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Chemical Compound Review

CHARCOAL     methane

Synonyms: Graphite, DIAMOND, Biogas, Carbon, Norit, ...
 
 
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Disease relevance of methane

 

Psychiatry related information on methane

 

High impact information on methane

  • This was an early example of oxidative phosphorylation in intact cells, and it required methylene blue and oxygen [11].
  • In cancer cells, as opposed to normal cells, the presence of this complex brings about the recruitment of DNA methyl transferases, leading to de novo methylation [12].
  • Here we quantitatively examine genetic interactions among 26 Saccharomyces cerevisiae genes conferring resistance to the DNA-damaging agent methyl methanesulfonate (MMS), as determined by chemogenomic fitness profiling of pooled deletion strains [13].
  • We used a combination of genetic (antisense and siRNA) and pharmacologic (5-aza-2'-deoxycytidine) inhibitors of DNA methyl transferases to study the contribution of the DNMT isotypes to cancer-cell methylation [14].
  • So is the methyl group a permanent mark on histones, or can it be removed by an active process necessary for regulated gene expression [15]?
 

Chemical compound and disease context of methane

 

Biological context of methane

  • This novel function of CRT in intracellular Ca2+ signaling may be regulated by Ca2+ occupancy of the high affinity binding site [21].
  • The methyl-accepting chemotaxis proteins of E. coli: a repellent-stimulated, covalent modification, distinct from methylation [22].
  • In striking contrast to this result, Hae III acted on formaldehyde-fixed minichromosomes to yield only one of the limit-digest fragments, F, which is located in the immediate vicinity of the origin of replication, spanning nucleotides 5169 and 250 on the DNA sequence map of Reddy et al [23].
  • The anticipated effect in stargazer mutants, inappropriate Ca2+ entry, may contribute to their more pronounced seizure phenotype compared with other mouse absence models with Ca2+-channel defects [24].
  • All other restriction endonucleases tested (Mbo I, Mbo II, Hind III, Hin II+III and Hinf I), for which there are no closely spaced recognition sequences in the above mentioned regions of the SV40 genome, did not produce any significant amount of limit-digest DNA fragments from formaldehyde-fixed minichromosomes [23].
 

Anatomical context of methane

  • The fact that anti-L3T4 antibodies inhibit antigen and Con A-stimulated Ca2+ transport and IL-2 production without affecting phosphatidylinositol turnover suggests that L3T4 may play a critical role in modulating the activation of the T cell receptor-associated Ca2+ transporter in T cell stimulus-response coupling [25].
  • In Xenopus oocytes, Ca(2+)-sensitive gating of the IP3 receptor (IP3R) produces repetitive waves of Ca2+ release [21].
  • It encodes a 36-kD protein (stargazin) with structural similarity to the gamma subunit of skeletal muscle voltage-gated calcium (Ca2+) channels [24].
  • A new procedure is described which allows selective reversal of formaldehyde cross-linking in both histone-histone and histone-DNA of nuclei isolated from calf thymus [26].
  • In the male germ line, these methyl moieties are removed during spermatogenesis, and this occurs before the programmed reactivation of Xist in the testis [27].
 

Associations of methane with other chemical compounds

  • Treatment of chromatin or nuclei with formaldehyde or glutaraldehyde results in the appearance of crosslinked histones as analyzed on SDS gels [28].
  • The finding that the methyl cytosine-binding protein MeCP2 binds to histone deacetylases and represses transcription in vivo supports a model in which MeCP2 recruits histone deacetylases to methylated DNA, resulting in histone deacetylation, chromatin condensation and transcriptional silencing [29].
  • The formation of alkali-labile sites in DNA lessened its ability to accept methyl groups in vitro, but the methylation reaction was much less sensitive to thymine dimers or double-strand breaks [30].
  • We examined the role of the luminal Ca(2+)-binding protein calreticulin (CRT) in IP3-mediated Ca2+ signaling by using Ca2+ wave activity as a sensitive Ca2+ release assay [21].
  • Effect of triglyceride levels on methyl and methylene envelope line widths in proton nuclear magnetic resonance spectroscopy of human plasma [31].
 

Gene context of methane

  • Mapping Polycomb-repressed domains in the bithorax complex using in vivo formaldehyde cross-linked chromatin [32].
  • Drosophila transient receptor potential (TRP) proteins and some mammalian homologues (TRPC proteins) are thought to mediate capacitative Ca2+ entry [33].
  • Using formaldehyde-based in vivo cross-linking, we show that the Gal4p activation domain recruits SAGA to the GAL1 UAS [34].
  • AFC (a specific inhibitor of prenyl-cysteine carboxyl methyl transferases) blocked the carboxyl methylation of CDC42 in five types of insulin-secreting cells, without blocking GTPgammaS-induced translocation, implying that methylation is a consequence (not a cause) of transfer to membrane sites [35].
  • We also show that a-factor, RAS1 and RAS2 are physiological methyl-accepting substrates for this enzyme by demonstrating that these proteins are not methylated in a ste14 null mutant [36].
 

Analytical, diagnostic and therapeutic context of methane

  • It is indistinguishable from histones in chromatin by its resistance to trypsin, pattern of reactivity with 125I. and ability to form specific crosslinked products after treatment with formaldehyde [37].
  • Both acetone and formaldehyde fixation were used for the immunofluorescence tests [38].
  • Using purified 32P-labeled RNA and 125I-labeled p12 protein, complexes that are stabilized by formaldehyde-cross-linking can be readily detected after velocity gradient centrifugation [39].
  • We have elaborated a method, based on the in vivo formaldehyde cross-linking technique, that allows a substantial enrichment for Pc-interacting sites by immunoprecipitation of the cross-linked chromatin with anti-Pc antibodies [32].
  • One of them binds specifically to methylated DNA in vitro and molecular cloning reveals a similarity to a known methyl CpG-binding protein [40].

References

  1. Different base/base mismatches are corrected with different efficiencies by the methyl-directed DNA mismatch-repair system of E. coli. Kramer, B., Kramer, W., Fritz, H.J. Cell (1984) [Pubmed]
  2. Formaldehyde-induced hemolysis during chronic hemodialysis. Orringer, E.P., Mattern, W.D. N. Engl. J. Med. (1976) [Pubmed]
  3. Mismatch repair and recombination in E. coli. Jones, M., Wagner, R., Radman, M. Cell (1987) [Pubmed]
  4. Chronic renal failure in children treated with methyl CCNU. Harmon, W.E., Cohen, H.J., Schneeberger, E.E., Grupe, W.E. N. Engl. J. Med. (1979) [Pubmed]
  5. The degree of breath methane production in IBS correlates with the severity of constipation. Chatterjee, S., Park, S., Low, K., Kong, Y., Pimentel, M. Am. J. Gastroenterol. (2007) [Pubmed]
  6. A genetic test of the natal homing versus social facilitation models for green turtle migration. Meylan, A.B., Bowen, B.W., Avise, J.C. Science (1990) [Pubmed]
  7. Alcohol, low-methionine--low-folate diets, and risk of colon cancer in men. Giovannucci, E., Rimm, E.B., Ascherio, A., Stampfer, M.J., Colditz, G.A., Willett, W.C. J. Natl. Cancer Inst. (1995) [Pubmed]
  8. Methylated cytosine and the brain: a new base for neuroscience. Tucker, K.L. Neuron (2001) [Pubmed]
  9. Response to 5% carbon dioxide in children and adolescents: relationship to panic disorder in parents and anxiety disorders in subjects. Pine, D.S., Klein, R.G., Roberson-Nay, R., Mannuzza, S., Moulton, J.L., Woldehawariat, G., Guardino, M. Arch. Gen. Psychiatry (2005) [Pubmed]
  10. Prostaglandin E2 and its methyl ester reduce cataplexy in canine narcolepsy. Nishino, S., Mignot, E., Fruhstorfer, B., Dement, W.C., Hayaishi, O. Proc. Natl. Acad. Sci. U.S.A. (1989) [Pubmed]
  11. 50 years of biological research--from oxidative phosphorylation to energy requiring transport regulation. Kalckar, H.M. Annu. Rev. Biochem. (1991) [Pubmed]
  12. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Schlesinger, Y., Straussman, R., Keshet, I., Farkash, S., Hecht, M., Zimmerman, J., Eden, E., Yakhini, Z., Ben-Shushan, E., Reubinoff, B.E., Bergman, Y., Simon, I., Cedar, H. Nat. Genet. (2007) [Pubmed]
  13. Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions. Onge, R.P., Mani, R., Oh, J., Proctor, M., Fung, E., Davis, R.W., Nislow, C., Roth, F.P., Giaever, G. Nat. Genet. (2007) [Pubmed]
  14. DNMT1 is required to maintain CpG methylation and aberrant gene silencing in human cancer cells. Robert, M.F., Morin, S., Beaulieu, N., Gauthier, F., Chute, I.C., Barsalou, A., MacLeod, A.R. Nat. Genet. (2003) [Pubmed]
  15. Histone methylation: dynamic or static? Bannister, A.J., Schneider, R., Kouzarides, T. Cell (2002) [Pubmed]
  16. Bhopal tragedy's health effects. A review of methyl isocyanate toxicity. Mehta, P.S., Mehta, A.S., Mehta, S.J., Makhijani, A.B. JAMA (1990) [Pubmed]
  17. Enzymatic methyl esterification of erythrocyte membrane proteins is impaired in chronic renal failure. Evidence for high levels of the natural inhibitor S-adenosylhomocysteine. Pema, A.F., Ingrosso, D., Zappia, V., Galletti, P., Capasso, G., De Santo, N.G. J. Clin. Invest. (1993) [Pubmed]
  18. Hepatic DNA methylation and liver tumor formation in male C3H mice fed methionine- and choline-deficient diets. Shivapurkar, N., Wilson, M.J., Hoover, K.L., Mikol, Y.B., Creasia, D., Poirier, L.A. J. Natl. Cancer Inst. (1986) [Pubmed]
  19. A role for spinal nitric oxide in mediating visceral hyperalgesia in the rat. Coutinho, S.V., Gebhart, G.F. Gastroenterology (1999) [Pubmed]
  20. Dissolution of calcium bilirubinate and calcium carbonate debris remaining after methyl tert-butyl ether dissolution of cholesterol gallstones. Nelson, P.E., Moyer, T.P., Thistle, J.L. Gastroenterology (1990) [Pubmed]
  21. Calreticulin inhibits repetitive intracellular Ca2+ waves. Camacho, P., Lechleiter, J.D. Cell (1995) [Pubmed]
  22. The methyl-accepting chemotaxis proteins of E. coli: a repellent-stimulated, covalent modification, distinct from methylation. Rollins, C., Dahlquist, F.W. Cell (1981) [Pubmed]
  23. A stretch of "late" SV40 viral DNA about 400 bp long which includes the origin of replication is specifically exposed in SV40 minichromosomes. Varshavsky, A.J., Sundin, O., Bohn, M. Cell (1979) [Pubmed]
  24. The mouse stargazer gene encodes a neuronal Ca2+-channel gamma subunit. Letts, V.A., Felix, R., Biddlecome, G.H., Arikkath, J., Mahaffey, C.L., Valenzuela, A., Bartlett, F.S., Mori, Y., Campbell, K.P., Frankel, W.N. Nat. Genet. (1998) [Pubmed]
  25. The role of the L3T4 molecule in mitogen and antigen-activated signal transduction. Rosoff, P.M., Burakoff, S.J., Greenstein, J.L. Cell (1987) [Pubmed]
  26. Studies on histone organization in the nucleosome using formaldehyde as a reversible cross-linking agent. Jackson, V. Cell (1978) [Pubmed]
  27. Gamete-specific methylation correlates with imprinting of the murine Xist gene. Ariel, M., Robinson, E., McCarrey, J.R., Cedar, H. Nat. Genet. (1995) [Pubmed]
  28. Identification of specific crosslinked histones after treatment of chromatin with formaldehyde. Van Lente, F., Jackson, J.F., Weintraub, H. Cell (1975) [Pubmed]
  29. Acetylated histones are associated with FMR1 in normal but not fragile X-syndrome cells. Coffee, B., Zhang, F., Warren, S.T., Reines, D. Nat. Genet. (1999) [Pubmed]
  30. Inhibition of DNA methylation by chemical carcinogens in vitro. Wilson, V.L., Jones, P.A. Cell (1983) [Pubmed]
  31. Effect of triglyceride levels on methyl and methylene envelope line widths in proton nuclear magnetic resonance spectroscopy of human plasma. Mims, M.P., Morrisett, J.D., Mattioli, C.A., Gotto, A.M. N. Engl. J. Med. (1989) [Pubmed]
  32. Mapping Polycomb-repressed domains in the bithorax complex using in vivo formaldehyde cross-linked chromatin. Orlando, V., Paro, R. Cell (1993) [Pubmed]
  33. Direct activation of human TRPC6 and TRPC3 channels by diacylglycerol. Hofmann, T., Obukhov, A.G., Schaefer, M., Harteneck, C., Gudermann, T., Schultz, G. Nature (1999) [Pubmed]
  34. SAGA is an essential in vivo target of the yeast acidic activator Gal4p. Bhaumik, S.R., Green, M.R. Genes Dev. (2001) [Pubmed]
  35. Glucose- and GTP-dependent stimulation of the carboxyl methylation of CDC42 in rodent and human pancreatic islets and pure beta cells. Evidence for an essential role of GTP-binding proteins in nutrient-induced insulin secretion. Kowluru, A., Seavey, S.E., Li, G., Sorenson, R.L., Weinhaus, A.J., Nesher, R., Rabaglia, M.E., Vadakekalam, J., Metz, S.A. J. Clin. Invest. (1996) [Pubmed]
  36. The Saccharomyces cerevisiae STE14 gene encodes a methyltransferase that mediates C-terminal methylation of a-factor and RAS proteins. Hrycyna, C.A., Sapperstein, S.K., Clarke, S., Michaelis, S. EMBO J. (1991) [Pubmed]
  37. Histones H2a, H2b, H3, and H4 form a tetrameric complex in solutions of high salt. Weintraub, H., Palter, K., Van Lente, F. Cell (1975) [Pubmed]
  38. Immunofluorescence on avian sarcoma virus-transformed cells: localization of the src gene product. Rohrschneider, L.R. Cell (1979) [Pubmed]
  39. Specific binding of the type C viral core protein p12 with purified viral RNA. Sen, A., Sherr, C.J., Todaro, G.J. Cell (1976) [Pubmed]
  40. Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Wade, P.A., Gegonne, A., Jones, P.L., Ballestar, E., Aubry, F., Wolffe, A.P. Nat. Genet. (1999) [Pubmed]
 
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