User:Galemu2/Sandbox

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Wikipedia's Five Pillars[edit]

The Five Guiding Principles[edit]

  1. Wikipedia is and encyclopedia - It contains general and/or specific information on different topics
  2. Impartial Point of View - Posts must be free of bias and must be presented in a balanced manner.
  3. All articles are freely licensed to the public
  4. Interact Respectfully with fellow editors
  5. The rules of Wikipedia are flexible

Galemu2 (talk) 23:29, 17 September 2013 (UTC)


Summary Of Characteristics of Target Article[edit]

Quality wikipedia article should content verifiable information.[1]

Article content must have natural point of view, and must acknowledge all major opposing view points of the topic.[1]

Article must be free of plagiarism [2]

  1. must acknowledge sources
  2. use quotation when using exact phrases
  3. must summarize or paraphrase sourced information

A class B or better article must is one without any major problems. The six criteria’s for this class include, that article must have inline citation, must cover topic with no obvious missing information about topic, it is organized and structured, must contain grammatical errors, article is supported with appropriate images, and is presented in a legible way for mass audience. [3]


Practice Citations[edit]

Chromosome Conformation Capture (3C) assay, is used to study the spatial organization of the genome.[4] The steps for the assay involve, fixing chromosome with formaldehyde, digestion of fixed chromosome, ligating digested chromosomes under low DNA concentration, followed by PCR to analyze ligation products.[4] Formaldehyde fixing preserves interacting sites of the chromosome.[4] Additionally, 4C-seq technology combines 3C principles mentioned here with the power of high-throughput sequencing.2[5] This technique allows for analysis of all the contacts made by genome site of interest.[5] 4C can be used to identify long-range DNA interactions of individual gene loci.[5] Furthermore, the technique can be applied to identify local regulatory sequence interaction.[5]

Ribose (left) and deoxyribose (right) sugars

Unit 12[edit]

Amino acid[edit]

Further information: Amino acid and Proteinogenic amino acid
The 20 standard amino acids

Protein is a polymer that is composed from amino acids that are linked by peptide bonds. There are more than 300 amino acids found in nature of which only twenty, known as the standard amino acids, are the building blocks for protein.[6] Only green plants and most microbes are able to synthesize all of the 20 standard amino acids that are needed by all living species. Mammals are can only synthesize ten of the twenty standard amino acids. The other amino acids, valine, methionine, leucine, isoleucine, phenylalanine, lysine, threonine and tryptophan for adults and histidine, and arginine for babies are obtained through diet.[7]

Amino acid basic structure[edit]

L-amino acid

The general structure of the standard amino acids includes a primary amino group, a carboxyl group and the functional group attached to the α-carbon. The different amino acids are identified by the functional group. As a result of the three different groups attached to the α-carbon, amino acids are asymetrical molecules. For all standard amino acids, except glycine, the α-carbon is a chiral center. In the case of glycine the α-carbon has two hydrogen atoms, thus adding symmetry to this molecule. All the amino acids, found in life, except proline, have the L-isoform conformation. Proline has a functional group on the α-carbon that forms a ring with the amino group.[6]

Nitrogen source[edit]

Glutamine oxoglutarate aminotransferase and Glutamine synthetase

One major step in amino acid biosynthesis involves incorporating a nitrogen group onto the α-carbon. In cells there are two major pathways of incorporating nitrogen groups. One pathway involves the enzyme Glutamine oxoglutarate aminotransferase, or abbreviated as GOGAT, which is able to removes the amide amino group of glutamine and transfer it onto 2-oxoglutarate resulting with two glutamate molecules. In this catalysis reaction glutamine serves as the nitrogen source. The other pathway for incorporating nitrogen onto α-carbon of amino acids involves the enzyme glutamate dehydrogenase (GDH). GDH is able to transfer ammonia onto 2-oxoglutarate and form glutamate. Furthermore, the enzyme glutamine synthetase (GS) is able to transfer ammonia onto glutamate and synthesize glutamine, replenishing glutamine.[8]

Unit 14[edit]

The glutamate family of amino acids[edit]

The glutamate family of amino acids includes the amino acids that derive some if not all of their amino acids from the amino acid glutamate. This family includes glutamate itself as well as glutamine, proline, and arginine. This family also includes the amino acid Lysine, which is derived from α-ketoglutarate. [9]

Glutamate and glutamine biosynthesis is a key step in nitrogen assimilation, which is presented above. The enzymes GOGAT and GDH catalyze the nitrogen assimilation reactions.

In bacterial the enzyme Glutamate 5-kinase initiates the biosynthesis of proline by transfering a phosphate gorup form ATP onto glutamate. The next reaction is catalyzed by the enzyme Pyrroline-5-carboxylate synthase (P5CS) catalyzes the reduction of the ϒ-carboxyl group of L-glutamate 5-phosphate that result in the formation of glutamate semialdehyde. Glutamate semialdehyde spontaneously cyclize to pyrroline-5-carboxylate. Pyrroline-5-carboxylate is further reduced by the enzyme pyrroline-5-carboxylate reductase (P5CR) to yield proline amino acid. [10]

In first step arginine biosynthesis in bacteria Glutamate is acetylated by transferring the acetyl group from acetyl-CoA at the N-α position, which prevents the spontaneously cyclization. The enzyme N-acetylglutamate synthase (Glutamate N-acetyltransferase) is responsible for catalyzing the acetylation step. Subsequent steps are catalyzed by the enzymes N-acetylglutamate kinase, N-acetyl-gamma-glutamyl-phosphate reductase, and acetylornithine/succinyldiamino pimelate aminotransferase and yield the N-acetyl-L-Ornithine. The acetyl group of Acetylornithine is removed by the enzyme acetylornithinase (AO) or ornithine acetyltransferase (OAT), which yields Ornithine. The enzymes citrulline and argininosuccinate convert Ornithine to arginine. .[11]

There are two distinct lysine biosynthetic pathways, the diaminopimelic acid pathway, and the α-amionoadipate pathway, which is not present in prokaryotes. The most common of the two synthetic pathway is the diaminopimelic acid pathway and consists of seven enzymatic reactions that add carbon groups to aspartate to yield lysine.[12]

The Diaminopimelic Acid Pathway
  1. The enzyme Aspartate kinase initiates the diaminopimelic acid pathway by phosphorylating aspartate and produceing aspartyl phosphate.
  2. The enzyme Aspartate semialdehyde dehydrogenase catalyzes the NADPH-dependent reduction of aspartyl phosphate to yield aspartate semialdehyde.
  3. The enzyme dihydrodipicolinate synthase catalyzes the condensation reaction of pyruvate with aspartate semialdehyde to yield 2,3-dihydrodipicolinate
  4. The enzyme Dihydrodipicolinate reductase catalyzes the reduction of 2,3-dihydrodipicolinate by NADPH to yield Δ’-piperideine-2,6-dicarboxylate.
  5. The enzyme Tetrahydrodipicolinate acyltransferase catalyzes the acetylation reaction that result in ring opening to yield N-acetyl α-amion-ε-ketopimelate
  6. The enzyme N-Succinyl-α-amion-ε-ketopimelate-glutamate aminotransaminase catalyzes the transamination reaction that removes the Keto group of N-acetyl α-amion-ε-ketopimelate and replaces it with an amino group to yield N-succinyl-L-diaminopimelate.[13]
  7. The enzyme N-Acyldiaminopimelate deacylase catalyzes the deacylation of N-succinyl-L-diaminopimelate to yield L,L-diaminopimelate.[14]
  8. the enzyme DAP epimerase catalyzes the conversion of L,L-diaminopimelate to the meso form of L,L-diaminopimelate. [15]
  9. The enzyme DAP decarboxylase catalyzes the removal of the carboxyl group yielding L-lysine.

The serine family of amino acids[edit]

The serine family of amino acid includes Serine as well as cysteine and glycine. In addition, most microorganisms and plants obtain the sulfur for synthesizing methionine from the amino acid cysteine. Furthermore, the conversion of serine to glycine provides the carbons needed for the biosynthesis of the methionine and histidine.[9]

During Serine biosynthesis[16] the enzyme phosphoglycerate dehydrogenase catalyzes the initial reaction that oxidizes 3-phospho-D-glycerate to yield 3-phosphonooxypyruvate. [17] The following reaction catalyzed by the enzyme Phosphoserine aminotransferase transferase an amino group from glutamate onto 3-phosphonooxypyruvate to yield L-phosphoserine. [18] The final step is catalyzed by the enzyme phosphoserine phosphatase that dephosphorylates of L-phosphoserine to yield L-serine.[19]

There are two known pathways for the biosynthesis of Glycine. One pathway known as ‘glyconeogenic’ pathway is used to synthesis glycine by organisms that use ethanol and acetate as the major carbon source. The other pathway of glycine biosynthesis is known as ‘glycolytic’ pathway. This pathway converts serine synthesised from the intermediates of glycolysis to glycine. In the ‘glycolytic’ pathway the enzyme Serine hydroxymethyltransferase catalyzes the cleavage of serine to yield glycine. The enzyme transfers the cleaved carbon group of serine onto tetrahydrofolate and forms 5,10-methylene-tetrahydrofolate.[20]

Cysteine biosynthesis is a two-step reaction that involves the incorporation of inorganic sulfur. In microorganisms and plants the enzyme Serine acetyltransferase catalyzes the transfer of acetyl group from acetyl-CoA onto L-serine to yield O-acetyl-L-serine.[21] The following reaction step catalyzed by the enzyme O-acetyl serine (thiol) lyase, replaces the acetyl group of O-acetyl-L-serine with sulfide to yield cysteine.[22]

The aspartate family of amino acids[edit]

The aspartate family of amino acids includes Threonine, lysine, methionine, and isoleucine as well as aspartate. Lysine and isoleucine are considered part of the aspartate family even though part of their carbon skeleton is derived from pyruvate. In the case of methionine the methyl carbon is derived from serine and the surfer group, in most organisms, is derived from cysteine.[9]

The biosynthesis aspartate is a one step reaction that is catalyzed by a single enzyme. The enzyme aspartate aminotransferase catalyzes the transfer of an amino group from aspartate onto α-ketoglutarate to yield glutamate and oxaloacetate. (Ref.2)[23] Asparagine is synthesized by an ATP dependent addition of an amino group onto aspartate. The enzyme asparagine synthetase catalyzes addition of the nitrogen from glutamine or soluble ammonia on to aspartate to yield asparagine. (ref. 3)[24]

The Diaminopimelic acid biosynthetic pathway of lysine belongs to the aspartate family of amino acids. This pathway involves nine enzyme-catalyzed reactions that convert aspartate to lysine. [25] (ref. 4*)

The Diaminopimelic Acid Lysine Biosynthetic Pathway
  1. The enzyme aspartate kinase catalyzes the initial step in Diaminopimelic acid pathway by transferring a phosphoryl from ATP onto the carboxylate group of aspartate to yield aspartyl-β-phosphate. (ref 5)[26]
  2. The enzyme Aspartate-semialdehyde dehydrogenase catalyzes reduction reaction by dephosphorylation of aspartyl-β-phosphate to yield aspartate-β-semialdehyde. (ref. 6)[27]
  3. The enzyme Dihydrodipicolinate Synthase catalyzes the condensation reaction of aspartate-β-semialdehyde with pyruvate to yield dihydrodipicolinic acid. (ref. 7)[28]
  4. The enzyme 4-hydroxy-tetrahydrodipicolinate reductase catalyzes the reduction of dihydrodipicolinic acid to yield tetrahydrodipicolinic acid. (ref. 8)[29]
  5. The enzyme Tetrahydrodipicolinate N-Succinyltransferase catalyzes the transfer of a succinyl group from succinyl-CoA on to tetrahydrodipicolinic acid to yield N-succinyl-L-2,6-diaminoheptanedioate. (Ref. 9)[30]
  6. The enzyme N-succinyldiaminopimelate aminotransferase catalyzes the transfer of an amino group from glutamate onto N-succinyl-L-2,6-diaminoheptanedioate to yield N-succinyl-L,L-diaminopimelic acid. (ref. 10)[31]
  7. The enzyme succinyl-diaminopimelate desuccinylase catalyzes the removal of acyl group from N-succinyl-L,L-diaminopimelic acid to yield L,L-diaminopimelic acid. (Ref. 11)[32]
  8. The enzyme Diaminopimelate epimerase catalyzes the inversion of the α-carbon of L,L-diaminopimelic acid to yield meso-diaminopimelic acid. (ref. 12)[33]
  9. The enzyme Diaminopimelate decarboxylase catalyzes the final step in lysine biosynthesis that removes carbon dioxide group form meso-diaminopimelic acid to yield L-lysine. (ref. 13)[34]


Refs

  1. ^ a b Training For Student:Verifiability
  2. ^ Let's get serious about plagiarism
  3. ^ WikiProject article quality grading
  4. ^ a b c Gavrilov, A.; Eivazova, E.; Priozhkova, I.; Lipinski, M.; Razin, S.; Vassetzky, Y. (2009). Chromosome conformation capture (from 3C to 5C) and its ChIP-based modification. Methods in Molecular Biology (Clifton, N.J.). Vol. 567. pp. 171–88. doi:10.1007/978-1-60327-414-2_12. ISBN 978-1-60327-413-5. PMID 19588093.
  5. ^ a b c d Van De Werken, H. J.; De Vree, P. J.; Splinter, E.; Holwerda, S. J.; Klous, P.; De Wit, E.; De Laat, W. (2012). "4C technology: protocols and data analysis". Methods in Enzymology. 513: 89–112. doi:10.1016/B978-0-12-391938-0.00004-5. ISBN 9780123919380. PMID 22929766.
  6. ^ a b Wu, G (2009 May). "Amino acids: metabolism, functions, and nutrition". Amino Acids. 37 (1): 1–17. doi:10.1007/s00726-009-0269-0. PMID 19301095. {{cite journal}}: Check date values in: |date= (help)
  7. ^ Mousdale, David M.; Coggins, John R. (1991). "Amino Acid Synthesis". Target Sites for Herbicide Action: 29-56. doi:10.1007/978-1-4899-2433-9_2. ISBN 978-1-4899-2435-3. Retrieved 26 November 2013.{{cite journal}}: CS1 maint: date and year (link)
  8. ^ Miflin, B. J.; Lea, P. J. (1977). "Amino Acid Metabolism". Annual Review of Plant Physiology. 28: 299-329. doi:10.1146/annurev.pp.28.060177.001503. Retrieved 26 November 2013.{{cite journal}}: CS1 maint: date and year (link)
  9. ^ a b c Umbarger, HE (1978). "Amino acid biosynthesis and its regulation". Annual Review of Biochemistry. 47: 532–606. doi:10.1146/annurev.bi.47.070178.002533. PMID 354503.
  10. ^ Pérez-Arellano, I.; Carmona-Alvarez, F.; Martínez, A. I.; Rodríguez-Díaz, J.; Cervera, J. (2010 Mar). "Pyrroline-5-carboxylate synthase and proline biosynthesis: from osmotolerance to rare metabolic disease". Protein Science : A Publication of the Protein Society. 19 (3): 372–82. doi:10.1002/pro.340. PMC 2866264. PMID 20091669. {{cite journal}}: Check date values in: |date= (help)
  11. ^ Xu, Y.; Labedan, B.; Glansdorff, N. (2007 Mar). "Surprising arginine biosynthesis: a reappraisal of the enzymology and evolution of the pathway in microorganisms". Microbiology and Molecular Biology Reviews : MMBR. 71 (1): 36–47. doi:10.1128/MMBR.00032-06. PMC 1847373. PMID 17347518. {{cite journal}}: Check date values in: |date= (help)
  12. ^ Xu, H.; Andi, B.; Qian, J.; West, A. H.; Cook, P. F. (2006). "The alpha-aminoadipate pathway for lysine biosynthesis in fungi". Cell Biochemistry and Biophysics. 46 (1): 43–64. doi:10.1385/CBB:46:1:43. PMID 16943623.
  13. ^ PETERKOFSKY B; GILVARG C (1961 May). "N-Succinyl-L-diaminopimelic-glutamic transaminase". The Journal of Biological Chemistry. 236 (5): 1432–8. doi:10.1016/S0021-9258(18)64192-4. PMID 13734750. {{cite journal}}: Check date values in: |date= (help)
  14. ^ KINDLER SH; GILVARG C (1960 Dec). "N-Succinyl-L-2,6-diaminopimelic acid deacylase". The Journal of Biological Chemistry. 235: 3532–5. doi:10.1016/S0021-9258(18)64502-8. PMID 13756049. {{cite journal}}: Check date values in: |date= (help)
  15. ^ Born, T. L.; Blanchard, J. S. (1999 Oct). "Structure/function studies on enzymes in the diaminopimelate pathway of bacterial cell wall biosynthesis". Current Opinion in Chemical Biology. 3 (5): 607–13. doi:10.1016/s1367-5931(99)00016-2. PMID 10508663. {{cite journal}}: Check date values in: |date= (help)
  16. ^ "Escherichia coli K-12 substr. MG1655". serine biosynthesis. SRI International. Retrieved 12 December 2013.
  17. ^ Bell, JK (2004 Mar 30). "Multiconformational states in phosphoglycerate dehydrogenase". Biochemistry. 43 (12): 3450–8. doi:10.1021/bi035462e. PMID 15035616. {{cite journal}}: Check date values in: |date= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
  18. ^ Dubnovitsky, A. P.; Kapetaniou, E. G.; Papageorgiou, A. C. (2005 Jan). "Enzyme adaptation to alkaline pH: atomic resolution (1.08 A) structure of phosphoserine aminotransferase from Bacillus alcalophilus". Protein Science : A Publication of the Protein Society. 14 (1): 97–110. doi:10.1110/ps.041029805. PMC 2253317. PMID 15608117. {{cite journal}}: Check date values in: |date= (help)
  19. ^ Wang, W.; Kim, R.; Jancarik, J.; Yokota, H.; Kim, S. H. (2001 Jan 10). "Crystal structure of phosphoserine phosphatase from Methanococcus jannaschii, a hyperthermophile, at 1.8 A resolution". Structure (London, England : 1993). 9 (1): 65–71. doi:10.1016/s0969-2126(00)00558-x. PMID 11342136. {{cite journal}}: Check date values in: |date= (help)
  20. ^ Monschau, N.; Stahmann, K. P.; Sahm, H.; McNeil, J. B.; Bognar, A. L. (1997 May 1). "Identification of Saccharomyces cerevisiae GLY1 as a threonine aldolase: a key enzyme in glycine biosynthesis". FEMS Microbiology Letters. 150 (1): 55–60. doi:10.1111/j.1574-6968.1997.tb10349.x. PMID 9163906. {{cite journal}}: Check date values in: |date= (help)
  21. ^ Pye, V. E.; Tingey, A. P.; Robson, R. L.; Moody, P. C. (2004 Sep 24). "The structure and mechanism of serine acetyltransferase from Escherichia coli". The Journal of Biological Chemistry. 279 (39): 40729–36. doi:10.1074/jbc.M403751200. PMID 15231846. {{cite journal}}: Check date values in: |date= (help)
  22. ^ Huang, B.; Vetting, M. W.; Roderick, S. L. (2005 May). "The active site of O-acetylserine sulfhydrylase is the anchor point for bienzyme complex formation with serine acetyltransferase". Journal of Bacteriology. 187 (9): 3201–5. doi:10.1128/JB.187.9.3201-3205.2005. PMC 1082839. PMID 15838047. {{cite journal}}: Check date values in: |date= (help)
  23. ^ McPhalen, C. A.; Vincent, M. G.; Picot, D.; Jansonius, J. N.; Lesk, A. M.; Chothia, C. (1992 Sep 5). "Domain closure in mitochondrial aspartate aminotransferase". Journal of Molecular Biology. 227 (1): 197–213. doi:10.1016/0022-2836(92)90691-c. PMID 1522585. {{cite journal}}: Check date values in: |date= (help)
  24. ^ Larsen, T. M.; Boehlein, S. K.; Schuster, S. M.; Richards, N. G.; Thoden, J. B.; Holden, H. M.; Rayment, I. (1999 Dec 7). "Three-dimensional structure of Escherichia coli asparagine synthetase B: a short journey from substrate to product". Biochemistry. 38 (49): 16146–57. doi:10.1021/bi9915768. PMID 10587437. {{cite journal}}: Check date values in: |date= (help)
  25. ^ Velasco, AM (2002 Oct). "Molecular evolution of the lysine biosynthetic pathways". Journal of Molecular Evolution. 55 (4): 445–59. doi:10.1007/s00239-002-2340-2. PMID 12355264. {{cite journal}}: Check date values in: |date= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
  26. ^ Kotaka, M.; Ren, J.; Lockyer, M.; Hawkins, A. R.; Stammers, D. K. (2006 Oct 20). "Structures of R- and T-state Escherichia coli aspartokinase III. Mechanisms of the allosteric transition and inhibition by lysine". The Journal of Biological Chemistry. 281 (42): 31544–52. doi:10.1074/jbc.M605886200. PMID 16905770. {{cite journal}}: Check date values in: |date= (help)
  27. ^ Hadfield, A.; Kryger, G.; Ouyang, J.; Petsko, G. A.; Ringe, D.; Viola, R. (1999 Jun 18). "Structure of aspartate-beta-semialdehyde dehydrogenase from Escherichia coli, a key enzyme in the aspartate family of amino acid biosynthesis". Journal of Molecular Biology. 289 (4): 991–1002. doi:10.1006/jmbi.1999.2828. PMID 10369777. {{cite journal}}: Check date values in: |date= (help)
  28. ^ Mirwaldt, C.; Korndörfer, I.; Huber, R. (1995 Feb 10). "The crystal structure of dihydrodipicolinate synthase from Escherichia coli at 2.5 A resolution". Journal of Molecular Biology. 246 (1): 227–39. doi:10.1006/jmbi.1994.0078. PMID 7853400. {{cite journal}}: Check date values in: |date= (help)
  29. ^ Cirilli, M.; Zheng, R.; Scapin, G.; Blanchard, J. S. (2003 Sep 16). "The three-dimensional structures of the Mycobacterium tuberculosis dihydrodipicolinate reductase-NADH-2,6-PDC and -NADPH-2,6-PDC complexes. Structural and mutagenic analysis of relaxed nucleotide specificity". Biochemistry. 42 (36): 10644–50. doi:10.1021/bi030044v. PMID 12962488. {{cite journal}}: Check date values in: |date= (help)
  30. ^ Beaman, TW (1997 Jan 21). "Three-dimensional structure of tetrahydrodipicolinate N-succinyltransferase". Biochemistry. 36 (3): 489–94. doi:10.1021/bi962522q. PMID 9012664. {{cite journal}}: Check date values in: |date= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
  31. ^ Weyand, S (2007 Mar 30). "The three-dimensional structure of N-succinyldiaminopimelate aminotransferase from Mycobacterium tuberculosis". Journal of Molecular Biology. 367 (3): 825–38. doi:10.1016/j.jmb.2007.01.023. PMID 17292400. {{cite journal}}: Check date values in: |date= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
  32. ^ Nocek, B. P.; Gillner, D. M.; Fan, Y.; Holz, R. C.; Joachimiak, A. (2010 Apr 2). "Structural basis for catalysis by the mono- and dimetalated forms of the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase". Journal of Molecular Biology. 397 (3): 617–26. doi:10.1016/j.jmb.2010.01.062. PMC 2885003. PMID 20138056. {{cite journal}}: Check date values in: |date= (help)
  33. ^ Pillai, B.; Cherney, M.; Diaper, C. M.; Sutherland, A.; Blanchard, J. S.; Vederas, J. C.; James, M. N. (2007 Nov 23). "Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase". Biochemical and Biophysical Research Communications. 363 (3): 547–53. doi:10.1016/j.bbrc.2007.09.012. PMID 17889830. {{cite journal}}: Check date values in: |date= (help)
  34. ^ Gokulan, K.; Rupp, B.; Pavelka Jr, M. S.; Jacobs Jr, W. R.; Sacchettini, J. C. (2003 May 16). "Crystal structure of Mycobacterium tuberculosis diaminopimelate decarboxylase, an essential enzyme in bacterial lysine biosynthesis". The Journal of Biological Chemistry. 278 (20): 18588–96. doi:10.1074/jbc.M301549200. PMID 12637582. {{cite journal}}: Check date values in: |date= (help)


References[edit]

References[edit]

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