Topoisomerase = enzyme which unwinds DNA so DNA replication and gene transcription can take place

Connections: In lecture, we learned how chemotherapeutic agents act by inhibiting enzymes in the nucleotide biosynthesis pathway because cancer cells have a greater requirement for nucleotides as DNA precursors. Glutamine analogs such as azaserine and acivicin inhibit glutamine amidotransferase, making it impossible for glutamine to act as a nitrogen donor. We discussed how thymidylate synthase and dihydrofolate reductase were good targets for chemotherapeutic agents and are inhibited by fluorouracil and methotrexate respectively. Although cancer cells grow fast, they’re weak and if distressed can be defeated.

Resource #3: Purine and Pyrimidine Metabolism Disorders http://www.merck.com/mmpe/sec19/ch296/ch296i.html

Main Focus: Under normal conditions, nucleotides act as components of cellular energy systems, signaling, and DNA and RNA production. However, when an enzyme has a defect causing it to malfunction leading to accumulation of compounds in blood, urine, or tissues, this can result in diseased states which can severely affect people and their everyday lives. This resource discusses several disorders of nucleotide metabolism; including disorders of purine salvage, purine nucleotide synthesis, purine catabolism, and pyrimidine metabolism. Not only is the nature of several deficiencies discussed, but diagnosis as well as possible treatment and diet adjustments are mentioned. Lesch-Nyhan syndrome is a disorder of purine salvage and results from a deficiency in the hypoxanthine-guanine phosphoribosyl transferase (HPRT) enzyme which normally aids in salvage pathway for hypoxanthine and guanine leading to uric acid overproduction. Adenosine deaminase deficiency is a disorder of purine catabolism, which results in accumulation of adenosine due to inability of enzyme to convert adenosine and deoxyadenosine to inosine and deoxyinosine. High levels of adenosine causes an increase in levels of ATP and dATP, and the latter inhibits ribonucleotide reductase causing underproduction of the other deoxribunucleotides compromising DNA replication. Immune cells are sensitive to this and this deficiency causes Severe Combined Immunodeficiency. This can be treated by stem cell transplantation and enzyme replacement. Xanthine oxidase deficiency is also a disorder of purine catabolism in which there is a buildup of xanthine due to the incapability of the enzyme to produce uric acid from xanthine and hypoxanthine. This deficiency causes painful xanthine stones and blood in urine.

New Terms: Lesch – Nyhan syndrome = x-linked recessive disorder caused by deficiency of hypoxanthine-guanine phosphoribosyl transferase (HPRT) Hypoxanthine-guanine phosphoribosyl transferase = enzyme involved in purine metabolism, more specifically the salvage pathway for hypoxanthine and guanine Hyperuricemia = presence of high levels of uric acid in the blood Gout = disease caused by deposits of uric acid crystals in the cartilage and tendons leading to inflammation and excruciating pain Allopurinol = xanthine oxidase inhibitor, prevents conversion of hypoxanthine to uric acid, can also prevent oxidation of adenine Adenine phosphoribosyltransferase deficiency = rare autosomal recessive disorder, results in inability to salvage adenine for purine synthesis Phosphoribosylpyrophosphate synthetase superactivity = x-linked recessive disorder, causes purine overproduction Adenylosuccinase deficiency = autosomal recessive disorder, causes mental retardation, autistic behavior, and seizures Myoadenylate deaminase deficiency = inability for the enzyme to convert AMP to inosine and ammonia Myalgia = muscle pain Adenosine deaminase deficiency = inability of enzyme to convert adenosine and deoxyadenosine to inosine and deoxyinosine Purine nucleoside phosphorylase deficiency = rare, autosomal recessive deficiency, immunodeficiency with severe T-cell dysfunction and neurologic symptoms Xanthine oxidase deficiency = inability of enzyme to produce uric acid from xanthine and hypoxanthine leading to precipitation of xanthine in the urine Uridine monophosphate synthase deficiency = causes accumulation of orotic acid

Connections: In class we’ve emphasized the importance of regulation of metabolic pathways and how if there is a disruption or defect in this regulation it can lead to diseased states. Often times enzymes can have or acquire mutations, which prevent them from performing properly. This often leads to accumulation of intermediates in blood or urine, which can lead to diseases. We briefly discussed phenylketonuria (PKU) in class, a genetic defect of amino acid metabolism in which there is a defect in the enzyme phenylalanine hydroxylase (involved in first step of catabolic pathway for phenylalanine). Under normal conditions, the enzyme would convert phenylalanine to tyrosine, but the genetic defect results in accumulation of phenylalanine. PKU can be detected at infancy and impairs normal development of brain causing severe mental retardation. Alkaptonuria (AKU) is also an inheritable disease of phenylalanine catabolism. The defective enzyme is homogentisate 1,2-dioxygenase, normally it would convert homogentisate to maleyloacetoacetate, but the diseased state leads to accumulation of homogentisate which is excreted in urine and turns black upon oxidation. These examples of a lack of regulation caused by enzyme defects in amino acid metabolism are very similar to those of nucleotide metabolism mentioned in this resource. For instance, Lesch-Nyhan syndrome involves accumulation of uric acid in blood due to a defective enzyme, adenosine deaminase deficiency involves accumulation of adenosine and compromise of DNA replication due to a defective enzyme, and xanthine oxidase deficiency involves precipitation of xanthine in urine causing stones due to a defective enzyme. In class, we also discussed various ways in which enzyme activity can be altered and these include allosteric regulation, association with a regulatory protein, sequestration or compartmentation, or covalent modification such as phosphorylation.

Peer-Reviewed Free Full Text Articles:

Article #1: Enhanced Activity of the Purine Nucleotide Cycle of the Exercising Muscle in Patients with Hyperthyroidism

http://jcem.endojournals.org/cgi/content/full/86/5/2205

Main Focus: This article discusses a study in which the purine nucleotide cycle is examined as a possible mechanism for causing muscular weakness in patients with hyperthyroidism. A semiischemic forearm exercise test was performed in order to measure metabolites related to the purine nucleotide cycle, ammonia and hypoxanthine, and metabolites of glycolysis, lactate and pyruvate. The levels of the previously mentioned metabolites were measure in the blood at rest, immediately after exercise, and 10 minutes later for four different groups. The four groups examined were; healthy volunteers (control group), patients with untreated thyrotoxic Graves’ disease (untreated group), patients with Graves’ disease treated with methimazole (treated group), and patients in remission (remission group). This study found that lactate and pyruvate levels were elevated in patients with hyperthyroidism after exercise indicating that muscle ATP content decreases, enhancing glycolysis and glycogenolysis. Hypoxanthine and ammonia levels were elevated in patients with hyperthyroidism after exercise, indicating acceleration of the purine nucleotide cycle in hyperthyroidism patients. Hypoxanthine levels were only slightly elevated in patients with hyperthyroidism in comparison to healthy controls and the hypoxanthine production didn’t parallel that of ammonia, which it should have, but the article suggests multiple possibilites to explain this. This study provides evidence of accelerated glycolysis and purine nucleotide catabolism, performed by purine nucleotide cycle, in hyperthyroidism.

New Terms: Myopathy = neuromuscular disease, muscle fibers don’t function resulting in muscular weakness Hyperthyroidism = overactive thyroid gland, result of excessive thyroid hormone production Grave’s disease = thyroid disorder caused by antibody mediated auto-immune reaction Deamination = removal of amine group Semiischemic forearm exercise test = induction of a rapid decrease in ATP content of muscle, stimulating the purine nucleotide cycle Muscle hypotonia = condition of low muscle tone Amyotrophy = progressive wasting of muscle tissue Thyrotoxicosis = condition resulting from excessive concentrations of thyroid hormones in the body Glycolysis = catabolic pathway by which a molecule of glucose is broken down into two molecules of pyruvate Glycogenolysis = catabolism of glycogen by removing glucose monomers Hypokalemia = low concentration of potassium in blood Hypophosphatemia = abnormally low level of phosphate in blood due to electrolyte imbalance

Connections: This article emphasizes ATP balance in skeletal muscles and how the purine nucleotide cycle contributes to this. During exercise, glycogen is consumed and ATP consumption by skeletal muscles increases to a rate faster than that of ATP synthesis. This is when the nucleotide cycle comes in and tries to replenish the insufficient ATP supply. In class we’ve discussed how organisms have regulatory mechanisms that allow them to maintain homeostasis, a steady state. Keeping a constant supply and concentration of ATP can aid in maintaining homeostasis. Reactions are often controlled by the ATP:ADP ratio. Many reactions involve ATP, therefore, if the concentration of ATP were to dramatically drop, many pathways and reactions in our bodies, which act to keep us alive, would not be capable of being carried out and our cells would most likely die. It seems that the same concept can be applied to the purine nucleotide cycle and how it tries to achieve energy balance in the muscles. It was even suggested in the article that the acceleration of purine catabolism in hyperthyroidism is a regulatory mechanism set in place to avoid rapid collapse of ATP balance.

Article #2: Hypoxanthine-guanine phosophoribosyltransferase (HPRT) deficiency: Lesch-Nyhan syndrome

http://www.pubmedcentral.nih.gov/picrender.fcgi?tool=pmcentrez&artid=2234399&blobtype=pdf

Main Focus: Lesch-Nyhan syndrome is an inborn error of metabolism and is due to complete deficiency of hypoxanthine-guanine phosphoribosyltransferase (HPRT) activity. This review article provides detailed descriptions of the nature of this disease, common symptoms (including motor disorder, cognitive impairment, and compulsive self-injurious behavior), classification with basis of severity of neurological manifestations and enzyme defect, mechanisms that contribute to the uric acid overproduction caused by the enzyme deficiency, methods for diagnosing patients as well as treatment and prognosis of the disease. The most pertinent of these topics are the mechanisms that contribute to this disease. The deficiency in the HPRT enzyme is the root cause of the uric acid overproduction in children diagnosed with Lesch-Nyhan syndrome and there are multiple mechanisms to explain this. Hypoxanthine and guanine are purine bases from which inosine monophosphate (IMP) and guanosine monophosphate (GMP) are synthesized respectively in the salvage pathway catalyzed by HPRT. A co-substrate, 5’-phosphoribosyl-1-pyrophosphate, (PRPP) is utilized in the reaction. The inherited defect in the HPRT enzyme leads to accumulation of hypoxanthine and guanine. These two purine bases are converted to uric acid in a reaction catalyzed by xanthine oxidase. Since the PRPP co-substrate is not needed in the salvage pathway, it’s available for PRPP amidotransferase, an enzyme which is part of the de novo synthesis of purine nucleotides. Consequently, purine synthesis increases, but since the feedback inhibitors of the de novo synthesis pathway, IMP and GMP, aren’t being synthesized, this pathway runs unregulated resulting in an increase of purine nucleotides.

New Terms: Hypoxanthine-guanine phosphoribosyl transferase = enzyme involved in purine metabolism, more specifically the salvage pathway for hypoxanthine and guanine Lesch – Nyhan syndrome = x-linked recessive disorder caused by deficiency of hypoxanthine-guanine phosphoribosyl transferase (HPRT) Dystonia = abnormal tone of any tissue caused by prolonged repetitive muscle contractions Choreoathetosis = nervous disturbance marked by involuntary and uncontrollable movement of body Ballismus = condition involving twisting, shaking, and jerking motions Aetiology = study of causes or origins Feedback Inhibition = inhibition of an allosteric enzyme at the beginning of a metabolic sequence by the end product of the sequence Amniocentesis = surgical procedure to obtain amniotic cells in order to perform tests in order to detect genetic abnormalities Allopurinol = xanthine oxidase inhibitor that blocks conversion of xanthine and hypoxanthine into uric acid Xanthine lithiasis = accumulation of xanthine stones in body due to administration of too high of a dose of allopurinol Benzodiazepine = family of minor tranquilizers that act against anxiety and convulsions and produce muscle relaxation and sedation Baclofen = used as a reactant of skeletal muscle often used in treating spasticity

Connections: This review article discusses mechanisms leading to overproduction of uric acid in patients diagnosed with Lesch-Nyhan syndrome. This places importance on regulation of metabolic pathways, and illustrates how, a defective enzyme or lack of regulation can cause accumulation of an intermediate, in this case guanine and hypoxanthine, resulting in a diseased state. There was also a term mentioned in the article that we’ve discussed in class multiple times regarding regulation, and this is feedback inhibition. Feedback inhibition is the inhibition of an allosteric enzyme at the beginning of a metabolic sequence by the end product of the sequence. There are actually three feedback mechanisms involved in regulating the overall rate of de novo purine synthesis, one of which was briefly mentioned in this article. The reaction involving the conversion of PRPP to 5-Phosphoribosylamine by transfer of an amino group is inhibited by the end products of the pathway, IMP, AMP, and GMP. A second control mechanism is when excess GMP inhibits xanthylate synthesis from inosate. The third mechanism, that GTP is required to convert IMP to AMP and ATP is required to convert IMP to GMP considered to be a reciprocal substrate relationship. Feedback inhibition is used a tool for regulation in many pathways including glycolysis, gluconeogenesis, and the citric acid cycle. It was mentioned that the co-substrate referred to as PRPP plays a role in the purine salvage pathway. Throughout this entire course we’ve focused on properties of activated intermediates. This co-substrate, PRPP, is an activated intermediate because of the phosphate group and the presence of the phosphoanhydride bond, which can be cleaved to generate energy. Once an amino group donated by glutamine is attached to PRPP, 5-phosphoribosylamine is formed and the purine ring is built upon the structure of this sugar.

Article #3: Anaplerotic processes in human skeletal muscle during brief dynamic exercise

http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1159539&blobtype=pdf

Main Focus: Although under normal conditions, anaplerotic reactions, which replenish tricarboxylic acid cycle intermediates, and cataplerotic reactions, which remove cycle intermediates, counteract each other mediating the constant concentration of tricarboxylic acid cycle intermediates (TCAIs), this does not seem to be the case during contraction of mammalian skeletal muscle. Under these circumstances the concentration of some TCAIs increase. The main focus of this article is to determine which mechanism plays the largest role and is most influential in the increase in TCAIs at the onset of exercise in human skeletal muscle. Possible mechanisms include the purine nucleotide cycle and reactions catalyzed by alanine aminotransferase, pyruvate carboxylase, glutamate dehydrogenase, malic enzyme, and phosphoenolpyruvate carboxykinase. The knee extensor exercise model was utilized in order to determine and compare concentrations of metabolites. The mechanism proposed to be responsible for the net increase in pool size of TCAIs during contraction was the purine nucleotide cycle which consists of three reactions. Throughout the cycle, GTP is consumed, aspartate is deaminated and NH3 along with fumarate are produced. When a competitive inhibitor of aspartate, hadacidin, was used to block the purine nucleotide cycle in the hindlimb muscle of a rat there was a 53% reduction in accumulation of malate and fumarate compared to control animals that weren’t treated with this inhibitor. Although this seems like strong evidence, there is controversy because of two reasons. There was no measurable change in aspartate concentrations during exercise which is required to reanimate IMP and produce fumarate, and there was only a small increase in NH3 formation. This indicates that the purine nucleotide cycle contributed only a minor amount to the increase in TCAI pool size. Instead, the alanine aminotransferase reaction may be the major anaplerotic reaction causing this increase in TCAI pool size in initial muscle contraction of humans.

New Terms: Tricarboxylic acid = organic acid containing three carboxyl groups Tricarboxylic acid cycle (TCA cycle) = cyclic system of enzymatic reactions for the oxidation of acetyl residues to carbon dioxide (also known as citric acid cycle or Krebs cycle) Carboxylation = introduction of a carboxyl group into a compound Decarboxylation = removal of carboxyl group from chemical compound, usually replacing it with hydrogen Cataplerotic reactions = reactions involved in disposal of tricarboxylic acid cycle (TCA cycle) (taken from http://www.jbc.org/cgi/content/full/277/34/30409) Anaplerotic reactions = series of enzymatic reactions that replenish the pools of metabolic intermediates in the tricarboxylic acid cycle (TCA cycle)(taken from http://www.jbc.org/cgi/content/full/277/34/30409)

Connections: In our study of the citric acid cycle we learned that the intermediates are drawn off to serve as biosynthetic precursors. For instance, ?-Ketoglutarate and oxaloacetate act as precursors of aspartate and glutamate, which are amino acids, and through these amino acids are used to build other amino acids and nucleotides. Oxaloacetate can be converted to glucose in gluconeogenesis and succinyl-CoA acts in synthesis of the porphyrin ring of heme groups. Citrate can also be siphoned off to synthesize fatty acids and sterols. When these intermediates are removed, they are replenished by anaplerotic reactions in order to keep the concentrations of the citric acid cycle intermediates constant. The anaplerotic reaction that is most essential to the proper functioning of the citric acid cycle is the carboxylation of pyruvate to form oxaloacetate catalyzed by pyruvate carboxylase, because the citric acid cycle requires oxaloacetate in order to function. The production of fumarate from aspartate in the purine nucleotide cycle also acts as an anaplerotic reaction to replenish an intermediate of the citric acid cycle.

MetaCyc Pathways:

Purine nucleotides de novo biosynthesis I http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=DENOVOPURINE2-PWY

Purine nucleotides de novo biosynthesis II http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-841

de novo biosynthesis of pyrimidine ribonucleotides http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY0-162

Pyrimidine ribonucleotides interconversion http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-5687

de novo biosynthesis of pyrimidine deoxyribonucleotides http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY0-166

Salvage pathways of purine and pyrimidine nucleotides http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=P1-PWY

Salvage pathways of pyrimidine ribonucleotides http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY0-163

Salvage pathways of pyrimidine deoxyribonucleotides http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY0-181

Articles and Web Pages for Review and Inclusion
Peer-Reviewed Article #1:

'UPLC-ESI-TOFMS-Based Metabolomics and Gene Expression Dynamics Inspector Self-Organizing Metabolomic Maps as Tools for Understanding the Cellular Response to Ionizing Radiation

'''Anal. Chem., 2008, 80 (3), pp 665–674'''

Main Focus

 * Identify the main focus of the resource. Possible answers include specific organisms, database design, intergration of information, but there are many more possibilities as well.

New Terms

 * New Term 1: Definition. (source: http://)
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 * New Term 4: Definition. (source: http://)
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Summary

 * Enter your article summary here. Please note that the punctuation is critical at the start (and sometimes at the end) of each entry. It should be 300-500 words. What are the main points of the article? What questions were they trying to answer? Did they find a clear answer? If so, what was it? If not, what did they find or what ideas are in tension in their findings?

Relevance to a Traditional Metabolism Course

 * Enter a 100-150 word description of how the material in this article connects to a traditional metabolism course. Does the article relate to particular pathways (e.g., glycolysis, the citric acid cycle, steroid synthesis, etc.) or to regulatory mechanisms, energetics, location, integration of pathways? Does it talk about new analytical approaches or ideas? Does the article show connections to the human genome project (or other genome projects)?

title: Metabolomics/Metabolites/Nucleotides


text:
More C++ Idioms/Barton-Nackman trick

= Barton-Nackman trick =

Intent
Support overloaded operators without relying on namespaces or function template overload resolution.

Also Known As
The inventors originally referred to it as Restricted Template Expansion, though this term has never been widely used.

Motivation
John Barton and Lee Nackman first published this idiom in 1994 in order to work around limitations of the C++ implementations available at the time. Though it is no longer necessary for its original purpose, the current standard retains support for it.

At the time Barton and Nackman originally developed the idiom, C++ did not support overloading of function templates and many implementations still didn't support namespaces. This caused problems when defining operator overloads for class templates. Consider the following class:

The most natural way to define the equality operator is as a non-member function at namespace scope (and since compilers at the time didn't support namespaces, therefore at global scope). Defining  as a non-member function means that the two arguments are treated symmetrically, which doesn't happen if one argument is a   pointer to the object. Such an equality operator might look like this:

However, since function templates couldn't be overloaded at the time, and since putting the function in its own namespace wouldn't work on all platforms, this would mean that only one class could have such an equality operator. Doing the same thing for a second type would cause an ambiguity.

Solution and Sample Code
The solution works by defining an operator in the class as a friend function:

Instantiating the template now causes a non-template function to be injected into global scope with the argument types being concrete, fixed types. This non-template function can be selected through function overload resolution the same way as any other non-template function.

The implementation can be generalised by providing the friend functions as part of a base class that is inherited from via the Curiously Recurring Template Pattern:

Known Uses

 * Boost.Operators library

Related Idioms

 * Curiously Recurring Template Pattern

title: More C++ Idioms/Barton-Nackman trick


text:
Iranian History/The Islamic Conquest of Iran

The advent of Islam in the 7th century AD made a decisive change in the course of Iran's history. Apart from introducing a new religion into the country, it changed the nation's culture, language, script and civilization beyond recognition. The two centuries of Arab rule in Iran had a larger impact on its culture and mindset than had the invasions of the Romans or Alexander prior to it. It created a new Persian Muslim civilization and identity introducing a vast array of new theological and cultural concepts into the existing Iranian society.

Early Interaction between Muslims and Sassanid Iran
Most of the modern-day Arabia had been conquered by Khusro Anushirvan and added to the Empire during his military campaign against Yemen. The Prophet of Islam, Muhammad was born in 570 during the reign of Khusro Anushirvan and was hence, a subject of the Sassanid Empire. Later, in his life, he is said to have expressed a sense of pride and good fortune in being born during the reign of an enlightened monarch as Khusro Anushirvan.

Muhammad's Letter to Khusro Perviz
Muslim missionaries claim that Prophet Muhammad sent Khusro Perviz the Sassanian monarch a messenger with a letter exhorting him to convert to Islam. Khusro Perviz reportedly tore them apart and contemptuously dismissed the messenger at which Prophet Muhammad is said to have remarked: "May his kingdom tear apart". Devout Muslims believe that this was the reason that Khusro was imprisoned and killed later and that the realm of the Imperial Sassanids itself crumbled to pieces.

Salman Al Farsi
Moid Salman or Salman Al Farsi (Salman the Persian) was born Ruzbeh in a small village called Jayyan in the province of Isfahan in Sassanid Iran during the reign of Khusro Anushirvan. His father was the dehkan (an army officer and petty landlord) of the village. His family descended from a line of Sassanian nobles and from an early age, Ruzbeh was inducted into the Magian faith and tended to the keep of the holy fire.

Very early in his life, he came under the influence of some Iranian Christians and converted to Christianity. Under the advice of these people, he made a pilgrimage to Syria upon hearing that Syria was the home of the Christian faith. On his journey to Syria, he was captured and sold into slavery. Transported to Mecca, he made a chance acquaintance with Prophet Muhammad and was convinced that Muhammad was the Messiah. He immediately converted to Islam and became one of the Companions of the Prophet who released him from slavery. He travelled along with him and fought in the Battle of the Ditch against the Meccans and the capture of Damascus and in the battles of Al Qadesiyah and Nehavend against the Persian Sassanian Empire. He died at the age of 88 and was buried near Ctesiphon according to some accounts, in the year 35 of Hijra, or 655 AD.

The Story of Princess Shahrbanu
According to sources, Shahrbanu was one of the three daughters of Yazdegerd III, the last Sassanian Emperor who was captured along with her sisters following the Islamic conquest of Persia. The sources relate that she was brought in person before the Caliph Umar who decreed that she be condemned to a life of servitude but was rescued by Ali, whose son Hussain, she married. Sources also relate that she was present at the Battle of Karbala in 680 in which Hussain ibn Ali was killed. Shahrbanu reportedly fled to the mountains of Rayy pursued by the troops of the Caliphate. But sources say that as the enemy caught up with her, the mountain split open and swallowed her up. There is a shrine built at the place where she was reportedly swallowed by the mountains which is an important place of worship for Shiites.

Western academic historians have cast serious doubts on the legend. According to the Encyclopedia Iranica:

"Neither do any of the scholars of ancient history that have chronicled, at times with great attention to detail, the invasion of Persia by Muslim troops and the fate of the last Sasanian sovereign and her family, establish any relationship between the wife of Imam Hussain and one of the daughters of Yazdgerd III"

Earlier sources such as Ibn Sad and Ebn Qotayba describe Husayn's wife as a slave, originally from Sindh, and make no reference to her being a princess. The first scholar to explicitly describe her as being of the Persian royal family was the 9th Century Arab philologist Mobarrad.

Battle of Chains
This was not the first conflict between the newborn Rashidun Caliphate and the Imperial Sassanid Empire. The confrontation was the result of a series of incursions made into Persian territory by the Arabs. The battle was fought in modern-day Kuwait in the year 633. The Caliphate forces were commanded by Khalid ibn Walid while the Sassanian army was commanded by Hormuz. The Sassanian soldiers linked themselves with chains to prevent the Arab cavalry from breaking through. This gave the battle the name 'Battle of the Chains'.

In the lead up to the battle, Hormuz challenged Khalid to a duel and was slain. The Persian troops fell upon the Arab army but were routed and forced to retreat. They were heavy casualties on the Persian side.

Battle of the River
A second battle was fought between the forces of the Caliphate and the Sassanid Empire in Mesapotamia (modern-day Iraq) in 633. The Persians were led by Karinz while the forces of the Caliphate were led by Khalid. The Persians were defeated once again.

Battle of Walaja
Following the defeat at the Battle of the Chains and the Battle of the River, the Sassanian Emperor Yazdegerd III sent two large armies under Andarzagar and Bahman respectively to fight the Arabs near the town of Walaja to the west of the Euphrates in Iraq. Khalid adopted the tactic of double-envelopment first practised by Hannibal against the Romans in the Punic Wars. Khalid came under vigorous Persian assault and was forced to retreat but the Persians were surprised by two bodies of the Arab army which attacked from the rear. After a hotly contested battle, the Persians were defeated and slaughtered in large numbers. Andarzgar fled from the battlefield and escaped into the Arabian desert but died of thirst soon afterwards. It was a resounding win for the Arabs as the Persian troops numbered 30,000-50,000 men and the Arabs just 15,000. The Battle of Walaja was also one of the longest and fiercest battles fought by the Rashidun Caliphate, prior to Qadesiyah and Nehavend.

Battle of Ullais
The defeated Sassanian troops under Bahman and their Christian Arab auxilaries who had escaped the battlefield retreated across the Euphrates and gave battle to the pursuing Arabs at a place called Ullais. The Sassanian troops were heavily reinforced by troops from Ctesiphon under Jaban. The Christian Arab contingent was led by Abdul Aswad. The combined army numbered artound 70,000 compared to the Muslim army of 15,000. The battle was fierce and raged on for many days. At length, the Arabs won the upper hand and the remaining Persian soldiers were cut to pieces. The residents of Ullais were compelled to pay jizya and act as spies for the Muslims.

Battle of Al Hira
Soon after the conquest of Ullais, the forces of the Caliphate proceeded further eastward and gave battle at Al Hira, the capital of the now defunct Lakhimid kingdom. In May 633, Khalid attacked the fortress-city. The Lakhimid soldiers responded by hurling projectiles. But at length, the Lakhimids surredered and consented to pay jizya. With the victory at Al Hira, the conquest of Iraq was complete.

Battle of Al Anbar
Al Anbar or Perisabor or Firuz Shapur is a town in Iraq. It was built by the Sassanian king Shapur I. In 633, Khalid attacked the fortress of Anbar which was defended by a large Persian army commanded by Shirazad. The Battle of Al Anbar is often known as the "Action of the Eye" as the Muslim archers targetted the eyes of the defending Persian soldiers.The battle resulted in one more victory for the forces of the Caliphate.

Battle of Ein-ul-Tamr
Following the successful siege of the fortress of Al Anbar, Khalid attacked the frontier post of Ein-ul-Tamr to the west of Anbar. Ein-ul-Tamr was garrisoned by a body of Sassanians and their Arab Christian auxiliaries commanded by one Aqqa ibn Qais ibn Bashir an Arab Christian. The Arabs successfully conquered the town and captured Aqqa.

Battle of Daumat-ul-Jandal
Daumat-ul-Jandal was one of the large commercial towns of Arabia, widely known for its rich and much-frequented market. It was also an important communication centre, a meeting point of routes from Central Arabia, Iraq and Syria. The city was defended by a garrison of Christian Arabs.

In August 633, Abu Bakr sent an army under Ayadh bin Ghanam to capture the city. But the siege lasted many days without any result. Ayadh appealed to Khalid for help. Khalid obliged and made way for Daumat-ul-Jandal. The battle lasted many days but the Christian Arabs were overwhelmed and slaughtered in large numbers.

Battle of Muzayyah
When Khalid ibn Walid left from Ain-ul-Tamr to Daumat ul jandal for the help of Ayadh, the Persian court believed that Khalid had returned to Arabia with a large part of his army. So Bahman was sent with an army of 15,000-20,000 men to fight the Arabs and drive them out of Iraq. There were two other Persian armies waiting at Saniyy and Zubail to support Bahman. In the last week of September 633, Khalid arrived at Hira from Daumat ul Jandal to fight the Persians. Khalid responded by dividing his army into three divisions and sent two of them against the Persians at Saniyy and Zubail while he himself fought Bahman's army. Khalid attacked the Persians initially but was unsuccessful. So he resorted to strategem and ordered a three pronged attacked by the Arabs on the encamped Persian troops at night by the three different divisions from three separate directions. Thousands were slaughtered but most of the Persians managed to escape in the darkness of the night. The Christian Arab armies at Saniyy and Zumail were vanquished in very much the same way.

Battle of Firaz
In January 634, the Persians allied with the Christian Arabs and Byzantine Empire and launched an attack on the Arabs. But in the battle which was consequently fought at Firaz the combined army was defeated and annihilated by the Arab troops led by Khalid. This decisive victory resulted in the Arab conquest of Iraq and was the prelude to the victory at Qadesiyah.

Battle of the Bridge
In October 634, emboldened by their early successes, the Arabs under Abu Ubaid launched an attack across the Sassanian frontier. The Sassanian general Bahman immediately took position near Kufa on the Euphrates. Intending to give battle, Abu Ubaid marched at the head of 10,000 troops and crossed the Euphrates on November 28, 634 by preparing a bridge of boats.

When the battle began, the Arab cavalry advanced but were opposed by the Persian war elephants. The Arabs soon lost ground and were forced to flee. Abu Ubaid was killed in the melee and the Arabs were forced to retreat. When Muthanna gathered his soldiers on the other side of the Euphrates only 3,000 Arab soldiers regrouped. The rest had either been killed or had fled the battlefield. This was the last Persian victory against the Arabs prior to the defeat of Yazdegerd in 636 and 642.

Preparations
During the last few battles when Khalid was absent from Iraq, the Persians under their general Rostam sought to re-establish Persian authority by seething discontent among the inhabitants of the provinces along the western frontiers of the Islamic Caliphate.

The Persians administered a crushing defeat on the Arabs in the Battle of the Bridge, but internal dissention and discontent foiled their dreams of recovering lost territory. The Arabs made a splendid recovery during this period as reinforcements arrived from Arabia. Muthanna gave battle on the canal Al Boweib and succeeded in defeating them. The beaten army recrossed the Euphrates, and returned to Ctesiphon without suffering further losses. But the conquest of Iraq by the Arabs was complete and the whole of the Sassanian Empire was open to the invaders.

The Battle
In the year 636, the Persians made an extraordinary effort to recover lost territory. They dispatched an army of 60,000 under the command of the able and experienced Rostam Farrokhzad. The army crossed the Euphrates without much difficulty and entered the territory known as Sawad which was retaken with ease. The Arabs were driven back and gave battle at a place called Qadesiyah or Kadesia. They were lead by the great genera Sa'ad ibn Abi Waqas since Muthanna had passed away.

Rostam divided the Persian army into three division: the first under himself which comprised around 20,000 troops, the second and third under Jalenus and Bendsuwan respectively. Rostam himself took position at the centre while positioning his lieutenants on his right and left respectively. The Arab army was, meanwhile, made of 36,000 troops commanded by Khalid in the absence of Sa'ad who  was injured.

The Arab cavalry charged first but was repulsed by the line of elephants which guarded the Sassanian rear. The Persians advanced pushing the Arabs back seeking to repeat the tactics of the Battle of the Bridge against the Arabs who were driven close to annihilation. However, the archers under Asim came to the rescue of their cavalry by shooting arrows at the Persian elephants. The day was, however, won by the Persians. The Arabs 500 men on the day.

On the second day, with fresh reinforcements from Syria, the Arabs attacked the Persians once again. The Persians charged with their elephants but were repulsed. There were light skirmishes and individual duels in which two of the leading Persian commanders Bendsuwan and Bahman Djulhadjib lost their lives. The Arabs conspired to capture Rostam himself but the latter was saved. The Persians had lost 10,000 in killed and wounded on the second day, the Arabs no more than 2000.

On the third day, the Persians reequipped their elephants to launch an all-out attack. But the horses of the Arabs had grown accustomed to the giant beasts. Morever, the Arabs adopted a new tactic to fight the elephant corps, which was to a fair degree, successful. They concentrated on injuring the elephants in their eyes or proboscis and this was fairly successful as when two of the elephants on the forefront were shot at by the Arabs the others too panicked and fled. The Arab cavalry pursued the fleeing Persians across the El Atik stream but the elephant corps was saved by the timely interposition of the Persian foot and horse regiments. The day came to an end without any of the sides taking a decisive advantage.

On the night of the third day, as the Persians slept soundly in their camps, they were attacked by two Arab contingents under Toleicha and Amr' killing a number of Persian soldiers.

On the fourth day, the Persians fought the Arabs with their backs to the east. This seemed to be a right move as they held the advantage for the early part of the day. However, about noon, all of a sudden a sandstorm broke out from the west blowing sand into the eyes of the Persians. The Arabs, who had their backs to the eye of the storm, were relatively unaffected by the violent gusts ofn wind. Hormuzan, Satrap of Susiana, and Firuzan, fell back. Rostam dismounted his throne to protect himself from the sandstorm and took refuge amongst his mules. However, he was spotted by the Arab general Hillal who pursued the fleeing commander across the El Atiq stream and slaying him, mounted his throne shouting aloud:

"By the lord of the Ka'aba, I have killed Rustam"

There was a general panic and the bulk of the Persian troops tried to flee by crossing the El Atik stream but were cut to pieces by the Arab assailants. As many as 10,000 Persian troops perished in the El Atik stream, either by drowning or to the sword of the Arabs. A few of them stood their ground firmly and fought to the last while others managed to reach the other bank safely. The fourth day of battle resulted in a decisive victory for the Arabs; 36,000 Arab troops had annihilated a Sassanian army of 60,000

Aftermath
The retreat of the Persian army was conducted by Jalenus. Sa'ad sent three bodies of troops across the Atik who came up with this division and slaughtered it to a man. The remainder of the troops sought refuge within the walls of Ctesiphon.

Fall of Ctesiphon
In 637, a large Arab army comprising of 20,000 men crossed the Euphrates and penetrated into Sassanian territory once more. Yazdegerd III hurriedly vacated Ctesiphon for the safety of the mountains of Northern Iran. He barely had the time to package his personal belongings and a very small quantity of the treasures accumulated by his ancestors. Sa'ad meanwhile overran Mesapotamia and the Euphrates and entered the abandoned Persian capital of Ctesiphon finding the city undefended.

Ctesiphon was a coveted prize and the city was plundered in its entirety. Later, when the plunder was distributed equally amongst the 60,000 soldiers whom Sa'ad commanded, each soldier's share was found to amount to 12,000 dirhems. This had a huge impact on the empire's exchequer and it became imminent that the end of the state was near.

At the same time, the Arabs encountered such greatness and grandeur which was beyond all their imagination and eagerly grabbed all that they could lay their hands upon. Gibson describes the plunder in his usual anti-Islamic, offensive manner.

After the conquest of Ctesiphon, Hisham and El Qaqa were sent with 12,000 men against the fugitive Yazdegerd. The Sassanian general Mihran confronted him at the town of Jalula near Holwan with an army of 100,000 men. Jalula was taken by the Arabs with great slaughter -- over hundred thousand Persians were reported to have perished in the onslaught. The town was plundered andeach soldier was given a share of 10,000 dirhems.

After the defeat at Jalula, Yazdegerd withdrew from Holwan to the town of Rayy. Holwan was taken in a few days along with Shirwan, Mahsabadan and Tikrit.

In 639, the Arabs launched campaigns against Susa and Persia proper. The former was successful and they successfully captured the cioty of Ahvaz. However, the latter failed to achieve its objectives. In 640, Hormuzan the Persian satrap of Susa allied with Shahrek, the satrap of Persia proper and attacked the Arabs unawares. However,the rebellion was subdued and Hormuzan captured and enslaved. He was transported to Medina where he converted to Islam.

Battle of Nehavend
In 641, Sa'ad was recalled by the Caliph Umar who replaced him with Ammar Ibn Yaser. Taking advantage of this change, Yazdegerd conspired to recover his lost throne and sent envoys all over the provinces of Media, Azerbaijan, Khorasan, Gorgan, Tabaristan, Merv, Bactria, Sistan, Kirman and Persia proper (Pars). Within a few months, he was able to accumulate an army of 50,000 men. The Arabs deputed Noman, the Governor of Ahvaz, to repel a possible Sassanid invasion and he encamped near Nehavend with 30,000 men. Here, the troops faced each other for around two months, one of the two sides willinjg to initiate hostilities. At length, by a clever st5rategem, Noman, set afloat the rumor that the Caliph Umar was dead. Firouzan, who commanded the Sassanid troops, regarding it as an opportune moment to strike the encamped Arab troops, attacked them. The battle raged on for many days but at length, the Persians had to flee. Noman was killed by the retreating Persian troops but this had no effect on the result of the battle. The Sassanid army was trapped in the mountain passes and slaughtered to the last man. This extinguished the Persian army. Yazdegerd fled to Merv sending emissaries to India and China for help but to no avail. He made a last stand at MKerv till he was killed in 651. Merv fell to the Arabs in a few years thereby ending the Sassanian Empire.

Completion of the Conquest
Between 641 and 651, the Arabs conquered the rest of Iran. Persia proper (Pars) fell during the reign of Caliph Uthmann, Sistan a few years later and Merv, after the death of Yazdegerd III. In 656, the Arabs completed the conquest of Greater Khorasan with successful siege of Herat. Herat formed the Eastern frontier of the Rashidun Caliphate till it was replaced by the Umayyad Caliphate. Under the Umayyads, the Arabs expanded further and conquered Zabul, Bamiyan, Baluchistan, Makran and Sindh upto the banks of the river Indus.

Consequences
The process of conquest of the Sassanian Empire began in 633 and came to an end in 656. Still, however, there existed principalities in Tabaristan (the modern day Tabriz) which never became a part of the Rashidun or the Umayyad Caliphates.

The Islamization of the conquered provinces began soon after the conquest and went on for hundreds of years. Poll tax or jizya' was imposed on non-Muslims thereby encouraging the populace to convert. The Persian language was identified with a quasi-national feeling and was prohibited by the Umayyads, its usage being substituted by Arabic. Persians were reduced to a position of slavery and subordination. The nation was plundered to the extremes to fill the coffers of Damascus.

However, Umayyad rule was brought was brought to an end by the revolt of the Abbasids. Despite the fact that it was fought for the replacement of one Arab dynasty by another, the movement itself was organized by Iranians and led by an Iranian general Abu Muslim.

Viewpoints about the Islamic Conquest of Iran
The two principal viewpoints about the Islamic invasions have been explained in detail by Professor Bernard Lewis:

"Arab Muslims conquests have been variously seen in Iran: by some as a blessing, the advent of the true faith, the end of the age of ignorance and heathenism; by others as a humiliating national defeat, the conquest and subjugation of the country by foreign invaders, and the eradication of Persian identity, religion (Zoroastrianism) and civilization. Both perceptions are of course valid, depending on one's angle of vision… Iran was indeed Islamized, but it was not Arabized. Persians remained Persians. And after an interval of silence, Iran reemerged as a separate, different and distinctive element within Islam, eventually adding a new element even to Islam itself. Culturally, politically, and most remarkable of all even religiously, the Iranian contribution to this new Islamic civilization is of immense importance. The work of Iranians can be seen in every field of cultural endeavor, including Arabic poetry, to which poets of Iranian origin composing their poems in Arabic made a very significant contribution. In a sense, Iranian Islam is a second advent of Islam itself, a new Islam sometimes referred to as Islam-i Ajam. It was this Persian Islam, rather than the original Arab Islam, that was brought to new areas and new peoples: to the Turks, first in Central Asia and then in the Middle East in the country which came to be called Turkey, and of course to India. The Ottoman Turks brought a form of Iranian civilization to the walls of Vienna."


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Muggles' Guide to Harry Potter/Major Events/Viktor Krum

Overview
Viktor Krum arrives with the delegation from Durmstrang Institute to take part in the Triwizard Tournament. He becomes attracted to Hermione, making Ron jealous, though Ron does not realize this at the time. Though Viktor is quite clearly trying to take things to the next stage with Hermione, she gently rebuffs him, and they stay pen-pals until Ron and Hermione become a couple. Viktor then suggests, in Harry's hearing, that he would like to meet Ginny. Harry tells him that Ginny is going out with someone very big who gets angry easily.

Goblet of Fire
Viktor Krum arrives for the Triwizard Tournament as part of the delegation from Durmstrang Institute. He seems to be spending significant time in the library, something that irritates Hermione because of the gaggle of giggling girls that seems to follow him around.

At the Yule Ball, we discover that Hermione has been asked to the ball by Viktor Krum. Ron is quite upset by this, saying that Hermione is "consorting with the enemy".

In the Second Task of the Triwizard Tournament, the four Champions must each retrieve something valuable to them from the bottom of the lake. The thing that is valuable to Viktor is Hermione. Having rescued Hermione, Viktor is apparently having a fairly intense conversation with her on the shore. An article that appears in Witch Weekly shortly afterwards, written by Rita Skeeter, says that Krum has invited Hermione to spend the summer with him. Hermione admits that this is true, but wonders how Rita had found out.

Viktor takes Harry aside in late May and asks him if Hermione is his girlfriend. Harry is rather surprised by this, and says no. Viktor says that Hermione is always talking about Harry, and Harry insists that it is because they are friends.

We don't see much other interaction between Viktor and Hermione, but by this time it is pretty clear that Viktor is romantically interested in Hermione.

Order of the Phoenix
While Viktor Krum does not play any particular role in this book, we see that Hermione is writing a very long letter to him as Christmas holidays approach. Hermione says that he's just a pen-pal, but Ron comments that he would like to be a lot more than that.

Half-Blood Prince
Harry and Ron catch Ginny and Dean snogging in a corridor. In the ensuing quarrel, Ginny says that Harry has snogged Cho, Hermione has snogged Viktor, and Ron is simply jealous because he doesn't have anyone to snog.

Deathly Hallows
Viktor has been invited to Bill and Fleur's wedding. Hermione is taken aback to see him there. Harry, in disguise, stops to talk with him. Viktor is looking sourly at Ron and Hermione out on the dance floor. Seeing Ginny, he asks if Harry knows her. Harry replies that she is going out with somebody large and bad-tempered. Viktor angrily asks what is the point of being famous if all the best girls are already taken?

Notable Consequences
Krum's ongoing attempts to become more than a pen-pal to Hermione eventually result in Ron's committing himself. It is entirely possible that Ron would leave his relationship with Hermione languishing if Krum had not been trying to take Hermione for himself.

It is unknown whether Krum would have attended Bill and Fleur's wedding if Hermione was not likely to be present. It is certain that she seems more surprised that he will be attending than he is at finding her there. If Krum's appearance at the wedding is a consequence of this relationship, then so also are Harry's discoveries about the identity of Gregorovitch, and the use of the symbol of the Deathly Hallows as the mark of Grindelwald.

Analysis
There is no way of knowing exactly how much has been going on between Viktor and Hermione. True, Ginny does tell Ron that Hermione and Viktor have been snogging, but this is not conclusive, as Ginny at the time is mid-quarrel with Ron, and is trying to hurt him with words. It is entirely possible that Ginny is going from what is public knowledge and expanding on it for effect. It is certainly true, as we see later, that Viktor would like to spend time snogging with Hermione; what is not so certain is whether he actually has done so. Hermione, as we see here, has clearly set her sights on Ron early in the series, and it is uncertain whether she would choose to jeopardize her relationship with Ron by being known to be snogging with Viktor.

Greater Picture
Key to the enjoyment of any piece of fiction is belief in its characters; without believable characters, one simply does not care about the story. The author had plotted out this story to cover a span of nearly seven years, in the lives of characters starting the series at age 11. Knowing that her characters were going to go through adolescence, she also chose to write their relationships as an integral part of the story, rather than simply ignoring them in favour of the main quest, as is common in heroic fiction. As Viktor is an incidental figure and off stage for much of the series, of course, we cannot get much of a feel for his character's growth; in fact, his behaviour at Bill and Fleur's wedding would indicate that he has matured very little since we first met him, three years earlier. Krum still seems to evince the belief that he is irresistible to women on account of his fame as the Bulgarian national Quidditch team Seeker. While we cannot say this shows perceptiveness on the part of the author, as many sports professionals exhibit a similar behaviour, it is certainly true that the author has managed to write this character most convincingly.


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Muggles' Guide to Harry Potter/Magic/Ancient Runes

Overview
Ancient Runes is the study of runic writing. Runes are characters designed to be scratched onto hard surfaces such as rock, and are almost entirely made up of straight lines. This subject is offered as an elective, taught in years three, four, and five; those with sufficiently high O.W.L. marks in the course can then go on to N.E.W.T.-level study in years 6 and 7.

Extended Description
We first hear mention of Ancient Runes as a course in Harry Potter and the Chamber of Secrets, around Easter. The first two years of Harry's education have been taken up with the basics: Defence Against the Dark Arts, Potions, Charms, Transfiguration, Herbology, History of Magic, and Astronomy, with Flying taking the place of Muggle physical education. As the beginning of the third year approaches, students must choose a set of electives to add to these core subjects. Hermione chooses all the available subjects, including Ancient Runes, and stays with Ancient Runes until the end of her time at Hogwarts.

Hermione makes use of her understanding of Ancient Runes in Harry Potter and the Deathly Hallows, where she is bequeathed an ancient copy of The Tales of Beedle the Bard. It is her ability to decipher these runes that allows us to hear the Tale of the Three Brothers, and so become enlightened in the nature of the Deathly Hallows.

As only Hermione takes this class, we do not see any of it. It is possible that it is taught by Bathsheba Babbling, but we never meet the professor of the course.

Analysis
The sole purpose of the introduction of this course seems to be to allow Hermione to be able to read the copy of the Tales of Beedle the Bard bequeathed to her by Professor Dumbledore. One would think that the purpose of this legacy could have been equally carried out by a version of the book written in English. However, creating of the book in runes serves two purposes. First, it indicates in no uncertain terms that the book is extremely old, being written in an alphabet no longer used. This serves, among other things, to reinforce that the tales in this edition are as close to the original as is possible. Second, it requires Hermione to spend time trying to figure out the meaning of the sigil of the Deathly Hallows as it appears over the one tale in that book, requiring that she bring Harry into her thoughts about the symbol, and thus connecting it to Grindelwald's mark, Xeno Lovegood, and the signature on one of Dumbledore's letters as reproduced in Rita Skeeter's book.

The only other place we see ancient runes is on Dumbledore's Pensieve. Though Harry notes them, we don't think Hermione ever does, and they play no part in the story except as decoration, and possibly an indication of the Pensieve's age.


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Muggles' Guide to Harry Potter/Magic/Banishing Charm

Overview
Banishing Charms are the opposite of Summoning Charms, and are used to send an object away from the caster.

Extended Description
Banishing charms are more difficult than summoning charms as you are not only impelling an object to move, but ideally you are also telling it where to move to. In Professor Flitwick's class, we see that while nearly everyone has managed to send objects away from themselves (though in the case of Neville's efforts, sometimes it is the wrong object), only the best of the students is able to send their pillows unerringly into the box where they are intended to go.

We never hear the actual invocation of the banishing charm.


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Korean/Commands

How to make command form (명령형 [命令形])of verbs

First, we must specify if we are speaking to someone who is older or higher in position than us, or to someone who is younger or lower in position. With children, we may use the less polite (verb stem + 라) form. This form is also used when someone is angry or when giving military commands.

음식을 먹으세요!

Eat your meal!

When you are asking someone politely to do something for you, use (verb stem + 어/아 주다) form:

보여 주세요!

Please show me.

주다 literally means "to give," but does not translate directly.

When we want to talk modestly about ourselves we use the (verb stem + 드리다) form instead. "드리다" also means "to give," but is an honorific verb.

책을 보여 드렸어요

I have shown the book.

title: Korean/Commands


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Iranian History/Ayatollah Khomeini and The Islamic Revolution

The Iranian Revolution (also known as the Islamic Revolution,  Persian: انقلاب اسلامی, Enghelābe Eslāmi) was the revolution that transformed Iran from a monarchy under Shah Mohammad Reza Pahlavi to an Islamic republic under Ayatollah Ruhollah Khomeini, the leader of the revolution and founder of the Islamic Republic. It has been called "the third great revolution in history," following the French and Bolshevik revolutions, and an event that "made Islamic fundamentalism a political force ... from Morocco to Malaysia."


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