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Sample records for methylated caffeine-silveri complex

  1. Photoluminescence properties of a cationic trinuclear zinc(II) complex with the tetradentate Schiff base ligand 6-methyl-2-({[(pyridin-2-yl)methyl]imino}methyl)phenolate.

    PubMed

    Kim, Young Inn; Song, Young Kwang; Kim, Daeyoung; Kang, Sung Kwon

    2015-10-01

    Metal complexes with Schiff base ligands have been suggested as potential phosphors in electroluminescent devices. In the title complex, tetrakis[6-methyl-2-({[(pyridin-2-yl)methyl]imino}methyl)phenolato-1:2?(8)N,N',O:O;3:2?(8)N,N',O:O]trizinc(II) hexafluoridophosphate methanol monosolvate, [Zn3(C14H13N2O)4](PF6)2·CH3OH, the Zn(II) cations adopt both six- and four-coordinate geometries involving the N and O atoms of tetradentate 6-methyl-2-({[(pyridin-2-yl)methyl]imino}methyl)phenolate ligands. Two terminal Zn(II) cations adopt distorted octahedral geometries and the central Zn(II) cation adopts a distorted tetrahedral geometry. The O atoms of the phenolate ligands bridge three Zn(II) cations, forming a dicationic trinuclear metal cluster. The title complex exhibits a strong emission at 469?nm with a quantum yield of 15.5%. PMID:26422221

  2. Author's personal copy Examination of a dicationic rhodium methyl aquo complex

    E-print Network

    Jones, William D.

    Author's personal copy Examination of a dicationic rhodium methyl aquo complex Kimberly A. Manbeck Available online 8 December 2012 Keywords: Rhodium C­H activation Bipyridine a b s t r a c t A cationic rhodium aquo methyl complex, [Rh(bpy)(CH3)(H2O)3]2+ Á2[BF4]À , was prepared and examined for activity

  3. DNA methylation in complex disease: applications in nursing research, practice, and policy.

    PubMed

    Wright, Michelle L; Ralph, Jody L; Ohm, Joyce E; Anderson, Cindy M

    2013-01-01

    DNA methylation is an epigenomic modification that is essential to normal human development and biological processes. DNA methylation patterns are heritable and dynamic throughout the life span. Environmental exposures can alter DNA methylation patterns, contributing to the development of complex disease. Identification and modulation of environmental factors influencing disease susceptibility through alterations in DNA methylation are amenable to nursing intervention and form the basis for individualized patient care. Here we describe the evidence supporting the translation of DNA methylation analyses as a tool for screening, diagnosis, and treatment of complex disease in nursing research and practice. The ethical, legal, social, and economic considerations of advances in genomics are considered as a model for epigenomic policy. We conclude that contemporary and informed nurse scientists and clinicians are uniquely poised to apply innovations in epigenomic research to clinical populations and develop appropriate policies that guide equitable and ethical use of new strategies to improve patient care. PMID:23849553

  4. Methylated Re(I) tetrazolato complexes: photophysical properties and Light Emitting Devices.

    PubMed

    Werrett, Melissa V; Huff, Gregory S; Muzzioli, Sara; Fiorini, Valentina; Zacchini, Stefano; Skelton, Brian W; Maggiore, Antonio; Malicka, Joanna M; Cocchi, Massimo; Gordon, Keith C; Stagni, Stefano; Massi, Massimiliano

    2015-05-14

    The irreversible reaction of methyl triflate with neutral Re(I) tetrazolato complexes of the type fac-[Re(diim)(CO)3(L)], where diim is either 1,10-phenanthroline or 2,2'-bipyridine and L is a para substituted 5-aryltetrazolate, yielded the corresponding cationic methylated complexes. While methylation occurred regioselectively at the N4 position of the tetrazole ring, the cationic complexes were found to exist in solution as equilibrating mixtures of linkage isomers, where the Re(i) centre was bound to either the N1 or N2 atom of the tetrazole ring. The existence of these isomers was highlighted both by NMR and X-ray crystallography studies. On the other hand, the two isomers appeared indistinguishable by IR, UV-Vis and luminescence spectroscopy. The prepared cationic complexes are all brightly phosphorescent in fluid and rigid solutions, with emission originating from triplet metal-to-ligand charge transfer excited states. Compared to their neutral precursors, which emit from admixtures of triplet metal-to-ligand and ligand-to-ligand charge transfer states, the methylated complexes exhibit blue-shifted emission characterised by elongated excited state lifetimes and increased quantum yields. The nature of the excited states for both the neutral and the methylated complexes was probed by resonance Raman spectroscopy and with the aid of time-dependent density functional theory calculations. Lastly, both the neutral and the methylated species were used as emitting phosphors in the fabrication of Organic Light Emitting Diodes and Light Emitting Electrochemical Cells. PMID:25582581

  5. INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis

    SciTech Connect

    Ausin, Israel; Greenberg, Maxim V.C.; Simanshu, Dhirendra K.; Hale, Christopher J.; Vashisht, Ajay A.; Simon, Stacey A.; Lee, Tzuu-fen; Feng, Suhua; Española, Sophia D.; Meyers, Blake C.; Wohlschlegel, James A.; Patel, Dinshaw J.; Jacobsen, Steven E.

    2012-10-23

    At least three pathways control maintenance of DNA cytosine methylation in Arabidopsis thaliana. However, the RNA-directed DNA methylation (RdDM) pathway is solely responsible for establishment of this silencing mark. We previously described INVOLVED IN DE NOVO 2 (IDN2) as being an RNA-binding RdDM component that is required for DNA methylation establishment. In this study, we describe the discovery of two partially redundant proteins that are paralogous to IDN2 and that form a stable complex with IDN2 in vivo. Null mutations in both genes, termed IDN2-LIKE 1 and IDN2-LIKE 2 (IDNL1 and IDNL2), result in a phenotype that mirrors, but does not further enhance, the idn2 mutant phenotype. Genetic analysis suggests that this complex acts in a step in the downstream portion of the RdDM pathway. We also have performed structural analysis showing that the IDN2 XS domain adopts an RNA recognition motif (RRM) fold. Finally, genome-wide DNA methylation and expression analysis confirms the placement of the IDN proteins in an RdDM pathway that affects DNA methylation and transcriptional control at many sites in the genome. Results from this study identify and describe two unique components of the RdDM machinery, adding to our understanding of DNA methylation control in the Arabidopsis genome.

  6. Characterization of DNA methylation as a function of biological complexity via dinucleotide inter-distances

    E-print Network

    Paci, Giulia; Monti, Barbara; Lenci, Marco; Esposti, Mirko Degli; Castellani, Gastone C; Remondini, Daniel

    2015-01-01

    We perform a statistical study of the distances between successive occurrencies of a given dinucleotide in the DNA sequence for a number of organisms of different complexity. Our analysis highlights peculiar features of the dinucleotide CG distribution in mammalian DNA, pointing towards a connection with the role of such dinucleotide in DNA methylation. While the CG distributions of mammals exhibit exponential tails with comparable parameters, the picture for the other organisms studied (e.g., fish, insects, bacteria and viruses) is more heterogeneous, possibly because in these organisms DNA methylation has different functional roles. Our analysis suggests that the distribution of the distances between dinucleotides CG provides useful insights in characterizing and classifying organisms in terms of methylation functionalities.

  7. Rotational Spectrum of the Methyl Salicylate-Water Complex: the Missing Conformer and the Tunneling Motions

    NASA Astrophysics Data System (ADS)

    Ghosh, Supriya; Thomas, Javix; Xu, Yunjie; Jäger, Wolfgang

    2015-06-01

    Methyl salicylate is a naturally occurring organic ester produced by wintergreen and other plants. It is also found in many over-the-counter remedies, such as muscle ache creams. The rotational spectrum of the methyl salicylate monomer was reported previously, where the most stable, dominant conformer was identified. The methyl salicylate-water complex was first studied using fluorescence-detected infrared spectroscopy; only one monohydrate conformer was found in that work. In the present study, we employed both broadband chirped and cavity based Fourier transform microwave spectroscopy to examine the competition between intra- and intermolecular hydrogen-bonding interactions and possible large amplitude motions associated with the methyl group and the water subunit. In contrast to the previous infrared study, two monohydrate conformers were identified, with carbonyl O or hydroxyl O as the hydrogen bond acceptors. Detailed analyses of the observed hyperfine structures will be presented, as well as our efforts to extend the study to larger methyl salicylate hydration clusters. S. Melandri, B. M. Giuliano, A. Maris, L. B. Favero, P. Ottaviani, B. Velino, W. Caminati, J. Phys. Chem. A. 2007, 111, 9076. A. Mitsuzuka, A. Fujii, T. Ebata, N. Mikami, J. Phys. Chem. A 1998, 102, 9779.

  8. METHYLATION OF 5' UNTRANSLATED EXON AND INTRON IN UBIL PROMOTER COMPLEX IS CORRELATED WITH TRANSCRIPTIONAL TRANSGENE SILENCING IN BARLEY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA methylation of the promoter is often associated with transcriptional silencing of transgenes. Here we report a case in which methylation of the first untranslated exon and intron in the maize ubiquitin promoter complex, but not of the promoter region itself, is correlated with differential trans...

  9. Dinuclear lanthanide(iii)/zinc(ii) complexes with methyl 2-pyridyl ketone oxime.

    PubMed

    Anastasiadis, Nikolaos C; Polyzou, Christina D; Kostakis, George E; Bekiari, Vlasoula; Lan, Yanhua; Perlepes, Spyros P; Konidaris, Konstantis F; Powell, Annie K

    2015-11-18

    The first use of methyl 2-pyridyl ketone oxime (mpkoH) in zinc(ii)/lanthanide(iii) chemistry leads to the [ZnLn(mpko)3(mpkoH)3](ClO4)2 and [ZnLn(NO3)2(mpko)3(mpkoH)] families of dinuclear Zn(II)Ln(III) complexes displaying blue-green, ligand-based photoluminescence; the Zn(II)Dy(III) compound shows field-induced relaxation of magnetization. PMID:26537457

  10. Influence of the preparation method on the physicochemical properties of indomethacin and methyl-?-cyclodextrin complexes.

    PubMed

    Rudrangi, Shashi Ravi Suman; Bhomia, Ruchir; Trivedi, Vivek; Vine, George J; Mitchell, John C; Alexander, Bruce David; Wicks, Stephen Richard

    2015-02-20

    The main objective of this study was to investigate different manufacturing processes claimed to promote inclusion complexation between indomethacin and cyclodextrins in order to enhance the apparent solubility and dissolution properties of indomethacin. Especially, the effectiveness of supercritical carbon dioxide processing for preparing solid drug-cyclodextrin inclusion complexes was investigated and compared to other preparation methods. The complexes were prepared by physical mixing, co-evaporation, freeze drying from aqueous solution, spray drying and supercritical carbon dioxide processing methods. The prepared complexes were then evaluated by scanning electron microscopy, differential scanning calorimetry, X-ray powder diffraction, solubility and dissolution studies. The method of preparation of the inclusion complexes was shown to influence the physicochemical properties of the formed complexes. Indomethacin exists in a highly crystalline solid form. Physical mixing of indomethacin and methyl-?-cyclodextrin appeared not to reduce the degree of crystallinity of the drug. The co-evaporated and freeze dried complexes had a lower degree of crystallinity than the physical mix; however the lowest degree of crystallinity was achieved in complexes prepared by spray drying and supercritical carbon dioxide processing methods. All systems based on methyl-?-cyclodextrin exhibited better dissolution properties than the drug alone. The greatest improvement in drug dissolution properties was obtained from complexes prepared using supercritical carbon dioxide processing, thereafter by spray drying, freeze drying, co-evaporation and finally by physical mixing. Supercritical carbon dioxide processing is well known as an energy efficient alternative to other pharmaceutical processes and may have application for the preparation of solid-state drug-cyclodextrin inclusion complexes. It is an effective and economic method that allows the formation of solid complexes with a high yield, without the use of organic solvents and problems associated with their residues. PMID:25579867

  11. Complexes of polyadenylic acid and the methyl esters of amino acids

    NASA Technical Reports Server (NTRS)

    Khaled, M. A.; Mulins, D. W., Jr.; Swindle, M.; Lacey, J. C., Jr.

    1983-01-01

    A study of amino acid methyl esters binding to polyadenylic acid supports the theory that the genetic code originated through weak but selective affinities between amino acids and nucleotides. NMR, insoluble complex analysis, and ultraviolet spectroscopy are used to illustrate a correlation between the hydrophybicities of A amino acids and their binding constants, which, beginning with the largest, are in the order of Phe (having nominally a hydrophobic AAA anticodon), Ile, Leu, Val and Gly (having a hydrophilic anticodon with no A). In general, the binding constants are twice the values by Reuben and Polk (1980) for monomeric AMP, which suggests that polymer amino acids are interacting with only one base. No real differences are found betwen poly A binding for free Phe, Phe methyl ester or Phe amide, except that the amide value is slightly lower.

  12. Rare-earth-metal methyl, amide, and imide complexes supported by a superbulky scorpionate ligand.

    PubMed

    Schädle, Dorothea; Maichle-Mössmer, Cäcilia; Schädle, Christoph; Anwander, Reiner

    2015-01-01

    The reaction of monomeric [(Tp(tBu,Me) )LuMe2 ] (Tp(tBu,Me) =tris(3-Me-5-tBu-pyrazolyl)borate) with primary aliphatic amines H2 NR (R=tBu, Ad=adamantyl) led to lutetium methyl primary amide complexes [(Tp(tBu,Me) )LuMe(NHR)], the solid-state structures of which were determined by XRD analyses. The mixed methyl/tetramethylaluminate compounds [(Tp(tBu,Me) )LnMe({?2 -Me}AlMe3 )] (Ln=Y, Ho) reacted selectively and in high yield with H2 NR, according to methane elimination, to afford heterobimetallic complexes: [(Tp(tBu,Me) )Ln({?2 -Me}AlMe2 )(?2 -NR)] (Ln=Y, Ho). X-ray structure analyses revealed that the monomeric alkylaluminum-supported imide complexes were isostructural, featuring bridging methyl and imido ligands. Deeper insight into the fluxional behavior in solution was gained by (1) H and (13) C?NMR spectroscopic studies at variable temperatures and (1) H-(89) Y HSQC NMR spectroscopy. Treatment of [(Tp(tBu,Me) )LnMe(AlMe4 )] with H2 NtBu gave dimethyl compounds [(Tp(tBu,Me) )LnMe2 ] as minor side products for the mid-sized metals yttrium and holmium and in high yield for the smaller lutetium. Preparative-scale amounts of complexes [(Tp(tBu,Me) )LnMe2 ] (Ln=Y, Ho, Lu) were made accessible through aluminate cleavage of [(Tp(tBu,Me) )LnMe(AlMe4 )] with N,N,N',N'-tetramethylethylenediamine (tmeda). The solid-state structures of [(Tp(tBu,Me) )HoMe(AlMe4 )] and [(Tp(tBu,Me) )HoMe2 ] were analyzed by XRD. PMID:25392940

  13. Intermediate-Valence Tautomerism in Decamethylytterbocene Complexes of Methyl-Substituted Bipyridines

    SciTech Connect

    Booth, Corwin H.; Kazhdan, Daniel; Werkema, Evan L.; Walter, Marc D.; Lukens, Wayne W.; Bauer, Eric D.; Hu, Yung-Jin; Maron, Laurent; Eisenstein, Odile; Head-Gordon, Martin; Andersen, Richard A.

    2011-01-25

    Multiconfigurational, intermediate valent ground states are established in several methyl-substituted bipyridine complexes of bispentamethylcyclopentadienylytterbium, Cp*{sub 2} Yb(Me{sub x}-bipy). In contrast to Cp*{sub 2} Yb(bipy) and other substituted-bipy complexes, the nature of both the ground state and the first excited state are altered by changing the position of the methyl or dimethyl substitutions on the bipyridine rings. In particular, certain substitutions result in multiconfigurational, intermediate valent open-shell singlet states in both the ground state and the first excited state. These conclusions are reached after consideration of single-crystal x-ray diffraction (XRD), the temperature dependence of x-ray absorption near-edge structure (XANES), extended x-ray absorption fine-structure (EXAFS), and magnetic susceptibility data, and are supported by CASSCF-MP2 calculations. These results place the various Cp*{sub 2}Yb(bipy) complexes in a new tautomeric class, that is, intermediate-valence tautomers.

  14. Metal-Alkane Complexes. Rapid Exchange of Hydrogen Atoms between Hydride and Methyl

    E-print Network

    Girolami, Gregory S.

    of the osmium(II) alkyl (C5Me5)Os(dmpm)(CH3), where dmpm is bis(dimethylphosphino)methane,2 with 1 equiv of the carbon acid H2C(SO2CF3)2 in CDFCl2 3 at -120 °C yields the osmium(IV) methyl/hydride complex [(C5Me5)Os, see: Hall, C.; Perutz, R. N. Chem. ReV. 1996, 96, 3125-3146. (2) This osmium(II) alkyl can be prepared

  15. Study on inclusion complex of cyclodextrin with methyl xanthine derivatives by fluorimetry

    NASA Astrophysics Data System (ADS)

    Wei, Yan-Li; Ding, Li-Hua; Dong, Chuan; Niu, Wei-Ping; Shuang, Shao-Min

    2003-10-01

    The inclusion complexes of ?-cyclodextrin (?-CD) and HP-?-cyclodextrin (HP-?-CD) with caffeine, theophylline and theobromine were investigated by fluorimetry. Various factors affecting the formation of inclusion complexes were discussed in detail including forming time, pH effect and temperature. The results indicate that inclusion process was affected seriously by laying time and pH. The forming time of ?-CD inclusion complexes is much longer than that of HP-?-CD. The optimum pH range is about 7-12 for caffeine, 8-10 for TP, 10.5-12 for TB. The intensities of their fluorescence increase with the decreasing of temperature. Their maximum excitation wavelengths are all in the range of 280-290 nm. The emission wavelength of caffeine and theophylline are both in the range of 340-360 nm, and that of theobromine is about 325 nm. The fluorescence signals are intensified with the increasing concentration of CD. The stoichiometry of the inclusion complexes of CD with these three methyl xanthine derivatives are all 1:1 and the formation constant are all calculated.

  16. Cationic scandium methyl complexes supported by a beta-diketiminato ("Nacnac") ligand framework.

    PubMed

    Hayes, Paul G; Piers, Warren E; McDonald, Robert

    2002-03-13

    The base-free dimethyl scandium complex supported by the bulky beta-diketiminato ligand ArNC((t)Bu)CHC((t)Bu)NAr (Ar = 2,6-(i)Pr(2)C(6)H(3), 1) reacts with various equivalencies of the strong organometallic Lewis acid B(C(6)F(5))(3) to give scandium alkyl cations. With 0.5 equiv, a monocationic mu-methyl dimer (2) was observed spectroscopically. Reaction with a further 0.5 equiv of borane gives the monomeric methyl cation 3, which was fully characterized, including via X-ray crystallography. This compound is fluxional on the NMR time scale via a "ligand flip" mechanism. Reaction with another equivalent of borane gives the unique dication 4, which exhibits a static structure on the NMR time scale. Dimethyl compound 1 is a highly active catalyst precursor for ethylene polymerization under borane or MAO-type activation. Activities for this group 3 metal based catalyst approach those observed for group 4 based metallocene systems. PMID:11878964

  17. Gas Phase Conformations and Methyl Internal Rotation for 2-PHENYLETHYL Methyl Ether and its Argon Van Der Waals Complex from Fourier Transform Microwave Spectroscopy

    NASA Astrophysics Data System (ADS)

    Gurusinghe, Ranil M.; Tubergen, Michael

    2015-06-01

    A mini-cavity microwave spectrometer was used to record the rotational spectra arising from 2-phenylethyl methyl ether and its weakly bonded argon complex in the frequency range of 10.5 - 22 GHz. Rotational spectra were found for two stable conformations of the monomer: anti-anti and gauche-anti, which are 1.4 kJ mol-1 apart in energy at wB97XD/6-311++G(d,p) level. Doubled rotational transitions, arising from internal motion of the methyl group, were observed for both conformers. The program XIAM was used to fit the rotational constants, centrifugal distortion constants, and barrier to internal rotation to the measured transition frequencies of the A and E internal rotation states. The best global fit values of the rotational constants for the anti-anti conformer are A= 3799.066(3) MHz, B= 577.95180(17) MHz, C= 544.7325(3) MHz and the A state rotational constants of the gauche-anti conformer are A= 2676.1202(7) MHz, B= 760.77250(2) MHz, C= 684.78901(2) MHz. The rotational spectrum of 2-phenylethyl methyl ether - argon complex is consistent with the geometry where argon atom lies above the plane of the benzene moiety of gauche-anti conformer. Tunneling splittings were too small to resolve within experimental accuracy, likely due to an increase in three fold potential barrier when the argon complex is formed. Fitted rotational constants are A= 1061.23373(16) MHz, B= 699.81754(7) MHz, C= 518.33553(7) MHz. The lowest energy solvated ether - water complex with strong intermolecular hydrogen bonding has been identified theoretically. Progress on the assignment of the water complex will also be presented.

  18. Electrospinning of functional poly(methyl methacrylate) nanofibers containing cyclodextrin-menthol inclusion complexes

    NASA Astrophysics Data System (ADS)

    Uyar, Tamer; Nur, Yusuf; Hacaloglu, Jale; Besenbacher, Flemming

    2009-03-01

    Electrospinning of nanofibers with cyclodextrin inclusion complexes (CD-ICs) is particularly attractive since distinct properties can be obtained by combining the nanofibers with specific functions of the CD-ICs. Here we report on the electrospinning of poly(methyl methacrylate) (PMMA) nanofibers containing cyclodextrin-menthol inclusion complexes (CD-menthol-ICs). These CD-menthol-IC functionalized nanofibers were developed with the purpose of producing functional nanofibers that contain fragrances/flavors with high temperature stability, and menthol was used as a model fragrance/flavor material. The PMMA nanofibers were electrospun with CD-menthol-ICs using three type of CD: ?-CD, ?-CD, and ?-CD. Direct pyrolysis mass spectrometry (DP-MS) studies showed that the thermal evaporation of menthol occurred over a very high and a broad temperature range (100-355 °C) for PMMA/CDmenthol-IC nanowebs, demonstrating the complexation of menthol with the CD cavity and its high temperature stability. Furthermore, as the size of CD cavity increased in the order ?-CD?-CD>?-CD.

  19. Structural impact of complete CpG methylation within target DNA on specific complex formation of the inducible transcription factor Egr-1.

    PubMed

    Zandarashvili, Levani; White, Mark A; Esadze, Alexandre; Iwahara, Junji

    2015-07-01

    The inducible transcription factor Egr-1 binds specifically to 9-bp target sequences containing two CpG sites that can potentially be methylated at four cytosine bases. Although it appears that complete CpG methylation would make an unfavorable steric clash in the previous crystal structures of the complexes with unmethylated or partially methylated DNA, our affinity data suggest that DNA recognition by Egr-1 is insensitive to CpG methylation. We have determined, at a 1.4-Å resolution, the crystal structure of the Egr-1 zinc-finger complex with completely methylated target DNA. Structural comparison of the three different methylation states reveals why Egr-1 can recognize the target sequences regardless of CpG methylation. PMID:25999311

  20. Structure-function properties of amylose-oleic acid inclusion complexes grafted with poly(methyl acrylate)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Spherulites, produced by steam jet-cooking high-amylose starch and oleic acid, were grafted with methyl acrylate, both before and after removal of un-complexed amylopectin. For comparison, granular high-amylose corn starch was graft polymerized in a similar manner. The amount of grafted and ungrafte...

  1. Beta-Phosphinoethylboranes as Ambiphilic Ligands in Nickel-Methyl Complexes

    SciTech Connect

    Fischbach, Andreas; Bazinet, Patrick R.; Waterman, Rory; Tilley, T. Don

    2007-10-28

    The ambiphilic {beta}-phosphinoethylboranes Ph{sub 2}PCH{sub 2}CH{sub 2}BR{sub 2} (BR{sub 2} = BCy{sub 2} (1a), BBN (1b)), which feature a ethano spacer CH{sub 2}CH{sub 2} between the Lewis acidic boryl and Lewis basic phosphino groups, were synthesized in nearly quantitative yields via the hydroboration of vinyldiphenylphosphine. Compounds 1a and 1b were fully characterized by elemental analysis, and by NMR and IR spectroscopy. X-ray crystallographic studies of compound 1b revealed infinite helical chains of the molecules connected through P{hor_ellipsis}B donor-acceptor interactions. The ability of these ambiphilic ligands to concurrently act as donors and acceptors was highlighted by their reactions with (dmpe)NiMe{sub 2}. Zwitterionic complexes (dmpe)NiMe(Ph{sub 2}PCH{sub 2}CH{sub 2}BCy{sub 2}Me) (2a) and (dmpe)NiMe(Ph{sub 2}PCH{sub 2}CH{sub 2}[BBN]Me) (2b) were generated via the abstraction of one of the methyl groups, forming a borate, and intramolecular coordination of the phosphine moiety to the resulting cationic metal center. Compound 2b was characterized by X-ray crystallography. Furthermore, B(C{sub 6}F{sub 5}){sub 3} abstracts the methyl group of a coordinated borate ligand to generate a free, 3-coordinate borane center in [(dmpe)NiMe(1a)]{sup +}[MeB(C{sub 6}F{sub 5}){sub 3}]{sup -} (3).

  2. Carbocation ? interaction with Car Parrinello molecular dynamics: Ab initio molecular dynamics investigation of complex of methyl cation with benzene

    NASA Astrophysics Data System (ADS)

    Zheng, Fei; Sa, Rongjian; Cheng, Jiagao; Jiang, Hualiang; Shen, Jianhua

    2007-02-01

    Cation-? interaction plays an important role as a general noncovalent binding force in a wide range of systems. To examine the more stable state of carbocation-? complex, we have carried out Car-Parrinello molecular dynamics (CPMD) simulations of six models. These results are proved to be reliable from the comparison with those of investigations by ab initio calculations. Charge transfer and molecular orbital interaction are discussed to depict the interaction modes of different models. From our CPMD studies without restraints, the methyl group moves toward the side of the benzene forming a stable ?-complex. However, if the methyl group is maintained above benzene, the inter-conversions among different models of CHsbnd CH3+ complex, which are determined from ab initio optimization, are observed; and distances between the carbon of methyl group and the center of benzene range from 2.67 Å to 3.61 Å. Our results provide a dynamic process concerning the motion of methyl group above the benzene ring.

  3. ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments.

    PubMed

    Cozen, Aaron E; Quartley, Erin; Holmes, Andrew D; Hrabeta-Robinson, Eva; Phizicky, Eric M; Lowe, Todd M

    2015-09-01

    High-throughput RNA sequencing has accelerated discovery of the complex regulatory roles of small RNAs, but RNAs containing modified nucleosides may escape detection when those modifications interfere with reverse transcription during RNA-seq library preparation. Here we describe AlkB-facilitated RNA methylation sequencing (ARM-seq), which uses pretreatment with Escherichia coli AlkB to demethylate N(1)-methyladenosine (m(1)A), N(3)-methylcytidine (m(3)C) and N(1)-methylguanosine (m(1)G), all commonly found in tRNAs. Comparative methylation analysis using ARM-seq provides the first detailed, transcriptome-scale map of these modifications and reveals an abundance of previously undetected, methylated small RNAs derived from tRNAs. ARM-seq demonstrates that tRNA fragments accurately recapitulate the m(1)A modification state for well-characterized yeast tRNAs and generates new predictions for a large number of human tRNAs, including tRNA precursors and mitochondrial tRNAs. Thus, ARM-seq provides broad utility for identifying previously overlooked methyl-modified RNAs, can efficiently monitor methylation state and may reveal new roles for tRNA fragments as biomarkers or signaling molecules. PMID:26237225

  4. PRMT4 blocks myeloid differentiation by assembling a methyl-RUNX1-dependent repressor complex.

    PubMed

    Vu, Ly P; Perna, Fabiana; Wang, Lan; Voza, Francesca; Figueroa, Maria E; Tempst, Paul; Erdjument-Bromage, Hediye; Gao, Rui; Chen, Sisi; Paietta, Elisabeth; Deblasio, Tony; Melnick, Ari; Liu, Yan; Zhao, Xinyang; Nimer, Stephen D

    2013-12-26

    Defining the role of epigenetic regulators in hematopoiesis has become critically important, because recurrent mutations or aberrant expression of these genes has been identified in both myeloid and lymphoid hematological malignancies. We found that PRMT4, a type I arginine methyltransferase whose function in normal and malignant hematopoiesis is unknown, is overexpressed in acute myelogenous leukemia patient samples. Overexpression of PRMT4 blocks the myeloid differentiation of human stem/progenitor cells (HSPCs), whereas its knockdown is sufficient to induce myeloid differentiation of HSPCs. We demonstrated that PRMT4 represses the expression of miR-223 in HSPCs via the methylation of RUNX1, which triggers the assembly of a multiprotein repressor complex that includes DPF2. As part of the feedback loop, PRMT4 expression is repressed posttranscriptionally by miR-223. Depletion of PRMT4 results in differentiation of myeloid leukemia cells in vitro and their decreased proliferation in vivo. Thus, targeting PRMT4 holds potential as a novel therapy for acute myelogenous leukemia. PMID:24332853

  5. Fluorescence of 5-arylvinyl-5'-methyl-2,2'-bipyridyl ligands and their zinc complexes.

    PubMed

    Younes, Ali H; Zhang, Lu; Clark, Ronald J; Zhu, Lei

    2009-11-20

    The photophysical properties of 5-arylvinyl-5'-methyl-2,2'-bipyridyls (AVMBs, 1-9, 11) and their zinc complexes were studied. Similar 2,2'-bipyridyl-based ligands have been applied as optical sensors for metal ions and sensitizers for solar energy conversion. The goal of this investigation is to reveal the factors that determine the emission band shift and fluorescence quantum yield change of the title ligand system upon zinc binding. The outcome of this study will not only advance the fundamental understanding of the coordination-driven photophysical processes embodied in the AVMB platform but facilitate the rational design of fluorescent probes for metal ions, particularly zinc. The AVMB ligands were synthesized using the Horner-Wadsworth-Emmons reaction. AVMBs containing electron-donating aryl groups show absorption and emission in the visible region, which can be assigned to charge-transfer transitions as supported by solvent-dependency and computational studies. The binding between AVMB ligands and zinc ion in acetonitrile was studied using isothermal titration calorimetry (ITC). A multicomponent equilibrium model is suggested that explains the multiple transitions evidenced in fluorescence titration isotherms. Coordination to zinc ion stabilizes the charge-transfer excited state of an AVMB ligand with an electron-donating aryl substituent, consequently results in bathochromic shifts in both absorption and emission. However, unlike the emission band shift, the fluorescence quantum yield change upon zinc complex formation does not have an intuitive correlation with the electronic nature of the aryl group. Lifetime measurements using the Time-Correlated Single Photon Counting method enabled the determination of nonradiative and radiative decay rate constants. Both rates of an AVMB ligand decrease upon zinc binding. The collective effect gives rise to the change in fluorescence quantum yield with the apparent lack of correlation with the electronic property of the aryl group. PMID:19852467

  6. Ultraviolet spectrophotometric characterization of copper(II) complexes with imidazole N-methyl derivatives of ?-histidine in aqueous solution

    NASA Astrophysics Data System (ADS)

    Prenesti, Enrico; Berto, Silvia; Daniele, Pier Giuseppe

    2003-01-01

    In this study we considered ?-methyl- L-histidine (?-methis) and ?-methyl- L-histidine (?-methis) as ligands for copper(II) ion, in order to clarify, by means of ultraviolet (UV) spectroscopy in aqueous solution ( T=25 °C, I=0.1 M), some aspects of the co-ordination mode with respect to other ligands of a previous study in which copper(II) complexes of L-histidine, N-acetyl- L-histidine, histamine, L-histidine methyl ester or carnosine were investigated. Particularly, UV spectra (300-400 nm) were recorded on solutions at various pH values, containing each binary system Cu-L; afterwards, an UV absorption spectrum for single complexes was calculated, taking into account the chemical model previously assessed, in order to fulfil a correct spectrum-structure correlation. The problem related to the eventual superimposition of the CT shoulder (?330 nm) to copper(II) of OH - and imidazole pyridine nitrogen groups were now solved by means of a comparison of the UV spectra of dimer species formed by both ?-methis or ?-methis. Finally, copper(II) complex formation with 2,2'-bipyridine was taken into account to compare the behaviour of pyridine (from 2,2'-bipyridine) and pyridine imidazole nitrogens (from ?-methis or ?-methis) with respect to the UV charge transfer process to copper(II) ion.

  7. Synthesis, photophysical and electroluminescent properties of novel iridium (III) complexes based on 5-methyl-2-phenylbenzo[d]oxazole derivatives

    NASA Astrophysics Data System (ADS)

    Li, Xiao; Chi, Hai-Jun; Dong, Yan; Xiao, Guo-Yong; Lei, Peng; Zhang, Dong-Yu; Cui, Zheng

    2013-12-01

    A new series of phosphorescent iridium (III) complexes based on 5-methyl-2-phenylbenzo[d]oxazole derivatives as main ligands, i.e. bis(5-methyl-2- phenylbenzo[d]oxazole-N,C2?)iridium(acetylacetonate) [(mpbo)2Ir(acac)], bis(2-(4-fluorophenyl)-5-methylbenzo[d]oxazole-N,C2?)iridium(acetylacetonate) [(fmbo)2Ir(acac)] and bis(5-methyl-2-p-tolylbenzo[d]oxazole-N,C2?) iridium(acetylacetonate) [(mtbo)2Ir(acac)], were synthesized for organic light-emitting diodes (OLEDs), and their photophysical, electroluminescent properties were investigated. All complexes have high thermal stability and emit intense phosphorescence from green to yellow at room temperature with high quantum efficiencies and relatively short lifetimes. The OLED based on (fmbo)2Ir(acac) as dopant emitter showed very high luminance of 26,004 cd m-2 and luminance efficiency of 18.5 cd A-1. The evidences indicated that this series of iridium (III) complexes were potential candidates for applications in organic electroluminescent devices.

  8. DNA binding, DNA cleavage, antioxidant and cytotoxicity studies on ruthenium(II) complexes of benzaldehyde 4-methyl-3-thiosemicarbazones

    NASA Astrophysics Data System (ADS)

    Sampath, Krishnan; Sathiyaraj, Subbaiyan; Jayabalakrishnan, Chinnasamy

    2013-03-01

    Four new ruthenium(II) complexes with N(4)-methyl thiosemicarbazone ligands, (E)-2-(2-chlorobenzylidene)-N-methylhydrazinecarbothioamide (HL1) and (E)-N-methyl-2-(2-nitrobenzylidene)hydrazinecarbothioamide (HL2), were prepared and fully characterized by various spectro-analytical techniques. The Schiff bases act as bidentate, monobasic chelating ligands with S and N as the donor sites and are preferably found in the thiol form in all the complexes studied. The molecular structure of HL1 and HL2 were determined by single crystal X-ray diffraction method. DNA binding of the compounds was investigated by absorption spectroscopy which indicated that the complexes bind to DNA via intercalation. The oxidative cleavage of the complexes with CT-DNA inferred that the effects of cleavage are dose dependent. Antioxidant studies of the ligands and complexes showed the significant antioxidant activity against DPPH radical. In addition, the in vitro cytotoxicity of the ligands and complexes against MCF-7 cell line was assayed which showed higher cytotoxic activity with the lower IC50 values indicating their efficiency in killing the cancer cells even at low concentrations.

  9. DNA binding, DNA cleavage, antioxidant and cytotoxicity studies on ruthenium(II) complexes of benzaldehyde 4-methyl-3-thiosemicarbazones.

    PubMed

    Sampath, Krishnan; Sathiyaraj, Subbaiyan; Jayabalakrishnan, Chinnasamy

    2013-03-15

    Four new ruthenium(II) complexes with N(4)-methyl thiosemicarbazone ligands, (E)-2-(2-chlorobenzylidene)-N-methylhydrazinecarbothioamide (HL(1)) and (E)-N-methyl-2-(2-nitrobenzylidene)hydrazinecarbothioamide (HL(2)), were prepared and fully characterized by various spectro-analytical techniques. The Schiff bases act as bidentate, monobasic chelating ligands with S and N as the donor sites and are preferably found in the thiol form in all the complexes studied. The molecular structure of HL(1) and HL(2) were determined by single crystal X-ray diffraction method. DNA binding of the compounds was investigated by absorption spectroscopy which indicated that the complexes bind to DNA via intercalation. The oxidative cleavage of the complexes with CT-DNA inferred that the effects of cleavage are dose dependent. Antioxidant studies of the ligands and complexes showed the significant antioxidant activity against DPPH radical. In addition, the in vitro cytotoxicity of the ligands and complexes against MCF-7 cell line was assayed which showed higher cytotoxic activity with the lower IC(50) values indicating their efficiency in killing the cancer cells even at low concentrations. PMID:23376221

  10. Complexation of NpO2+ with N-methyl-iminodiacetic Acid: in Comparison with Iminodiacetic and Dipicolinic Acids

    SciTech Connect

    Tian, Guoxin; Rao, Linfeng

    2010-10-01

    Complexation of Np(V) with N-methyl-iminodiacetic acid (MIDA) in 1 M NaClO{sub 4} solution was studied with multiple techniques including potentiometry, spectrophotometry, and microcalorimetry. The 1:2 complex, NpO{sub 2}(MIDA){sub 2}{sup 3-} was identified for the first time in aqueous solution. The correlation between its optical absorption properties and symmetry was discussed, in comparison with Np(V) complexes with two structurally related nitrilo-dicarboxylic acids, iminodiacetic acid (IDA) and dipicolinic acid (DPA). The order of the binding strength (DPA > MIDA > IDA) is explained by the difference in the structural and electronic properties of the ligands. In general, the nitrilo-dicarboxylates form stronger complexes with Np(V) than oxy-dicarboxylates due to a much more favorable enthalpy of complexation.

  11. Evaluating the Identity and Diiron Core Transformations of a (?-Oxo)diiron(III) Complex Supported by Electron-Rich Tris(pyridyl-2-methyl)amine Ligands

    E-print Network

    Do, Loi Hung

    The composition of a (?-oxo)diiron(III) complex coordinated by tris[(3,5-dimethyl-4-methoxy)pyridyl-2-methyl]amine (R[subscript 3]TPA) ligands was investigated. Characterization using a variety of spectroscopic methods and ...

  12. Structure of DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation

    PubMed Central

    Song, Jikui; Rechkoblit, Olga; Bestor, Timothy H.; Patel, Dinshaw J.

    2015-01-01

    Maintenance of genomic methylation patterns is mediated primarily by DNA methyltransferase-1 (DNMT1). We have solved structures of mouse and human DNMT1 composed of CXXC, tandem bromo-adjacent homology (BAH1/2), and methyltransferase domains bound to DNA-containing unmethylated CpG sites. The CXXC specifically binds to unmethylated CpG dinucleotide and positions the CXXC–BAH1 linker between the DNA and the active site of DNMT1, preventing de novo methylation. In addition, a loop projecting from BAH2 interacts with the target recognition domain (TRD) of the methyltransferase, stabilizing the TRD in a retracted position and preventing it from inserting into the DNA major groove. Our studies identify an autoinhibitory mechanism, in which unmethylated CpG dinucleotides are occluded from the active site to ensure that only hemimethylated CpG dinucleotides undergo methylation. PMID:21163962

  13. Structure of DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation

    SciTech Connect

    Song, Jikui; Rechkoblit, Olga; Bestor, Timothy H.; Patel, Dinshaw J.

    2011-09-06

    Maintenance of genomic methylation patterns is mediated primarily by DNA methyltransferase-1 (DNMT1). We have solved structures of mouse and human DNMT1 composed of CXXC, tandem bromo-adjacent homology (BAH1/2), and methyltransferase domains bound to DNA-containing unmethylated CpG sites. The CXXC specifically binds to unmethylated CpG dinucleotide and positions the CXXC-BAH1 linker between the DNA and the active site of DNMT1, preventing de novo methylation. In addition, a loop projecting from BAH2 interacts with the target recognition domain (TRD) of the methyltransferase, stabilizing the TRD in a retracted position and preventing it from inserting into the DNA major groove. Our studies identify an autoinhibitory mechanism, in which unmethylated CpG dinucleotides are occluded from the active site to ensure that only hemimethylated CpG dinucleotides undergo methylation.

  14. Structure of DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation

    SciTech Connect

    J Song; O Rechkoblit; T Bestor; D Patel

    2011-12-31

    Maintenance of genomic methylation patterns is mediated primarily by DNA methyltransferase-1 (DNMT1). We have solved structures of mouse and human DNMT1 composed of CXXC, tandem bromo-adjacent homology (BAH1/2), and methyltransferase domains bound to DNA-containing unmethylated CpG sites. The CXXC specifically binds to unmethylated CpG dinucleotide and positions the CXXC-BAH1 linker between the DNA and the active site of DNMT1, preventing de novo methylation. In addition, a loop projecting from BAH2 interacts with the target recognition domain (TRD) of the methyltransferase, stabilizing the TRD in a retracted position and preventing it from inserting into the DNA major groove. Our studies identify an autoinhibitory mechanism, in which unmethylated CpG dinucleotides are occluded from the active site to ensure that only hemimethylated CpG dinucleotides undergo methylation.

  15. Spectroscopic studies of inclusion complexes of methyl- p-dimethylaminobenzoate and its ortho derivative with ?- and ?-cyclodextrins

    NASA Astrophysics Data System (ADS)

    Lazarowska, Agata; Józefowicz, Marek; Heldt, Janina R.; Heldt, Józef

    2012-02-01

    The effects of ?- and ?-cyclodextrins (CDs) on the both emission modes (LE - locally excited and TICT - twisted intramolecular charge transfer) of the fluorescence spectrum of methyl- p-dimethylaminobenzoate (I) and its o-methoxy (II) derivative in aqueous solution have been investigated using steady-state and time-resolved fluorescence techniques. It is found that the intensity of both fluorescence bands increases with increasing concentration of ?- and ?-CD. The stoichiometries and equilibrium constants of the fluorophore-cyclodextrin inclusion complexes have been determined by steady-state fluorescence measurements. Performed spectroscopic studies demonstrate that in the case of I in ?-CD and ?-CD, both 1:1 and 1:2 inclusion complexes are formed, whereas only 1:1 inclusion complex is formed between II and ?-CD.

  16. STRUCTURES AND BINDING ENERGIES OF METHYL TERT-BUTYL ETHER-WATER COMPLEXES

    EPA Science Inventory

    Methyl tert-butyl ether (MTBE) is a well-known environmental contaminant owing to its high solubility in water. Since the early 1990s, MTBE has been added to gasoline to improve air quality in some metropolitan areas of the United States. Improved air quality was, however, achiev...

  17. A TDG/CBP/RAR? Ternary Complex Mediates the Retinoic Acid-dependent Expression of DNA Methylation-sensitive Genes

    PubMed Central

    Léger, Hélène; Smet-Nocca, Caroline; Attmane-Elakeb, Amel; Morley-Fletcher, Sara; Benecke, Arndt G.; Eilebrecht, Sebastian

    2014-01-01

    The thymine DNA glycosylase (TDG) is a multifunctional enzyme, which is essential for embryonic development. It mediates the base excision repair (BER) of G:T and G:U DNA mismatches arising from the deamination of 5-methyl cytosine (5-MeC) and cytosine, respectively. Recent studies have pointed at a role of TDG during the active demethylation of 5-MeC within CpG islands. TDG interacts with the histone acetylase CREB-binding protein (CBP) to activate CBP-dependent transcription. In addition, TDG also interacts with the retinoic acid receptor ? (RAR?), resulting in the activation of RAR? target genes. Here we provide evidence for the existence of a functional ternary complex containing TDG, CBP and activated RAR?. Using global transcriptome profiling, we uncover a coupling of de novo methylation-sensitive and RA-dependent transcription, which coincides with a significant subset of CBP target genes. The introduction of a point mutation in TDG, which neither affects overall protein structure nor BER activity, leads to a significant loss in ternary complex stability, resulting in the deregulation of RA targets involved in cellular networks associated with DNA replication, recombination and repair. We thus demonstrate for the first time a direct coupling of TDG’s epigenomic and transcription regulatory function through ternary complexes with CBP and RAR?. PMID:24394593

  18. DNA Methylation in the Exon 1 Region and Complex Regulation of Twist1 Expression in Gastric Cancer Cells

    PubMed Central

    Sakamoto, Ayuna; Akiyama, Yoshimitsu; Shimada, Shu; Zhu, Wei-Guo; Yuasa, Yasuhito; Tanaka, Shinji

    2015-01-01

    Twist1 overexpression is frequently observed in various cancers including gastric cancer (GC). Although DNA methylation of the Twist1 gene has been reported in cancer cells, the mechanisms underlying transcriptional activation remain uncertain. In this study, we first examined epigenetic alterations of the Twist1 using Twist1 transcription-positive and -negative cell lines that are derived from our established diffuse-type GC mouse model. Treatment with a DNA demethylation agent 5-aza-dC re-activated Twist1 expression in Twist1 expression-negative GC cells. According to methylation-specific PCR and bisulfite sequencing analysis, methylation at the CpG-rich region within Twist1 coding exon 1, rather than its promoter region, was tightly linked to transcriptional silencing of the Twist1 expression in mouse GC cells. Chromatin immunoprecipitation assays revealed that active histone mark H3K4me3 was enriched in Twist1 expression-positive cells, and inactive histone mark H3K9me3 was enriched in Twist1 expression-negative cells. The expression levels of Suv39h1 and Suv39h2, histone methyltransferases for H3K9me3, were inversely correlated with Twist1 expression, and knockdown of Suv39h1 or Suv39h2 induced Twist1 expression. Moreover, Sp1 transcription factor bound to the exon 1 CpG-rich region in Twist1 expression-positive cell lines, and Twist1 expression was diminished by mithramycin, which that interferes with Sp1 binding to CpG-rich regulatory sequences. Our studies suggested that the Twist1 transcription in GC cells might be regulated through potential cooperation of DNA methylation, histone modification in complex with Sp1 binding to CpG-rich regions within the exon 1 region. PMID:26695186

  19. Molecular Insights into Inhibition of the Methylated Histone-Plant Homeodomain Complexes by Calixarenes.

    PubMed

    Ali, Muzaffar; Daze, Kevin D; Strongin, Daniel E; Rothbart, Scott B; Rincon-Arano, Hector; Allen, Hillary F; Li, Janessa; Strahl, Brian D; Hof, Fraser; Kutateladze, Tatiana G

    2015-09-18

    Plant homeodomain (PHD) finger-containing proteins are implicated in fundamental biological processes, including transcriptional activation and repression, DNA damage repair, cell differentiation, and survival. The PHD finger functions as an epigenetic reader that binds to posttranslationally modified or unmodified histone H3 tails, recruiting catalytic writers and erasers and other components of the epigenetic machinery to chromatin. Despite the critical role of the histone-PHD interaction in normal and pathological processes, selective inhibitors of this association have not been well developed. Here we demonstrate that macrocyclic calixarenes can disrupt binding of PHD fingers to methylated lysine 4 of histone H3 in vitro and in vivo. The inhibitory activity relies on differences in binding affinities of the PHD fingers for H3K4me and the methylation state of the histone ligand, whereas the composition of the aromatic H3K4me-binding site of the PHD fingers appears to have no effect. Our approach provides a novel tool for studying the biological roles of methyllysine readers in epigenetic signaling. PMID:26229108

  20. MBD3L2 interacts with MBD3 and components of the NuRD complex and can oppose MBD2-MeCP1-mediated methylation silencing.

    PubMed

    Jin, Seung-Gi; Jiang, Chun-Ling; Rauch, Tibor; Li, Hongwei; Pfeifer, Gerd P

    2005-04-01

    MBD2 and MBD3 are two proteins that contain methyl-CpG binding domains and have a transcriptional repression function. Both proteins are components of a large CpG-methylated DNA binding complex named MeCP1, which consists of the nucleosome remodeling and histone deacetylase complex Mi2-NuRD and MBD2. MBD3L2 (methyl-CpG-binding protein 3-like 2) is a protein with substantial homology to MBD2 and MBD3, but it lacks the methyl-CpG-binding domain. Unlike MBD3L1, which is specifically expressed in haploid male germ cells, MBD3L2 expression is more widespread. MBD3L2 interacts with MBD3 in vitro and in vivo, co-localizes with MBD3 but not MBD2, and does not localize to methyl-CpG-rich regions in the nucleus. In glutathione S-transferase pull-down assays, MBD3L2 is found associated with several known components of the Mi2-NuRD complex, including HDAC1, HDAC2, MTA1, MBD3, p66, RbAp46, and RbAp48. Gel shift experiments with nuclear extracts and a CpG-methylated DNA probe indicate that recombinant MBD3L2 can displace a form of the MeCP1 complex from methylated DNA. MBD3L2 acts as a transcriptional repressor when tethered to a GAL4-DNA binding domain. Repression by GAL4-MBD3L2 is relieved by MBD2 and vice versa, and repression by MBD2 from a methylated promoter is relieved by MBD3L2. The data are consistent with a role of MBD3L2 as a transcriptional modulator that can interchange with MBD2 as an MBD3-interacting component of the NuRD complex. Thus, MBD3L2 has the potential to recruit the MeCP1 complex away from methylated DNA and reactivate transcription. PMID:15701600

  1. Impact of methyl rotor in the excited state level mixing of doubly hydrogen-bonded complexes of 2-pyridone.

    PubMed

    Hazra, Montu K; Chakraborty, Tapas

    2008-02-14

    We have presented in this paper the laser-induced fluorescence excitation and resolved fluorescence spectra of five 1:1 hydrogen-bonded complexes of 2-pyridone (2PY) with formic acid (FA), acetic acid (AA), propanoic acid (PA), formamide (FM), and acetamide (AM). The resolved fluorescence spectra, measured following excitation to different single vibronic levels of the dimers indicate that the intermolecular hydrogen bond vibrations undergo mixing with a number of intramolecular modes of the 2PY moiety in the excited state. A comparison of the emission spectral features of these dimers clearly indicates that the methyl groups belonging to the AA and AM moieties spectacularly accelerate the vibrational energy redistribution (IVR) in the 2PY moiety. On the other hand, although the molecular size of PA is bigger than AA, the spectral features of the 2PY-PA dimer bear signatures of a slower IVR rate compared to those of 2PY-AA. We propose that hyperconjugation of the methyl group with the cyclic hydrogen-bonded network involving AA and AM is responsible for the observed phenomenon. PMID:18205339

  2. Noncovalent interactions determine the conformation of aurophilic complexes with 2-mercapto-4-methyl-5-thiazoleacetic acid ligands.

    PubMed

    Hapka, Micha?; Dranka, Maciej; Or?owska, Katarzyna; Cha?asi?ski, Grzegorz; Szcz??niak, Ma?gorzata M; Zachara, Janusz

    2015-08-14

    We report the synthesis of three gold(i) complexes [Au(H(2)-mmta)(2)]Cl·(3)H(2)O (1), Na(3)[Au(mmta)(2)]·6H(2)O (2) and Na(3)[Au(mmta)(2)]·10.5H(2)O (3) (H(2)-mmta = 2-mercapto-4-methyl-5-thiazoleacetic acid) in which the Au(i) centre is incorporated either in cationic or anionic units of the [Au(SR)(2)](+/-) type depending on the protonation state of the ligand. All structures were characterized by single crystal X-ray analysis and found to exhibit unsupported aurophilic interactions leading to the formation of dimeric [Au(2)(H(2)-mmta)(4)](2+) and [Au(2)(mmta)(4)](6-) species. By applying several ab initio interpretative techniques we examine the character of the intermolecular interactions stabilizing the eclipsed arrangement of the aurophilic dimers formed in 1-3. PMID:26144218

  3. Integrated analyses of a major histocompatibility complex, methylation and transcribed ultra-conserved regions in systemic lupus erythematosus.

    PubMed

    Lin, Hua; Sui, Weiguo; Tan, Qiupei; Chen, Jiejing; Zhang, Yue; Ou, Minglin; Xue, Wen; Li, Fengyan; Cao, Cuihui; Sun, Yufeng; Dai, Yong

    2016-01-01

    Systemic lupus erythematosus (SLE) is a multifactorial autoimmune disease which affects different organs and systems that, has a complex genetic inheritance, and is affected by both epigenetic and environmental risk factors. Previous studies on SLE have lacked the statistical power and genetic resolution to fully determine the influence of major histocompatibility complex (MHC) on SLE. In this study, in order to determine this influence, a total of 15 patients with SLE and 15 healthy controls were enrolled. MHC region capture technology, hMeDIP-chip, transcribed ultra-conserved region (T-UCR) microarray and bioinformatics analysis were utilized for both groups. The results revealed methylated CpG enrichment at 6 loci in the MHC segment of SLE. We found 4 single-nucleotide polymorphisms (SNPs) in the CpG promoter of human leukocyte antigen-B (HLA-B) and 2 SNPs in chr6:29521110?29521833. No significant GO term or KEGG pathway enrichment was noted for an immune-correlated process in the SLE patients for the corresponding CpG-methylated genes. In this study, T-UCR was not discovered in the MHC segment. The analysis of SNPs (rs1050683, rs12697943, rs17881210, rs1065378, rs17184255 and rs16895070) and gene expression in peripheral blood lymphocytes indicated that these SNPs were associated with the occurrence of SLE. Further studies are warranted to examine the roles of these SNPs in the pathogenesis of SLE. Integrative analysis technology provided a view of the molecular signaling pathways in SLE. PMID:26717903

  4. Electronic and optical response of Ru(II) complexes functionalized by methyl, carboxylate groups: joint theoretical and experimental study

    SciTech Connect

    Tretiak, Sergei

    2008-01-01

    New photovoltaic and photocatalysis applications have been recently proposed based on the hybrid Ru(II)-bipyridine-complex/semiconductor quantum dot systems. In order to attach the complex to the surface of a semiconductor, a linking bridge - a carboxyl group - is added to one or two of the 2,2{prime}-bipyridine ligands. Such changes in the ligand structure, indeed, affect electronic and optical properties and consequently, the charge transfer reactivity of Ru-systems. In this study, we apply both theoretical and experimental approaches to analyze the effects brought by functionalization of bipyridine ligands with the methyl, carboxyl, and carboxilate groups on the electronic structure and optical response of the Ru(II) bipyridine complex. First principle calculations based on density functional theory (DFT) and linear response time dependent density functional theory (TDDFT) are used to simulate the ground and excited-state structures of functionalized Ru-complexes in the gas phase, as well as in acetonitrile solution. In addition, an inelaborate Frenkel exciton model is used to explain the optical activity and splitting patterns of the low-energy excited states. All theoretical results nicely complement experimental absorption spectra of Ru-complexes and contribute to their interpretation. We found that the carboxyl group breaks the degeneracy of two low-energy optically bright excited states and red-shifts the absorption spectrum, while leaves ionization and affinity energies of complexes almost unchanged. Experimental studies show a high probability of deprotonation of the carbboxyl group in the Ru-complexes resulted in a slight blue shift and decrease of intensities of the low energy absorption peaks. Comparison of experimental and theoretical linear response spectra of deprotanated complexes demonstrate strong agreement when acetonitrile solvent is used in simulations. A polar solvent is found to play an important role in calculations of optical spectra: it stabilizes the energy of states localized on the carboxyl or carboxylate groups eliminating artificial charge transport states, which typically appear in TDDFT calculations. Thus, it is validated that the excited-state structure of the functionalized Ru-complexes, specifically in the case of the deprotonated functions, can be accurately modeled by TDDFT with the addition of a dielectric continuum in simulations.

  5. Lithium Di- and trimethyl dimolybdenum(II) complexes with Mo-Mo quadruple bonds and bridging methyl groups.

    PubMed

    Curado, Natalia; Carrasco, Mario; Álvarez, Eleuterio; Maya, Celia; Peloso, Riccardo; Rodríguez, Amor; López-Serrano, Joaquín; Carmona, Ernesto

    2015-09-30

    New dimolybdenum complexes of composition [Mo2{?-Me}2Li(S)}(?-X)(?-N^N)2] (3a-3c), where S = THF or Et2O and N^N represents a bidentate aminopyridinate or amidinate ligand that bridges the quadruply bonded molybdenum atoms, were prepared from the reaction of the appropriate [Mo2{?-O2CMe}2(?-N^N)2] precursors and LiMe. For complex 3a, X = MeCO2, while in 3b and 3c, X = Me. Solution NMR studies in C6D6 solvent support formulation of the complexes as contact ion pairs with weak agostic Mo-CH3···Li interactions, which were also evidenced by X-ray crystallography in the solid-state structures of the molecules of 3a and 3b. Samples of 3c enriched in (13)C (99%) at the metal-bonded methyl sites were also prepared and investigated by NMR spectroscopy employing C6D6 and THF-d8 solvents. Crystallization of 3c from toluene:tetrahydrofuran mixtures provided single crystals of the solvent separated ion pair complex [Li(THF)4] [Mo2(Me)2(?-Me){?-HC(NDipp)2}2] (4c), where Dipp stands for 2,6-iPr2C6H3. A computational analysis of the Mo2(?-Me)2Li core of complexes 3a and 3b has been developed, which is consistent with a small but non-negligible electron-density sharing between the C and Li atoms of the mainly ionic CH3···Li interactions. PMID:26305709

  6. An intrinsically disordered region of methyl-CpG binding domain protein 2 (MBD2) recruits the histone deacetylase core of the NuRD complex

    PubMed Central

    Desai, Megha A.; Webb, Heather D.; Sinanan, Leander M.; Scarsdale, J. Neel; Walavalkar, Ninad M.; Ginder, Gordon D.; Williams, David C.

    2015-01-01

    The MBD2-NuRD (Nucleosome Remodeling and Deacetylase) complex is an epigenetic reader of DNA methylation that regulates genes involved in normal development and neoplastic diseases. To delineate the architecture and functional interactions of the MBD2-NuRD complex, we previously solved the structures of MBD2 bound to methylated DNA and a coiled-coil interaction between MBD2 and p66? that recruits the CHD4 nucleosome remodeling protein to the complex. The work presented here identifies novel structural and functional features of a previously uncharacterized domain of MBD2 (MBD2IDR). Biophysical analyses show that the MBD2IDR is an intrinsically disordered region (IDR). However, despite this inherent disorder, MBD2IDR increases the overall binding affinity of MBD2 for methylated DNA. MBD2IDR also recruits the histone deacetylase core components (RbAp48, HDAC2 and MTA2) of NuRD through a critical contact region requiring two contiguous amino acid residues, Arg286 and Leu287. Mutating these residues abrogates interaction of MBD2 with the histone deacetylase core and impairs the ability of MBD2 to repress the methylated tumor suppressor gene PRSS8 in MDA-MB-435 breast cancer cells. These findings expand our knowledge of the multi-dimensional interactions of the MBD2-NuRD complex that govern its function. PMID:25753662

  7. A role for repressive complexes and H3K9 di-methylation in PRDM5-associated brittle cornea syndrome.

    PubMed

    Porter, Louise F; Galli, Giorgio G; Williamson, Sally; Selley, Julian; Knight, David; Elcioglu, Nursel; Aydin, Ali; Elcioglu, Mustafa; Venselaar, Hanka; Lund, Anders H; Bonshek, Richard; Black, Graeme C; Manson, Forbes D

    2015-12-01

    Type 2 brittle cornea syndrome (BCS2) is an inherited connective tissue disease with a devastating ocular phenotype caused by mutations in the transcription factor PR domain containing 5 (PRDM5) hypothesized to exert epigenetic effects through histone and DNA methylation. Here we investigate clinical samples, including skin fibroblasts and retinal tissue from BCS2 patients, to elucidate the epigenetic role of PRDM5 and mechanisms of its dysregulation in disease. First we report abnormal retinal vascular morphology in the eyes of two cousins with BCS2 (PRDM5 ? exons 9-14) using immunohistochemistry, and mine data from skin fibroblast expression microarrays from patients with PRDM5 mutations p.Arg590* and ? exons 9-14, as well as from a PRDM5 ChIP-sequencing experiment. Gene ontology analysis of dysregulated PRDM5-target genes reveals enrichment for extracellular matrix (ECM) genes supporting vascular integrity and development. Q-PCR and ChIP-qPCR confirm upregulation of critical mediators of ECM stability in vascular structures (COL13A1, COL15A1, NTN1, CDH5) in patient fibroblasts. We identify H3K9 di-methylation (H3K9me2) at these PRDM5-target genes in fibroblasts, and demonstrate that the BCS2 mutation p.Arg83Cys diminishes interaction of PRDM5 with repressive complexes, including NuRD complex protein CHD4, and the repressive chromatin interactor HP1BP3, by co-immunoprecipitation combined with mass spectrometry. We observe reduced heterochromatin protein 1 binding protein 3 (HP1BP3) staining in the retinas of two cousins lacking exons 9-14 by immunohistochemistry, and dysregulated H3K9me2 in skin fibroblasts of three patients (p.Arg590*, p.Glu134* and ? exons 9-14) by western blotting. These findings suggest that defective interaction of PRDM5 with repressive complexes, and dysregulation of H3K9me2, play a role in PRDM5-associated disease. PMID:26395458

  8. Spectrophotometric determination of benzydamine HCl, levamisole HCl and mebeverine HCl through ion-pair complex formation with methyl orange.

    PubMed

    El-Didamony, Akram M

    2008-03-01

    A simple, rapid and sensitive spectrophotometric method has been proposed for the assay of benzydamine HCl (BENZ), levamisole HCl (LEV) and mebeverine HCl (MBV) in bulk and pharmaceutical formulations. The method based on the reaction of the selected drugs with methyl orange (MO) in buffered aqueous solution at pH 3.6. The formed yellow ion-pair complexes were extracted with dichloromethane and measured quantitatively with maximum absorption at 422 nm. The analytical parameters and their effects on the reported systems are investigated. The extracts are intensely colored and very stable at room temperature. The calibration graphs were linear over the concentration range of 2-10 microg ml(-1) for BENZ, 6-24 microg ml(-1) for LEV and 4-14 microg ml(-1) for MBV. The stoichiometry of the reaction was found to be 1:1 in all cases and the conditional stability constant (K(f)) of the complexes have been calculated. The proposed method was successfully extended to pharmaceutical preparations-tablets. Excipients used as additive in commercial formulations did not interfere in the analysis. The proposed method can be recommended for quality control and routine analysis where time, cost effectiveness and high specificity of analytical technique are of great importance. PMID:17625955

  9. Spectrophotometric determination of benzydamine HCl, levamisole HCl and mebeverine HCl through ion-pair complex formation with methyl orange

    NASA Astrophysics Data System (ADS)

    El-Didamony, Akram M.

    2008-03-01

    A simple, rapid and sensitive spectrophotometric method has been proposed for the assay of benzydamine HCl (BENZ), levamisole HCl (LEV) and mebeverine HCl (MBV) in bulk and pharmaceutical formulations. The method based on the reaction of the selected drugs with methyl orange (MO) in buffered aqueous solution at pH 3.6. The formed yellow ion-pair complexes were extracted with dichloromethane and measured quantitatively with maximum absorption at 422 nm. The analytical parameters and their effects on the reported systems are investigated. The extracts are intensely colored and very stable at room temperature. The calibration graphs were linear over the concentration range of 2-10 ?g ml -1 for BENZ, 6-24 ?g ml -1 for LEV and 4-14 ?g ml -1 for MBV. The stoichiometry of the reaction was found to be 1:1 in all cases and the conditional stability constant ( Kf) of the complexes have been calculated. The proposed method was successfully extended to pharmaceutical preparations-tablets. Excipients used as additive in commercial formulations did not interfere in the analysis. The proposed method can be recommended for quality control and routine analysis where time, cost effectiveness and high specificity of analytical technique are of great importance.

  10. Structural studies of MeCP2 in complex with methylated DNA 

    E-print Network

    Ho, Kok Lian

    2009-01-01

    synchrotron sources. It belongs to space group C2 with unit cell dimensions: a = 79.71Å, b = 53.60Å, c = 65.73Å, and ? = 132.1°. The X-ray structure of the MeCP2 MBD-DNA complex was solved using the SAD method. Structural analyses of the refined X...

  11. Time-resolved electron paramagnetic resonance spectra of photoexcited triplet states of electron-donor-acceptor complexes in frozen solution: Methylated benzenes and chlorinated phthalic anhydrides

    NASA Astrophysics Data System (ADS)

    Murai, Hisao; Minami, Masashi; I'Haya, Yasumasa J.

    1994-09-01

    Phthalic anhydride (PA) and chlorinated PAs in frozen methyl substituted benzenes provided the time-resolved electron paramagnetic resonance (TREPR) spectra of the electron-donor-acceptor (EDA) complexes. The chlorine substitution of PA reduced the zero-field splitting parameters, D, due to the contribution of the spin-orbit interaction caused by heavy atoms such as chlorine. The increase of the number of methyl group on benzene, which apparently reduced the ionization potential, worked to decrease the D value of the EDA complex. The charge-transfer (CT) ratios were measured more exactly by the absolute value of (Delta m(sub s)) = 1 transition of the triplet states. The major axes of these systems were also safely presumed. The sign of the 100% charge transferred EDA complex was found negative because of the CT ratio plots and the spin-polarization pattern of the TREPR spectra.

  12. Synthesis, crystal structures and intermolecular interactions of two Mn(II) complexes with 4,4?-bipy and methyl benzoates

    NASA Astrophysics Data System (ADS)

    Xin-Jian, Wu; Yi-Ping, Chen; Ze-Min, Xia; Su-Zhi, Ge; Feng, Chai; Ling-Yan, Zhao; Jian-Zhong, Chen

    2013-03-01

    Two manganese complexes containing 4,4'-bipyridine and methyl benzoate as ligands have been prepared and crystallized by solvent evaporation method in DMF. The single crystal X-ray crystallographic analyses reveal that the complexes crystallize in monoclinic system. Crystal of 1 [Mn2(4,4'-bipy)2 (o-MBA)4]n has space group of P21/c with unit cell parameters of a = 17.508 (Å), b = 11.6229 (Å), c = 27.983 (Å), ? = 128.123°, V = 4.4797 nm3, empirical formula: C52H44Mn2N4O8, Mr = 962.79, Z = 4, Dc = 1.428 g/cm3, ? = 0.625 mm-1, and F(000) = 1992. The crystal of 2 [Mn (4,4'-bipy)(m-MBA)2]n belongs to space group C2/c with a = 16.079 (Å), b = 11.652 (Å), c = 24.887 (Å), ? = 92.02°, V = 4.660 nm3, empirical formula: C26H22MnN2O4, Mr = 481.40, Z = 8, Dc = 1.372 g/cm3, ? = 1.179 mm-1, F(000) = 1992. The weak interactions in structures are observed from the X-ray crystallographic data. These include the Csbnd H⋯O hydrogen bonds, ?-? stacking and Csbnd H⋯? interactions found in 1. The different strength of intermolecular interaction in the structures is reflected on their different thermal stability of the two complexes measured by thermal gravimetric analysis and the 2D-IR correlation spectroscopy. The study of weak interactions is meaningful to provide supporting data for potential application in molecular biology.

  13. (1-Methyl-2-(thiophen-2-yl)-1H-benzo[d]imidazole) and its three copper complexes: Synthesis, characterization and fluorescence properties

    NASA Astrophysics Data System (ADS)

    Demir, Selçuk; Eren, Bilge; Ho?y?ska, Ma?gorzata

    2015-02-01

    (1-Methyl-2-(thiophen-2-yl)-1H-benzo[d]imidazole) (C12H10N2S) (L) ligand and its three copper complexes [(Cu2(L)2I2] (1), [(Cu(L)2X2] (X = Cl- (2), and NO3- (3)) were synthesized and characterized by elemental analysis and IR measurements. The structures of the complexes 1-3 were determined by single crystal X-ray diffraction. The complex molecules interact with each other's via weak Csbnd H⋯X hydrogen bonds (X = I for the complex 1, X = Cl for the complex 2 and X = O for the complex 3). Upon excitation with a wavelength of 350 nm at room temperature, free L and complex 1 emit fluorescence at 420 and 560 nm, respectively.

  14. '2+1' tricarbonyltechnetium(I)/tricarbonylrhenium(I) mixed-ligand complexes with methyl thiosalicylate and isocyanide ligands as potential precursors of radiopharmaceuticals.

    PubMed

    Ko?mi?ski, Przemys?aw; Gniazdowska, Ewa; Fuks, Leon; Kowalska, Sylwia

    2011-02-01

    The complexes of [(99m)Tc]-tricarbonyltechnetium(I) and [(188)Re]-tricarbonylrhenium(I), of the '2+1' type, with methyl thiosalicylate as an anionic bidentate ligand and with either tert-butyl 3-isocyanopropionate or glycine-glycine-tyrosine 4-isocyanobutyrate as monodentate ligands, have been prepared on the n.c.a. scale. The complexes exhibit different lipophilicity and high stability in neutral aqueous solutions. Based on the results of the challenge experiment with histidine, cysteine and glutathione the studied complexes might be considered to be promising models for radiopharmaceutical precursors. PMID:21129987

  15. Preparation of olanzapine and methyl-?-cyclodextrin complexes using a single-step, organic solvent-free supercritical fluid process: An approach to enhance the solubility and dissolution properties.

    PubMed

    Rudrangi, Shashi Ravi Suman; Trivedi, Vivek; Mitchell, John C; Wicks, Stephen Richard; Alexander, Bruce David

    2015-10-15

    The purpose of this study was to evaluate a single-step, organic solvent-free supercritical fluid process for the preparation of olanzapine-methyl-?-cyclodextrin complexes with an express goal to enhance the dissolution properties of olanzapine. The complexes were prepared by supercritical carbon dioxide processing, co-evaporation, freeze drying and physical mixing. The prepared complexes were then analysed by differential scanning calorimetry, X-ray powder diffraction, scanning electron microscopy, solubility and dissolution studies. Computational molecular docking studies were performed to study the formation of molecular inclusion complexation of olanzapine with methyl-?-cyclodextrin. All the binary mixtures of olanzapine with methyl-?-cyclodextrin, except physical mixture, exhibited a faster and greater extent of drug dissolution than the drug alone. Products obtained by the supercritical carbon dioxide processing method exhibited the highest apparent drug dissolution. The characterisation by different analytical techniques suggests complete complexation or amorphisation of olanzapine and methyl-?-cyclodextrin complexes prepared by supercritical carbon dioxide processing method. Therefore, organic solvent-free supercritical carbon dioxide processing method proved to be novel and efficient for the preparation of solid inclusion complexes of olanzapine with methyl-?-cyclodextrin. The preliminary data also suggests that the complexes of olanzapine with methyl-?-cyclodextrin will lead to better therapeutic efficacy due to better solubility and dissolution properties. PMID:26315120

  16. Investigations of iridium-mediated reversible C-H bond cleavage: characterization of a 16-electron iridium(III) methyl hydride complex.

    PubMed

    Bernskoetter, Wesley H; Hanson, Susan Kloek; Buzak, Sara K; Davis, Zoe; White, Peter S; Swartz, Rodney; Goldberg, Karen I; Brookhart, Maurice

    2009-06-24

    New iridium complexes of a tridentate pincer ligand, 2,6-bis(di-tert-butylphosphinito)pyridine (PONOP), have been prepared and used in the study of hydrocarbon C-H bond activation. Intermolecular oxidative addition of a benzene C-H bond was directly observed with [(PONOP)Ir(I)(cyclooctene)][PF(6)] at ambient temperature, resulting in a cationic five-coordinate iridium(III) phenyl hydride product. Protonation of the (PONOP)Ir(I) methyl complex yielded the corresponding iridium(III) methyl hydride cation, a rare five-coordinate, 16-valence electron transition metal alkyl hydride species which was characterized by X-ray diffraction. Kinetic studies of C-H bond coupling and reductive elimination reactions from the five-coordinate complexes have been carried out. Exchange NMR spectroscopy measurements established a barrier of 17.8(4) kcal/mol (22 degrees C) for H-C(aryl) bond coupling in the iridium(III) phenyl hydride cation and of 9.3(4) kcal/mol (-105 degrees C) for the analogous H-C(alkyl) coupling in the iridium(III) methyl hydride cation. The origin of the higher barrier of H-C(aryl) relative to H-C(alkyl) bond coupling is proposed to be influenced by a hindered rotation about the Ir-C(aryl) bond, a result of the sterically demanding PONOP ligand. PMID:19489584

  17. Spectroscopic studies on Co(II) and Cu(II) complexes of 6-amino-1-methyl-5-nitrosouracil and its 6-methylamine derivative

    NASA Astrophysics Data System (ADS)

    Teleb, Said M.

    2004-11-01

    Four complexes are obtained during the reactions of 6-amino-1-methyl-5-nitrosouracil and its 6-methylamine derivative with Co(II) and Cu(II) ions. Theses complexes were characterized through their elemental, thermal analysis, infrared and 1H NMR spectroscopes. The obtained results indicate that, the exocyclic oxygen and nitrogen atoms are the most probable binding sites rather than ring nitrogen atoms. For cobalt complexes, the two pyrimidine bases act as bidentate ligands in the anionic form with the dissociation of iminic or N(3) proton depending upon the nature of substituents on the pyrimidine ring. For copper complexes, the pyrimidine bases interact in the neutral form as monodentate ligands. Octahedral geometries are proposed for all of these complexes.

  18. Two nickel(II) bis[(pyridin-2-yl)methyl]amine complexes with homophthalic and benzene-1,2,4,5-tetracarboxylic acids.

    PubMed

    Atria, Ana María; Garland, Maria Teresa; Baggio, Ricardo

    2014-06-01

    Two new Ni(II) complexes involving the ancillary ligand bis[(pyridin-2-yl)methyl]amine (bpma) and two different carboxylate ligands, i.e. homophthalate [hph; systematic name: 2-(2-carboxylatophenyl)acetate] and benzene-1,2,4,5-tetracarboxylate (btc), namely catena-poly[[aqua{bis[(pyridin-2-yl)methyl]amine-?(3)N,N',N''}nickel(II)]-?-2-(2-carboxylatophenyl)aceteto-?(2)O:O'], [Ni(C9H6O4)(C12H13N3)(H2O)]n, and (?-benzene-1,2,4,5-tetracarboxylato-?(4)O(1),O(2):O(4),O(5))bis(aqua{bis[(pyridin-2-yl)methyl]amine-?(3)N,N',N''}nickel(II)) bis(triaqua{bis[(pyridin-2-yl)methyl]amine-?(3)N,N',N''}nickel(II)) benzene-1,2,4,5-tetracarboxylate hexahydrate, [Ni2(C10H2O8)(C12H13N3)2(H2O)2]·[Ni(C12H13N3)(H2O)3]2(C10H2O8)·6H2O, (II), are presented. Compound (I) is a one-dimensional polymer with hph acting as a bridging ligand and with the chains linked by weak C-H···O interactions. The structure of compound (II) is much more complex, with two independent Ni(II) centres having different environments, one of them as part of centrosymmetric [Ni(bpma)(H2O)]2(btc) dinuclear complexes and the other in mononuclear [Ni(bpma)(H2O)3](2+) cations which (in a 2:1 ratio) provide charge balance for btc(4-) anions. A profuse hydrogen-bonding scheme, where both coordinated and crystal water molecules play a crucial role, provides the supramolecular linkage of the different groups. PMID:24898954

  19. Synthesis and complexation properties of DTPA-N,N''-bis[bis(n-butyl)]-N'-methyl-tris(amide). Kinetic stability and water exchange of its Gd3+ complex.

    PubMed

    Jaszberényi, Z; Tóth, E; Kálai, T; Király, R; Burai, L; Brücher, E; Merbach, A E; Hideg, K

    2005-02-21

    A novel DTPA-tris(amide) derivative ligand, DTPA-N,N''-bis[bis(n-butyl)]-N'-methyl-tris(amide)(H2L3) was synthesized. With Gd3+, it forms a positively charged [Gd(L3)]+ complex, whereas with Cu2+ and Zn2+ [ML3], [MHL3]+ and [M2L3]2+ species are formed. The protonation constants of H2L3 and the stability constants of the complexes were determined by pH potentiometry. The stability constants are lower than those for DTPA-N,N''-bis[bis(n-butyl)amide)](H3L2), due to the lower negative charge and reduced basicity of the amine nitrogens in (L3)2-. The kinetic stability of [Gd(L3)]+ was characterised by the rates of metal exchange reactions with Eu3+, Cu2+ and Zn2+. The exchange reactions, which occur via proton and metal ion assisted dissociation of [Gd(L3)]+, are significantly slower than for [Gd(DTPA)]2-, since the amide groups cannot be protonated and interact only weakly with the attacking metal ions. The relaxivities of [Gd(L2)] and [Gd(L3)]+ are constant between 10-20 degrees C, indicating a relatively slow water exchange. Above 25 degrees C, the relaxivities decrease, similarly to other Gd3+ DTPA-bis(amide) complexes. The pH dependence of the relaxivities for [Gd(L3)]+ shows a minimum at pH approximately 9, thus differs from the behaviour of Gd3+-DTPA-bis(amides) which have constant relaxivities at pH 3-8 and an increase below and above. The water exchange rates for [Gd(L2)(H2O)] and [Gd(L3)(H2O)]+, determined from a variable temperature (17)O NMR study, are lower than that for [Gd(DTPA)(H2O)]2-. This is a consequence of the lower negative charge and decreased steric crowding at the water binding site in amides as compared to carboxylate analogues. Substitution of the third acetate of DTPA5- with an amide, however, results in a less pronounced decrease in kex than substitution of the first two acetates. The activation volumes derived from a variable pressure (17)O NMR study prove a dissociative interchange and a limiting dissociative mechanism for [Gd(L2)(H2O)] and [Gd(L3)(H2O)]+, respectively. PMID:15702179

  20. Formation of molecular complexes of salicylic acid, acetylsalicylic acid, and methyl salicylate in a mixture of supercritical carbon dioxide with a polar cosolvent

    NASA Astrophysics Data System (ADS)

    Petrenko, V. E.; Antipova, M. L.; Gurina, D. L.; Odintsova, E. G.

    2015-08-01

    The solvate structures formed by salicylic acid, acetylsalicylic acid, and methyl salicylate in supercritical (SC) carbon dioxide with a polar cosolvent (methanol, 0.03 mole fractions) at a density of 0.7 g/cm3 and a temperature of 318 K were studied by the molecular dynamics method. Salicylic and acetylsalicylic acids were found to form highly stable hydrogen-bonded complexes with methanol via the hydrogen atom of the carboxyl group. For methyl salicylate in which the carboxyl hydrogen is substituted by a methyl radical, the formation of stable hydrogen bonds with methanol was not revealed. The contribution of other functional groups of the solute to the interactions with the cosolvent was much smaller. An analysis of correlations between the obtained data and the literature data on the cosolvent effect on the solubility of the compounds in SC CO2 showed that the dissolving ability of SC CO2 with respect to a polar organic substance in the presence of a cosolvent increased only when stable hydrogen-bonded complexes are formed between this substance and the cosolvent.

  1. Construction of two Cd(II) complexes by flexible adipic acid plus 2-((benzoimidazol-yl)methyl)-1H-tetrazole ligand

    NASA Astrophysics Data System (ADS)

    Duan, Wanlu; Zhang, Yuhong; Wang, Xiuxiu; Meng, Xiangru

    2015-10-01

    Two new complexes with the formulas [Cd(bimt)(adi)]n (1) and {[Cd(bimt)(adi)0.5Br]·H2O}n (2) were synthesized through reactions of 2-((benzoimidazol-yl)methyl)-1H-tetrazole (bimt) with Cd(II) salts in the presence of adipic acid (H2adi). Single crystal X-ray analysis reveals that complex 1 shows a 1D chain structure in which adipate ligand coordinates to Cd(II) ions with ?3-bridging mode. Complex 2 displays a 2D layer structure with 4-connected (44·62) topology in which adipate ligand coordinates to Cd(II) ions with ?2-bridging mode. These results reveal that the versatile coordination modes of adipate ligands play an important role in controlling the structures of the complexes. In addition, their IR spectra, element analyses, PXRD patterns and luminescent properties are investigated.

  2. Exposing the Molecular Complexity of Sgr B2(N): The Interstellar Detection of Methyl Isocyanate (CH3NCO) from the GBT PRIMOS Survey

    NASA Astrophysics Data System (ADS)

    Pulliam, Robin; Remijan, A. J.; Loomis, R. A.

    2013-01-01

    CH3NCO is one of just a few interstellar molecules that contain H, C, N, and O, all of which are constituents of the simple amino acid, glycine, a species that has yet to be detected in the interstellar medium. Methyl isocyanate is thus an important molecule in bridging the gap to more complex, organic biomolecules. Using data from the publicly available Green Bank Telescope Prebiotic Interstellar Molecular Survey (PRIMOS) towards Sgr B2(N), we have observed, for the first time, 20 rotational transitions of methyl isocyanate. The spectral regions are free of molecular line confusion and the features observed are consistent with the source structure of this source with an LSR velocity of +64 and +73 km/s. It is likely that CH3NCO is produced in a neutral-radical reaction with the neutral reactant HNCO, which is ubiquitous in SgrB2(N), and the radicals CH2 or CH3.

  3. Stereospecific ligands and their complexes. Part XIX. Synthesis, characterization, circular dichroism and antimicrobial activity of oxalato and malonato-(S,S)-ethylenediamine-N,N?-di-2-(3-methyl)butanoato-chromate(III) complexes

    NASA Astrophysics Data System (ADS)

    Ili?, Dragoslav; Jevti?, Verica V.; Radojevi?, Ivana D.; Vasi?, Sava M.; Stefanovi?, Olgica D.; ?omi?, Ljiljana R.; Vasojevi?, Miorad M.; Jeli?, Miodrag Ž.; Koval'chuk, Tatyana V.; Loginova, Natalia V.; Trifunovi?, Sre?ko R.

    2013-10-01

    The s-cis-[Cr(S,S-eddv)L]-complexes (1,2) (S,S-eddv = (S,S)-ethylenediamine-N,N?-di-2-(3-methyl)butanoato ion; L = oxalate or malonate ion) were prepared. The complexes were purified by ion-exchange chromatography. The geometry of the complexes has been supposed on the basis of the infrared and electronic absorption spectra, and the absolute configurations of the isolated s-cis-[Cr(S,S-eddv)L]-complexes have been predicted on the basis of their circular dichroism (CD) spectra. Also, the results of thermal decomposition have been discussed. Antimicrobial activity of the prepared complexes (1-4) was investigated against 28 species of microorganisms. Testing was performed by microdilution method and minimum inhibitory concentrations (MIC) and minimum microbicidal concentration (MMC) have been determined. Complexes demonstrated in generally low antibacterial and antifungal activity.

  4. Synthesis, characterization, antimicrobial activity and carbonic anhydrase enzyme inhibitor effects of salicilaldehyde-N-methyl p-toluenesulfonylhydrazone and its Palladium(II), Cobalt(II) complexes

    NASA Astrophysics Data System (ADS)

    Alyar, Saliha; Adem, ?evki

    2014-10-01

    We report the synthesis of the ligand, salicilaldehyde-N-methyl p-toluenesulfonylhydrazone (salptsmh) derived from p-toluenesulfonicacid-1-methylhydrazide (ptsmh) and its Pd(II) and Co(II) metal complexes were synthesized for the first time. The structure of the ligand and their complexes were investigated using elemental analysis, magnetic susceptibility, molar conductance and spectral (IR, NMR and LC-MS) measurements. Salptsmh has also been characterized by single crystal X-ray diffraction. 1H and 13C shielding tensors for crystal structure were calculated with GIAO/DFT/B3LYP/6-311++G(d,p) methods in CDCl3. The complexes were found to have general composition [ML2]. The results of elemental analysis showed 1:2 (metal/ligand) stoichiometry for all the complex. Magnetic and spectral data indicate a square planar geometry for Pd(II) complex and a distorted tetrahedral geometry for Co(II) complexes. The ligand and its metal chelates have been screened for their antimicrobial activities using the disk diffusion method against the selected Gram positive bacteria: Bacillus subtilis, Bacillus cereus, Staphylococcus aureus, Enterococcus faecalis, Gram negative bacteria: Eschericha coli, Pseudomonas aeruginosa, Klebsiella pneumonia. The inhibition activities of these compounds on carbonic anhydrase II (CA II) and carbonic anhydrase I (CA I) have been investigated by comparing IC50 and Ki values and it has been found that Pd(II) complex have more enzyme inhibition efficiency than salptsmh and Co(II) complex.

  5. Synthesis, spectroscopic, anticancer, antibacterial and antifungal studies of Ni(II) and Cu(II) complexes with hydrazine carboxamide, 2-[3-methyl-2-thienyl methylene

    NASA Astrophysics Data System (ADS)

    Chandra, Sulekh; Vandana; Kumar, Suresh

    2015-01-01

    Schiff's base ligand(L) hydrazine carboxamide, 2-[3-methyl-2-thienyl methylene] and its metal complexes have been synthesized and characterized by elemental analysis, molar conductance, various spectroscopic techniques such as electronic, IR, 1H NMR, mass, EPR. Molar conductance of complexes in DMF solution corresponds to non-electrolyte. Complexes have general composition [M(L)2X2], where M = Ni(II) and Cu(II), X = Cl-, NO3-, CH3COO- and ½SO42-. On the basis of above spectral studies, an octahedral geometry has been assigned for Ni(II) complexes and tetragonal geometry for Cu(II) complexes except [Cu(L)2SO4] which possesses five coordinated trigonal bipyramidal geometry. These metal complexes were also tested for their anticancer, antibacterial and antifungal activities to assess their inhibition potential. Anticancer activity of ligand and its metal complexes were evaluated using SRB fluorometric assay and Adriamycin (ADR) was applied as positive control. Schiff's base ligand and its metal complexes were screened for their antibacterial and antifungal activity against Escherichia coli, Bacillus cereus and Aspergillus niger, Aspergillus flavus, respectively. Kirby-Bauer single disk susceptibility test was used for antibacterial activity and well diffusion method for antifungal activity of the compounds on the used fungi.

  6. "Stripping" the Carbon Atom of Methyl Halide by a Cationic Holmium Complex: A Gas-Phase Study.

    PubMed

    Zhou, Shaodong; Schlangen, Maria; Li, Jilai; Wu, Xiao-Nan; Schwarz, Helmut

    2015-10-01

    Mechanistic aspects of an unusual reaction of [HoC6 H4 S](+) with CH3 X (X=Cl, Br, I) have been investigated using Fourier-transform ion cyclotron resonance mass spectrometry combined with density functional theory (DFT) calculations. In this thermal process, all four bonds of the methyl halides are cleaved. PMID:26331900

  7. Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression

    PubMed Central

    Horton, John R.; Zhang, Xing; Blumenthal, Robert M.; Cheng, Xiaodong

    2015-01-01

    DNA adenine methyltransferase (Dam) is widespread and conserved among the ?-proteobacteria. Methylation of the Ade in GATC sequences regulates diverse bacterial cell functions, including gene expression, mismatch repair and chromosome replication. Dam also controls virulence in many pathogenic Gram-negative bacteria. An unexplained and perplexing observation about Escherichia coli Dam (EcoDam) is that there is no obvious relationship between the genes that are transcriptionally responsive to Dam and the promoter-proximal presence of GATC sequences. Here, we demonstrate that EcoDam interacts with a 5-base pair non-cognate sequence distinct from GATC. The crystal structure of a non-cognate complex allowed us to identify a DNA binding element, GTYTA/TARAC (where Y = C/T and R = A/G). This element immediately flanks GATC sites in some Dam-regulated promoters, including the Pap operon which specifies pyelonephritis-associated pili. In addition, Dam interacts with near-cognate GATC sequences (i.e. 3/4-site ATC and GAT). Taken together, these results imply that Dam, in addition to being responsible for GATC methylation, could also function as a methylation-independent transcriptional repressor. PMID:25845600

  8. Polycomb Repressive Complex 2 and H3K27me3 Cooperate with H3K9 Methylation To Maintain Heterochromatin Protein 1? at Chromatin

    PubMed Central

    Boros, Joanna; Arnoult, Nausica; Stroobant, Vincent; Collet, Jean-François

    2014-01-01

    Methylation of histone H3 on lysine 9 or 27 is crucial for heterochromatin formation. Previously considered hallmarks of, respectively, constitutive and facultative heterochromatin, recent evidence has accumulated in favor of coexistence of these two marks and their cooperation in gene silencing maintenance. H3K9me2/3 ensures anchorage at chromatin of heterochromatin protein 1? (HP1?), a main component of heterochromatin. HP1? chromoshadow domain, involved in dimerization and interaction with partners, has additional but still unclear roles in HP1? recruitment to chromatin. Because of previously suggested links between polycomb repressive complex 2 (PRC2), which catalyzes H3K27 methylation, and HP1?, we tested whether PRC2 may regulate HP1? abundance at chromatin. We found that the EZH2 and SUZ12 subunits of PRC2 are required for HP1? stability, as knockdown of either protein led to HP1? degradation. Similar results were obtained upon overexpression of H3K27me2/3 demethylases. We further showed that binding of HP1?/?/? to H3K9me3 peptides is greatly increased in the presence of H3K27me3, and this is dependent on PRC2. These data fit with recent proteomic studies identifying PRC2 as an indirect H3K9me3 binder in mouse tissues and suggest the existence of a cooperative mechanism of HP1? anchorage at chromatin involving H3 methylation on both K9 and K27 residues. PMID:25047840

  9. Polycomb repressive complex 2 and H3K27me3 cooperate with H3K9 methylation to maintain heterochromatin protein 1? at chromatin.

    PubMed

    Boros, Joanna; Arnoult, Nausica; Stroobant, Vincent; Collet, Jean-François; Decottignies, Anabelle

    2014-10-01

    Methylation of histone H3 on lysine 9 or 27 is crucial for heterochromatin formation. Previously considered hallmarks of, respectively, constitutive and facultative heterochromatin, recent evidence has accumulated in favor of coexistence of these two marks and their cooperation in gene silencing maintenance. H3K9me2/3 ensures anchorage at chromatin of heterochromatin protein 1? (HP1?), a main component of heterochromatin. HP1? chromoshadow domain, involved in dimerization and interaction with partners, has additional but still unclear roles in HP1? recruitment to chromatin. Because of previously suggested links between polycomb repressive complex 2 (PRC2), which catalyzes H3K27 methylation, and HP1?, we tested whether PRC2 may regulate HP1? abundance at chromatin. We found that the EZH2 and SUZ12 subunits of PRC2 are required for HP1? stability, as knockdown of either protein led to HP1? degradation. Similar results were obtained upon overexpression of H3K27me2/3 demethylases. We further showed that binding of HP1?/?/? to H3K9me3 peptides is greatly increased in the presence of H3K27me3, and this is dependent on PRC2. These data fit with recent proteomic studies identifying PRC2 as an indirect H3K9me3 binder in mouse tissues and suggest the existence of a cooperative mechanism of HP1? anchorage at chromatin involving H3 methylation on both K9 and K27 residues. PMID:25047840

  10. Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: Potential implications for methylation-independent transcriptional repression

    DOE PAGESBeta

    Horton, John R.; Zhang, Xing; Blumenthal, Robert M.; Cheng, Xiaodong

    2015-04-06

    DNA adenine methyltransferase (Dam) is widespread and conserved among the ?-proteobacteria. Methylation of the Ade in GATC sequences regulates diverse bacterial cell functions, including gene expression, mismatch repair and chromosome replication. Dam also controls virulence in many pathogenic Gram-negative bacteria. An unexplained and perplexing observation about Escherichia coli Dam (EcoDam) is that there is no obvious relationship between the genes that are transcriptionally responsive to Dam and the promoter-proximal presence of GATC sequences. Here, we demonstrate that EcoDam interacts with a 5-base pair non-cognate sequence distinct from GATC. The crystal structure of a non-cognate complex allowed us to identify amore »DNA binding element, GTYTA/TARAC (where Y = C/T and R = A/G). This element immediately flanks GATC sites in some Dam-regulated promoters, including the Pap operon which specifies pyelonephritis-associated pili. In addition, Dam interacts with near-cognate GATC sequences (i.e. 3/4-site ATC and GAT). All together, these results imply that Dam, in addition to being responsible for GATC methylation, could also function as a methylation-independent transcriptional repressor.« less

  11. Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: Potential implications for methylation-independent transcriptional repression

    SciTech Connect

    Horton, John R.; Zhang, Xing; Blumenthal, Robert M.; Cheng, Xiaodong

    2015-04-06

    DNA adenine methyltransferase (Dam) is widespread and conserved among the ?-proteobacteria. Methylation of the Ade in GATC sequences regulates diverse bacterial cell functions, including gene expression, mismatch repair and chromosome replication. Dam also controls virulence in many pathogenic Gram-negative bacteria. An unexplained and perplexing observation about Escherichia coli Dam (EcoDam) is that there is no obvious relationship between the genes that are transcriptionally responsive to Dam and the promoter-proximal presence of GATC sequences. Here, we demonstrate that EcoDam interacts with a 5-base pair non-cognate sequence distinct from GATC. The crystal structure of a non-cognate complex allowed us to identify a DNA binding element, GTYTA/TARAC (where Y = C/T and R = A/G). This element immediately flanks GATC sites in some Dam-regulated promoters, including the Pap operon which specifies pyelonephritis-associated pili. In addition, Dam interacts with near-cognate GATC sequences (i.e. 3/4-site ATC and GAT). All together, these results imply that Dam, in addition to being responsible for GATC methylation, could also function as a methylation-independent transcriptional repressor.

  12. Mononuclear zinc(II) complexes of 2-((2-(piperazin-1-yl)ethylimino)methyl)-4-substituted phenols: Synthesis, structural characterization, DNA binding and cheminuclease activities

    NASA Astrophysics Data System (ADS)

    Ravichandran, J.; Gurumoorthy, P.; Karthick, C.; Kalilur Rahiman, A.

    2014-03-01

    Four new zinc(II) complexes [Zn(HL1-4)Cl2] (1-4), where HL1-4 = 2-((2-(piperazin-1-yl)ethylimino)methyl)-4-substituted phenols, have been isolated and fully characterized using various spectro-analytical techniques. The X-ray crystal structure of complex 4 shows the distorted trigonal-bipyramidal coordination geometry around zinc(II) ion. The crystal packing is stabilized by intermolecular NH⋯O hydrogen bonding interaction. The complexes display no d-d electronic band in the visible region due to d10 electronic configuration of zinc(II) ion. The electrochemical properties of the synthesized ligands and their complexes exhibit similar voltammogram at reduction potential due to electrochemically innocent Zn(II) ion, which evidenced that the electron transfer is due to the nature of the ligand. Binding interaction of complexes with calf thymus DNA was studied by UV-Vis absorption titration, viscometric titration and cyclic voltammetry. All complexes bind with CT DNA by intercalation, giving the binding affinity in the order of 2 > 1 ? 3 > 4. The prominent cheminuclease activity of complexes on plasmid DNA (pBR322 DNA) was observed in the absence and presence of H2O2. Oxidative pathway reveals that the underlying mechanism involves hydroxyl radical.

  13. Antioxidant, DNA binding and nuclease activities of heteroleptic copper(II) complexes derived from 2-((2-(piperazin-1-yl)ethylimino)methyl)-4-substituted phenols and diimines

    NASA Astrophysics Data System (ADS)

    Ravichandran, J.; Gurumoorthy, P.; Imran Musthafa, M. A.; Kalilur Rahiman, A.

    2014-12-01

    A series of heteroleptic copper(II) complexes of the type [CuL1-4(diimine)](ClO4)2 (1-8) [L1-4 = 2-((2-(piperazin-1-yl)ethylimino)methyl)-4-substituted phenols, and diimine = 2,2?-bipyridyl (bpy) or 1,10-phenanthroline (phen)], have been synthesized and characterized by spectroscopic methods. The IR spectra of complexes indicate the presence of uncoordinated perchlorate anions and the electronic spectra revealed the square pyramidal geometry with N4O coordination environment around copper(II) nuclei. Electrochemical studies of the mononuclear complexes evidenced one-electron irreversible reduction wave in the cathodic region. The EPR spectra of complexes with g|| (2.206-2.214) and A|| (154-172 × 10-4 cm-1) values support the square-based CuN3O coordination chromophore and the presence of unpaired electron localized in dx-y ground state. Antioxidant studies against DPPH revealed effective radical scavenging properties of the synthesized complexes. Binding studies suggest that the heteroleptic copper(II) complexes interact with calf thymus DNA (CT-DNA) through minor-groove and electrostatic interaction, and all the complexes display pronounced nuclease activity against supercoiled pBR322 DNA.

  14. Mixed ligand ruthenium(III) complexes of benzaldehyde 4-methyl-3-thiosemicarbazones with triphenylphosphine/triphenylarsine co-ligands: Synthesis, DNA binding, DNA cleavage, antioxidative and cytotoxic activity

    NASA Astrophysics Data System (ADS)

    Sampath, K.; Sathiyaraj, S.; Raja, G.; Jayabalakrishnan, C.

    2013-08-01

    The new ruthenium(III) complexes with 4-methyl-3-thiosemicarbazone ligands, (E)-2-(2-chlorobenzylidene)-N-methylhydrazinecarbothioamide (HL1) and (E)-2-(2-nitrobenzylidene)-N-methylhydrazinecarbothioamide (HL2), were prepared and characterized by various physico-chemical and spectroscopic methods. The title compounds act as bidentate, monobasic chelating ligands with S and N as the donor sites and are preferably found in the thiol form in all the complexes studied. The molecular structure of HL1 and HL2 were determined by single crystal X-ray diffraction method. DNA binding of the ligands and complexes were investigated by absorption spectroscopy and IR spectroscopy. It reveals that the compounds bind to nitrogenous bases of DNA via intercalation. The oxidative cleavage of the complexes with CT-DNA inferred that the effects of cleavage are dose dependent. Antioxidant study of the ligands and complexes showed the significant antioxidant activity against DPPH radical. In addition, the in vitro cytotoxicity of the ligands and complexes against MCF-7 cell line was assayed which showed higher cytotoxic activity with the lower IC50 values indicating their efficiency in killing the cancer cells even at low concentrations.

  15. Protective effect of melatonin against the 1-methyl-4-phenylpyridinium-induced inhibition of complex I of the mitochondrial respiratory chain.

    PubMed

    Absi, E; Ayala, A; Machado, A; Parrado, J

    2000-08-01

    In the present study, a novel property of melatonin is shown: a protective effect of melatonin on the respiratory chain in isolated rat liver mitochondria and in striatal synaptosomes treated with 1-methyl-4-phenylpyridinium ion (MPP+). The cellular damage caused by MPP+, a compound that produces a Parkinsonian-like syndrome in humans, is the result of the mitochondrial respiration inhibition at the Complex I level and oxidative stress induction. Treatment of mitochondria with MPP+ inhibits the respiration rate. This effect was prevented by the inclusion of melatonin in the incubation mixture. This preventive effect, which is not related to the antioxidative properties of melatonin, seems to be due to the fact that melatonin prevents MPP+ interaction with Complex I. These results suggest that melatonin may protect against the effect of several Parkinsonogenic compounds that are associated with progressive impairment of mitochondrial function and increased oxidative damage. PMID:10949539

  16. Mixed Ligand Complexes of N-Methyl-N-phenyl Dithiocarbamate: Synthesis, Characterisation, Antifungal Activity, and Solvent Extraction Studies of the Ligand

    PubMed Central

    Ekennia, Anthony C.; Onwudiwe, Damian C.; Ume, Cyril; Ebenso, Eno E.

    2015-01-01

    A series of mixed ligand dithiocarbamate complexes with a general formula [ML2(py)2], where M = Mn(II), Co(II), Ni(II), and Cu(II), py = pyridine, and L = N-methyl-N-phenyl dithiocarbamate have been prepared and characterised by elemental analysis, FTIR and Uv spectroscopy, magnetic moment, and thermogravimetric and conductance analysis. The infrared spectra showed that symmetrical bidentate coordination occurred with the dithiocarbamate moiety through the sulfur atoms, while neutral monodentate coordination occurred through the nitrogen atom for the pyridine molecule in the complexes. The electronic spectra, elemental analysis, and magnetic moment results proved that the complexes adopted octahedral geometry. The conductance measurement showed that the complexes are nonelectrolytes proving their nonionic nature. The compounds were screened for three human pathogenic fungi: Aspergillus flavus, Aspergillus niger, and Candida albicans. The cobalt complex showed the best antifungal activity among the test compounds. Liquid-liquid extractive abilities of the ligand towards copper and nickel ions in different solvent media were investigated. The ligand showed a strong binding affinity towards the metals ions with an extractive efficiency of about 99%. PMID:26543441

  17. Iron(III) complexes of bis (benzimidazol-2-yl) methyl) thiophene-2,5-dicarboxamide: synthesis, spectral and oxidation of o-phenylenediamine.

    PubMed

    Tyagi, Nidhi; Mathur, Pavan

    2012-10-01

    Iron(III) complexes of a potentially pentadentate ligand N(2), N(5)-bis ((1H-benzo [d] imidazol-2-yl) methyl) thiophene-2,5-dicarboxamide are synthesized with an exogenous anion X=Cl(-), NO(3)(-). Mössbauer and EPR spectroscopy indicates axially distorted complexes. These complexes were utilized for the oxidation of o-phenylenediamine to 2,3-diaminophenazine in presence of H(2)O(2). The initial rate of reaction is dependent on the concentration of o-phenylenediamine as well as the iron(III) complex. Rates of reaction were found to be at least five times higher for the Cl(-) bound complex. The effect of an added anion like acetate, azide and citrate is found to inhibit the rate of reaction. This suggests that one of the factors affecting the rate determining step is the binding of these anions on a vacant site at the iron(III) centre. The oxidation of o-phenylenediamine to 2,3-diaminophenazine is reminiscent of the functioning of horse radish peroxidase. PMID:22885893

  18. Iron(III) complexes of bis (benzimidazol-2-yl) methyl) thiophene-2,5-dicarboxamide: Synthesis, spectral and oxidation of o-phenylenediamine

    NASA Astrophysics Data System (ADS)

    Tyagi, Nidhi; Mathur, Pavan

    2012-10-01

    Iron(III) complexes of a potentially pentadentate ligand N2, N5-bis ((1H-benzo [d] imidazol-2-yl) methyl) thiophene-2,5-dicarboxamide are synthesized with an exogenous anion X = Cl-, NO3-. Mössbauer and EPR spectroscopy indicates axially distorted complexes. These complexes were utilized for the oxidation of o-phenylenediamine to 2,3-diaminophenazine in presence of H2O2. The initial rate of reaction is dependent on the concentration of o-phenylenediamine as well as the iron(III) complex. Rates of reaction were found to be at least five times higher for the Cl- bound complex. The effect of an added anion like acetate, azide and citrate is found to inhibit the rate of reaction. This suggests that one of the factors affecting the rate determining step is the binding of these anions on a vacant site at the iron(III) centre. The oxidation of o-phenylenediamine to 2,3-diaminophenazine is reminiscent of the functioning of horse radish peroxidase.

  19. Synthesis, growth, spectral, and thermal studies of a new organic molecular charge transfer complex crystal: 3-nitroaniline 4-methyl benzene sulfonate.

    PubMed

    Selvakumar, E; Anandha babu, G; Ramasamy, P; Chandramohan, A

    2014-03-25

    A new organic intermolecular charge transfer complex 3-nitroaniline 4-methyl benzene sulfonate (NATS) has been successfully synthesized and good optical quality single crystals grown by slow solvent evaporation solution growth technique at room temperature using methanol as the solvent. The (1)H and (13)C NMR spectra were recorded to establish the molecular structure of the title complex. The crystal structure of NATS has been determined by single crystal XRD analysis and it belongs to orthorhombic crystal system with space group Pbca. Fourier transform infrared (FT-IR) spectral study has been carried out to confirm the presence of various functional groups present in the complex. Electronic absorption spectrum was recorded to find the prevalent charge transfer activity in the complex. The UV-Vis-NIR transmission spectrum was recorded in the range 200-2500 nm, to find the optical transmittance window and lower cut off wavelength of the title crystal. The thermal stability of the title complex crystal was studied by using thermo-gravimetric and differential thermal analyses and found that the compound is stable up to 215 °C. PMID:24322759

  20. Synthesis, characterization and properties of tetra((1-hydroxyimino-methylnaphthalen-2-yloxy)methyl)ethene and its homo-dinuclear metal complexes: A combined experimental and theoretical investigation

    NASA Astrophysics Data System (ADS)

    Serbest, Kerim; Karao?lu, Kaan; Erman, Murat; Er, Mustafa; De?irmencio?lu, ?smail

    2010-10-01

    Tetra((1-hydroxyiminomethylnaphthalen-2-yloxy)methyl)ethene (THIMNYOME), H 4L, was synthesized by the agents of 2-hydroxy-1-naphtaldehyde, tetra(bromomethyl)ethene and hydroxylamine hydrochloride in two steps. Characterization of THIMNYOME and its dinuclear complexes was made by elemental analyses, IR, 1H- and 13C NMR, UV-vis, electrospray ionisation mass spectra, molar conductivities and magnetic susceptibility measurements. In the light of these results, it was suggested that the ligand coordinate to each metal atom by the two ether oxygen, two nitrogen atoms of oxime imine (C dbnd N) and an axial oxygen of perchlorate to form pseudo square-pyramidal complexes with Ni(II), Cu(II) and Zn(II). Molar conductivity measurements reveal that all the complexes are non-electrolytes. In addition, the full geometric optimization of the tetraoxime ligand ( 4) has been made by the B3LYP/6-31G(d) level in order to establish a stable conformation. Additionally, all the complex structures have been studied in the B3LYP/LANL2DZ level. NBO charge distribution and the characteristics of frontier molecular orbitals of these complexes have also been investigated in order to see the electrons movement between ligand and metal atom in the same level.

  1. Guanine nucleobase adducts formed by a monofunctional complex: [Pt(N-(6-methyl-2-picolyl)-N-(2-picolyl)amine)Cl]Cl.

    PubMed

    Andrepont, Chase; Marzilli, Patricia A; Pakhomova, Svetlana; Marzilli, Luigi G

    2015-12-01

    Monofunctional Pt(II) complexes bind to G residues in DNA and, if the carrier ligands are bulky, cause DNA structural distortions that lead to anticancer activity. We assessed the steric effects of the tridentate carrier ligand, N(H)6-Medpa (N-(6-methyl-2-picolyl)-N-(2-picolyl)amine), bearing a 6-methyl group and a 6'-proton projecting toward the nucleobase in Pt(N(H)6-Medpa)G adducts (G=9-ethylguanine, 3'-GMP, 5'-GMP, 5'-GTP). Pt(N(H)6-Medpa)G adducts form syn and anti rotamers with the guanine O6 and the central N-H of N(H)6-Medpa on the same or opposite side of the coordination plane, respectively. Pt(N(H)6-Medpa)G adducts have some properties (ease of rotamer interchange and extent of conversion to bis adducts, Pt(N(H)6-Medpa)G2) intermediate to properties reported for analogs having a tridentate ligand with zero or two methyl groups. However, in comparison, the syn rotamer of Pt(N(H)6-Medpa)G adducts has an unexpectedly high abundance. This result is attributable to guanine base canting, such that the 6-membered guanine ring is positioned away from the bulky 6-Me group. This canting both relieves electrostatic repulsion between the partially positive H6' and the guanine H8 protons and creates a favorable electrostatic attraction between the H6' proton and the partially negative guanine O6. This combined information provides insight useful for designing monofunctional anticancer agents. PMID:26239547

  2. Critical analysis of spectral solvent shifts calculated by the contemporary PCM approaches of a representative series of charge-transfer complexes between tetracyanoethylene and methylated benzenes.

    PubMed

    Budzák, Šimon; Mach, Pavel; Medved', Miroslav; Kysel', Ondrej

    2015-07-21

    Applications of contemporary polarisable continuum model (PCM) quantum chemical approaches to account for the solvent shifts of UV-Vis absorption charge transfer (CT) transitions in electron donor-acceptor (EDA) complexes (as well as to account for their stability and other properties in solvents) have been rather rare until now. In this study, we systematically applied different - mainly state-specific - PCM approaches to examine excited state properties, namely, solvatochromic excitation energy shifts in a series of EDA complexes of a tetracyanoethylene (TCNE) acceptor with methyl substituted benzenes with different degrees of methylation N (NMB). For these complexes, representative and reliable experimental data exist both for the gas phase and in solution (dichloromethane). We have found that the linear response (LR) solvent shifts are too small compared to the experimental values, while self-consistent SS approaches give values that are too large. The best agreement with experimental values was obtained by corrected LR (cLR). The transition energies were calculated by means of TD-DFT methodology with PBE0, CAM-B3LYP and M06-2X functionals as well as the wave function CC2 method for the gas phase, and the PCM solvent shifts were added to account for the solvent effects. The best results for transition energies in solvents were obtained using the CC2 method complemented by CAM-B3LYP/cLR for the gas phase transition energy red solvent shift, while all three TD-DFT approaches used gave insufficient values (ca. 50%) of the slope of the dependence of the transition energies on N compared to experimental values. PMID:26051338

  3. Theoretical and experimental studies of phenol oxidation by ruthenium complex with N,N,N-tris(benzimidazol-2yl-methyl)amine.

    PubMed

    Hernandez, J Guadalupe; Silva, Antonio Romero; Thangarasu, Pandiyan; Najera, Rafael Herrera; Moreno, Alfonso Duran; Ledesma, M Teresa Orta; Cruz-Borbolla, Julian; Singh, Narinder

    2015-09-01

    The ruthenium complex with (N,N,N-tris(benzimidazol-2yl-methyl)amine, L(1)) was prepared, and characterized. Fukui data were used to localize the reactive sites on the ligand. The structural and electronic properties of the complex were analyzed by DFT in different oxidation states in order to evaluate its oxidant properties for phenol oxidation. The results show that the hard Ru(IV) cation bonds preferentially with a hard base (Namine = amine nitrogen, or axial chloride ion), and soft Ru(II) with a soft base (Nbzim = benzimidazole nitrogen or axial triphenyl phosphine). Furthermore, the Jahn-Teller effect causes an elongation of the axial bond in the octahedral structure. The bonding nature and the orbital contribution to the electronic transitions of the complex were studied. The experimental UV-visible bands were interpreted by using TD-DFT studies. The complex oxidizes phenol to benzoquinone in the presence of H2O2 and the intermediate was detected by HPLC and (13)C NMR. A possible mechanism and rate law are proposed for the oxidation. The adduct formation of phenol with [Ru(O)L(1)](2+) or [Ru(OH)L(1)](+) is theoretically analyzed to show that [Ru(OH)L(1)-OPh](+) could produce the phenol radical. PMID:26252971

  4. Spectroscopic, structural and antibacterial properties of copper(II) complexes with bio-relevant 5-methyl-3-formylpyrazole N(4)-benzyl-N(4)-methylthiosemicarbazone.

    PubMed

    Sau, Dhiman Kumar; Butcher, Ray J; Chaudhuri, Siddhartha; Saha, Nityananda

    2003-11-01

    The coordination behaviour of the title ligand, 5-methyl-3-formylpyrazole N(4)-benzyl-N(4)-methylthiosemicarbazone (HMPz4BM), is reported with solid state isolation of copper(II) complexes, [Cu(HMPz4BM)X2] (X = Cl, Br, NO3, ClO4 and BF4) which have been spectroscopically and structurally characterised. I.r. data for the free ligand and its Cu(II) complexes indicate that HMPz4BM exhibits a neutral NNS tridentate function via the pyrazolyl nitrogen(tertiary), azomethine nitrogen and thione sulphur. Electronic spectral data are suggestive of a square pyramidal environment for the seemingly pentacoordinated Cu(II) species. E.s.r parameters (RT and LNT) of the reported copper(II) complexes are indicative of a dx2-y2 ground state for the reported species. Cyclic voltammograms of Cu(II) complexes show a quasireversible CuII/CuIII couple and also an irreversible CuII/CuI couple. X-ray crystallography of a representative species, [Cu(HMPz4BM)(NO3)2] (C2/c, monoclinic), has unambiguously documented the conjectural findings from i.r. data that coordinating sites of the title ligand are pyrazolyl (tertiary) nitrogen, azomethine nitrogen and the thione sulphur (NNS); and the oxygen of one of the nitrate ions has occupied the basal plane; the fifth coordination position has been occupied by the oxygen of another nitrate ion in a square pyramidal geometry. The antibacterial properties of the ligand and its copper(II) complexes studied on microorganism, Staphylococcus aureus have pointed out that most of the complexes have higher activities than that of the free ligand. PMID:14619952

  5. Accurate Computer Simulation of Phase Equilibrium for Complex Fluid Mixtures. Application to Binaries Involving Isobutene, Methanol, Methyl tert-Butyl Ether, and

    E-print Network

    Lisal, Martin

    to Binaries Involving Isobutene, Methanol, Methyl tert-Butyl Ether, and n-Butane Martin Li´sal,*,, William R + methyl tert-butyl ether (MTBE) and the binaries formed by methanol with isobutene, MTBE, and n

  6. Resolution and characterization of helicate dimer and trimer complexes of 1,3-bis(9-methyl-1,10-phenanthrolin-2-yl)propane with copper(I).

    PubMed

    Lemus, Luis; Guerrero, Juan; Costamagna, Juan; Lorca, Romina; Jara, Danilo H; Ferraudi, Guillermo; Oliver, Allen; Lappin, A Graham

    2013-08-28

    Complexation of copper(I) with the binucleating ligand, 1,3-bis(9-methyl-1,10-phenanthrolin-2-yl)propane, mphenpr, result in formation of helical dimers, [Cu2(mphenpr)2](2+). The resolution of the enantiomeric forms of the dimers has been carried out with ?-[As(cat)3](-) as resolving agent and X-ray structures for two compounds, P-[Cu2(mphenpr)2](?-[As(cat)3])2 and P-[Cu2(mphenpr)2](?-[As(cat)3])2·4(CH3CN), are reported. The rate of racemization in poorly-coordinating solvents has been examined by (1)H NMR, and is slow. At saturating concentrations of [[Cu2(mphenpr)2](2+)] in acetonitrile, crystals of the helical trimeric complex [Cu3(mphenpr)3](ClO4)3 are obtained. The X-ray structure of the trimer is reported. This species has also been resolved. As with the helical dimer, racemization in poorly-coordinating solvents is slow, and circular dichroism and (1)H NMR spectra are reported. The absolute configuration of the resolved complex, P-[Cu3(mphenpr)3](?-[As(cat)3])3, has been determined by X-ray crystallography. PMID:23824074

  7. Methyl Iodide

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Methyl iodide (MeI, iodomethane, CH3I) was reported as a potential alternative to the stratospheric ozone-depleting fumigant methyl bromide (MeBr) in the mid-1990s (Sims et al., 1995; Ohr et al., 1996). It has since received significant research attention to determine its environmental fate and tran...

  8. Homogeneous solvation controlled photoreduction of cobalt(III) complexes in aqueous 2-methyl-2-propanol solutions linear solvation energy relationship and cyclic voltammetric analyses.

    PubMed

    Anbalagan, K; Lydia, I Sharmila

    2008-03-01

    The effect of solvent participation on the ligand-to-metal charge transfer (LMCT, L-->Co(III)) reduction of the of Co(III)(en)(2)Br(RC(6)H(4)NH(2))(2+) where R=m-OCH(3), p-F, H, m-CH(3), p-CH(3,)p-OC(2)H(5) and p-OCH(3) were examined in aqueous 2-methyl-2-propanol (Bu(t)OH) solutions. The change in the reduction behavior of Co(III) centre was also examined through cyclic voltammetric studies. The observed reduction in quantum yield due to LMCT excitation can mainly be accounted using linear solvation energy relationship (LSER) comprising model correlation equations. These consist of empirical parameters such as Grunwald-Winstein's solvent ionizing power, Y, Dimroth-Richardt's solvent micro-polarity parameter, E(T)(N), Gutmann's donor number, DN(N), along with Kamlet-Taft's solvatochromic parameters (hydrogen bond acceptor acidity/basicity alpha/beta and solvent dipolarity/polarizability, pi*). The origin of solvent effect is found to be due to microscopic interaction between the solvent donor and the nitrogen-bound hydrogen of the ligand. Cyclic voltammograms show an irreversible reduction of Co(III) in DMF using Glassy Carbon Electrode, GCE, the redox peaks for the aniline complexes appear at -0.20 and 0.525V. Irradiation of the complexes with UV light (lambda=254nm) in binary mixtures produce Co(II)(aq) and the concentration of this species are highly dependent on x(alc) (x(alc)=mole fraction of alcohol). The observed quantum yield (logPhi(Co(II))) is found to be linearly related to mole fraction of organic co-solvent added in the mixture, therefore, logPhi(Co(II))=26.41 x 10(-2) when x(2)=0.0094 and 43.75 x 10(-2) when x(2)=0.076 for a typical complex Co(III)(en)(2)Br(p-OCH(3)C(6)H(4)NH(2))(2+) in aqueous 2-methyl-2-propanol at 300K. Cyclic voltammetry and LSER analyses illustrate the variation of reduction property of Co(III) by the aryl ligand and homogeneous solvation of the excited state of the complex Co(III)(en)(2)Br(RC(6)H(4)NH(2))(2+) in H(2)O/Bu(t)OH mixtures. PMID:17698408

  9. Homogeneous solvation controlled photoreduction of cobalt(III) complexes in aqueous 2-methyl-2-propanol solutions. Linear solvation energy relationship and cyclic voltammetric analyses

    NASA Astrophysics Data System (ADS)

    Anbalagan, K.; Lydia, I. Sharmila

    2008-03-01

    The effect of solvent participation on the ligand-to-metal charge transfer (LMCT, L ? Co III) reduction of the of Co III(en) 2Br(RC 6H 4NH 2) 2+ where R = m-OCH 3, p-F, H, m-CH 3, p-CH 3,p-OC 2H 5 and p-OCH 3 were examined in aqueous 2-methyl-2-propanol (Bu tOH) solutions. The change in the reduction behavior of Co III centre was also examined through cyclic voltammetric studies. The observed reduction in quantum yield due to LMCT excitation can mainly be accounted using linear solvation energy relationship (LSER) comprising model correlation equations. These consist of empirical parameters such as Grunwald-Winstein's solvent ionizing power, Y, Dimroth-Richardt's solvent micro-polarity parameter, ETN, Gutmann's donor number, DN N, along with Kamlet-Taft's solvatochromic parameters (hydrogen bond acceptor acidity/basicity ?/ ? and solvent dipolarity/polarizability, ?*). The origin of solvent effect is found to be due to microscopic interaction between the solvent donor and the nitrogen-bound hydrogen of the ligand. Cyclic voltammograms show an irreversible reduction of Co III in DMF using Glassy Carbon Electrode, GCE, the redox peaks for the aniline complexes appear at -0.20 and 0.525 V. Irradiation of the complexes with UV light ( ? = 254 nm) in binary mixtures produce Co IIaq and the concentration of this species are highly dependent on xalc ( xalc = mole fraction of alcohol). The observed quantum yield (log ?Co(II)) is found to be linearly related to mole fraction of organic co-solvent added in the mixture, therefore, log ?Co(II) = 26.41 × 10 -2 when x2 = 0.0094 and 43.75 × 10 -2 when x2 = 0.076 for a typical complex Co III(en) 2Br( p-OCH 3C 6H 4NH 2) 2+ in aqueous 2-methyl-2-propanol at 300 K. Cyclic voltammetry and LSER analyses illustrate the variation of reduction property of Co(III) by the aryl ligand and homogeneous solvation of the excited state of the complex Co III(en) 2Br(RC 6H 4NH 2) 2+ in H 2O/Bu tOH mixtures.

  10. Methyl chloroform

    SciTech Connect

    Wray, T.K.

    1994-04-01

    Methyl chloroform is identified as a Class 1 ozone-depleting substance under Title VI of the CAA Amendments. On Nov. 30, 1993, EPA ordered the phaseout of Class 1 ozone-depleting substances -- chlorofluorocarbons (CFCs), halons, carbon tetrachloride and methyl chloroform -- by Jan. 1, 1996. Methyl chloroform and other Class 1 substances may be used after the dead-line if sources can be found through recycling or existing inventories. Methyl chloroform is listed as a hazardous air pollutant under CAA. It also is a SARA Title III, Sec. 313 compound with a reportable quantity of 1,000 pounds. OSHA and the American Conference of Government Industrial Hygienists have set 350 ppm as the time-weighted average airborne exposure level for methyl chloroform. NIOSH lists its immediately dangerous to life or health'' concentration as 1,000 parts per million. DOT identifies the substance as a hazardous material, Class 6.1 (poison).

  11. Ruthenium Polypyridyl Complexes Containing a Conjugated Ligand LDQ (LDQ ) 1-[4-(4-methyl)-2,2-bipyridyl]-2-[4-(4-N,N-tetramethylene-2,2-bipyridinum)]ethene): Synthesis,

    E-print Network

    Dutta, Prabir K.

    Ruthenium Polypyridyl Complexes Containing a Conjugated Ligand LDQ (LDQ ) 1-[4-(4-methyl)-2. In this study, the focus is on the ruthenium polypyridyl compound [(bpy)2RuLDQ]4+ (where bpy ) bipyridine ruthenium(II) as an electron donor and bipyridinium ions as electron acceptors have been extensively

  12. Synthesis and crystal structure of a dinuclear yttrium(III)- (lanthanide(III)-) copper(II) complex with an unusual 2-methyl-2,4,6-tris(trifluoromethyl)-1,3-dioxane-4,6-diolato ligand

    SciTech Connect

    Wang, S.; Pang, Z.; Smith, K.D.L. )

    1993-11-10

    A dinuclear Ln[sup III]-Cu[sup II] complex with an unusual 2-methyl-2,4,6-tris(trifluoromethyl)-1,3-dioxane-4,6-diolato ligand has been synthesized and characterized structurally. The 1,3-dioxane-4,6-diolato ligand is the product of cycloaddition of 1,1,1-trifluoro-2,2-propanediol to a hexafluoroacetylacetonato ligand promoted by the metal complex.

  13. Characterization of Albendazole-Randomly Methylated-?-Cyclodextrin Inclusion Complex and In Vivo Evaluation of Its Antihelmitic Activity in a Murine Model of Trichinellosis

    PubMed Central

    García, Agustina; Leonardi, Darío; Vasconi, María D.; Hinrichsen, Lucila I.; Lamas, María C.

    2014-01-01

    Albendazole is a benzimidazole carbamate extensively used in oral chemotherapy against intestinal parasites, due to its broad spectrum activity, good tolerance and low cost. However, the drug has the disadvantage of poor bioavailability due to its very low solubility in water; as a consequence, a very active area of research focuses on the development of new pharmaceutical formulations to increase its solubility, dissolution rate, and bioavailability. The primary objective of this study was to prepare randomly methylated ?-cyclodextrins inclusion complexes to increase albendazole dissolution rate, in order to enhance its antiparasitic activity. This formulation therapeutic efficacy was contrasted with that of the pure drug by treating Trichinella spiralis infected mice during the intestinal phase of the parasite cycle, on days five and six post-infection. This protocol significantly decreased muscle larval burden measured in the parenteral stage on day 30 post-infection, when compared with the untreated control. Thus, it could be demonstrated that the inclusion complexes improve the in vivo therapeutic activity of albendazole. PMID:25406084

  14. The proto-oncoprotein FBI-1 interacts with MBD3 to recruit the Mi-2/NuRD-HDAC complex and BCoR and to silence p21WAF/CDKN1A by DNA methylation

    PubMed Central

    Choi, Won-Il; Jeon, Bu-Nam; Yoon, Jae-Hyeon; Koh, Dong-In; Kim, Myung-Hwa; Yu, Mi-Young; Lee, Kyung-Mi; Kim, Youngsoo; Kim, Kyunggon; Hur, Sujin Susanne; Lee, Choong-Eun; Kim, Kyung-Sup; Hur, Man-Wook

    2013-01-01

    The tumour-suppressor gene CDKN1A (encoding p21Waf/Cip1) is thought to be epigenetically repressed in cancer cells. FBI-1 (ZBTB7A) is a proto-oncogenic transcription factor repressing the alternative reading frame and p21WAF/CDKN1A genes of the p53 pathway. FBI-1 interacts directly with MBD3 (methyl-CpG–binding domain protein 3) in the nucleus. We demonstrated that FBI-1 binds both non-methylated and methylated DNA and that MBD3 is recruited to the CDKN1A promoter through its interaction with FBI-1, where it enhances transcriptional repression by FBI-1. FBI-1 also interacts with the co-repressors nuclear receptor corepressor (NCoR), silencing mediator for retinoid and thyroid receptors (SMRT) and BCL-6 corepressor (BCoR) to repress transcription. MBD3 regulates a molecular interaction between the co-repressor and FBI-1. MBD3 decreases the interaction between FBI-1 and NCoR/SMRT but increases the interaction between FBI-1 and BCoR. Because MBD3 is a subunit of the Mi-2 autoantigen (Mi-2)/nucleosome remodelling and histone deacetylase (NuRD)-HDAC complex, FBI-1 recruits the Mi-2/NuRD-HDAC complex via MBD3. BCoR interacts with the Mi-2/NuRD-HDAC complex, DNMTs and HP1. MBD3 and BCoR play a significant role in the recruitment of the Mi-2/NuRD-HDAC complex– and the NuRD complex–associated proteins, DNMTs and HP. By recruiting DNMTs and HP1, Mi-2/NuRD-HDAC complex appears to play key roles in epigenetic repression of CDKN1A by DNA methylation. PMID:23658227

  15. Cytosine methylation is the most common covalent modification of DNA in eukaryotes. DNA methylation has an

    E-print Network

    3959 Cytosine methylation is the most common covalent modification of DNA in eukaryotes. DNA to transcriptional silencing. Complex multicellular eukaryotes (plants and animals) primarily methylate DNA reports have considerably expanded our knowledge of eukaryotic DNA methylation (Bibikova et al., 2006a

  16. Synthesis, characterization, and electronic structures of a methyl germyliumylidene ion and germylone-group VI metal complexes.

    PubMed

    Su, Bochao; Ganguly, Rakesh; Li, Yongxin; Kinjo, Rei

    2016-01-11

    The reaction of germylone (L)Ge (1) [L = 3-Ad-1-{C((t)Bu) = N(Mes)}C3H4N2] with 1 equivalent of MeOTf afforded a germyliumylidene ion [(L)GeMe](+)OTf(-) (2), while reactions with M(CO)5(thf) (M = Cr, Mo, W) gave the corresponding germylone-metal complexes [(L)Ge]M(CO)5 (3-5). The former possesses a pyramidal Ge center, whereas the latter display a planar geometry around the Ge atom. Computational studies showed a unique bonding interaction between 1 and the M(CO)5 unit, which involves a ?-donation as well as a weak ?-back-donation. PMID:26552365

  17. The Influence of Linker Geometry on Uranyl Complexation by Rigidly-Linked Bis(3-hydroxy-N-methyl-pyridin-2-one)

    SciTech Connect

    Szigethy, Geza; Raymond, Kenneth

    2010-04-22

    A series of bis(3-hydroxy-N-methyl-pyridin-2-one) ligands was synthesized, and their respective uranyl complexes were characterized by single crystal X-ray diffraction analyses. These structures were inspected for high-energy conformations and evaluated using a series of metrics to measure co-planarity of chelating moieties with each other and the uranyl coordination plane, as well as to measure coordinative crowding about the uranyl dication. Both very short (ethyl, 3,4-thiophene and o-phenylene) and very long ({alpha},{alpha}{prime}-m-xylene and 1,8-fluorene) linkers provide optimal ligand geometries about the uranyl cation, resulting in planar, unstrained molecular arrangements. The planarity of the rigid linkers also suggests there is a degree of pre-organization for a planar coordination mode that is ideal for uranyl-selective ligand design. Comparison of intramolecular N{sub amide}-O{sub phenolate} distances and {sup 1}H NMR chemical shifts of amide protons supports earlier results that short linkers provide the optimal geometry for intramolecular hydrogen bonding.

  18. Highly Selective Anti-Cancer Activity of Cholesterol-Interacting Agents Methyl-?-Cyclodextrin and Ostreolysin A/Pleurotolysin B Protein Complex on Urothelial Cancer Cells

    PubMed Central

    Resnik, Nataša; Repnik, Urška; Kreft, Mateja Erdani; Sep?i?, Kristina; Ma?ek, Peter; Turk, Boris; Verani?, Peter

    2015-01-01

    Cholesterol content can vary distinctly between normal and cancer cells, with elevated levels in cancer cells. Here, we investigated cholesterol sequestration with methyl-?-cyclodextrin (MCD), and pore-formation with the ostreolysin A/pleurotolysin B (OlyA/PlyB) protein complex that binds to cholesterol/sphingomyelin-rich membrane domains. We evaluated the effects on viability of T24 invasive and RT4 noninvasive human urothelial cancer cells and normal porcine urothelial (NPU) cells. Cholesterol content strongly correlated with cancerous transformation, as highest in the T24 high-grade invasive urothelial cancer cells, and lowest in NPU cells. MCD treatment induced prominent cell death of T24 cells, whereas OlyA/PlyB treatment resulted in greatly decreased viability of the RT4 low-grade noninvasive carcinoma cells. Biochemical and transmission electron microscopy analyses revealed that MCD and OlyA/PlyB induce necrotic cell death in these cancer cells, while viability of NPU cells was not significantly affected by either treatment. We conclude that MCD is more toxic for T24 high-grade invasive urothelial cancer cells, and OlyA/PlyB for RT4 low-grade noninvasive urothelial cancer cells, and neither is toxic for NPU cells. The cholesterol and cholesterol/sphingomyelin-rich membrane domains in urothelial cancer cells thus constitute a selective therapeutic target for elimination of urothelial cancer cells. PMID:26361392

  19. DNA Methylation

    PubMed Central

    Marinus, M.G.; Løbner-Olesen, A.

    2014-01-01

    The DNA of E. coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcm methyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during repair of replication errors, controlling the frequency of initiation of chromosome replication at oriC, and regulation of transcription initiation at promoters containing GATC sequences. In contrast, there is no known function for Dcm methylation although Dcm recognition sites constitute sequence motifs for Very Short Patch repair of T/G base mismatches. In certain bacteria (e.g., Vibrio cholerae, Caulobacter crescentus) adenine methylation is essential and in C. crescentus, it is important for temporal gene expression which, in turn, is required for coordinating chromosome initiation, replication and division. In practical terms, Dam and Dcm methylation can inhibit restriction enzyme cleavage; decrease transformation frequency in certain bacteria; decrease the stability of short direct repeats; are necessary for site-directed mutagenesis; and to probe eukaryotic structure and function. PMID:25405210

  20. A STUDY OF FUNDAMENTAL REACTION PATHWAYS FOR TRANSITION METAL ALKYL COMPLEXES. I. THE REACTION OF A NICKEL METHYL COMPLEX WITH ALKYNES. II. THE MECHANISM OF ALDEHYDE FORMATION IN THE REACTION OF A MOLYBDENUM HYDRIDE WITH MOLYBDENUM ALKYLS

    SciTech Connect

    Huggins, John Mitchell

    1980-06-01

    I. This study reports the rapid reaction under mild conditions of internal or terminal alkynes with methyl (acetyl~ acetonato) (triphenylphosphine) nickel (1) in either aromatic or ether solvents. In all cases vinylnickel products 2 are formed by insertion of the alkyne into the nickel=methyl bond. These complexes may be converted into a variety of organic products (e.g. alkenes, esters, vinyl halides) by treatment with appropriate reagents. Unsymmetrical alkynes give selectively the one regioisomer with the sterically largest substituent next to the nickel atom. In order to investigate the stereochemistry of the initial insertion, a x-ray diffraction study of the reaction of 1 with diphenylacetylene was carried out. This showed that the vinylnickel complex formed by overall trans insertion was the product of the reaction. Furthermore, subsequent slow isomerization of this complex, to a mixture of it and the corresponding cis isomer, demonstrated that this trans addition product is the kinetic product of the reaction. In studies with other alkynes, the product of trans addition was not always exclusively (or even predominantly) formed, but the ratio of the stereoisomers formed kinetically was substantially different from the thermodynamic ratio. Isotope labeling, added phosphine, and other experiments have allowed us to conclude that the mechanism of this reaction does involve initial cis addition. However, a coordinatively unsaturated vinylnickel complex is initially formed which can undergo rapid, phosphine-catalyzed cis-trans isomerization in competition with its conversion to the isolable phosphine-substituted kinetic reaction products. II. The reaction of CpMo(CO){sub 3}H (1a) with CpMo(CO){sub 3}R (2, R= CH{sub 3}, C{sub 2}H{sub 5}) at 50{degrees} C in THF gives the aldehyde RCHO and the dimers [CpMo(CO){sub 3}]{sub 2} (3a) and [CpMo(CO){sub 2}]{sub 2} (4a). Labeling one of the reactants with a methylcyclopentadienyl ligand it was possible to show that the mixed dimers MeCpMo(CO){sub 3}-(CO){sub 3}MoCp (3b) and MeCpMo(CO){sub 2}{triple_bond}(CO){sub 2}MoCp (4b) are the predominant kinetic products of the reaction. Additionally labeling the carbonyl ligands of 1a with {sup 13}CO led to the conclusion that all three of the carbonyl ligands in 1a end up in the tetracarbonyl dimers 4a if the reaction is carried out under a continuous purge of argon Trapping studies failed to find any evidence for the intermediacy of either [CpMo(CO){sub 3}]{sup -} or [CpMo(CO){sub 3}]{sup +} in this reaction. A mechanism is proposed that involves the initial migration of the alkyl ligand in 2 to CO forming an unsaturated acyl complex which reacts with 1a to give a binuclear complex containing a three center-two electron Mo-H-Mo bond. This complex then selectively looses a carbonyl from the acyl molybdenum, migrates the hydride to that same metal, and forms a metal-metal bond. This binuclear complex with the hydride and acyl ligands on one metal reductively eliminates aldehyde, and migrates a carbonyl ligand, to give 4a directly. The other product 3a is formed by addition of two molecules of free CO to 4a.

  1. Methyl methacrylate

    Integrated Risk Information System (IRIS)

    Methyl methacrylate ; CASRN 80 - 62 - 6 ( 03 / 02 / 98 ) Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments f

  2. Methyl parathion

    Integrated Risk Information System (IRIS)

    Methyl parathion ; CASRN 298 - 00 - 0 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic

  3. Methyl acrylate

    Integrated Risk Information System (IRIS)

    Methyl acrylate ; CASRN 96 - 33 - 3 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic Ef

  4. Methyl chloride

    Integrated Risk Information System (IRIS)

    EPA / 635 / R01 / 003 TOXICOLOGICAL REVIEW OF METHYL CHLORIDE ( CAS No . 74 - 87 - 3 ) In Support of Summary Information on the Integrated Risk Information System ( IRIS ) June 2001 U.S . Environmental Protection Agency Washington , DC DISCLAIMER This document has been reviewed in accordance with U.

  5. Methyl iodide

    Integrated Risk Information System (IRIS)

    Methyl iodide ; CASRN 74 - 88 - 4 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic Effe

  6. Methyl chlorocarbonate

    Integrated Risk Information System (IRIS)

    Methyl chlorocarbonate ; CASRN 79 - 22 - 1 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinog

  7. Methyl isocyanate

    Integrated Risk Information System (IRIS)

    Methyl isocyanate ; CASRN 624 - 83 - 9 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic

  8. Magnetic property and thermal analysis of a Mn(II) complex with [Mn(CO2)]n chains based on 4,4?-bis(1H-imidazol-1-yl-methyl)biphenyl

    NASA Astrophysics Data System (ADS)

    Zhang, Ming-Dao; Zheng, Bao-Hui; Wang, Zhe; Jiao, Yan; Chen, Min-Dong

    2014-11-01

    Magnetic coordination polymers have attracted considerable interest due to their novel structures and potential applications. In this paper, one new 2D magnetic manganese coordination polymer {[Mn(bimb)(OBA)]}n (1) was synthesized under solvothermal conditions based on 4,4?-bis(1H-imidazol-1-yl-methyl)biphenyl (bimb) and 4,4?-oxybis(benzoate) (H2OBA). Complex 1 contains [Mn(CO2)]n 1D chains and magnetic susceptibility measurements indicate that compound 1 exhibits an antiferromagnetic coupling interaction. In addition, complex 1 exhibits solid-state photoluminescence and high thermal stability.

  9. Structural and spectral studies of some coordination complexes of a phenol-functionalized diazamesocyclic ligand 1,4-bis-(3- tert-butyl-5-methyl-2-hydroxybenzyl)-1,4-diazacycloheptane ( H2L)

    NASA Astrophysics Data System (ADS)

    Guo, Ya-Mei; Du, Miao; Wang, Gui-Chang; Bu, Xian-He

    2002-12-01

    A series of four-coordinated monomeric Cu II, Co II, and Ni II complexes of a tetradentate diazamesocyclic ligand containing bulky phenolate donor pendants, [Cu L] ( 1), [Cu( HL)]ClO 4 ( 2), [Co L] ( 3), and [Ni L] ( 4), where H2L=1,4-bis-(3- tert-butyl-5-methyl-2-hydroxybenzyl)-1,4-diazacycloheptane, have been synthesized and characterized by elemental analyses, IR, UV-vis and ESR spectra. The crystal structure of complex 1 has been determined by X-ray diffraction analysis.

  10. Metal nitrosyl complexes of bioinorganic, catalytic, and environmental relevance: A novel single-step synthesis of dinitrosylmolybdenum(0) complexes of {Mo(NO) 2} 6 electron configuration involving Schiff bases derived from 4-acyl-3-methyl-1-phenyl-2-pyrazolin-5-one and 4-aminoantipyrine, directly from molybdate(VI) and their characterization

    NASA Astrophysics Data System (ADS)

    Maurya, R. C.; Pandey, A.; Chaurasia, J.; Martin, H.

    2006-10-01

    This paper reports the synthesis of five new hexa-coordinated mixed-ligand dinitrosyl complexes of molybdenum(0) of the composition [Mo(NO) 2(L)(OH)], where LH = N-(3'-methyl-1'-phenyl-4'-valerylidene-2'-pyrazolin-5'-one)-4-aminoantipyrine (mphvp-aapH), N-(4'-benzoylidene-3'-methyl-1'-phenyl-2 '-pyrazolin-5'-one)-4-aminoantipyrine (bmphp-aapH), N-(3'-methyl-1'-phenyl-4'-propionylidene-2'-pyrazolin-5'-one)-4-aminoantipyrine (mphpp-aapH), N-(4'-acetylidene-3'-methyl-1'-phenyl-2'-pyrazolin-5 '-one)-4-aminoantipyrine (amphp-aapH) or N-(-4'- iso-butyrylidene-3'-methyl-1'-phenyl-2'-pyrazolin-5'-one)-4-aminoantipyrine ( iso-bumphp-aapH) directly from molybdate (VI) in a single step and in a single pot. The compounds so obtained have been characterized by elemental analyses, molar conductance, decomposition temperature and magnetic measurements, thermogravimetric analyses, infrared and electronic spectral studies. They were found to contain low-spin [Mo(NO) 2] 6 electron configuration. A cis-octahedral structure has been proposed for these complexes. The 3D molecular modeling and analysis for bond lengths and bond angles have also been carried out for one of the representative compounds, [Mo(NO) 2(bmphp-aap)(OH)] ( 2).

  11. Mechanism of DNA methylation-directed histone methylation by KRYPTONITE

    PubMed Central

    Groth, Martin; Feng, Suhua; Hale, Christopher J.; Li, Sisi; Vashisht, Ajay A.; Wohlschlegel, James A.; Patel, Dinshaw J.; Jacobsen, Steven E.

    2014-01-01

    SUMMARY In Arabidopsis, CHG DNA methylation is controlled by the H3K9 methylation mark through a self-reinforcing loop between DNA methyltransferase CHROMOMETHYLASE3 (CMT3) and H3K9 histone methyltransferase KRYPTONITE/SUVH4 (KYP). We report on the structure of KYP in complex with methylated DNA, substrate H3 peptide and cofactor SAH, thereby defining the spatial positioning of the SRA domain relative to the SET domain. The methylated DNA is bound by the SRA domain with the 5mC flipped out of the DNA, while the H3(1-15) peptide substrate binds between the SET and post-SET domains, with the ?-ammonium of K9 positioned adjacent to bound SAH. These structural insights complemented by in vivo functional data on key mutants of residues lining the 5mC and H3K9-binding pockets within KYP, establish how methylated DNA recruits KYP to the histone substrate. Together, the structures of KYP and previously reported CMT3 complexes provide insights into molecular mechanisms linking DNA and histone methylation. PMID:25018018

  12. Sterically hindered complexes of platinum(II) with planar heterocyclic nitrogen donors. A novel complex with 1-methyl-cytosine has a spectrum of activity different from cisplatin and is able of overcoming acquired cisplatin resistance.

    PubMed

    Margiotta, Nicola; Natile, Giovanni; Capitelli, Francesco; Fanizzi, Francesco P; Boccarelli, Angelina; De Rinaldis, Pietro; Giordano, Domenico; Coluccia, Mauro

    2006-11-01

    A very interesting series of water soluble platinum compounds violating some of the classical structure-activity relationships, but still showing antitumor activity, was reported by Hollis and collaborators some 25 years ago [L.S. Hollis, A.R. Amundsenm, E.W. Stern. J. Med. Chem. 32 (1989) 128-136]. The compounds, having formula [PtClA(2)L](+) (A(2)=two monodentate or a bidentate amine, L=a secondary or tertiary amine or a N-donor heterocycle), were characterized by a positive charge and three non-labile N-donor ligands. We have extended the investigation to analogous compounds in which 2,9-dimethyl-1,10-phenanthroline has taken the place of the A(2) ligand(s) and L is 2-picoline (1), 6-amino-2-picoline (2), or 1-methyl-cytosine (3). The X-ray analysis of 2 has revealed a bow-like distortion of the phenanthroline plane, a sloping of the phenanthroline plane with respect to the coordination plane, and an overall shielding of the metallic core by the ortho substituents of the phenanthroline and pyridine ligands. In vitro grow inhibition assays have been performed on the most water soluble complex 3. The results indicate that this complex is characterized by a potent growth inhibitory activity with mean IC(50) value (in a panel of 11 human tumor cell lines) of 1.1 microM to be compared with a mean value of 3.8 microM for cisplatin. The same compound also appears to completely overcome the acquired cisplatin resistance stemming from reduced uptake or a multifocal mechanism, thus pointing to a mechanism of action distinctly different from that of cisplatin. PMID:16959321

  13. Synthesis, spectroscopic characterization, DNA interaction and biological activities of Mn(II), Co(II), Ni(II) and Cu(II) complexes with [(1H-1,2,4-triazole-3-ylimino)methyl]naphthalene-2-ol

    NASA Astrophysics Data System (ADS)

    Gaber, Mohamed; El-Wakiel, Nadia A.; El-Ghamry, Hoda; Fathalla, Shaimaa K.

    2014-11-01

    Manganese(II), cobalt(II), nickel(II) and copper(II) complexes of [(1H-1,2,4-triazole-3-ylimino)methyl]naphthalene-2-ol have been synthesized. The structure of complexes have been characterized by elemental analysis, molar conductance, magnetic moment measurements and spectral (IR, 1H NMR, EI-mass, UV-Vis and ESR), and thermal studies. The results showed that the chloro and nitrato Cu(II) complexes have octahedral geometry while Ni(II), Co(II) and Mn(II) complexes in addition to acetato Cu(II) complex have tetrahedral geometry. The possible structures of the metal complexes have been computed using the molecular mechanic calculations using the hyper chem. 8.03 molecular modeling program to confirm the proposed structures. The kinetic and thermodynamic parameters of the thermal decomposition steps were calculated from the TG curves. The binding modes of the complexes with DNA have been investigated by UV-Vis absorption titration. The results showed that the mode of binding of the complexes to DNA is intercalative or non-intercalative binding modes. Schiff base and its metal complexes have been screened for their in vitro antimicrobial activities against Gram positive bacteria (Staphylococcus aureus), Gram negative bacteria (Escherichia coli and Pesudomonas aeruginosa), fungi (Asperigllus flavus and Mucer) and yeast (Candida albicans and Malassezia furfur).

  14. Synthesis and spectral characterization of mono- and binuclear copper(II) complexes derived from 2-benzoylpyridine-N?-methyl-3-thiosemicarbazone: crystal structure of a novel sulfur bridged copper(II) box-dimer.

    PubMed

    Jayakumar, K; Sithambaresan, M; Aiswarya, N; Kurup, M R Prathapachandra

    2015-03-15

    Mononuclear and binuclear copper(II) complexes of 2-benzoylpyridine-N(4)-methyl thiosemicarbazone (HL) were prepared and characterized by a variety of spectroscopic techniques. Structural evidence for the novel sulfur bridged copper(II) iodo binuclear complex is obtained by single crystal X-ray diffraction analysis. The complex [Cu2L2I2], a non-centrosymmetric box dimer, crystallizes in monoclinic C2/c space group and it was found to have distorted square pyramidal geometry (Addison parameter, ?=0.238) with the square basal plane occupied by the thiosemicarbazone moiety and iodine atom whereas the sulfur atom from the other coordinated thiosemicarbazone moiety occupies the apical position. This is the first crystallographically studied system having non-centrosymmetrical entities bridged via thiolate S atoms with Cu(II)I bond. The tridentate thiosemicarbazone coordinates in mono deprotonated thionic tautomeric form in all complexes except in sulfato complex, [Cu(HL)(SO4)]·H2O (1) where it binds to the metal centre in neutral form. The magnetic moment values and the EPR spectral studies reflect the binuclearity of some of the complexes. The spin Hamiltonian and bonding parameters are calculated based on EPR studies. In all the complexes g||>g?>2.0023 and the g values in frozen DMF are consistent with the d(x2-y2) ground state. The thermal stabilities of some of the complexes were also determined. PMID:25546494

  15. Synthesis and spectral characterization of mono- and binuclear copper(II) complexes derived from 2-benzoylpyridine-N4-methyl-3-thiosemicarbazone: Crystal structure of a novel sulfur bridged copper(II) box-dimer

    NASA Astrophysics Data System (ADS)

    Jayakumar, K.; Sithambaresan, M.; Aiswarya, N.; Kurup, M. R. Prathapachandra

    2015-03-01

    Mononuclear and binuclear copper(II) complexes of 2-benzoylpyridine-N4-methyl thiosemicarbazone (HL) were prepared and characterized by a variety of spectroscopic techniques. Structural evidence for the novel sulfur bridged copper(II) iodo binuclear complex is obtained by single crystal X-ray diffraction analysis. The complex [Cu2L2I2], a non-centrosymmetric box dimer, crystallizes in monoclinic C2/c space group and it was found to have distorted square pyramidal geometry (Addison parameter, ? = 0.238) with the square basal plane occupied by the thiosemicarbazone moiety and iodine atom whereas the sulfur atom from the other coordinated thiosemicarbazone moiety occupies the apical position. This is the first crystallographically studied system having non-centrosymmetrical entities bridged via thiolate S atoms with Cu(II)sbnd I bond. The tridentate thiosemicarbazone coordinates in mono deprotonated thionic tautomeric form in all complexes except in sulfato complex, [Cu(HL)(SO4)]·H2O (1) where it binds to the metal centre in neutral form. The magnetic moment values and the EPR spectral studies reflect the binuclearity of some of the complexes. The spin Hamiltonian and bonding parameters are calculated based on EPR studies. In all the complexes g|| > g? > 2.0023 and the g values in frozen DMF are consistent with the dx2-y2 ground state. The thermal stabilities of some of the complexes were also determined.

  16. Synthesis, Characterization, and Biological Activity of N?-[(Z)-(3-Methyl-5-oxo-1-phenyl-1,5-dihydro-4H-pyrazol-4-ylidene)(phenyl)methyl]benzohydrazide and Its Co(II), Ni(II), and Cu(II) Complexes

    PubMed Central

    Asegbeloyin, Jonnie N.; Ujam, Oguejiofo T.; Okafor, Emmanuel C.; Babahan, Ilknur; Coban, Esin Poyrazoglu; Özmen, Ali; Biyik, Halil

    2014-01-01

    Reaction of 1-phenyl-3-methyl-4-benzoyl-pyrazol-5-one and benzoyl hydrazide in refluxing ethanol gave N?-[(Z)-(3-methyl-5-oxo-1-phenyl-1,5-dihydro-4H-pyrazol-4-ylidene)(phenyl)methyl]benzohydrazide (HL1), which was characterized by NMR spectroscopy and single-crystal X-ray structure study. X-ray diffraction analyses of the crystals revealed a nonplanar molecule, existing in the keto-amine form, with intermolecular hydrogen bonding forming a seven-membered ring system. The reaction of HL1 with Co(II), Ni(II), and Cu(II) halides gave the corresponding complexes, which were characterized by elemental analysis, molar conductance, magnetic measurements, and infrared and electronic spectral studies. The compounds were screened for their in vitro cytotoxic activity against HL-60 human promyelocytic leukemia cells and antimicrobial activity against some bacteria and yeasts. Results showed that the compounds are potent against HL-60 cells with the IC50 value ?5??M, while some of the compounds were active against few studied Gram-positive bacteria. PMID:25332694

  17. Crystal structure of a dinuclear CoII complex with bridging fluoride ligands: di-?-fluorido-bis­{tris­[(6-methyl­pyridin-2-yl)meth­yl]amine}­dicobalt(II) bis­(tetra­fluorido­borate)

    PubMed Central

    Inomata, Masataka; Suenaga, Yusaku

    2014-01-01

    Reaction of Co(BF4)2·6H2O with tris­[(6-methyl­pyridin-2-yl)meth­yl]amiine in methanol results in a fluoride abstraction from BF4 ?, yielding the unexpected title compound, [Co2F2(C21H24N4)2](BF4)2. The complex cation consists of two inversion-related [Co(C21H24N4)]2+ moieties bridged by a pair of fluoride ligands. The CoII cation is six-coordinated in a distorted octa­hedral geometry and forms a +II high-spin state. In the crystal, the complex cation and the BF4 ? anion are connected by C—H?F hydrogen bonds, forming a three-dimensional network. An intra­molecular C—H?F hydrogen bond is also observed. PMID:25484774

  18. Synthesis, characterization, antimicrobial, DNA-cleavage and antioxidant activities of 3-((5-chloro-2-phenyl-1H-indol-3-ylimino)methyl)quinoline-2(1H)-thione and its metal complexes

    NASA Astrophysics Data System (ADS)

    Vivekanand, B.; Mahendra Raj, K.; Mruthyunjayaswamy, B. H. M.

    2015-01-01

    Schiff base 3-((5-chloro-2-phenyl-1H-indol-3-ylimino)methyl)quinoline-2(1H)-thione and its Cu(II), Co(II), Ni(II), Zn(II) and Fe(III), complexes have been synthesized and characterized by elemental analysis, UV-Visible, IR, 1H NMR, 13C NMR and mass spectra, molar conductance, magnetic susceptibility, ESR and TGA data. The ligand and its metal complexes have been screened for their antibacterial activity against Staphylococcus aureus and Pseudomonas aeruginosa, antifungal activity against Aspergillus niger and Aspergillus flavus in minimum inhibition concentration (MIC) by cup plate method respectively, antioxidant activity using 1,1-diphenyl-2-picryl hydrazyl (DPPH), which was compared with that of standard drugs vitamin-C and vitamin-E and DNA cleavage activity using calf-thymus DNA.

  19. Synthesis, spectroscopic, crystal structure and DNA binding of Ru(II) complexes with 2-hydroxy-benzoic acid [1-(4-hydroxy-6-methyl-2-oxo-2H-pyran-3-yl)-ethylidene]-hydrazide

    NASA Astrophysics Data System (ADS)

    Chitrapriya, Nataraj; Sathiya Kamatchi, Thangavel; Zeller, Matthias; Lee, Hyosun; Natarajan, Karuppannan

    2011-10-01

    Reactions of 2-hydroxy-benzoic acid [1-(4-hydroxy-6-methyl-2-oxo-2H-pyran-3-yl)-ethylidene]-hydrazide (H 2L) with [RuHCl(CO)(EPh 3) 3] (E = P or As) were carried out and the new complexes obtained were characterized by elemental analysis, electronic, IR, 1H NMR and 13C NMR spectroscopic techniques and single crystal X-ray diffraction studies. Complex ( 1) crystallizes in the monoclinic space group P2(1)/ c with unit cell dimensions a = 18.6236(17) Å, b = 12.8627(12) Å, c = 21.683(2) Å, ? = 90.00, ? = 114.626(2), ? = 90.00 V = 4721.8(8) Å, Z = 4. The crystal structure of the complex shows Ru(II) atom is six-coordinated, forming a slightly distorted octahedral geometry with two P atoms in axial positions, and three chelating donor atoms of the tridentate Schiff base ligand and one carbonyl group located in the equatorial plane. The molecular structure is stabilized by intramolecular O—H···N interactions. No intermolecular hydrogen bond was observed. The intramolecular hydrogen bond exists between the oxygen atom from salicylic acid moiety and nitrogen from the same moiety. A variety of solution studies were carried out for the determination of DNA binding mode of the complexes. The results suggest that both complexes bind to Herring sperm DNA via non intercalative mode.

  20. Analytical Methodologies for Detection of Gamma-valerolactone, Delta-valerolactone, Acephate, and Azinphos Methyl and their Associated Metabolites in Complex Biological Matrices

    SciTech Connect

    Zink, Erika M.; Clark, Ryan J.; Grant, Karen E.; Campbell, James A.; Hoppe, Eric W.

    2005-01-01

    Non-invasive biomonitoring for chemicals of interest in law enforcement and similar monitoring of pesticides together with their metabolites can not only save money but can lead to faster medical attention for individuals exposed to these chemicals. This study describes methods developed for the analysis of gamma-valerolactone (GVL), delta-valerolactone (DVL), acephate, and azinphos methyl in saliva and serum. Liquid chromatography/mass spectrometry (LC/MS) operated in the negative ion mode and in the positive ion mode and gas chromatography/mass spectrometry (GC/MS) were used to analyze GVL and DVL. Although both analytical techniques worked well, lower detection limits were obtained with GC/MS. The lactones and their corresponding sodium salts were spiked into both saliva and serum. The lactones were isolated from saliva or serum using newly developed extraction techniques and then subsequently analyzed using GC/MS. The sodium salts of the lactones are nonvolatile and require derivatization prior to analysis by this method. N-methyl-N-(t-butyldimethylsilyl)-trifluoroacetamide (MTBSTFA) was ultimately selected as the reagent for derivatization because the acidic conditions required for reactions with diazomethane caused the salts to undergo intramolecular cyclization to the corresponding lactones. In vitro studies were conducted using rat liver microsomes to determine other metabolites associated with these compounds. Azinphos methyl and acephate are classified as organophosphate pesticides, and are known to be cholinesterase inhibitors in humans and insects, causing neurotoxicity. For this reason they have both exposure and environmental impact implications. These compounds were spiked into serum and saliva and prepared for analysis by GC/MS. Continuation of this research would include analysis by GC/MS under positive ion mode to determine the parent ions of the unknown metabolites. Further research is planned through an in vivo analysis of the lactones and pesticides. These methodologies could be extended for further analysis of other similar compounds as well as chemical and biological warfare agents.

  1. Analytical Methodologies for Detection of Gamma-Valerolactone, Delta-Valerolactone, Acephate and Azinphos Methyl and Their Associated Metabolites in Complex Biological Matrices

    SciTech Connect

    Zink, E.; Clark, R.; Grant, K.; Campbell, J.; Hoppe, E.

    2005-01-01

    Non-invasive biomonitoring for chemicals of interest in law enforcement and similar monitoring of pesticides, together with their metabolites, can not only save money but can lead to faster medical attention for individuals exposed to these chemicals. This study describes methods developed for the analysis of gamma-valerolactone (GVL), delta-valerolactone (DVL), acephate, and azinphos methyl in saliva and serum. Liquid chromatography/mass spectrometry (LC/MS) operated in the negative and positive ion mode and gas chromatography/mass spectrometry (GC/MS) were used to analyze GVL and DVL. Although both analytical techniques worked well, lower detection limits were obtained with GC/MS. The lactones and their corresponding sodium salts were spiked into both saliva and serum. The lactones were isolated from saliva or serum using newly developed extraction techniques and then subsequently analyzed using GC/MS. The sodium salts of the lactones are nonvolatile and require derivatization prior to analysis by this method. N-methyl-N-(t-butyldimethylsilyl)-trifluoroacetamide (MTBSTFA) was ultimately selected as the reagent for derivatization because the acidic conditions required for reactions with diazomethane caused the salts to undergo intramolecular cyclization to the corresponding lactones. In vitro studies were conducted using rat liver microsomes to determine other metabolites associated with these compounds. Azinphos methyl and acephate are classified as organophosphate pesticides, and are known to be cholinesterase inhibitors in humans and insects, causing neurotoxicity. For this reason they have both exposure and environmental impact implications. These compounds were spiked into serum and saliva and prepared for analysis by GC/MS. Continuation of this research would include analysis by GC/MS under positive ion mode to determine the parent ions of the unknown metabolites. Further research is planned through an in vivo analysis of the lactones and pesticides. These methodologies could be extended for further analysis of other similar compounds.

  2. Crystal structure of zwitterionic 4-(ammonio­methyl)­benzoate: a simple mol­ecule giving rise to a complex supra­molecular structure

    PubMed Central

    Atria, Ana María; Garland, Maria Teresa; Baggio, Ricardo

    2014-01-01

    The asymmetric unit of the title compound, C8H9NO2·H2O consists of an isolated 4-(ammonio­meth­yl)benzoate zwitterion derived from 4-amino­methyl­benzoic acid through the migration of the acidic proton, together with a water molecule of crystallization that is disordered over three sites with occupancy ratios (0.50:0.35:0.15). In the crystal structure, N—H?O hydrogen bonds together with ?–? stacking of the benzene rings [centroid–centroid distance = 3.8602?(18)?Å] result in a strongly linked, compact three-dimensional structure. PMID:25484753

  3. IRM-GCMS analysis of thermally stressed oils containing {sup 13}C methyl labelled 4-methyl dibenzothiophene

    SciTech Connect

    Filley, T.R.; Filley, R.M.; Eser, S.

    1995-12-31

    4-methyl dibenzothiophene with 100% {sup 13}C methyl was added to a decant oil, which is a feedstock for petroleum coking. The mixture was heated to 500{degrees}C for 15, 30, 45, and 60 minutes in a tubing bomb under autogenous pressure. Analysis by irm-GCMS of the resultant maltene fraction showed redistribution of the {sup 13}C-labelled methyl group to other aromatic hydrocarbons as well as formation of {sup 13}C labelled di- and tri-methyl dibenzothiophenes. The extent of uptake of labelled methyl varied considerably among different aromatic hydrocarbons as did the reactions of specific methyl isomers with the same aromatic backbone. By tracking the redistribution of the labelled methyl with time we can determine the reactivities; of specific sites within a complex chemical mixture. This application of stable isotope analysis will substantially aid in the understanding of mechanisms associated with complex systems such as catalytic cracking, catalytic desulfurization and petroleum coking.

  4. The origins of atmospheric methyl mercury

    SciTech Connect

    Prestbo, E.M.; Bloom, N.S.

    1995-12-31

    Methyl Hg in precipitation shows strong regional patterns, with highest volume weighted mean values (0.4 ng/L) in the Pacific Northwest and lowest values in Florida (<0.01 ng/l). Over most of the North Central region, average values range from 0.05 to 0.2 ng/L. Several potential sources of methyl Hg to the atmosphere have been investigated, including direct anthropogenic emissions, atmospheric methylation of Hg{sup o} or Hg(II), and emissions of methyl or dimethyl Hg from natural surfaces (oceans, bogs, or forests). Direct measurements of major total Hg sources such as coal and waste combustors, and sewage treatment facilities suggest that direct anthropogenic emissions are an insignificant source of methyl Hg to the atmosphere. The gas phase reaction of methyl halides with Hg{sup o} also appears to be an insignificant source of methyl Hg to the atmosphere. Recent laboratory experiments have provided a likely mechanism for atmospheric Hg methylation via a complex reaction involving acetate, sulfite, and iron. From a series of field measurements, another source appears to be the degradation of dimethyl mercury emitted by the upwelling of deep ocean water.

  5. [On the biological action of transition metal complexes. 2. The antiviral activity of 4-methyl-2-amino-pyridine-palladium-chloride (IV)].

    PubMed

    Tonew, M; Tonew, E; Schröer, H P; Heyn, B

    1981-01-01

    4-methyl-2-amino-pyridine-palladiumchlorid (IV) showed an inactivation of cell-free enveloped DNA and RNA viruses in serum-free saline such as vaccinia, pseudorabies, herpes type 1, Newcastle disease and influenza virus A/fowl plague, human influenza type A and B and vesicular stomatitis viruses, and adenovirus, a naked DNA virus, too. Picorna viruses were not inactivated, the inactivation of other viruses failed in medium with 10% serum. However the replication of enveloped viruses as checked with vaccinia and fowl plague viruses was inhibited, also when the compound was present only for 1 h after infection. Contrary to this the multiplication of adenovirus was depressed only with 90%. For the inactivation of viruses high concentrations were necessary than for the inhibition of replication. Therefore more than one kind of mode of action have to be taken into consideration. PMID:6797148

  6. Methyl formate in star forming regions

    NASA Astrophysics Data System (ADS)

    Occhiogrosso, A.; Viti, S.; Modica, P.; Palumbo, M. E.

    2011-05-01

    Methyl formate is an important organic complex molecule that has been detected in hot cores and hot corinos, two different regions in the interstellar medium. Chemical model based only on gas-phase reactions are unable to account for the observed abundances of methyl formate, and it is believed that gas-grain chemical models are therefore needed. We update the gas-grain model UCL/CHEM (Viti et al. 2004) to include recent experiments involving methyl formate and present in this poster a chemical model for a sample of hot cores and hot corinos. The work presented here is a part of the LASSIE European Network.

  7. Methyl salicylate overdose

    MedlinePLUS

    Methyl salicylate is a wintergreen-scented chemical found in many over-the-counter products, including muscle ache creams. Methyl salicylate overdose occurs when someone accidentally or intentionally takes ...

  8. Comparison of reactivity of Pt(II) center in the mononuclear and binuclear organometallic diimineplatinum complexes toward oxidative addition of methyl iodide

    NASA Astrophysics Data System (ADS)

    Hashemi, Majid

    2016-01-01

    The reactivities of Pt(II) center in a series of organometallic mononuclear Pt(II), binuclear Pt(II) and binuclear mixed-valence Pt(II)-Pt(IV) complexes toward oxidative addition of MeI have been compared from a theoretical point of view. The nucleophilicity index and electron-donation power were calculated for each of these complexes. The energies of HOMO and dZ2 orbital were determined for these complexes. Very good correlations were found between logk2 (k2 is the experimentally determined second order rate constant for the oxidative addition of MeI on these complexes) and nucleophilicity index or electron-donation power for these complexes. The correlation between logk2 and the energy of HOMO or the energy of dZ2 orbital were also very good. The condensed-to-atom Fukui functions for electrophilic attack on these complexes showed that the Pt(II) center is the preferred site for the oxidative addition of MeI. All of these observations are in agreement with the proposed SN2 type mechanism in the oxidative addition of MeI on the Pt(II) center in these complexes.

  9. Intramolecular energy transfer in actinide complexes of 6-methyl-2-(2-pyridyl)-benzimidazole (biz): comparison between Cm{sup 3+} and Tb{sup 3+} systems

    SciTech Connect

    Assefa, Zerihun . E-mail: assefaz@ornl.gov; Yaita, T.; Haire, R.G.; Tachimori, S.

    2005-02-15

    Coordination of the 6-methyl-2-(2-pyridyl)-benzimidazole ligand with actinide and lanthanide species can produce enhanced emission due to increased efficiency of intramolecular energy transfer to metal centers. A comparison between the curium and terbium systems indicates that the position of the ligand's triplet state is critical for the enhanced emission. The energy gap between the ligand's triplet state and the acceptor level in curium is about 1000cm{sup -1}, as compared to a {approx}600cm{sup -1} gap in the terbium system. Due to the larger gap, the back transfer with curium is reduced and the radiative yield is significantly higher. The quantum yield for this 'sensitized' emission increases to 6.2%, compared to the 0.26% value attained for the metal centered excitation prior to ligand addition. In the terbium case, the smaller donor/acceptor gap enhances back transfer and the energy transfer is less efficient than with the curium system.

  10. Strategy to enhance efficacy of doxorubicin in solid tumor cells by methyl-?-cyclodextrin: Involvement of p53 and Fas receptor ligand complex

    PubMed Central

    Mohammad, Naoshad; Vikram Singh, Shivendra; Malvi, Parmanand; Chaube, Balkrishna; Athavale, Dipti; Vanuopadath, Muralidharan; Nair, Sudarslal Sadasivan; Nair, Bipin; Bhat, Manoj Kumar

    2015-01-01

    Doxorubicin (DOX) is one of the preferred drugs for treating breast and liver cancers. However, its clinical application is limited due to severe side effects and the accompanying drug resistance. In this context, we investigated the effect on therapeutic efficacy of DOX by cholesterol depleting agent methyl-?-cyclodextrin (MCD), and explored the involvement of p53. MCD sensitizes MCF-7 and Hepa1–6 cells to DOX, Combination of MCD and marginal dose of DOX reduces the cell viability, and promoted apoptosis through induction of pro-apoptotic protein, Bax, activation of caspase-8 and caspase-7, down regulation of anti-apoptotic protein Bcl-2 and finally promoting PARP cleavage. Mechanistically, sensitization to DOX by MCD was due to the induction of FasR/FasL pathway through p53 activation. Furthermore, inhibition of p53 by pharmacological inhibitor pifithrin-? (PFT-?) or its specific siRNA attenuated p53 function and down-regulated FasR/FasL, thereby preventing cell death. Animal experiments were performed using C57BL/6J mouse isografted with Hepa1–6 cells. Tumor growth was retarded and survival increased in mice administered MCD together with DOX to as compared to either agent alone. Collectively, these results suggest that MCD enhances the sensitivity to DOX for which wild type p53 is an important determinant. PMID:26149967

  11. Structural Basis for Methyl Transfer by a Radical SAM Enzyme

    SciTech Connect

    Boal, Amie K.; Grove, Tyler L.; McLaughlin, Monica I.; Yennawar, Neela H.; Booker, Squire J.; Rosenzweig, Amy C.

    2014-10-02

    The radical S-adenosyl-l-methionine (SAM) enzymes RlmN and Cfr methylate 23S ribosomal RNA, modifying the C2 or C8 position of adenosine 2503. The methyl groups are installed by a two-step sequence involving initial methylation of a conserved Cys residue (RlmN Cys{sup 355}) by SAM. Methyl transfer to the substrate requires reductive cleavage of a second equivalent of SAM. Crystal structures of RlmN and RlmN with SAM show that a single molecule of SAM coordinates the [4Fe-4S] cluster. Residue Cys{sup 355} is S-methylated and located proximal to the SAM methyl group, suggesting the SAM that is involved in the initial methyl transfer binds at the same site. Thus, RlmN accomplishes its complex reaction with structural economy, harnessing the two most important reactivities of SAM within a single site.

  12. [Research advances in methyl bromide in the ocean].

    PubMed

    Du, Hui-na; Xie, Wen-xia; Cui, Yu-qian; Chen, Jian-lei; Ye, Si-yuan

    2014-12-01

    Methyl bromide is an important atmospheric trace gas, which plays significant roles in the global warming and atmospheric chemistry. The ocean plays important and complex roles in the global biogeochemical cycles of methyl bromide, not only the source of atmospheric methyl bromide, but also the sink. Therefore, developing the chemical research of the soluble methyl bromide in the ocean, will not only have a certain guiding significance to the atmospheric ozone layer protection, but also provide a theoretical basis for estimating methyl bromide's contribution to the global environmental change on global scale. This paper reviewed the research advances on methyl bromide in the ocean, from the aspects of the biogeochemical cycle of methyl bromide in the ocean, the analysis and determination method, the concentration distribution, the sea-to-air flux and its sources and sinks in the atmosphere. Some deficiencies in the current studies were put forward, and the directions of the future studies were prospected. PMID:25876424

  13. Synthesis, characterization and biological activities of 2-((E)-(benzo[d][1,3]dioxol-6-ylimino)methyl)-6-ethoxyphenol and its metal complexes.

    PubMed

    Sundararajan, M L; Anandakumaran, J; Jeyakumar, T

    2014-05-01

    Metal complexes of Zn(II), Cd(II), Ni(II), Cu(II), and Fe(III) have been synthesized from the Schiff base ligand derived by the condensation of 3,4-(methylenedioxy)aniline and 3-ethoxy salicylaldehyde. The compounds have been characterized by using elemental analysis, molar conductance, IR, UV-Visible, (1)H NMR, (13)C NMR, mass spectra and thermal analysis (TG/DTA). The elemental analysis suggests the stoichiometry to be 1:1 (metal:ligand). The IR, (1)H NMR, (13)C NMR and UV-Visible spectral data suggest that the ligand coordinate to the metal atom by imino nitrogen and phenolic oxygen as bidentate manner. The mass spectral data also strengthen the formation of the metal complexes. The thermal behaviors of the complexes prove the presence of lattice as well as coordinated water molecules in the complexes. The in vitro biological screening effects of the synthesized compounds are tested against five bacterial species and three fungal species by well diffusion method. Antioxidant activities have also been performed for all the compounds. Metal complexes show more pronounced biological activity than the free ligand. PMID:24531110

  14. Complexes of (?(6)-benzene)ruthenium(ii) with 1,4-bis(phenylthio/seleno-methyl)-1,2,3-triazoles: synthesis, structure and applications in catalytic activation of oxidation and transfer hydrogenation.

    PubMed

    Saleem, Fariha; Rao, Gyandshwar K; Kumar, Satyendra; Singh, Mahabir Pratap; Singh, Ajai K

    2015-11-28

    1,4-Bis(phenylthio/seleno methyl)-1,2,3-triazoles (L1-L4) synthesized by a 'Click' reaction react with [{(?(6)-C6H6)RuCl(?-Cl)}]2 and NH4PF6 resulting in complexes [(?(6)-C6H6)RuClL]PF6 (1-4 for L = L1-L4) in which the ligands coordinate in a bidentate mode through S/Se and N of triazole. The CH2EPh (E = S or Se) attached to nitrogen of triazole remains pendent. Ligands and complexes have been authenticated with multinuclei NMR, IR and HR-MS. Single crystal structures of complexes 1-4 have been solved. The Ru-S and Ru-Se bond lengths (Å) are respectively 2.388(2)/2.3902(19) and 2.5007(4)/2.5262(19). The disposition of benzene ring, N, S/Se and Cl around Ru is of a piano stool type. For catalytic oxidation of alcohols [Oppenauer-type and with N-methylmorpholine-N-oxide (NMO)] and transfer hydrogenation (TH) of carbonyl compounds [with 2-propanol and glycerol] all the four complexes have been found efficient. The optimum catalyst loadings (in mol%) are: 0.01 (NMO), 0.1 (Oppenauer), 0.01 (TH with 2-propanol) and 0.5 (TH with glycerol). Interestingly, time profiles (under optimum conditions) of two catalytic oxidations and TH's are almost similar, suggesting that they are competitive on appropriate catalyst loading. DFT calculations are consistent with somewhat low reactivity of 1 in comparison to those of 2-4. PMID:26477509

  15. Synthesis and characterization of complexes of p-isopropyl benzaldehyde and methyl 2-pyridyl ketone thiosemicarbazones with Zn(II) and Cd(II) metallic centers. Cytotoxic activity and induction of apoptosis in Pam-ras cells.

    PubMed

    Pérez, J M; Matesanz, A I; Martín-Ambite, A; Navarro, P; Alonso, C; Souza, P

    1999-07-15

    It is known that metallic complexes of methyl 2-pyridyl ketone thiosemicarbazone (HL1) and p-isopropyl benzaldehyde thiosemicarbazone (HL2) may have potential antitumor activity. We have prepared complexes of HL1 and HL2 with Zn(II) and Cd(II). The cytotoxic activity shown by these compounds against cell lines sensitive and resistant to cis-diamminedichloroplatinum(II) (cis-DDP) indicates that coupling of HL1 and HL2 to Zn(II) and Cd(II) centers may result in metallic complexes with important biological properties since they display IC50 values in a microM range similar to that of the antitumor drug cis-DDP. Moreover, it is interesting to note that the Zn/HL2 complex exhibits specific cytotoxic activity against Pam-ras cells (cis-DDP resistant cells which over-express the H-ras oncogene) with an in vitro therapeutic index of 3.26 versus 0.78 for cis-DDP. Treatment of Pam-ras cells with the IC50 value of the Zn/HL2 compound induces a 'DNA ladder' (fragmentation of genomic DNA in nucleosome units) indicative of apoptosis in this ras-transformed cell line. In contrast, a 'DNA smear' (non-specific fragmentation of genomic DNA) is observed in Pam 212 normal cells treated with the IC50 of this compound. The analysis by circular dichroism (CD) spectroscopy of the interaction of the Zn/HL2 compound with calf thymus DNA (CT DNA) indicates that it produces stronger alterations on the double helix conformation than cis-DDP. So, these results suggest that Zn/HL2 may be considered a potential antitumor agent. PMID:10499288

  16. A complex study of 5-amino-3-methyl-4-[2-(5-amino-1,3,4-oxadiazolo)]-isoxazole monohydrate: A new low-molecular-weight immune response modifier

    NASA Astrophysics Data System (ADS)

    Ryng, Stanis?aw; Zimecki, Micha?; Jezierska-Mazzarello, Aneta; Panek, Jaros?aw J.; M?czy?ski, Marcin; G?owiak, Tadeusz; Sawka-Dobrowolska, Wanda; Koll, Aleksander

    2011-07-01

    A new potential lead structure with immunological activity, 5-amino-3-methyl-4-[2-(5-amino-1,3,4-oxadiazolo)]-isoxazole monohydrate, was synthesized. A detailed description of synthesis is presented together with X-ray structural analysis. In vitro assays showed that the compound had a potent immunosuppressive activity. Next, Density Functional Theory (DFT) was employed to shed a light on molecular properties of the investigated isoxazole derivative. The molecular modeling part included geometric as well as electronic structure descriptions: (i) the conformational analysis was performed to localize the most appropriate conformation; (ii) the coordination energy and Basis Set Superposition Error (BSSE) were estimated for the complex of the isoxazole derivative interacting with water molecule; (iii) the potential energy distribution was used to assign molecular vibrations, and NBO population analysis served to describe the electronic structure; (iv) the electrostatic potential map was generated to provide the graphical presentation of regions exposed for intermolecular interactions. The contacts between the water molecule and the nitrogen atom of the isoxazole ring edge were present in the solid phase. On the other hand, the theoretical DFT prediction was that the oxygen atom of the edge should form a more stable complex with the water molecule.

  17. A Specialized Histone H1 Variant Is Required for Adaptive Responses to Complex Abiotic Stress and Related DNA Methylation in Arabidopsis1[OPEN

    PubMed Central

    Rutowicz, Kinga; Puzio, Marcin; Halibart-Puzio, Joanna; Lirski, Maciej; Kotli?ski, Maciej; Krote?, Magdalena A.; Knizewski, Lukasz; Lange, Bartosz; Muszewska, Anna; ?niegowska-?wierk, Katarzyna; Ko?cielniak, Janusz; Iwanicka-Nowicka, Roksana; Buza, Krisztián; Janowiak, Franciszek; ?muda, Katarzyna; Jõesaar, Indrek; Laskowska-Kaszub, Katarzyna; Fogtman, Anna; Kollist, Hannes; Zielenkiewicz, Piotr; Tiuryn, Jerzy; Siedlecki, Pawe?; Swiezewski, Szymon; Ginalski, Krzysztof; Koblowska, Marta; Archacki, Rafa?; Wilczynski, Bartek; Rapacz, Marcin; Jerzmanowski, Andrzej

    2015-01-01

    Linker (H1) histones play critical roles in chromatin compaction in higher eukaryotes. They are also the most variable of the histones, with numerous nonallelic variants cooccurring in the same cell. Plants contain a distinct subclass of minor H1 variants that are induced by drought and abscisic acid and have been implicated in mediating adaptive responses to stress. However, how these variants facilitate adaptation remains poorly understood. Here, we show that the single Arabidopsis (Arabidopsis thaliana) stress-inducible variant H1.3 occurs in plants in two separate and most likely autonomous pools: a constitutive guard cell-specific pool and a facultative environmentally controlled pool localized in other tissues. Physiological and transcriptomic analyses of h1.3 null mutants demonstrate that H1.3 is required for both proper stomatal functioning under normal growth conditions and adaptive developmental responses to combined light and water deficiency. Using fluorescence recovery after photobleaching analysis, we show that H1.3 has superfast chromatin dynamics, and in contrast to the main Arabidopsis H1 variants H1.1 and H1.2, it has no stable bound fraction. The results of global occupancy studies demonstrate that, while H1.3 has the same overall binding properties as the main H1 variants, including predominant heterochromatin localization, it differs from them in its preferences for chromatin regions with epigenetic signatures of active and repressed transcription. We also show that H1.3 is required for a substantial part of DNA methylation associated with environmental stress, suggesting that the likely mechanism underlying H1.3 function may be the facilitation of chromatin accessibility by direct competition with the main H1 variants. PMID:26351307

  18. A Specialized Histone H1 Variant Is Required for Adaptive Responses to Complex Abiotic Stress and Related DNA Methylation in Arabidopsis.

    PubMed

    Rutowicz, Kinga; Puzio, Marcin; Halibart-Puzio, Joanna; Lirski, Maciej; Kotli?ski, Maciej; Krote?, Magdalena A; Knizewski, Lukasz; Lange, Bartosz; Muszewska, Anna; ?niegowska-?wierk, Katarzyna; Ko?cielniak, Janusz; Iwanicka-Nowicka, Roksana; Buza, Krisztián; Janowiak, Franciszek; ?muda, Katarzyna; Jõesaar, Indrek; Laskowska-Kaszub, Katarzyna; Fogtman, Anna; Kollist, Hannes; Zielenkiewicz, Piotr; Tiuryn, Jerzy; Siedlecki, Pawe?; Swiezewski, Szymon; Ginalski, Krzysztof; Koblowska, Marta; Archacki, Rafa?; Wilczynski, Bartek; Rapacz, Marcin; Jerzmanowski, Andrzej

    2015-11-01

    Linker (H1) histones play critical roles in chromatin compaction in higher eukaryotes. They are also the most variable of the histones, with numerous nonallelic variants cooccurring in the same cell. Plants contain a distinct subclass of minor H1 variants that are induced by drought and abscisic acid and have been implicated in mediating adaptive responses to stress. However, how these variants facilitate adaptation remains poorly understood. Here, we show that the single Arabidopsis (Arabidopsis thaliana) stress-inducible variant H1.3 occurs in plants in two separate and most likely autonomous pools: a constitutive guard cell-specific pool and a facultative environmentally controlled pool localized in other tissues. Physiological and transcriptomic analyses of h1.3 null mutants demonstrate that H1.3 is required for both proper stomatal functioning under normal growth conditions and adaptive developmental responses to combined light and water deficiency. Using fluorescence recovery after photobleaching analysis, we show that H1.3 has superfast chromatin dynamics, and in contrast to the main Arabidopsis H1 variants H1.1 and H1.2, it has no stable bound fraction. The results of global occupancy studies demonstrate that, while H1.3 has the same overall binding properties as the main H1 variants, including predominant heterochromatin localization, it differs from them in its preferences for chromatin regions with epigenetic signatures of active and repressed transcription. We also show that H1.3 is required for a substantial part of DNA methylation associated with environmental stress, suggesting that the likely mechanism underlying H1.3 function may be the facilitation of chromatin accessibility by direct competition with the main H1 variants. PMID:26351307

  19. Properties of extruded starch-poly(methyl acrylate) graft copolymers prepared from spherulites formed from amylose-oleic acid inclusion complexes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mixtures of high amylose corn starch and oleic acid were processed by steam jet-cooking, and the dispersions were rapidly cooled to yield amylose-oleic acid inclusion complexes as sub-micron spherulites and spherulite aggregates. Dispersions of these spherulite particles were then graft polymerized ...

  20. Genome-Wide Methylation Profiling of Schizophrenia

    PubMed Central

    Rukova, B; Staneva, R; Hadjidekova, S; Stamenov, G; Milanova; Toncheva, D

    2014-01-01

    Schizophrenia is one of the major psychiatric disorders. It is a disorder of complex inheritance, involving both heritable and environmental factors. DNA methylation is an inheritable epigenetic modification that stably alters gene expression. We reasoned that genetic modifications that are a result of environmental stimuli could also make a contribution. We have performed 26 high-resolution genome-wide methylation array analyses to determine the methylation status of 27,627 CpG islands and compared the data between patients and healthy controls. Methylation profiles of DNAs were analyzed in six pools: 220 schizophrenia patients; 220 age-matched healthy controls; 110 female schizophrenia patients; 110 age-matched healthy females; 110 male schizophrenia patients; 110 age-matched healthy males. We also investigated the methylation status of 20 individual patient DNA samples (eight females and 12 males. We found significant differences in the methylation profile between schizophrenia and control DNA pools. We found new candidate genes that principally participate in apoptosis, synaptic transmission and nervous system development (GABRA2, LIN7B, CASP3). Methylation profiles differed between the genders. In females, the most important genes participate in apoptosis and synaptic transmission (XIAP, GABRD, OXT, KRT7), whereas in the males, the implicated genes in the molecular pathology of the disease were DHX37, MAP2K2, FNDC4 and GIPC1. Data from the individual methylation analyses confirmed, the gender-specific pools results. Our data revealed major differences in methylation profiles between schizophrenia patients and controls and between male and female patients. The dysregulated activity of the candidate genes could play a role in schizophrenia pathogenesis. PMID:25937794

  1. Isomer dependence in the assembly and lability of silver(I) trifluoromethanesulfonate complexes of the heteroditopic ligands, 2-, 3-, and 4-[di(1H-pyrazolyl)methyl]phenyl(di-p-tolyl)phosphine.

    PubMed

    Gardinier, James R; Hewage, Jeewantha S; Lindeman, Sergey V

    2014-11-17

    Three isomers of a new heteroditopic ligand that contains a di(1H-pyrazolyl)methyl (-CHpz2) moiety connected to a di(p-tolyl)phosphine group via a para-, meta-, or ortho-phenylene spacer (pL, mL, and oL, respectively) have been synthesized by using a palladium(0)-catalyzed coupling reaction between HP(p-tolyl)2 and the appropriate isomer of (IC6H4)CHpz2. The 1:1 complexes of silver(I) trifluoromethanesulfonate, Ag(OTf), were prepared to examine the nature of ligand coordination and the type of supramolecular isomer (monomeric, cyclic oligomeric, or polymeric) that would be obtained. The single crystal X-ray diffraction studies showed that [Ag(pL)](OTf), 1, and [Ag(mL)](OTf), 2, possessed cyclic dimeric dications, whereas [Ag(oL)](OTf), 3, was a coordination polymer. The polymeric chain in 3 could be disrupted by reaction with triphenylphosphine, and the resulting complex, [Ag(oL)(PPh3)](OTf), 4, possessed a monometallic cation where the ligand was bound to silver in a chelating ?(2)P,N- coordination mode. The solution structures of 1-4 were probed via a combination of IR, variable-temperature multinuclear ((1)H, (13)C, (31)P) NMR spectroscopy, as well as by electron spray ionization (ESI)(+) mass spectrometry. A related complex [Ag(m-IC6H4CHpz2)2](OTf), 5, was also prepared, and its solid-state and solution spectroscopic properties were studied for comparison purposes. These studies suggest that the cyclic structures of 1 and 2 are likely preserved but are dynamic in solution at room temperature. Moreover, both 3 and 4 have dynamic solution structures where 3 is likely extensively dissociated in CH3CN or acetone rather than being polymeric as in the solid state. PMID:25375040

  2. Iron and chromium complexes containing tridentate chelates based on nacnac and imino- and methyl-pyridine components: triggering C-X bond formation.

    PubMed

    Morris, Wesley D; Wolczanski, Peter T; Sutter, Jörg; Meyer, Karsten; Cundari, Thomas R; Lobkovsky, Emil B

    2014-07-21

    Nacnac-based tridentate ligands containing a pyridyl-methyl and a 2,6-dialkyl-phenylamine (i.e., (2,6-R2-C6H3N?C(Me)CH?C(Me)NH(CH2py); R = Et, {Et(nn)PM}H; R = (i)Pr, {(i)Pr(nn)PM}H) were synthesized by condensation routes. Treatment of M{N(TMS)2}THFn (M = Cr, n = 2; M = Fe, Co, n = 1; TMS = trimethylsilane; THF = tetrahydrofuran) with {(i)Pr(nn)PM}H) afforded {(i)Pr(nn)PM}MN(TMS)2 (1-M(iPr); M = Cr, Fe); {Et(nn)PM}MN(TMS)2 (1-M(Et); M = Fe, Co) was similarly obtained. {R(nn)PM}FeBr (R = (i)Pr, Et; 2-Fe(R)) were prepared from FeBr2 and {R(nn)PM}Li, and alkylated to generate {R(nn)PM}Fe(neo)Pe (R = (i)Pr, Et; 3-Fe(R)). Carbonylation of 3-Fe(R) provided {(i)Pr(nn)PM}Fe(CO(neo)Pe)CO (4-Fe(iPr)), and carbonylations of 1-Fe(R) (R = Et, (i)Pr) and 1-Cr(iPr) induced deamination to afford {R(nn)PI}Fe(CO)2 (R = (i)Pr, 5-Fe(iPr); Et, 5-Fe(Et)), where PI is pyridine-imine, and {?(2)-N,N-pyrim-pyr}Cr(CO)4 (6-Cr(iPr)), in which the aryl-amide side of the nacnac attacked the incipient PI group. Carbon-carbon bonds were formed at the imine carbon of the {R(nn)PI} ligand. Addition of [{(i)Pr(nn)PI}(2-)](K(+)(THF)x)2 to FeCl3 generated {(i)Pr(nn)CHpy}2Fe2Cl2 (7-Fe(iPr)), and TMSN3 induced the deamination of 1-Fe(Et), but with disproportionation to provide {[Et(nn)CHpy]2}Fe (8-Fe(Et)). Ph2CN2 induced C-C bond formation with 1-Fe(iPr) via its thermal degradation to ultimately afford {(i)Pr(nn)CHpy}2(FeN?CPh2)2 (9-Fe(iPr)). The compounds were examined by X-ray crystallography (1-M(iPr), M = Cr, Fe; 1-Co(Et); 2-Fe(iPr); 4-Fe(iPr); 5-Fe(iPr); 6-Cr(iPr); 7-Fe(iPr); 8-Fe(Et); 9-Fe(iPr)), Mössbauer spectroscopy, and NMR spectroscopy. Structural parameters assessing redox noninnocence are discussed, as are structural and mechanistic consequences of the various electronic environments. PMID:25010819

  3. In situ preparation of powder and the sorption behaviors of molecularly imprinted polymers through the complexation between polymer ion of methyl methacrylate/acrylic acid and Ca++ ion.

    PubMed

    Chough, Sung Hyo; Park, Kwang Ho; Cho, Seung Jin; Park, Hye Ryoung

    2014-09-01

    Molecularly imprinted polymer (MIP) powders were prepared using a simple complexation strategy between the polymer carboxylate groups and template molecule followed by metal cation cross-linking of residual polymer carboxylates. Polymer powders were formed in situ by templating carboxylic acid containing polymers with 4-ethylaniline (4-EA), followed by addition of an aqueous CaCl2 solution. The solution remained homogeneous. The powders were prepared by precipitation by slowly adding a non-solvent, H2O, to the mixture. The resulting particles were very porous with uptake capacity that approached the theoretical value. We suggest two types of complexes are formed between the template, 4-EA, and polymer. The isolated entry type forms well defined cavities for the template with high specific selectivity, while the adjacent entry type forms wider binding sites without specific sorption for isomeric molecules. To evaluate conditions for forming materials with high affinity and selectivity, three MIPs were prepared containing 0.5, 1.0, and 1.5 equivalents of template to the base polymer. The MIP containing 0.5 eq showed higher specific selectivity to 4-EA, but the MIP containing 1.5 eq had noticeably lower selectivity. The lower selectivity is attributed to poorly formed binding sites with little selective sorption to any isomer when the higher ratio of template was used. However at the lower ratio of template the isolated entry is preferably formed to produce well defined binding cavities with higher selectivity to template. PMID:25109865

  4. Synthesis and Characterization of Bioactive Acylpyrazolone Sulfanilamides and Their Transition Metal Complexes: Single Crystal Structure of 4-Benzoyl-3-methyl-1-phenyl-2-pyrazolin-5-one Sulfanilamide

    PubMed Central

    Idemudia, Omoruyi G.; Sadimenko, Alexander P.; Afolayan, Anthony J.; Hosten, Eric C.

    2015-01-01

    Two Schiff base ligands Ampp-Sn 1 and Bmpp-Sn 2, afforded by a condensation reaction between sulfanilamide and the respective acylpyrazolone carbonyl precursors, their Mn(II), Co(II), Ni(II), and Cu(II) complexes prepared by the reaction of ligands and corresponding metal salts in aqueous solutions, were synthesized and then characterized by both analytical and spectroscopic methods, in a view to developing new improved bioactive materials with novel properties. On the basis of elemental analysis, spectroscopic and TGA results, transition metal complexes, with octahedral geometry having two molecules of the bidentate keto-imine ligand each, have been proposed. The single crystal structure of Bmpp-Sn according to X-ray crystallography showed a keto-imine tautomer type of Schiff base, having three intramolecular bonds, one short N2?H2?O3 hydrogen bond of 1.90?Å and two long C13?H13?O2 and C32?H32?O3 hydrogen bonds of 2.48?Å. A moderate to low biological activities have been exhibited by synthesized compounds when compared with standard antimicrobial agents on screening the synthesized compounds against Staphylococcus aureus, Bacillus pumilus, Proteus vulgaris, and Aeromonas hydrophila for antibacterial activity and against free radical 1, 1-diphenyl-2-picryl-hydrazyl (DPPH) for antioxidant activity. PMID:26106285

  5. RNA-directed DNA methylation

    PubMed Central

    2010-01-01

    Epigenetic RNA based gene silencing mechanisms play a major role in genome stability and control of gene expression. Transcriptional gene silencing via RNA-directed DNA methylation (RdDM) guides the epigenetic regulation of the genome in response to disease states, growth, developmental and stress signals. RdDM machinery is composed of proteins that produce and modify 24-nt-long siRNAs, recruit the RdDM complex to genomic targets, methylate DNA and remodel chromatin. The final DNA methylation pattern is determined by either DNA methyltransferase alone or by the combined action of DNA methyltransferases and demethylases. The dynamic interaction between RdDM and demethylases may render the plant epigenome plastic to growth, developmental and environmental cues. The epigenome plasticity may allow the plant genome to assume many epigenomes and to have the right epigenome at the right time in response to intracellular or extracellular stimuli. This review discusses recent advances in RdDM research and considers future perspectives. PMID:20421728

  6. The Search for a Complex Molecule in a Selected Hot Core Region: a Rigorous Attempt to Confirm Trans-Ethyl Methyl Ether Toward W51 E1/E2

    NASA Astrophysics Data System (ADS)

    Carroll, Brandon; McGuire, Brett A.; Apponi, Aldo J.; Ziurys, Lucy; Blake, Geoffrey; Remijan, Anthony

    2014-06-01

    An extensive search has been conducted to confirm transitions of trans-ethyl methyl ether (tEME), (C_2H_5OCH_3), toward the high mass star forming region W51 e1/e2 using the 12 m Telescope of the Arizona Radio Observatory (ARO) at 2 mm and 3 mm wavelengths. Typical peak to peak noise levels for the present observations of W51e1/e2 were between 10 mK to 30 mK, indicating an upper limit of the tEME column density of ? 1.5 × 1015 cm-2, this would make tEME at least a factor 2 times less abundant than dimethyl ether (CH_3OCH_3) toward W51 e1/e2. We have also performed an extensive search for this species toward the high mass star forming region Sgr B2(N-LMH) with the NRAO 100 m Green Bank Telescope (GBT). No transitions of tEME were detected and we were able to set an upper limit to the tEME column density of ? 4 × 1014 cm-2 toward Sgr B2(N-LMH). We will discuss these observations in the context of detecting large complex organic species toward star forming regions with next generation telescopes such as ALMA.

  7. DNA Methylation Biomarkers: Cancer and Beyond

    PubMed Central

    Mikeska, Thomas; Craig, Jeffrey M.

    2014-01-01

    Biomarkers are naturally-occurring characteristics by which a particular pathological process or disease can be identified or monitored. They can reflect past environmental exposures, predict disease onset or course, or determine a patient’s response to therapy. Epigenetic changes are such characteristics, with most epigenetic biomarkers discovered to date based on the epigenetic mark of DNA methylation. Many tissue types are suitable for the discovery of DNA methylation biomarkers including cell-based samples such as blood and tumor material and cell-free DNA samples such as plasma. DNA methylation biomarkers with diagnostic, prognostic and predictive power are already in clinical trials or in a clinical setting for cancer. Outside cancer, strong evidence that complex disease originates in early life is opening up exciting new avenues for the detection of DNA methylation biomarkers for adverse early life environment and for estimation of future disease risk. However, there are a number of limitations to overcome before such biomarkers reach the clinic. Nevertheless, DNA methylation biomarkers have great potential to contribute to personalized medicine throughout life. We review the current state of play for DNA methylation biomarkers, discuss the barriers that must be crossed on the way to implementation in a clinical setting, and predict their future use for human disease. PMID:25229548

  8. A (pentafluoroethyl)(trifluoromethyl)carbene complex of iridium and reductive activation of its sp(3)?, ?, and ? carbon-fluorine bonds to give perfluoro-2-butyne, perfluoro-1,2,3-butatriene and perfluoro-1-irida-2-methyl-2-cyclobutene) complexes.

    PubMed

    Yuan, Jian; Hughes, Russell P; Rheingold, Arnold L

    2015-12-01

    The (pentafluoroethyl)(trifluoromethyl)carbene complex Cp*Ir(CO)[[double bond, length as m-dash]C(CF3)(C2F5)] was synthesized by the reductive activation of the ?-C-F bond in the perfluoro-sec-butyl-iridium complex Cp*Ir(CO)[CF(CF3)(C2F5)](I) with Na/Pb alloy. This compound exists as two geometric isomers in solution; the structure of one isomer has been determined by a single crystal X-ray diffraction study and contains two independent molecules in the asymmetric unit. Further reduction of this carbene complex with Na/Pb alloy afforded the perfluoro-2-butyne iridium complex Cp*Ir(CO)(?(2)-CF3C[triple bond, length as m-dash]CCF3) by an overall 2-electron reduction and elimination of two ?-fluorides. When magnesium graphite was utilized as the reducing agent for the further reduction, Cp*Ir(CO)(?(2)-CF3C[triple bond, length as m-dash]CCF3) was produced as a minor product and the major product was the perfluoroiridacyclobutene complex Cp*Ir(CO)(?(2,4)-CF3CCFCF2) resulting from a ?-C-F bond activation. Direct reduction of the precursor Cp*Ir(CO)[CF(CF3)(C2F5)](i) with magnesium graphite generated the tetrafluorobutatriene iridium complex Cp*Ir(CO)(?(2,3)-CF2[double bond, length as m-dash]C[double bond, length as m-dash]C[double bond, length as m-dash]CF2) along with the perfluoro-2-butyne complex and perfluoroiridacyclobutene complexes in a ratio of 1?:?2?:?6. These reductive inner-sphere pathways to unsaturated fluorocarbon ligands illustrate that carbon-fluorine bond activation can take place at ?-, ?- and ?-carbons but that selectivity in these heterogeneous reductions is difficult to control, with a variety of fluoride eliminations possible for complex perfluoroalkyl ligands. Density Functional Theory (DFT/B3LYP-D3/LACV3P**++) is used to explore the relative energetics of products and intermediates in these reactions. PMID:26158776

  9. 49 CFR 173.193 - Bromoacetone, methyl bromide, chloropicrin and methyl bromide or methyl chloride mixtures, etc.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ...chloropicrin and methyl bromide or methyl chloride mixtures, etc. 173.193 Section...chloropicrin and methyl bromide or methyl chloride mixtures, etc. (a) Bromoacetone...bromide mixtures, chloropicrin and methyl chloride mixtures, and chloropicrin...

  10. 49 CFR 173.193 - Bromoacetone, methyl bromide, chloropicrin and methyl bromide or methyl chloride mixtures, etc.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...chloropicrin and methyl bromide or methyl chloride mixtures, etc. 173.193 Section...chloropicrin and methyl bromide or methyl chloride mixtures, etc. (a) Bromoacetone...bromide mixtures, chloropicrin and methyl chloride mixtures, and chloropicrin...

  11. 49 CFR 173.193 - Bromoacetone, methyl bromide, chloropicrin and methyl bromide or methyl chloride mixtures, etc.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ...chloropicrin and methyl bromide or methyl chloride mixtures, etc. 173.193 Section...chloropicrin and methyl bromide or methyl chloride mixtures, etc. (a) Bromoacetone...bromide mixtures, chloropicrin and methyl chloride mixtures, and chloropicrin...

  12. 49 CFR 173.193 - Bromoacetone, methyl bromide, chloropicrin and methyl bromide or methyl chloride mixtures, etc.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...chloropicrin and methyl bromide or methyl chloride mixtures, etc. 173.193 Section...chloropicrin and methyl bromide or methyl chloride mixtures, etc. (a) Bromoacetone...bromide mixtures, chloropicrin and methyl chloride mixtures, and chloropicrin...

  13. 49 CFR 173.193 - Bromoacetone, methyl bromide, chloropicrin and methyl bromide or methyl chloride mixtures, etc.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...chloropicrin and methyl bromide or methyl chloride mixtures, etc. 173.193 Section...chloropicrin and methyl bromide or methyl chloride mixtures, etc. (a) Bromoacetone...bromide mixtures, chloropicrin and methyl chloride mixtures, and chloropicrin...

  14. ENZYMOLOGY OF ARSENIC METHYLATION

    EPA Science Inventory

    Enzymology of Arsenic Methylation

    David J. Thomas, Pharmacokinetics Branch, Experimental Toxicology Division, National
    Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park...

  15. Crystal Structure of the Human tRNA m(1)A58 Methyltransferase-tRNA3(Lys) Complex: Refolding of Substrate tRNA Allows Access to the Methylation Target.

    PubMed

    Finer-Moore, Janet; Czudnochowski, Nadine; O'Connell, Joseph D; Wang, Amy Liya; Stroud, Robert M

    2015-12-01

    Human tRNA3(Lys) is the primer for reverse transcription of HIV; the 3' end is complementary to the primer-binding site on HIV RNA. The complementarity ends at the 18th base, A58, which in tRNA3(Lys) is modified to remove Watson-Crick pairing. Motivated to test the role of the modification in terminating the primer-binding sequence and thus limiting run-on transcription, we asked how the modification of RNA could be accomplished. tRNA m(1)A58 methyltransferase (m(1)A58 MTase) methylates N1 of A58, which is buried in the T?C-loop of tRNA, from cofactor S-adenosyl-l-methionine. This conserved tRNA modification is essential for stability of initiator tRNA in Saccharomyces cerevisiae. Reported here, three structures of human tRNA m(1)A58 MTase in complex with human tRNA3(Lys) and the product S-adenosyl-l-homocysteine show a dimer of heterodimers in which each heterodimer comprises a catalytic chain, Trm61, and a homologous but noncatalytic chain, Trm6, repurposed as a tRNA-binding subunit that acts in trans; tRNAs bind across the dimer interface such that Trm6 from the opposing heterodimer brings A58 into the active site of Trm61. T-loop and D-loop are splayed apart showing how A58, normally buried in tRNA, becomes accessible for modification. This result has broad impact on our understanding of the mechanisms of modifying internal sites in folded tRNA. The structures serve as templates for design of inhibitors that could be used to test tRNA m(1)A58 MTase's impact on retroviral priming and transcription. PMID:26470919

  16. Array-based DNA methylation profiling in follicular lymphoma

    PubMed Central

    O’Riain, Ciarán; O’Shea, Derville M.; Yang, Youwen; Le Dieu, Rifca; Gribben, John G.; Summers, Karin; Yeboah-Afari, Johnson; Bhaw-Rosun, Leena; Fleischmann, Christina; Mein, Charles A.; Crook, Tim; Smith, Paul; Kelly, Gavin; Rosenwald, Andreas; Ott, German; Campo, Elias; Rimsza, Lisa M.; Smeland, Erlend B.; Chan, Wing C.; Johnson, Natalie; Gascoyne, Randy D.; Reimer, Sandra; Braziel, Rita M.; Wright, George W.; Staudt, Louis M.; Lister, T. Andrew; Fitzgibbon, Jude

    2009-01-01

    Quantitative methylation profiling was performed using the Illumina GoldenGate Assay in untreated Follicular Lymphoma (FL) (164), paired pre- and post-transformation FL (20), benign haematopoietic (24) samples and purified B & T cells from two FL cases. Methylation values allowed separation of untreated FL samples from controls with one exception based primarily on tumour-specific gains of methylation typically occurring within CpG islands. Genes which are targets for epigenetic repression in stem cells by Polycomb Repressor Complex 2 were significantly overrepresented among hypermethylated genes. Methylation profiles were conserved in sequential FL and t-FL biopsies suggesting that widespread methylation represents an early event in lymphomagenesis and may not contribute substantially to transformation. Significant (p<0.05) correlation between FL methylation values and reduced gene expression was demonstrated for up to 28% of loci. Methylation changes occurred predominantly in B cells with variability in the amount of non-malignant tissue between samples preventing conclusive correlation with survival. This represents an important caveat in attributing prognostic relevance to methylation and future studies in cancer will optimally require purified tumour populations to address the impact of methylation on clinical outcome. PMID:19587707

  17. Coagulation of methylated arsenic from drinking water: Influence of methyl substitution.

    PubMed

    Hu, Chengzhi; Chen, Qingxin; Liu, Huijuan; Qu, Jiuhui

    2015-08-15

    Methylated arsenic can be found in virtually all earth surface environments. So far, however, little information has been collected regarding their removal by coagulation. In this study, the removal of monomethylarsenate (MMA) and dimethylarsenate (DMA) from drinking water by coagulation was investigated from the viewpoint of methyl substitution. Results indicated that FeCl3 was more efficient than AlCl3 and polyaluminum chloride (PACl) in methylated As removal. For the initial arsenic concentration of 200 ?g/L, an FeCl3 dosage of 0.2 mmol Fe/L was sufficient to attain about 95% removal of MMA, while a dosage of 0.6 mmol Fe/L achieved about 57% removal of DMA. Arsenic removal efficiency was negatively correlated with the degree of methyl substitution. With the increase in methyl group number, the quantity of negatively charged arsenic species decreased and molecular size increased, leading to the decrease of methylated As removal by coagulation. Adsorption on preformed hydroxide flocs was the major mechanism during coagulation. Both FTIR and XPS results indicated that the As?O group of As might substitute the O?H group of Fe/Al hydroxide to form a Fe/Al?O?As complex. Furthermore, the use of traditional oxidants and coagulation aids exhibited limited help for improving coagulation removal of DMA. PMID:25855566

  18. Evolution of DNA Methylation Is Linked to Genetic Aberrations in Chronic Lymphocytic Leukemia

    PubMed Central

    Oakes, Christopher C.; Claus, Rainer; Gu, Lei; Assenov, Yassen; Hüllein, Jennifer; Zucknick, Manuela; Bieg, Matthias; Brocks, David; Bogatyrova, Olga; Schmidt, Christopher R.; Rassenti, Laura; Kipps, Thomas J.; Mertens, Daniel; Lichter, Peter; Döhner, Hartmut; Stilgenbauer, Stephan; Byrd, John C.; Zenz, Thorsten; Plass, Christoph

    2014-01-01

    Although clonal selection by genetic driver aberrations in cancer is well documented, the ability of epigenetic alterations to promote tumor evolution is undefined. We used 450k arrays and next-generation sequencing to evaluate intratumor heterogeneity and evolution of DNA methylation and genetic aberrations in chronic lymphocytic leukemia (CLL). CLL cases exhibit vast interpatient differences in intratumor methylation heterogeneity, with genetically clonal cases maintaining low methylation heterogeneity and up to 10% of total CpGs in a monoallelically methylated state. Increasing methylation heterogeneity correlates with advanced genetic subclonal complexity. Selection of novel DNA methylation patterns is observed only in cases that undergo genetic evolution, and independent genetic evolution is uncommon and is restricted to low-risk alterations. These results reveal that although evolution of DNA methylation occurs in high-risk, clinically progressive cases, positive selection of novel methylation patterns entails coevolution of genetic alteration(s) in CLL. PMID:24356097

  19. Paramutation of the r1 locus of maize is associated with increased cytosine methylation.

    PubMed Central

    Walker, E L

    1998-01-01

    In paramutation two alleles of a gene interact so that one of the alleles is epigenetically silenced. The silenced state is then genetically transmissible for many generations. The large (220 kbp) multigenic complex R-r is paramutable: its level of expression is changed during paramutation. R-r was found to exhibit increases in its level of cytosine methylation (C-methylation) following paramutation. These C-methylation changes are localized to the 5' portions of the two genes in the complex that are most sensitive to paramutation. These methylation changes flank a small region called sigma that is thought to have been derived from a transposon named doppia. A mutant derivative of R-r that has a deletion of the sigma region fails to become methylated under conditions in which R-r is heavily methylated. This suggests that the presence of sigma sequences at the locus is required for the methylation changes that are observed following paramutation. PMID:9560410

  20. Abiotic Formation of Methyl Halides in the Terrestrial Environment

    NASA Astrophysics Data System (ADS)

    Keppler, F.

    2011-12-01

    Methyl chloride and methyl bromide are the most abundant chlorine and bromine containing organic compounds in the atmosphere. Since both compounds have relatively long tropospheric lifetimes they can effectively transport halogen atoms from the Earth's surface, where they are released, to the stratosphere and following photolytic oxidation form reactive halogen gases that lead to the chemical destruction of ozone. Methyl chloride and methyl bromide account for more than 20% of the ozone-depleting halogens delivered to the stratosphere and are predicted to grow in importance as the chlorine contribution to the stratosphere from anthropogenic CFCs decline. Today methyl chloride and methyl bromide originate mainly from natural sources with only a minor fraction considered to be of anthropogenic origin. However, until as recently as 2000 most of the methyl chloride and methyl bromide input to the atmosphere was considered to originate from the oceans, but investigations in recent years have clearly demonstrated that terrestrial sources such as biomass burning, wood-rotting fungi, coastal salt marshes, tropical vegetation and organic matter degradation must dominate the atmospheric budgets of these trace gases. However, many uncertainties still exist regarding strengths of both sources and sinks, as well as the mechanisms of formation of these naturally occurring halogenated gases. A better understanding of the atmospheric budget of both methyl chloride and methyl bromide is therefore required for reliable prediction of future ozone depletion. Biotic and abiotic methylation processes of chloride and bromide ion are considered to be the dominant pathways of formation of these methyl halides in nature. In this presentation I will focus on abiotic formation processes in the terrestrial environment and the potential parameters that control their emissions. Recent advances in our understanding of the abiotic formation pathway of methyl halides will be discussed. This will include a consideration on how stable isotope studies assisted advancements in this subject area. For example, it has been shown that the methoxyl groups of lignin and pectin which together constitute the bulk of the C1 plant pool have a carbon isotope signature significantly depleted in 13C. Plant-derived C1 volatile organic compounds (VOCs) are also highly depleted in 13C compared with Cn+1 VOCs. These observations suggest that the plant methoxyl pool is the predominant source of methyl halides released from senescent and dead plant litter. The distinct 13C depletion of plant methoxyl groups and naturally produced methyl halides may provide a helpful tool in constraining complex environmental processes and therefore improve our understanding of the global cycles of atmospheric methyl halides.

  1. CpG methylation in the Fhit regulatory region: relation to Fhit expression in murine tumors.

    PubMed

    Han, Shuang-Yin; Iliopoulos, Dimitrios; Druck, Teresa; Guler, Gulnur; Grubbs, Clinton J; Pereira, Michael; Zhang, Zhongqiu; You, Ming; Lubet, Ronald A; Fong, Louise Y Y; Huebner, Kay

    2004-05-13

    To determine if: (1) 5' CpG island methylation is related to Fhit inactivation; (2) there are tumor or carcinogen-specific methylation patterns, we examined 35 CpG sites in the promoter, exon and intron 1 of the mouse Fhit gene. In primary tumors of lung, urinary bladder and tongue, induced by different carcinogens, 15-35% of sites were methylated, with specific methylation patterns associated with each cancer type, suggesting cancer- or tissue-specific methylation patterns. The methylation patterns were associated with reduced Fhit expression, as determined by immunohistochemical analyses. Methylation of rat Fhit 5' CpGs in mammary adenocarcinomas, detected by methylation specific PCR amplification, also correlated with reduced gene expression. Thus, there was an overall association between promoter/exon 1 methylation and decreased Fhit expression. In contrast, in cancer-derived cell lines 70-95% of the CpG sites were methylated. This is the first detailed study of the relationship between Fhit 5' CpG island methylation and Fhit expression in murine tumors, our main models for preclinical cancer studies, and provides evidence that loss of Fhit expression and methylation are correlated in these mouse models and these models will be useful to examine the complex relationships among gene expression, methylation patterns and organ specificity. PMID:15007387

  2. DNMT3L interacts with transcription factors to target DNMT3L/DNMT3B to specific DNA sequences: role of the DNMT3L/DNMT3B/p65-NF?B complex in the (de-)methylation of TRAF1.

    PubMed

    Pacaud, Romain; Sery, Quentin; Oliver, Lisa; Vallette, François M; Tost, Jörg; Cartron, Pierre-François

    2014-09-01

    DNMT3L i.e. DNA (cytosine-5)-methyltransferase 3-like protein, is devoid of cytosine methyltransferase activity, despite clear homology to DNMT3A and DNMT3B, due to the mutation of key catalytic residues. However, DNMT3L participates in de novo methylation reactions through its direct interaction with DNMT3A and DNMT3B. In the present study, we investigated if DNMT3L interacts also directly with transcription factors (TFs). Using TF arrays, we identified 73 TFs that interacted with DNMT3L, 13 of which (ASH2L, ATF1, ATF3, BLZF1, CDX2, CERM, E2F3, E2F4, GCNF, GTF2I, GTF3C5, NFkB-p65 and RXR?) interacted only with DNMT3L, but not with DNMT3A/B. By focusing on the interaction with NFkB-p65, we demonstrate that DNMT3L forms a complex with DNMT3B and NFkB-p65 and that this complex is required for the control of DNA methylation at the TRAF1 promoter in the T98G glioma cell line. In addition, our experiments describe the DNA methylation at TRAF1 as being dynamic with a demethylation phase involving TET3. Thus, our data suggests that DNMT3L can address DNMT3A/B to specific sites by directly interacting with TFs that do not directly interact with DNMT3A/B. In summary, our data provide a new avenue for the direction of site-specific de novo DNA methylation catalyzed by DNMT3A/B. PMID:24952347

  3. 40 CFR 721.6920 - Butyl acrylate, polymer with substituted methyl styrene, methyl methacrylate, and substituted...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...2014-07-01 false Butyl acrylate, polymer with substituted methyl styrene, methyl...Substances § 721.6920 Butyl acrylate, polymer with substituted methyl styrene, methyl...substance identified as butyl acrylate, polymer with substituted methyl styrene,...

  4. 40 CFR 721.6920 - Butyl acrylate, polymer with substituted methyl styrene, methyl methacrylate, and substituted...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...2013-07-01 false Butyl acrylate, polymer with substituted methyl styrene, methyl...Substances § 721.6920 Butyl acrylate, polymer with substituted methyl styrene, methyl...substance identified as butyl acrylate, polymer with substituted methyl styrene,...

  5. 40 CFR 721.6920 - Butyl acrylate, polymer with substituted methyl styrene, methyl methacrylate, and substituted...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...2010-07-01 false Butyl acrylate, polymer with substituted methyl styrene, methyl...Substances § 721.6920 Butyl acrylate, polymer with substituted methyl styrene, methyl...substance identified as butyl acrylate, polymer with substituted methyl styrene,...

  6. 40 CFR 721.6920 - Butyl acrylate, polymer with substituted methyl styrene, methyl methacrylate, and substituted...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...2011-07-01 false Butyl acrylate, polymer with substituted methyl styrene, methyl...Substances § 721.6920 Butyl acrylate, polymer with substituted methyl styrene, methyl...substance identified as butyl acrylate, polymer with substituted methyl styrene,...

  7. Aberrant methylation patterns in cancer: a clinical view

    PubMed Central

    Paska, Alja Videtic; Hudler, Petra

    2015-01-01

    Epigenetic mechanisms, such as DNA methylation, DNA hydroxymethylation, post-translational modifications (PTMs) of histone proteins affecting nucleosome remodelling, and regulation by small and large non-coding RNAs (ncRNAs) work in concert with cis and trans acting elements to drive appropriate gene expression. Advances in detection methods and development of dedicated platforms and methylation arrays resulted in an explosion of information on aberrantly methylated sequences linking deviations in epigenetic landscape with the initiation and progression of complex diseases. Here, we consider how DNA methylation changes in malignancies, such as breast, pancreatic, colorectal, and gastric cancer could be exploited for the purpose of developing specific diagnostic tools. DNA methylation changes can be applicable as biomarkers for detection of malignant disease in easily accessible tissues. Methylation signatures are already proving to be an important marker for determination of drug sensitivity. Even more, promoter methylation patterns of some genes, such as MGMT, SHOX2, and SEPT9, have already been translated into commercial clinical assays aiding in patient assessment as adjunct diagnostic tools. In conclusion, the changes in DNA methylation patterns in tumour cells are slowly gaining entrance into routine diagnostic tests as promising biomarkers and as potential therapeutic targets. PMID:26110029

  8. Optimized method for methylated DNA immuno-precipitation

    PubMed Central

    Guerrero-Bosagna, Carlos; Jensen, Per

    2015-01-01

    Methylated DNA immunoprecipitation (MeDIP) is one of the most widely used methods to evaluate DNA methylation on a whole genome scale, and involves the capture of the methylated fraction of the DNA by an antibody specific to methyl-cytosine. MeDIP was initially coupled with microarray hybridization to detect local DNA methylation enrichments along the genome. More recently, MeDIP has been coupled with next generation sequencing, which highlights its current and future applicability. In previous studies in which MeDIP was applied, the protocol took around 3 days to be performed. Given the importance of MeDIP for studies involving DNA methylation, it was important to optimize the method in order to deliver faster turnouts. The present article describes optimization steps of the MeDIP method. The length of the procedure was reduced in half without compromising the quality of the results. This was achieved by:•Reduction of the number of washes in different stages of the protocol, after a careful evaluation of the number of indispensable washes.•Reduction of reaction times for detaching methylated DNA fragments from the complex agarose beads:antibody.•Modification of the methods to purify methylated DNA, which incorporates new devices and procedures, and eliminates a lengthy phenol and chloroform:isoamyl alcohol extraction.

  9. Profile analysis and prediction of tissue-specific CpG island methylation classes

    PubMed Central

    2009-01-01

    Background The computational prediction of DNA methylation has become an important topic in the recent years due to its role in the epigenetic control of normal and cancer-related processes. While previous prediction approaches focused merely on differences between methylated and unmethylated DNA sequences, recent experimental results have shown the presence of much more complex patterns of methylation across tissues and time in the human genome. These patterns are only partially described by a binary model of DNA methylation. In this work we propose a novel approach, based on profile analysis of tissue-specific methylation that uncovers significant differences in the sequences of CpG islands (CGIs) that predispose them to a tissue- specific methylation pattern. Results We defined CGI methylation profiles that separate not only between constitutively methylated and unmethylated CGIs, but also identify CGIs showing a differential degree of methylation across tissues and cell-types or a lack of methylation exclusively in sperm. These profiles are clearly distinguished by a number of CGI attributes including their evolutionary conservation, their significance, as well as the evolutionary evidence of prior methylation. Additionally, we assess profile functionality with respect to the different compartments of protein coding genes and their possible use in the prediction of DNA methylation. Conclusion Our approach provides new insights into the biological features that determine if a CGI has a functional role in the epigenetic control of gene expression and the features associated with CGI methylation susceptibility. Moreover, we show that the ability to predict CGI methylation is based primarily on the quality of the biological information used and the relationships uncovered between different sources of knowledge. The strategy presented here is able to predict, besides the constitutively methylated and unmethylated classes, two more tissue specific methylation classes conserving the accuracy provided by leading binary methylation classification methods. PMID:19383127

  10. Genetic Sensor for Strong Methylating Compounds

    E-print Network

    Moser, Felix

    Methylating chemicals are common in industry and agriculture and are often toxic, partly due to their propensity to methylate DNA. The Escherichia coli Ada protein detects methylating compounds by sensing aberrant methyl ...

  11. Methyl isobutyl ketone (MIBK)

    Integrated Risk Information System (IRIS)

    Methyl Isobutyl Ketone ( MIBK ) ; CASRN 108 - 10 - 1 ; Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for

  12. Methyl ethyl ketone (MEK)

    Integrated Risk Information System (IRIS)

    EPA 635 / R - 03 / 009 www.epa.gov / iris TOXICOLOGICAL REVIEW OF METHYL ETHYL KETONE ( CAS No . 78 - 93 - 3 ) In Support of Summary Information on the Integrated Risk Information System ( IRIS ) September 2003 U.S . Environmental Protection Agency Washington , DC DISCLAIMER This document has been r

  13. Thiophanate-methyl

    Integrated Risk Information System (IRIS)

    Thiophanate - methyl ; CASRN 23564 - 05 - 8 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcino

  14. Pirimiphos-methyl

    Integrated Risk Information System (IRIS)

    Pirimiphos - methyl ; CASRN 29232 - 93 - 7 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinog

  15. Chloromethyl methyl ether (CMME)

    Integrated Risk Information System (IRIS)

    Chloromethyl methyl ether ( CMME ) ; CASRN 107 - 30 - 2 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments fo

  16. Haloxyfop-methyl

    Integrated Risk Information System (IRIS)

    Haloxyfop - methyl ; CASRN 69806 - 40 - 2 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinoge

  17. Kapok oil methyl esters

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The increased need for biodiesel feedstocks has caused various vegetable oils to be examined for this purpose. In the present work, the methyl esters of kapok (Ceiba pentandra) oil were prepared. The essential fuel properties were comprehensively determined and evaluated in comparison to specificati...

  18. Nutrients and DNA Methylation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Epigenetics is a new mechanism responsible for development, aging, and disease process such as cancer development. One major epigenetic phenomenon is DNA methylation, which attributes to gene expression and integrity. Deepening the knowledge on one-carbon metabolism is very important to understandin...

  19. Kenaf methyl esters

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Additional or alternative feedstocks are one of the major areas of interest regarding biodiesel. In this paper, for the first time, the fuel properties of kenaf (Hibiscus cannabinus L.) seed oil methyl esters are comprehensively reported. This biodiesel is also relatively unique by containing small ...

  20. Effects of coadministered sodium selenite on short-term distribution on methyl mercury in the rat

    SciTech Connect

    Thomas, D.J.; Smith, J.C.

    1984-08-01

    Adult male Sprague-Dawley rats received iv injections of 1 ..mu..mole of methyl mercury/kg alone or coadministered with 5 ..mu..mole of sodium selenite/kg. Tissue concentrations of methyl mercury were determined at 5, 20, and 60 min after treatment. Selenite treatment produced a significant increase in cerebral methyl mercury concentrations and a significant decrease in kidney methyl mercury concentrations at all time points. The concentration of methyl mercury in liver was significantly increased by selenite coadministration at 5 and 20 min but at 60 min after injection the concentration was not significantly different from that found in rats receiving methyl mercury alone. Selenite treatment also significantly lowered blood methyl mercury concentrations at all time points. This decrease was associated with a significant decrease in the concentration of methyl mercury in erythrocytes at 5, 20, and 60 min. Plasma methyl mercury levels at 5 min postinjection were slightly higher in selenite-treated rats but were significantly lower in treated animals at 20 and 60 min. Treatment of rats with selenite did not specifically alter the extent of methyl mercury binding to glutathione in the 108,000 g supernatant of cerebrum of in erythrocyte hemolysates. In rats receiving either methyl mercury alone or with selenite, low-molecular-weight methyl mercury complexes could not be detected in plasma 5 min after iv injection.

  1. Altered DNA Methylation in Leukocytes with Trisomy 21

    PubMed Central

    Kerkel, Kristi; Schupf, Nicole; Hatta, Kota; Pang, Deborah; Salas, Martha; Kratz, Alexander; Minden, Mark; Murty, Vundavalli; Zigman, Warren B.; Mayeux, Richard P.; Jenkins, Edmund C.; Torkamani, Ali; Schork, Nicholas J.; Silverman, Wayne; Croy, B. Anne; Tycko, Benjamin

    2010-01-01

    The primary abnormality in Down syndrome (DS), trisomy 21, is well known; but how this chromosomal gain produces the complex DS phenotype, including immune system defects, is not well understood. We profiled DNA methylation in total peripheral blood leukocytes (PBL) and T-lymphocytes from adults with DS and normal controls and found gene-specific abnormalities of CpG methylation in DS, with many of the differentially methylated genes having known or predicted roles in lymphocyte development and function. Validation of the microarray data by bisulfite sequencing and methylation-sensitive Pyrosequencing (MS-Pyroseq) confirmed strong differences in methylation (p<0.0001) for each of 8 genes tested: TMEM131, TCF7, CD3Z/CD247, SH3BP2, EIF4E, PLD6, SUMO3, and CPT1B, in DS versus control PBL. In addition, we validated differential methylation of NOD2/CARD15 by bisulfite sequencing in DS versus control T-cells. The differentially methylated genes were found on various autosomes, with no enrichment on chromosome 21. Differences in methylation were generally stable in a given individual, remained significant after adjusting for age, and were not due to altered cell counts. Some but not all of the differentially methylated genes showed different mean mRNA expression in DS versus control PBL; and the altered expression of 5 of these genes, TMEM131, TCF7, CD3Z, NOD2, and NPDC1, was recapitulated by exposing normal lymphocytes to the demethylating drug 5-aza-2?deoxycytidine (5aza-dC) plus mitogens. We conclude that altered gene-specific DNA methylation is a recurrent and functionally relevant downstream response to trisomy 21 in human cells. PMID:21124956

  2. Identification of differentially methylated regions using streptavidin bisulfite ligand methylation enrichment (SuBLiME), a new method to enrich for methylated DNA prior to deep bisulfite genomic sequencing

    PubMed Central

    Ross, Jason P.; Shaw, Jan M.; Molloy, Peter L.

    2013-01-01

    We have developed a method that enriches for methylated cytosines by capturing the fraction of bisulfite-treated DNA with unconverted cytosines. The method, called streptavidin bisulfite ligand methylation enrichment (SuBLiME), involves the specific labeling (using a biotin-labeled nucleotide ligand) of methylated cytosines in bisulfite-converted DNA. This step is then followed by affinity capture, using streptavidin-coupled magnetic beads. SuBLiME is highly adaptable and can be combined with deep sequencing library generation and/or genomic complexity-reduction. In this pilot study, we enriched methylated DNA from Csp6I-cut complexity-reduced genomes of colorectal cancer cell lines (HCT-116, HT-29 and SW-480) and normal blood leukocytes with the aim of discovering colorectal cancer biomarkers. Enriched libraries were sequenced with SOLiD-3 technology. In pairwise comparisons, we scored a total of 1,769 gene loci and 33 miRNA loci as differentially methylated between the cell lines and leukocytes. Of these, 516 loci were differently methylated in at least two promoter-proximal CpG sites over two discrete Csp6I fragments. Identified methylated gene loci were associated with anatomical development, differentiation and cell signaling. The data correlated with good agreement to a number of published colorectal cancer DNA methylation biomarkers and genomic data sets. SuBLiME is effective in the enrichment of methylated nucleic acid and in the detection of known and novel biomarkers. PMID:23257838

  3. Molecular coupling of DNA methylation and histone methylation

    PubMed Central

    Hashimoto, Hideharu; Vertino, Paula M; Cheng, Xiaodong

    2011-01-01

    The combinatorial pattern of DNA and histone modifications constitutes an epigenetic ‘code’ that shapes gene-expression patterns by enabling or restricting the transcriptional potential of genomic domains. DNA methylation is associated with histone modifications, particularly the absence of histone H3 lysine 4 methylation (H3K4me0) and the presence of H3K9 methylation. This article focuses on three protein domains (ATRX–Dnmt3–Dnmt3L [ADD], Cys–X–X–Cys [CXXC] and the methyl-CpG-binding domain [MBD]) and the functional implications of domain architecture in the mechanisms linking histone methylation and DNA methylation in mammalian cells. The DNA methyltransferase DNMT3a and its accessory protein DNMT3L contain a H3K4me0-interacting ADD domain that links the DNA methylation reaction with unmodified H3K4. The H3K4 methyltransferase MLL1 contains a CpG-interacting CXXC domain that may couple the H3K4 methylation reaction to unmethylated DNA. Another H3K4 methyltransferase, SET1, although lacking an intrinsic CXXC domain, interacts directly with an accessory protein CFP1 that contains the same domain. The H3K9 methyltransferase SETDB1 contains a putative MBD that potentially links the H3K4 methylation reaction to methylated DNA or may do so through the interaction with the MBD containing protein MBD1. Finally, we consider the domain structure of the DNA methyltransferase DNMT1, its accessory protein UHRF1 and their associated proteins, and propose a mechanism by which DNA methylation and histone methylation may be coordinately maintained through mitotic cell division, allowing for the transmission of parental DNA and for the histone methylation patterns to be copied to newly replicated chromatin. PMID:21339843

  4. Spectroscopic and biological studies of new binuclear metal complexes of a tridentate ONS hydrazone ligand derived from 4-amino-6-methyl-3-thioxo-3,4-dihydro-1,2,4-triazin-5(2H)-one and 4,6-diacetylresorcinol

    NASA Astrophysics Data System (ADS)

    Adly, Omima M. I.; Emara, Adel A. A.

    2014-11-01

    The binuclear hydrazone, H2L, ligand derived from 4-amino-6-methyl-3-thioxo-3,4-dihydro-1,2,4-triazin-5(2H)-one and 4,6-diacetylresorcinol, in the molar ratio 2:1, and its copper(II), nickel(II), cobalt(II), zinc(II), cadmium(II), cerium(III), iron(III), oxovanadium(IV) and dioxouranium(VI) complexes have been synthesized. Structures of the ligand and its metal complexes were characterized by elemental analyses, spectral (infrared, electronic, mass, 1H NMR and ESR) data, magnetic susceptibility, molar conductivity measurements and thermal gravimetric analysis (TGA). The ligand acts as dibasic with two ONS tridentate sites. The bonding sites are the azomethine nitrogen, phenolate oxygen and sulfur atoms. The metal complexes exhibit different geometrical arrangements such as square planer, tetrahedral and octahedral. The Coats-Redfern equation was used to calculate the kinetic and thermodynamic parameters for the different thermal decomposition steps of some complexes. The ligand and its metal complexes showed antimicrobial activity towards Gram-positive bacteria (Staphylococcus aureus and Bacillus subtilis), Gram-negative bacteria (Salmonella typhimurium and Escherichia coli), yeast (Candida albicans) and fungus (Aspergillus fumigatus). Structural parameters of the ligand and its metal complexes were theoretically computed on the basis of semiempirical PM3 level, and the results were correlated with their experimental data.

  5. Crystal structure of hexa­kis­(dmpu)-di-?2-hydroxido-dialuminium tetraiodide dmpu tetra­solvate [dmpu is 1,3-di­methyl­tetra­hydro­pyrimidin-2(1H)-one]: a centrosymmetric dinuclear aluminium complex containing AlO5 polyhedra

    PubMed Central

    Lundberg, Daniel; Lyczko, Krzysztof

    2015-01-01

    The structure of the title compound, [Al2(OH)2(C6H12N2O)6]I4·4C6H12N2O (systematic name: di-?2-hydroxido-bis­{tris­[1,3-di­methyl­tetra­hydro­pyrimidin-2(1H)-one-?O]aluminium} tetra­iodide 1,3-di­methyl­tetra­hydro­pyrimidin-2(1H)-one tetra­solvate), is composed of two Al(C6H12N2O)3 moieties linked into a centrosymmetric dinuclear unit by a pair of bridging hydroxide ions. The aluminium cations show a distorted trigonal bipyramidal AlO5 coordination environment formed only by monodentate ligands. The Al—O bond lengths are in the range 1.789?(2)–1.859?(2)?Å (mean bond length = 1.818?Å). The non-coordinating iodide anions compensate the charge of the complex cation. The remaining solvent mol­ecules and the iodide counter-anions inter­act with the complex cation by weak non-classical C—H?I and C—H?O hydrogen bonds. PMID:26396749

  6. Role of DNA methylation in colorectal carcinogenesis.

    PubMed

    Patai, Arpád V; Molnár, Béla; Kalmár, Alexandra; Schöller, Andrea; Tóth, Kinga; Tulassay, Zsolt

    2012-01-01

    Colorectal cancer is the most common malignancy of the gastrointestinal tract and a leading cause of cancer-related deaths worldwide. In order to detect early precursor lesions, colonoscopy is widely used. Unfortunately, patient adherence to colonoscopy is poor, which is partially due to the modest performance of currently used prescreening tests. Recently, epigenetics added an additional layer to the understanding of colorectal carcinogenesis. DNA methylation as part of the epigenetic gene-silencing complex is a universally occurring change in colorectal cancer and arises prior to the onset of recognizable preneoplastic changes, which may have huge preventive implications. Herein we discuss the major developments in the field of colorectal carcinogenesis and DNA methylation, including alterations in non-neoplastic conditions such as aging and ulcerative colitis. We try to demonstrate how this epigenetic modification can be harnessed to address some of the key issues impeding the successful clinical management of colorectal cancer. PMID:22722557

  7. Human papillomavirus type 16 E7 oncoprotein mediates CCNA1 promoter methylation

    PubMed Central

    Chalertpet, Kanwalat; Pakdeechaidan, Watcharapong; Patel, Vyomesh; Mutirangura, Apiwat; Yanatatsaneejit, Pattamawadee

    2015-01-01

    Human papillomavirus (HPV) oncoproteins drive distinctive promoter methylation patterns in cancer. However, the underlying mechanism remains to be elucidated. Cyclin A1 (CCNA1) promoter methylation is strongly associated with HPV-associated cancer. CCNA1 methylation is found in HPV-associated cervical cancers, as well as in head and neck squamous cell cancer. Numerous pieces of evidence suggest that E7 may drive CCNA1 methylation. First, the CCNA1 promoter is methylated in HPV-positive epithelial lesions after transformation. Second, the CCNA1 promoter is methylated at a high level when HPV is integrated into the human genome. Finally, E7 has been shown to interact with DNA methyltransferase 1 (Dnmt1). Here, we sought to determine the mechanism by which E7 increases methylation in cervical cancer by using CCNA1 as a gene model. We investigated whether E7 induces CCNA1 promoter methylation, resulting in the loss of expression. Using both E7 knockdown and overexpression approaches in SiHa and C33a cells, our data showed that CCNA1 promoter methylation decreases with a corresponding increase in expression in E7 siRNA-transfected cells. By contrast, CCNA1 promoter methylation was augmented with a corresponding reduction in expression in E7-overexpressing cells. To confirm whether the binding of the E7–Dnmt1 complex to the CCNA1 promoter induced methylation and loss of expression, ChIP assays were carried out in E7-, del CR3-E7 and vector control-overexpressing C33a cells. The data showed that E7 induced CCNA1 methylation by forming a complex with Dnmt1 at the CCNA1 promoter, resulting in the subsequent reduction of expression in cancers. It is interesting to further explore the genome-wide mechanism of E7 oncoprotein-mediated DNA methylation. PMID:26250467

  8. Interstellar methyl mercaptan

    NASA Technical Reports Server (NTRS)

    Linke, R. A.; Frerking, M. A.; Thaddeus, P.

    1979-01-01

    Methyl mercaptan (CH3SH) has been identified in Sgr B2 from observations of six lines in its millimeter-wave spectrum. The CH3SH rotational temperature and column density in Sgr B2 are T(rot) = 9 plus or minus 3 K and N = 1.5 plus or minus 0.2 x 10 to the 14th per sq cm, respectively. The CH3SH/CH3OH ratio is apparently not greatly different from the cosmic S/O ratio.

  9. Structure of a dinuclear cadmium complex with 2,2'-bi-pyridine, monodentate nitrate and 3-carb-oxy-6-methyl-pyridine-2-carboxyl-ate ligands: intra-molecular carbon-yl(lone pair)??(ring) and nitrate(?)??(ring) inter-actions.

    PubMed

    Granifo, Juan; Suarez, Sebastián; Baggio, Ricardo

    2015-08-01

    The centrosymmetric dinuclear complex bis-(?-3-carb-oxy-6-methyl-pyridine-2-carboxyl-ato)-?(3) N,O (2):O (2);?(3) O (2):N,O (2)-bis-[(2,2'-bi-pyridine-?(2) N,N')(nitrato-?O)cadmium] methanol monosolvate, [Cd2(C8H6NO4)2(NO3)2(C10H8N2)2]·CH3OH, was isolated as colourless crystals from the reaction of Cd(NO3)2·4H2O, 6-methyl-pyridine-2,3-di-carb-oxy-lic acid (mepydcH2) and 2,2'-bi-pyridine in methanol. The asymmetric unit consists of a Cd(II) cation bound to a ?-?(3) N,O (2):O (2)-mepydcH(-) anion, an N,N'-bidentate 2,2'-bi-pyridine group and an O-mono-dentate nitrate anion, and is completed with a methanol solvent mol-ecule at half-occupancy. The Cd complex unit is linked to its centrosymmetric image through a bridging mepydcH(-) carboxyl-ate O atom to complete the dinuclear complex mol-ecule. Despite a significant variation in the coordination angles, indicating a considerable departure from octa-hedral coordination geometry about the Cd(II) atom, the Cd-O and Cd-N distances in this complex are surprisingly similar. The crystal structure consists of O-H?O hydrogen-bonded chains parallel to a, further bound by C-H?O contacts along b to form planar two-dimensional arrays parallel to (001). The juxtaposed planes form inter-stitial columnar voids that are filled by the methanol solvent mol-ecules. These in turn inter-act with the complex mol-ecules to further stabilize the structure. A search in the literature showed that complexes with the mepydcH(-) ligand are rare and complexes reported previously with this ligand do not adopt the ?-?(3) coordination mode found in the title compound. PMID:26396748

  10. Structure of a dinuclear cadmium complex with 2,2?-bi­pyridine, monodentate nitrate and 3-carb­oxy-6-methyl­pyridine-2-carboxyl­ate ligands: intra­molecular carbon­yl(lone pair)??(ring) and nitrate(?)??(ring) inter­actions

    PubMed Central

    Granifo, Juan; Suarez, Sebastián; Baggio, Ricardo

    2015-01-01

    The centrosymmetric dinuclear complex bis­(?-3-carb­oxy-6-methyl­pyridine-2-carboxyl­ato)-?3 N,O 2:O 2;?3 O 2:N,O 2-bis­[(2,2?-bi­pyridine-?2 N,N?)(nitrato-?O)cadmium] methanol monosolvate, [Cd2(C8H6NO4)2(NO3)2(C10H8N2)2]·CH3OH, was isolated as colourless crystals from the reaction of Cd(NO3)2·4H2O, 6-methyl­pyridine-2,3-di­carb­oxy­lic acid (mepydcH2) and 2,2?-bi­pyridine in methanol. The asymmetric unit consists of a CdII cation bound to a ?-?3 N,O 2:O 2-mepydcH? anion, an N,N?-bidentate 2,2?-bi­pyridine group and an O-mono­dentate nitrate anion, and is completed with a methanol solvent mol­ecule at half-occupancy. The Cd complex unit is linked to its centrosymmetric image through a bridging mepydcH? carboxyl­ate O atom to complete the dinuclear complex mol­ecule. Despite a significant variation in the coordination angles, indicating a considerable departure from octa­hedral coordination geometry about the CdII atom, the Cd—O and Cd—N distances in this complex are surprisingly similar. The crystal structure consists of O—H?O hydrogen-bonded chains parallel to a, further bound by C—H?O contacts along b to form planar two-dimensional arrays parallel to (001). The juxtaposed planes form inter­stitial columnar voids that are filled by the methanol solvent mol­ecules. These in turn inter­act with the complex mol­ecules to further stabilize the structure. A search in the literature showed that complexes with the mepydcH? ligand are rare and complexes reported previously with this ligand do not adopt the ?-?3 coordination mode found in the title compound. PMID:26396748

  11. Supporting Information Surface residence and uptake of methyl chloride and methyl alcohol at the

    E-print Network

    1 Supporting Information Surface residence and uptake of methyl chloride and methyl alcohol spectra from flow experiments over water of methyl alcohol, methyl chloride, butyl alcohol, butyl chloride(a.u) 295029002850 Incident Infrared (cm -1 ) 0.6 0.4 0.2 0.0 Methyl alcohol Methyl chloride Butyl alcohol Butyl

  12. Radical SAM-Mediated Methylation of Ribosomal RNA.

    PubMed

    Stojkovi?, Vanja; Fujimori, Danica Galoni?

    2015-01-01

    While RNA methylation occurs in all kingdoms of life, the type and the distribution of different methylated species varies substantially among archaea, bacteria, and eukaryotes. The most prevalent type of RNA methylation is methylation of nucleobases. However, despite recent advances in our knowledge of these marks, the biological roles of such modifications are still incompletely understood (Machnicka et al., 2013; Motorin & Helm, 2011; Sergeeva et al., 2014; Sergiev et al., 2011). A number of mechanisms have evolved to enable RNA methylation, which are tuned to the electronic demands of the substrate. Herein, we provide an overview of methods for expression, purification, and activity analysis of a specific type of RNA methylating enzymes, radical SAM methylsynthases. These enzymes modify the amidine carbon atoms of an adenosine, A2503, in bacterial 23S rRNA. The activities of these enzymes have only been recently reconstituted (Yan et al., 2010), which can be attributed to the complex anaerobic catalysis that they perform. As the substrate A2503 is located at the nascent peptide exit tunnel of the bacterial ribosome, methylations catalyzed by these enzymes have profound impact on the biology of the host strain. RlmN, an endogenous protein found in all bacteria, methylates the C2 amidine carbon and contributes to the translational fidelity (Benitez-Paez et al., 2012; Ramu et al., 2011; Vazquez-Laslop, Ramu, Klepacki, Kannan, & Mankin, 2010). Cfr, found in pathogenic species, methylates the C8 amidine carbon, a modification that confers resistance to various classes of antibiotics (Giessing et al., 2009; Long et al., 2006; Smith & Mankin, 2008). Interestingly, C2 methylated adenosine was recently detected in a subset of tRNAs, raising the question of the physiological role of this modification (Benitez-Paez et al., 2012). With an increase in available whole genome sequences, the development of methods to identify target substrates of RNA methylating enzymes (Khoddami & Cairns, 2013; Meyer et al., 2012; Tim, Katharina, & Matthias, 2010), as well as advances in the characterization of their activities, we anticipate the coming years will unravel novel aspects of mechanisms of the RNA methylation and deepen insight into the function of the resulting modification. PMID:26253978

  13. Neural Tube Defects, Folic Acid and Methylation

    PubMed Central

    Imbard, Apolline; Benoist, Jean-François; Blom, Henk J.

    2013-01-01

    Neural tube defects (NTDs) are common complex congenital malformations resulting from failure of the neural tube closure during embryogenesis. It is established that folic acid supplementation decreases the prevalence of NTDs, which has led to national public health policies regarding folic acid. To date, animal studies have not provided sufficient information to establish the metabolic and/or genomic mechanism(s) underlying human folic acid responsiveness in NTDs. However, several lines of evidence suggest that not only folates but also choline, B12 and methylation metabolisms are involved in NTDs. Decreased B12 vitamin and increased total choline or homocysteine in maternal blood have been shown to be associated with increased NTDs risk. Several polymorphisms of genes involved in these pathways have also been implicated in risk of development of NTDs. This raises the question whether supplementation with B12 vitamin, betaine or other methylation donors in addition to folic acid periconceptional supplementation will further reduce NTD risk. The objective of this article is to review the role of methylation metabolism in the onset of neural tube defects. PMID:24048206

  14. A Search for Methyl Acetate in Hot Cores

    NASA Astrophysics Data System (ADS)

    Kelley, Matthew; Braakman, Rogier; Blake, Geoffrey

    2006-10-01

    We propose to search for methyl acetate, CH3COOCH3, in high mass hot cores. Methyl acetate is possibly synthesized through multiple reaction pathways from molecules previously detected in hot cores, most notably from acetic acid and methanol via esterification. Esterification, beyond the formation of methyl formate, has not yet been observed in the ISM. The project is already underway in nothern sources based on millimeter data from the Caltech Submillimeter Observatory (CSO). We hope to study the chemically rich southern source G327.3 (decl B1950=-54.49'15.6"), amongst others, using MOPRA and to search for acetic acid and methyl acetate. Observations are supported by laboratory studies of methyl acetate in the 3 mm and 1 mm and successful spectral fitting by the Blake group at Caltech. If detected, methyl acetate, consisting of 11 atoms, would be one of the larger complex organic molecules detected in the interstellar medium and could point to previously unconsidered reaction mechanisms.

  15. Leading Edge Reversing DNA Methylation

    E-print Network

    Zhang, Yi

    ). In mammals, new DNA methylation pattern is established by de novo DNA methyltransferases, DNMT3A and DNMT3B is faithfully maintained in daughter cells through the action of maintenance DNA methyltransferase DNMT1 and itsLeading Edge Review Reversing DNA Methylation: Mechanisms, Genomics, and Biological Functions Hao

  16. Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population

    PubMed Central

    Schmitz, Robert J.; He, Yupeng; Valdés-López, Oswaldo; Khan, Saad M.; Joshi, Trupti; Urich, Mark A.; Nery, Joseph R.; Diers, Brian; Xu, Dong; Stacey, Gary; Ecker, Joseph R.

    2013-01-01

    Cytosine DNA methylation is one avenue for passing information through cell divisions. Here, we present epigenomic analyses of soybean recombinant inbred lines (RILs) and their parents. Identification of differentially methylated regions (DMRs) revealed that DMRs mostly cosegregated with the genotype from which they were derived, but examples of the uncoupling of genotype and epigenotype were identified. Linkage mapping of methylation states assessed from whole-genome bisulfite sequencing of 83 RILs uncovered widespread evidence for local methylQTL. This epigenomics approach provides a comprehensive study of the patterns and heritability of methylation variants in a complex genetic population over multiple generations, paving the way for understanding how methylation variants contribute to phenotypic variation. PMID:23739894

  17. A Comparative Study of Tests for Homogeneity of Variances with Application to DNA Methylation Data

    PubMed Central

    Li, Xuan; Qiu, Weiliang; Morrow, Jarrett; DeMeo, Dawn L.; Weiss, Scott T.; Fu, Yuejiao; Wang, Xiaogang

    2015-01-01

    Variable DNA methylation has been associated with cancers and complex diseases. Researchers have identified many DNA methylation markers that have different mean methylation levels between diseased subjects and normal subjects. Recently, researchers found that DNA methylation markers with different variabilities between subject groups could also have biological meaning. In this article, we aimed to help researchers choose the right test of equal variance in DNA methylation data analysis. We performed systematic simulation studies and a real data analysis to compare the performances of 7 equal-variance tests, including 2 tests recently proposed in the DNA methylation analysis literature. Our results showed that the Brown-Forsythe test and trimmed-mean-based Levene's test had good performance in testing for equality of variance in our simulation studies and real data analyses. Our results also showed that outlier profiles could be biologically very important. PMID:26683022

  18. Methods of DNA methylation detection

    NASA Technical Reports Server (NTRS)

    Maki, Wusi Chen (Inventor); Filanoski, Brian John (Inventor); Mishra, Nirankar (Inventor); Rastogi, Shiva (Inventor)

    2010-01-01

    The present invention provides for methods of DNA methylation detection. The present invention provides for methods of generating and detecting specific electronic signals that report the methylation status of targeted DNA molecules in biological samples.Two methods are described, direct and indirect detection of methylated DNA molecules in a nano transistor based device. In the direct detection, methylated target DNA molecules are captured on the sensing surface resulting in changes in the electrical properties of a nano transistor. These changes generate detectable electronic signals. In the indirect detection, antibody-DNA conjugates are used to identify methylated DNA molecules. RNA signal molecules are generated through an in vitro transcription process. These RNA molecules are captured on the sensing surface change the electrical properties of nano transistor thereby generating detectable electronic signals.

  19. Methyl Halide Production by Fungi

    NASA Astrophysics Data System (ADS)

    Dailey, G. D.; Varner, R. K.; Blanchard, R. O.; Sive, B. C.; Crill, P. M.

    2005-12-01

    Methyl chloride (CH3Cl), methyl bromide (CH3Br) and methyl iodide (CH3I) are methyl halide gases that contribute significant amounts of halogen radicals to the atmosphere. In an effort to better understand the global budget of methyl halides and their impact on the atmosphere, we need to identify the natural sources in addition to the known anthropogenic sources of these compounds. We are investigating the role of fungi in the production of methyl halides in the soils and wetlands in southern New Hampshire, USA. Previous research has shown that wood decay fungi and ectomycorrhizal fungi, which are within a group of fungi called basidiomycetes, emit methyl halides. In our study, measurements of headspace gas extracted from flasks containing fungi grown in culture demonstrate that a variety of fungi, including basidiomycetes and non-basidiomycetes, emit methyl halides. Our research sites include four ecosystems: an agricultural field, a temperate forest, a fresh water wetland, and coastal salt marshes. We have collected and isolated fungi at each site by culturing tissue samples of fruiting bodies and plant material, by using wood baits, and from the direct culture of soil. We compared the rates of methyl halide emissions from the fungi in the four ecosystems. In addition, we measured emissions from previously assayed fungal isolates after reintroducing them to sterilized soils that were collected from their original environments. Fungal biomass was determined by substrate-induced respiration (SIR). The emission rate by the fungus was determined by a linear regression of the concentration of methyl halide in the sample headspace over time divided by the fungal biomass.

  20. Palladium-catalyzed substitution of (coumarinyl)methyl acetates with C-, N-, and S-nucleophiles

    E-print Network

    Chattopadhyay, Kalicharan; Fenster, Erik; Grenning, Alexander James; Tunge, Jon A.

    2012-07-27

    The palladium-catalyzed nucleophilic substitution of (coumarinyl)methyl acetates is described. The reaction proceeds though a palladium ?-benzyl-like complex and allows for many different types of C-, N-, and S-nucleophiles to be regioselectively...

  1. Methylation Abnormalities in Mammary Carcinoma: The Methylation Suicide Hypothesis

    PubMed Central

    O’Donnell, Anne H.; Edwards, John R.; Rollins, Robert A.; Vander Kraats, Nathan D.; Su, Tao; Hibshoosh, Hanina H.; Bestor, Timothy H.

    2015-01-01

    Promoter silencing by ectopic de novo methylation of tumor suppressor genes has been proposed as comparable or equivalent to inactivating mutations as a factor in carcinogenesis. However, this hypotheses had not previously been tested by high resolution, high-coverage whole-genome methylation profiling in primary carcinomas. We have determined the genomic methylation status of a series of primary mammary carcinomas and matched control tissues by examination of more than 2.7 billion CpG dinucleotides. Most of the tumors showed variable losses of DNA methylation from all sequence compartments, but increases in promoter methylation were infrequent, very small in extent, and were observed largely at CpG-poor promoters. De novo methylation at the promoters of proto-oncogenes and tumor suppressor genes occurred at approximately the same frequency. The findings indicate that tumor suppressor silencing by de novo methylation is much less common than currently believed. We put forward a hypothesis under which the demethylation commonly observed in carcinomas is a manifestation of a defensive system that kills incipient cancer cells. PMID:25960928

  2. Ni(II), Pd(II) and Pt(II) complexes of (1H-1,2,4-triazole-3-ylimino)methyl]naphthalene-2-ol. Structural, spectroscopic, biological, cytotoxicity, antioxidant and DNA binding.

    PubMed

    Gaber, M; El-Ghamry, H A; Fathalla, S K

    2015-03-15

    Metal complexes of the general formula [ML(H2O)Cl]nH2O; n=1 for M=Ni and Pt and n=2 for M=Pd, L=Schiff base (HL) derived from the condensation of 3-amino-1,2,4-triazole and 2-hydroxy-1-naphthaldehyde, were prepared. The synthesized ligand and its metal complexes were characterized on the basis of elemental analyses, spectral and magnetic studies as well as thermal analysis. The IR spectra revealed that the ligand is coordinated to the metal ions in bidentate manner via the N-atom of the azomethine group and the phenolic OH group. Square planar geometry was proposed for Pd(II) and Pt(II) complexes and tetrahedral for Ni(II) complex. The ligand and its metal complexes were screened against the sensitive organisms Escherichia coli as Gram-negative bacteria, Staphylococcus aureus as Gram-positive bacteria, Aspergillus flavus and Candida albicans as fungi. Moreover, the anticancer activity of the ligand and its metal complexes was evaluated in liver carcinoma (HEPG2) cell line. The results obtained indicated that the Schiff base ligand is more effective than its metal complexes towards the tested cell line. Ni(II), Pd(II) and Pt(II) complexes as well as the free Schiff base ligand were tested for their antioxidant activities. The DNA-binding properties of the studied complexes have been investigated by electronic absorption and viscosity measurements. PMID:25576936

  3. Ni(II), Pd(II) and Pt(II) complexes of (1H-1,2,4-triazole-3-ylimino)methyl]naphthalene-2-ol. Structural, spectroscopic, biological, cytotoxicity, antioxidant and DNA binding

    NASA Astrophysics Data System (ADS)

    Gaber, M.; El-Ghamry, H. A.; Fathalla, S. K.

    2015-03-01

    Metal complexes of the general formula [ML(H2O)Cl]nH2O; n = 1 for M = Ni and Pt and n = 2 for M = Pd, L = Schiff base (HL) derived from the condensation of 3-amino-1,2,4-triazole and 2-hydroxy-1-naphthaldehyde, were prepared. The synthesized ligand and its metal complexes were characterized on the basis of elemental analyses, spectral and magnetic studies as well as thermal analysis. The IR spectra revealed that the ligand is coordinated to the metal ions in bidentate manner via the N-atom of the azomethine group and the phenolic OH group. Square planar geometry was proposed for Pd(II) and Pt(II) complexes and tetrahedral for Ni(II) complex. The ligand and its metal complexes were screened against the sensitive organisms Escherichia coli as Gram-negative bacteria, Staphylococcus aureus as Gram-positive bacteria, Aspergillus flavus and Candida albicans as fungi. Moreover, the anticancer activity of the ligand and its metal complexes was evaluated in liver carcinoma (HEPG2) cell line. The results obtained indicated that the Schiff base ligand is more effective than its metal complexes towards the tested cell line. Ni(II), Pd(II) and Pt(II) complexes as well as the free Schiff base ligand were tested for their antioxidant activities. The DNA-binding properties of the studied complexes have been investigated by electronic absorption and viscosity measurements.

  4. DNA methylation pathways and their crosstalk with histone methylation

    PubMed Central

    Du, Jiamu; Johnson, Lianna M.; Jacobsen, Steven E.; Patel, Dinshaw J.

    2015-01-01

    Methylation of DNA and of histone 3 at Lys 9 (H3K9) are highly correlated with gene silencing in eukaryotes from fungi to humans. Both of these epigenetic marks need to be established at specific regions of the genome and then maintained at these sites through cell division. Protein structural domains that specifically recognize methylated DNA and methylated histones are key for targeting enzymes that catalyse these marks to appropriate genome sites. Genetic, genomic, structural and biochemical data reveal connections between these two epigenetic marks, and these domains mediate much of the crosstalk. PMID:26296162

  5. Photodissociation of methyl chloride and methyl bromide in the atmosphere

    NASA Technical Reports Server (NTRS)

    Robbins, D. E.

    1976-01-01

    Methyl chloride (CH3Cl) and methyl bromide (CH3Br) have been suggested to be significant sources of the stratospheric halogens. The breakup of these compounds in the stratosphere by photodissociation or reaction with OH releases halogen atoms which catalytically destroy ozone. Experimental results are presented for ultraviolet photoabsorption cross sections of CH3Cl and CH3Br. Calculations are presented of loss rates for the methyl halides due to photodissociation and reaction with OH and of mixing ratios of these species in the stratosphere.

  6. Hydridomethyl iridium complex

    DOEpatents

    Bergman, Robert G. (P.O. Box 7141, San Francisco, CA 94120-7141); Buchanan, J. Michael (P.O. Box 7141, San Francisco, CA 94120-7141); Stryker, Jeffrey M. (P.O. Box 7141, San Francisco, CA 94120-7141); Wax, Michael J. (P.O. Box 7141, San Francisco, CA 94120-7141)

    1989-01-01

    A process for functionalizing methane comprising: (a) reacting methane with a hydridoalkyl metal complex of the formula: CpIr[P(R.sub.1).sub.3 ]H(R.sub.2) wherein Cp represents a cyclopentadienyl or alkylcyclopentadienyl radical having from 1 to 5 carbon atoms; Ir represents an iridium atom; P represents a phosphorus atom; R.sub.1 represents an alkyl group; R.sub.2 represents an alkyl group having at least two carbon atoms; and H represents a hydrogen atom, in the presence of a liquid alkane R.sub.3 H having at least three carbon atoms to form a hydridomethyl complex of the formula: CpIr[P(R.sub.1).sub.3 ]HMe where Me represents a methyl radical. (b) reacting said hydridomethyl complex with an organic halogenating agent such as a tetrahalomethane or a haloform of the formulas: CX'X"X'"X"" or CHX'X"X'"; wherein X', X", X"', and X"" represent halogens selected from bromine, iodine and chlorine, to halomethyl complex of step (a) having the formula: CpIr[P(R.sub.1).sub.3 ]MeX: (c) reacting said halomethyl complex with a mercuric halide of the formula HgX.sub.2 to form a methyl mercuric halide of the formula HgMeX; and (d) reacting said methyl mercuric halide with a molecular halogen of the formula X.sub.2 to form methyl halide.

  7. Formation of a highly stable complex between BN 50730 [tetrahydro-4,7,8,10 methyl-1(chloro-2 phenyl)-6 (methoxy-4 phenyl-carbamoyl)-9 pyrido [4',3'-4,5] thieno [3,2-f] triazolo-1,2,4 [4,3-a] diazepine-1,4] and the platelet-activating factor receptor in rabbit platelet membranes.

    PubMed

    Silva, C L; Cruz, H N; Violante, F A; Cordeiro, R S; Martins, M A; Noël, F

    1996-01-26

    BN 50730 [tetrahydro-4,7,8,10 methyl-1(chloro-2 phenyl)-6 (methoxy-4 phenyl-carbamoyl)-9 pyrido [4',3'-4,5] thieno [3,2-f] triazolo-1,2,4 [4,3-alpha] diazepine-1,4], a novel platelet-activating factor (PAF) receptor antagonist with a hetrazepine structure, decreased the maximal number of binding sites (Bmax) of [3H]PAF in rabbit platelet membranes without altering its dissociation constant. Platelet aggregation induced by 1 microM PAF was prevented by preincubation with 1 microM BN 50730. The washing of the platelets preincubated with BN 50730 failed to revert its inhibitory effects. We conclude that BN 50730 acts as a non-competitive antagonist of the PAF receptor, due to the formation of a highly stable drug-receptor complex. PMID:8615889

  8. Conservation and divergence in eukaryotic DNA methylation

    E-print Network

    Conservation and divergence in eukaryotic DNA methylation Tzuu-fen Lee, Jixian Zhai, and Blake C of Delaware, Newark, DE 19711 C ytosine methylation is a com- mon DNA modification found in most eukaryotic conserved and divergent features of DNA methylation in eukaryotes. Although DNA methylation appears

  9. Synthesis of poly(2-methyl-3-hydroxyoctanoate) via anionic polymerization of alpha-methyl-beta-pentyl-beta-propiolactone.

    PubMed

    Arkin, A H; Hazer, B; Adamus, G; Kowalczuk, M; Jedli?ski, Z; Lenz, R W

    2001-01-01

    Synthesis of an alpha,beta-alkyl branched polyester, i.e., poly(2-methyl-3-hydroxyoctanoate), has been accomplished via anionic polymerization of alpha-methyl-beta-pentyl-beta-propiolactone mediated by supramolecular complexes of potassium methoxide or potassium hydroxide, respectively. The structure of resulting polymers has been established by electrospray ionization multistage mass spectrometry (ESI-MSn), FT-IR, NMR, and GPC analyses. Previously proposed addition-elimination mechanism of the polymerization of beta-lactones containing alpha-hydrogen by alkoxide anion has been confirmed to operate also in the case of beta-lactone having alkyl substituents in both alpha and beta positions. PMID:11710013

  10. Synthesis of platinum complexes with 2-(5-perfluoroalkyl-1,2,4-oxadiazol-3yl)-pyridine and 2-(3-perfluoroalkyl-1-methyl-1,2,4-triazole-5yl)-pyridine ligands and their in vitro antitumor activity.

    PubMed

    Rubino, Simona; Pibiri, Ivana; Costantino, Cristina; Buscemi, Silvestre; Girasolo, Maria Assunta; Attanzio, Alessandro; Tesoriere, Luisa

    2016-02-01

    Five new mononuclear Pt(II) complexes with 5-perfluoroalkyl-1,2,4-oxadiazolyl-pyridine and 3-perfluoroalkyl-1,2,4-triazolyl-pyridine ligands are reported. The ligands 2-(5-perfluoroheptyl-1,2,4-oxadiazole-3yl)-pyridine (pfhop), 2-(5-perfluoropropyl)-1,2,4-oxadiazole-3yl)-pyridine (pfpop), 2-(3-perfluoroheptyl-1-methyl-1,2,4-triazole-5yl)-pyridine (pfhtp), 2-(3-perfluoropropyl-1-methyl-1,2,4-triazole-5yl)-pyridine (pfptp) and their complexes [PtCl2(pfhop)2]·1.5 DMSO (2a), [PtCl2(pfpop)2]·1.5 DMSO (3a), [PtCl2(pfhtp)2]·1.5 DMSO (4a), PtCl2(pfhtp) (4b), [PtCl2(pfptp)2]·1.5 DMSO (5a) have been synthesized and structurally characterized. The complexes 2a, 3a, 4a and 5a have the same chemical environment of Pt(II) where PtCl2 moieties coordinate two molecules of ligand via N1 atom of pyridine in the case of pfhop and pfpop, and N2 atom of 1,2,4-triazole in the case of pfhtp and pfptp. For 4b, pfhtp behaves as bidentate ligand, coordinating Pt(II) ion via N4 atom of triazole and N1 atom of pyridine. All complexes have been tested in vitro by 3-(4,5-dimethyl-2-thiazolyl)bromide-2,5-diphenyl-2H-tetrazolium (MTT) test on four tumor cell lines MCF-7 (human breast cancer), HepG2 (human hepatocellular carcinoma), HCT116 (human colorectal carcinoma). Compounds 2a and 4b showed a dose-dependent anti-proliferative effect against the three tumor cell lines whereas did not affect viability of intestinal normal-like differentiated Caco-2 cells. The cell death of HepG2, MCF-7 and HCT116 induced by the compounds, was considered to be apoptotic by measuring the exposure of phosphatidylserine to the outer membrane and observing the typical apoptotic morphological change by acridine orange (AO)/ethidium bromide (EB) staining. PMID:26684582

  11. 21 CFR 177.2000 - Vinylidene chloride/methyl acrylate/methyl methacrylate polymers.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Vinylidene chloride/methyl acrylate/methyl... Vinylidene chloride/methyl acrylate/methyl methacrylate polymers. The vinylidene chloride/methyl acrylate... the provisions of this section. (a) Identity. For the purpose of this section, vinylidene...

  12. 21 CFR 177.2000 - Vinylidene chloride/methyl acrylate/methyl methacrylate polymers.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Vinylidene chloride/methyl acrylate/methyl... Vinylidene chloride/methyl acrylate/methyl methacrylate polymers. The vinylidene chloride/methyl acrylate... the provisions of this section. (a) Identity. For the purpose of this section, vinylidene...

  13. NOAA and University Scientists Study Methyl Bromide and Methyl Chloride Cycling in the Southern Ocean

    E-print Network

    Goodwin, Kelly D.

    NOAA and University Scientists Study Methyl Bromide and Methyl Chloride Cycling in the Southern, methyl chloride and other climatically important halocarbons in the Southern Ocean. Atmospheric methyl. Methyl chloride (CH3Cl) is the most abundant halocarbon in the atmosphere and is a naturally occurring

  14. Synthesis, spectral, antitumor, antioxidant and antimicrobial studies on Cu(II), Ni(II) and Co(II) complexes of 4-[(1H-Benzoimidazol-2-ylimino)-methyl]-benzene-1,3-diol

    NASA Astrophysics Data System (ADS)

    El-wakiel, Nadia; El-keiy, Mai; Gaber, Mohamed

    2015-08-01

    A new Schiff base of 2-aminobenzimidazole with 2,4-dihydroybezaldehyde (H3L), and its Cu(II), Ni(II) and Co(II) complexes have been synthesized and characterized by elemental analyses, molar conductance, thermal analysis (TGA), inductive coupled plasma (ICP), magnetic moment measurements, IR, EI-mass, UV-Vis. and ESR spectral studies. On the basis of spectral studies and analytical data, it is evident that the Schiff base acts as dibasic tridentate ligand coordinating via deprotonated OH, NH and azomethine nitrogen atom. The results showed that Co(II) and Ni(II) complexes have tetrahedral structure while Cu(II) complexes has octahedral geometry. The kinetic and thermodynamic parameters of the thermal decomposition stages have been evaluated. The studied complexes were tested for their in vitro antimicrobial activities against some bacterial strains. The anticancer activity of the ligand and its metal complexes is evaluated against human liver Carcinoma (HEPG2) cell. These compounds exhibited a moderate and weak activity against the tested HEPG2 cell lines with IC50 of 9.08, 18.2 and 19.7 ?g/ml for ligand, Cu(II) and Ni(II) complexes, respectively. In vitro antioxidant activity of the newly synthesized compounds has also been evaluated.

  15. [DNA methylation. From basic research to routine diagnostics].

    PubMed

    Lehmann, U

    2010-10-01

    On a molecular level cancer is characterized not only by genetic defects, such as deletions, mutations or translocations, but also by epigenetic lesions. The most important epigenetic mechanisms are DNA methylation, Polycomb/trithorax complexes, histon modifications, non-coding RNAs, and chromosomal territories. These epigenetic mechanisms contribute to a stable modification of gene expression without changes in primary DNA sequence. During the development and progression of human tumours a gene-specific hypermethylation with resulting repression of transcription can occur. At the same time, global hypomethylation can very often be observed which contributes to an increase in chromosomal instability. In tumour pathology, the detection of somatic hMLH1 hypermethylation is important for molecular diagnostics of Lynch syndrome. The detection of MGMT gene methylation is a good prognostic and predictive factor for glioblastoma patients. Performing DNA methylation assays for routine diagnostics requires technical as well as theoretical expertise. PMID:20824434

  16. Dynamic changes in histone modifications precede de novo DNA methylation in oocytes

    PubMed Central

    Stewart, Kathleen R.; Veselovska, Lenka; Kim, Jeesun; Huang, Jiahao; Saadeh, Heba; Tomizawa, Shin-ichi; Smallwood, Sébastien A.; Chen, Taiping; Kelsey, Gavin

    2015-01-01

    Erasure and subsequent reinstatement of DNA methylation in the germline, especially at imprinted CpG islands (CGIs), is crucial to embryogenesis in mammals. The mechanisms underlying DNA methylation establishment remain poorly understood, but a number of post-translational modifications of histones are implicated in antagonizing or recruiting the de novo DNA methylation complex. In mouse oogenesis, DNA methylation establishment occurs on a largely unmethylated genome and in nondividing cells, making it a highly informative model for examining how histone modifications can shape the DNA methylome. Using a chromatin immunoprecipitation (ChIP) and genome-wide sequencing (ChIP-seq) protocol optimized for low cell numbers and novel techniques for isolating primary and growing oocytes, profiles were generated for histone modifications implicated in promoting or inhibiting DNA methylation. CGIs destined for DNA methylation show reduced protective H3K4 dimethylation (H3K4me2) and trimethylation (H3K4me3) in both primary and growing oocytes, while permissive H3K36me3 increases specifically at these CGIs in growing oocytes. Methylome profiling of oocytes deficient in H3K4 demethylase KDM1A or KDM1B indicated that removal of H3K4 methylation is necessary for proper methylation establishment at CGIs. This work represents the first systematic study performing ChIP-seq in oocytes and shows that histone remodeling in the mammalian oocyte helps direct de novo DNA methylation events. PMID:26584620

  17. Evaluation of colorimetric assays for analyzing reductively methylated proteins: Biases and mechanistic insights.

    PubMed

    Brady, Pamlea N; Macnaughtan, Megan A

    2015-12-15

    Colorimetric protein assays, such as the Coomassie blue G-250 dye-binding (Bradford) and bicinchoninic acid (BCA) assays, are commonly used to quantify protein concentration. The accuracy of these assays depends on the amino acid composition. Because of the extensive use of reductive methylation in the study of proteins and the importance of biological methylation, it is necessary to evaluate the impact of lysyl methylation on the Bradford and BCA assays. Unmodified and reductively methylated proteins were analyzed using the absorbance at 280 nm to standardize the concentrations. Using model compounds, we demonstrate that the dimethylation of lysyl ?-amines does not affect the proteins' molar extinction coefficients at 280 nm. For the Bradford assay, the responses (absorbance per unit concentration) of the unmodified and reductively methylated proteins were similar, with a slight decrease in the response upon methylation. For the BCA assay, the responses of the reductively methylated proteins were consistently higher, overestimating the concentrations of the methylated proteins. The enhanced color formation in the BCA assay may be due to the lower acid dissociation constants of the lysyl ?-dimethylamines compared with the unmodified ?-amine, favoring Cu(II) binding in biuret-like complexes. The implications for the analysis of biologically methylated samples are discussed. PMID:26342307

  18. Dynamic changes in histone modifications precede de novo DNA methylation in oocytes.

    PubMed

    Stewart, Kathleen R; Veselovska, Lenka; Kim, Jeesun; Huang, Jiahao; Saadeh, Heba; Tomizawa, Shin-Ichi; Smallwood, Sébastien A; Chen, Taiping; Kelsey, Gavin

    2015-12-01

    Erasure and subsequent reinstatement of DNA methylation in the germline, especially at imprinted CpG islands (CGIs), is crucial to embryogenesis in mammals. The mechanisms underlying DNA methylation establishment remain poorly understood, but a number of post-translational modifications of histones are implicated in antagonizing or recruiting the de novo DNA methylation complex. In mouse oogenesis, DNA methylation establishment occurs on a largely unmethylated genome and in nondividing cells, making it a highly informative model for examining how histone modifications can shape the DNA methylome. Using a chromatin immunoprecipitation (ChIP) and genome-wide sequencing (ChIP-seq) protocol optimized for low cell numbers and novel techniques for isolating primary and growing oocytes, profiles were generated for histone modifications implicated in promoting or inhibiting DNA methylation. CGIs destined for DNA methylation show reduced protective H3K4 dimethylation (H3K4me2) and trimethylation (H3K4me3) in both primary and growing oocytes, while permissive H3K36me3 increases specifically at these CGIs in growing oocytes. Methylome profiling of oocytes deficient in H3K4 demethylase KDM1A or KDM1B indicated that removal of H3K4 methylation is necessary for proper methylation establishment at CGIs. This work represents the first systematic study performing ChIP-seq in oocytes and shows that histone remodeling in the mammalian oocyte helps direct de novo DNA methylation events. PMID:26584620

  19. Protein methylation and DNA repair.

    PubMed

    Lake, Aimee N; Bedford, Mark T

    2007-05-01

    DNA is under constant attack from intracellular and external mutagens. Sites of DNA damage need to be pinpointed so that the DNA repair machinery can be mobilized to the proper location. The identification of damaged sites, recruitment of repair factors, and assembly of repair "factories" is orchestrated by posttranslational modifications (PTMs). These PTMs include phosphorylation, ubiquitination, sumoylation, acetylation, and methylation. Here we discuss recent data surrounding the roles of arginine and lysine methylation in DNA repair processes. PMID:17306845

  20. Novel mixed ligand complexes of bioactive Schiff base (E)-4-(phenyl (phenylimino) methyl) benzene-1,3-diol and 2-aminophenol/2-aminobenzoic acid: Synthesis, spectral characterization, antimicrobial and nuclease studies

    NASA Astrophysics Data System (ADS)

    Subbaraj, P.; Ramu, A.; Raman, N.; Dharmaraja, J.

    2014-01-01

    A novel bidentate Schiff base ligand has been synthesized using 2,4-dihydroxybenzophenone and aniline. Its mixed ligand complexes of MAB type [M = Mn(II), Co(II), Ni(II), Cu(II) and Zn(II); HA = Schiff base and B = 2-aminophenol/2-aminobenzoic acid] have been synthesized and characterized on the basis of spectral data UV-Vis, IR, 1H NMR, FAB-Mass, EPR, SEM and magnetic studies. All the complexes were soluble in DMF and DMSO. Elemental analysis and molar conductance values indicate that the complexes are non-electrolytes. HA binds with M(II) ions through azomethine and deprotonated phenolic group and B binds through the primary amine group and deprotonated phenolic/carboxylic groups. Using FAB-Mass the cleavage pattern of the ligand (HA) has been established. All the complexes adopt octahedral geometry around the metal ions. It has been confirmed with the help of UV-Vis, IR, 1H NMR and FAB-Mass spectral data. DNA binding activities of the complexes 1d and 2d are studied by UV-Vis spectroscopy and cleavage studies of Schiff base ligand and its complexes 1d and 2d have been by agarose gel electrophoresis method. In vitro biological activities of the free ligand (HA) and their metal complexes (1a-1e and 2a-2e) were screened against few bacteria, Escherichia coli, Staphylococcus saphyphiticus, Staphylococcus aureus, Pseudomonas aeruginosa and fungi Aspergillus niger, Enterobacter species, Candida albicans by well diffusion technique.

  1. Novel mixed ligand complexes of bioactive Schiff base (E)-4-(phenyl (phenylimino) methyl) benzene-1,3-diol and 2-aminophenol/2-aminobenzoic acid: synthesis, spectral characterization, antimicrobial and nuclease studies.

    PubMed

    Subbaraj, P; Ramu, A; Raman, N; Dharmaraja, J

    2014-01-01

    A novel bidentate Schiff base ligand has been synthesized using 2,4-dihydroxybenzophenone and aniline. Its mixed ligand complexes of MAB type [M=Mn(II), Co(II), Ni(II), Cu(II) and Zn(II); HA=Schiff base and B=2-aminophenol/2-aminobenzoic acid] have been synthesized and characterized on the basis of spectral data UV-Vis, IR, (1)H NMR, FAB-Mass, EPR, SEM and magnetic studies. All the complexes were soluble in DMF and DMSO. Elemental analysis and molar conductance values indicate that the complexes are non-electrolytes. HA binds with M(II) ions through azomethine and deprotonated phenolic group and B binds through the primary amine group and deprotonated phenolic/carboxylic groups. Using FAB-Mass the cleavage pattern of the ligand (HA) has been established. All the complexes adopt octahedral geometry around the metal ions. It has been confirmed with the help of UV-Vis, IR, (1)H NMR and FAB-Mass spectral data. DNA binding activities of the complexes 1d and 2d are studied by UV-Vis spectroscopy and cleavage studies of Schiff base ligand and its complexes 1d and 2d have been by agarose gel electrophoresis method. In vitro biological activities of the free ligand (HA) and their metal complexes (1a-1e and 2a-2e) were screened against few bacteria, Escherichia coli, Staphylococcus saphyphiticus, Staphylococcus aureus, Pseudomonas aeruginosa and fungi Aspergillus niger, Enterobacter species, Candida albicans by well diffusion technique. PMID:23981416

  2. PGC?1? Promoter Methylation in Parkinson’s Disease

    PubMed Central

    Su, Xiaomin; Chu, Yaping; Kordower, Jeffrey H.; Li, Bin; Cao, Hong; Huang, Liang; Nishida, Maki; Song, Lei; Wang, Difei; Federoff, Howard J.

    2015-01-01

    The etiopathogenesis of sporadic Parkinson’s disease (PD) remains elusive although mitochondrial dysfunction has long been implicated. Recent evidence revealed reduced expression of peroxisome proliferator-activated receptor gamma coactivator?1 ? (PGC?1?) and downstream regulated nuclear encoded respiratory complex genes in affected brain tissue from PD patients. We sought to determine whether epigenetic modification of the PGC?1? gene could account for diminished expression. In substantia nigra from PD patients but not control subjects, we show significant promoter-proximal non-canonical cytosine methylation of the PGC?1? gene but not an adjacent gene. As neuroinflammation is a prominent feature of PD and a mediator of epigenetic change, we evaluated whether the pro-inflammatory fatty acid, palmitate, would stimulate PGC?1? promoter methylation in different cell types from the CNS. Indeed, in mouse primary cortical neurons, microglia and astrocytes, palmitate causes PGC?1? gene promoter non-canonical cytosine methylation, reduced expression of the gene and reduced mitochondrial content. Moreover, intracerebroventricular (ICV) injection of palmitate to transgenic human ??synuclein mutant mice resulted in increased PGC?1? promoter methylation, decreased PGC?1? expression and reduced mitochondrial content in substantia nigra. Finally we provide evidence that dysregulation of ER stress and inflammatory signaling is associated with PGC?1? promoter methylation. Together, these data strengthen the connection between saturated fatty acids, neuroflammation, ER stress, epigenetic alteration and bioenergetic compromise in PD. PMID:26317511

  3. The Fine LINE: Methylation Drawing the Cancer Landscape

    PubMed Central

    Miousse, Isabelle R.; Koturbash, Igor

    2015-01-01

    LINE-1 (L1) is the most abundant mammalian transposable element that comprises nearly 20% of the genome, and nearly half of the mammalian genome has stemmed from L1-mediated mobilization. Expression and retrotransposition of L1 are suppressed by complex mechanisms, where the key role belongs to DNA methylation. Alterations in L1 methylation may lead to aberrant expression of L1 and have been described in numerous diseases. Accumulating evidence clearly indicates that loss of global DNA methylation observed in cancer development and progression is tightly associated with hypomethylation of L1 elements. Significant progress achieved in the last several years suggests that such parameters as L1 methylation status can be potentially utilized as clinical biomarkers for determination of the disease stage and in predicting the disease-free survival in cancer patients. In this paper, we summarize the current knowledge on L1 methylation, with specific emphasis given to success and challenges on the way of introduction of L1 into clinical practice. PMID:26448926

  4. Neurospora Importin ? Is Required for Normal Heterochromatic Formation and DNA Methylation

    PubMed Central

    Klocko, Andrew D.; Rountree, Michael R.; Grisafi, Paula L.; Hays, Shan M.; Adhvaryu, Keyur K.; Selker, Eric U.

    2015-01-01

    Heterochromatin and associated gene silencing processes play roles in development, genome defense, and chromosome function. In many species, constitutive heterochromatin is decorated with histone H3 tri-methylated at lysine 9 (H3K9me3) and cytosine methylation. In Neurospora crassa, a five-protein complex, DCDC, catalyzes H3K9 methylation, which then directs DNA methylation. Here, we identify and characterize a gene important for DCDC function, dim-3 (defective in methylation-3), which encodes the nuclear import chaperone NUP-6 (Importin ?). The critical mutation in dim-3 results in a substitution in an ARM repeat of NUP-6 and causes a substantial loss of H3K9me3 and DNA methylation. Surprisingly, nuclear transport of all known proteins involved in histone and DNA methylation, as well as a canonical transport substrate, appear normal in dim-3 strains. Interactions between DCDC members also appear normal, but the nup-6dim-3 allele causes the DCDC members DIM-5 and DIM-7 to mislocalize from heterochromatin and NUP-6dim-3 itself is mislocalized from the nuclear envelope, at least in conidia. GCN-5, a member of the SAGA histone acetyltransferase complex, also shows altered localization in dim-3, raising the possibility that NUP-6 is necessary to localize multiple chromatin complexes following nucleocytoplasmic transport. PMID:25793375

  5. High methylation rates of mercury bound to cysteine by Geobacter sulfurreducens

    NASA Astrophysics Data System (ADS)

    Schaefer, Jeffra K.; Morel, François M. M.

    2009-02-01

    Methylmercury bioaccumulates in aquatic food chains and is able to cross the blood-brain barrier, making this organometallic compound a much more worrisome pollutant than inorganic mercury. We know that methylation of inorganic mercury is carried out by microbes in the anoxic layers of sediments and water columns, but the factors that control the extent of this methylation are poorly known. Mercury methylation is generally thought to be catalysed accidentally by some methylating enzyme, and it has been suggested that cellular mercury uptake results from passive diffusion of neutral mercury complexes. Here, we show that mercury methylation by the bacterium Geobacter sulfurreducens is greatly enhanced in the presence of low concentrations of the amino acid cysteine. The formation of a mercury-cysteine complex promotes both the uptake of inorganic mercury by the bacteria and the enzymatic formation of methylmercury, which is subsequently released to the external medium. Our results suggest that mercury uptake and methylation by microbes are controlled more tightly by biological mechanisms than previously thought, and that the formation of specific mercury complexes in anoxic waters modulates the efficiency of the microbial methylation of mercury.

  6. Genome-wide methylation study on depression: differential methylation and variable methylation in monozygotic twins

    PubMed Central

    Córdova-Palomera, A; Fatjó-Vilas, M; Gastó, C; Navarro, V; Krebs, M-O; Fañanás, L

    2015-01-01

    Depressive disorders have been shown to be highly influenced by environmental pathogenic factors, some of which are believed to exert stress on human brain functioning via epigenetic modifications. Previous genome-wide methylomic studies on depression have suggested that, along with differential DNA methylation, affected co-twins of monozygotic (MZ) pairs have increased DNA methylation variability, probably in line with theories of epigenetic stochasticity. Nevertheless, the potential biological roots of this variability remain largely unexplored. The current study aimed to evaluate whether DNA methylation differences within MZ twin pairs were related to differences in their psychopathological status. Data from the Illumina Infinium HumanMethylation450 Beadchip was used to evaluate peripheral blood DNA methylation of 34 twins (17 MZ pairs). Two analytical strategies were used to identify (a) differentially methylated probes (DMPs) and (b) variably methylated probes (VMPs). Most DMPs were located in genes previously related to neuropsychiatric phenotypes. Remarkably, one of these DMPs (cg01122889) was located in the WDR26 gene, the DNA sequence of which has been implicated in major depressive disorder from genome-wide association studies. Expression of WDR26 has also been proposed as a biomarker of depression in human blood. Complementarily, VMPs were located in genes such as CACNA1C, IGF2 and the p38 MAP kinase MAPK11, showing enrichment for biological processes such as glucocorticoid signaling. These results expand on previous research to indicate that both differential methylation and differential variability have a role in the etiology and clinical manifestation of depression, and provide clues on specific genomic loci of potential interest in the epigenetics of depression. PMID:25918994

  7. Tunable Luminescence and Application in Dye-Sensitized Solar Cells of Zn(II)/Hg(II) Complexes: Methyl Substitution-Induced Supramolecular Structures Based on (E)-N-(6-Methoxypyridin-2-ylmethylene)arylamine Derivatives.

    PubMed

    Dong, Yu-Wei; Fan, Rui-Qing; Wang, Ping; Wei, Li-Guo; Wang, Xin-Ming; Gao, Song; Zhang, Hui-Jie; Yang, Yu-Lin; Wang, Yu-Lei

    2015-08-17

    Using Schiff-base ligands (E)-N-(6-methoxypyridin-2-yl)(CH?NAr) (where Ar = C6H5, L1; 2-MeC6H4, L2; 2,4,6-Me3C6H2, L3), six Zn(II)/Hg(II) complexes, namely, [ZnL1Cl2] (Zn1), [HgL1Cl2] (Hg1), [ZnL2Cl2] (Zn2), [HgL2Cl2] (Hg2), [ZnL3Cl2] (Zn3), and [HgL3Cl2] (Hg3) have been synthesized under solvothermal conditions. The structures of six complexes have been established by X-ray single-crystal analysis and further physically characterized by EA, FT-IR, (1)H NMR, and ESI-MS. The crystal structures of these complexes indicate that noncovalent interactions, such as hydrogen bonds, C-H···Cl, and ?···? stacking, play essential roles in constructing the resulting supramolecular structures (1D for Hg3; 2D for Zn2, Hg2; 3D for Zn1, Hg1, and Zn3). Upon irradiation with UV light, the emission of complexes Zn1-Zn3 and Hg1-Hg3 could be finely tuned from green (480-540 nm) in the solid state to blue (402-425 nm) in acetonitrile solution. It showed that the ligand and metal cation can influence the structures and luminescence properties of complexes such as emission intensities and maximum wavelengths. Since these ligands and complexes could compensate for the absorption of N719 in the low-wavelength region of the visible spectrum and reduce charge recombination of the injected electron, the ligands L1-L3 and complexes Zn3/Hg3 were employed to prepare cosensitized dye-sensitized solar cells devices for investigating the influences of the electron-donating group and coordination on the DSSCs performance. Compared to DSSCs only being sensitized by N719, these prepared ligands and complexes chosen to cosensitize N719 in solar cell do enhanced its performance by 11-41%. In particular, a DSSC using L3 as cosensitizer displays better photovoltaic performance with a short circuit current density of 18.18 mA cm(-2), corresponding to a conversion efficiency of 7.25%. It is much higher than that for DSSCs only sensitized by N719 (5.14%). PMID:26207930

  8. The Search for a Complex Molecule in a Selected Hot Core Region: A Rigorous Attempt to Confirm Trans-ethyl Methyl Ether toward W51 e1/e2

    NASA Astrophysics Data System (ADS)

    Carroll, P. Brandon; McGuire, Brett A.; Blake, Geoffrey A.; Apponi, A. J.; Ziurys, L. M.; Remijan, Anthony

    2015-01-01

    An extensive search has been conducted to confirm transitions of trans-ethyl methyl ether (tEME, C2H5OCH3), toward the high-mass star forming region W51 e1/e2 using the 12 m Telescope of the Arizona Radio Observatory at wavelengths from 2 mm and 3 mm. In short, we cannot confirm the detection of tEME toward W51 e1/e2 and our results call into question the initial identification of this species by Fuchs et al. Additionally, re-evaluation of the data from the original detection indicates that tEME is not present toward W51 e1/e2 in the abundance reported by Fuchs and colleagues. Typical peak-to-peak noise levels for the present observations of W51 e1/e2 were between 10 and 30 mK, yielding an upper limit of the tEME column density of <=1.5 × 1015 cm-2. This would make tEME at least a factor of two times less abundant than dimethyl ether (CH3OCH3) toward W51 e1/e2. We also performed an extensive search for this species toward the high-mass star forming region Sgr B2(N-LMH) with the National Radio Astronomy Observatory 100 m Green Bank Telescope. No transitions of tEME were detected and we were able to set an upper limit to the tEME column density of <=4 × 1014 cm-2 toward this source. Thus, we are able to show that tEME is not a new molecular component of the interstellar medium and that an exacting assessment must be carried out when assigning transitions of new molecular species to astronomical spectra to support the identification of large organic interstellar molecules.

  9. THE SEARCH FOR A COMPLEX MOLECULE IN A SELECTED HOT CORE REGION: A RIGOROUS ATTEMPT TO CONFIRM TRANS-ETHYL METHYL ETHER TOWARD W51 e1/e2

    SciTech Connect

    Carroll, P. Brandon; McGuire, Brett A.; Blake, Geoffrey A.; Apponi, A. J.; Ziurys, L. M.; Remijan, Anthony

    2015-01-20

    An extensive search has been conducted to confirm transitions of trans-ethyl methyl ether (tEME, C{sub 2}H{sub 5}OCH{sub 3}), toward the high-mass star forming region W51 e1/e2 using the 12 m Telescope of the Arizona Radio Observatory at wavelengths from 2 mm and 3 mm. In short, we cannot confirm the detection of tEME toward W51 e1/e2 and our results call into question the initial identification of this species by Fuchs et al. Additionally, re-evaluation of the data from the original detection indicates that tEME is not present toward W51 e1/e2 in the abundance reported by Fuchs and colleagues. Typical peak-to-peak noise levels for the present observations of W51 e1/e2 were between 10 and 30 mK, yielding an upper limit of the tEME column density of ?1.5 × 10{sup 15} cm{sup –2}. This would make tEME at least a factor of two times less abundant than dimethyl ether (CH{sub 3}OCH{sub 3}) toward W51 e1/e2. We also performed an extensive search for this species toward the high-mass star forming region Sgr B2(N-LMH) with the National Radio Astronomy Observatory 100 m Green Bank Telescope. No transitions of tEME were detected and we were able to set an upper limit to the tEME column density of ?4 × 10{sup 14} cm{sup –2} toward this source. Thus, we are able to show that tEME is not a new molecular component of the interstellar medium and that an exacting assessment must be carried out when assigning transitions of new molecular species to astronomical spectra to support the identification of large organic interstellar molecules.

  10. Synthesis, structural characterization, superoxide dismutase and antimicrobial activities studies of copper (II) complexes with 2-(E)-(2-(2-aminoethylamino) methyl)-4-bromophenol and (19E, 27E)-N1, N2-bis (phenyl (pyridine-2-yl)-methylene)-ethane-1, 2-diamine as ligands

    NASA Astrophysics Data System (ADS)

    Choudhary, Mukesh; Patel, R. N.; Rawat, S. P.

    2014-07-01

    Three new copper (II) complexes, [Cu(L)(H2O)]ClO4 (1), [Cu(L1)(ClO4)]+ (2) and [Cu(L1)]2+ (3), where HL = 2-(E)-(2-(2-aminoethylamino)methyl)-4-bromophenol, L1 =(19E, 27E)-N1,N2-bis(phenyl(pyridine-2-yl)-methylene)-ethane-1, 2-diamine, have been synthesized and characterized by using various physic-chemical and spectroscopic methods. The solid-state structures of 1 and 2 were determined by single crystal X-ray crystallography. Infrared spectra, ligand field spectra and magnetic susceptibility measurements agree with the observed crystal structures. The molecular structure of copper complexes showed that the ligands occupies the basal plane of square pyramidal geometry with the H2O of 1 or the ClO4 of 2 occupying the remaining apical position. Complexes 1 and 2 crystallize in the monoclinic system of the space group P21/c, a = 10.5948(6)Å, b = 19.6164(11)Å, c = 8.6517(5)Å, ? = 90°, ? = 108.213(2)°, ? = 90° and Z = 4 for 1, a = 9.5019(3)Å, b = 11.3 801(3)Å, c = 25.3168(14)Å, ? = 90°, ? = 100.583(4)°, ? = 90°, and Z = 4 for 2. The synthesized Schiff base (HL/L1) was behaves as tetradentate ON3/N4 ligands with donor groups suitable placed for forming 2 or 3 five membered chelate rings. Copper (II) complexes display X-band EPR spectra in 100% DMSO at 77 K giving g|| > g? > 2.0023 indicating dx2-y2 ground state. The half-wave potential values for Cu (II)/Cu (I) redox couple obtained in the reaction of the copper (II) complexes with molecular oxygen and superoxide radical (O2-) electronegated in DMSO are in agreement with the SOD-like activity of the copper (II) complexes. In vitro antimicrobial activities of the complexes against the two bacteria (Escherichia coli, Salmonella typhi) and the two fungi (Penicillium, Aspergillus sp.) have been investigated comparing with the Schiff base ligands.

  11. Comparisons of Non-Gaussian Statistical Models in DNA Methylation Analysis

    PubMed Central

    Ma, Zhanyu; Teschendorff, Andrew E.; Yu, Hong; Taghia, Jalil; Guo, Jun

    2014-01-01

    As a key regulatory mechanism of gene expression, DNA methylation patterns are widely altered in many complex genetic diseases, including cancer. DNA methylation is naturally quantified by bounded support data; therefore, it is non-Gaussian distributed. In order to capture such properties, we introduce some non-Gaussian statistical models to perform dimension reduction on DNA methylation data. Afterwards, non-Gaussian statistical model-based unsupervised clustering strategies are applied to cluster the data. Comparisons and analysis of different dimension reduction strategies and unsupervised clustering methods are presented. Experimental results show that the non-Gaussian statistical model-based methods are superior to the conventional Gaussian distribution-based method. They are meaningful tools for DNA methylation analysis. Moreover, among several non-Gaussian methods, the one that captures the bounded nature of DNA methylation data reveals the best clustering performance. PMID:24937687

  12. Genome wide analysis of DNA methylation and gene expression changes in the mouse lung following subchronic arsenate exposure

    EPA Science Inventory

    Alterations in DNA methylation have been proposed as a mechanism for the complex toxicological effects of arsenic. In this study, whole genome DNA methylation and gene expression changes were evaluated in lungs from female mice exposed for 90 days to 50 ppm arsenate (As) in drink...

  13. Synthesis of 3-Methyl-4-(4-methylbenzoyl)-1-phenyl-pyrazol-5-One: How to Avoid O-Acylation

    ERIC Educational Resources Information Center

    Kurteva, Vanya B.; Petrova, Maria A.

    2015-01-01

    In this laboratory experiment, students synthesize 3-methyl-4-(4-methylbenzoyl)-1-phenyl-pyrazol-5-one by selective C-acylation of 3-methyl-1-phenyl-1H-pyrazol-5-one. Calcium hydroxide is used to push the tautomeric equilibrium toward the enol form, to protect the hydroxyl functionality as a complex, to trap the liberated hydrogen chloride, and to…

  14. PCMdb: Pancreatic Cancer Methylation Database

    NASA Astrophysics Data System (ADS)

    Nagpal, Gandharva; Sharma, Minakshi; Kumar, Shailesh; Chaudhary, Kumardeep; Gupta, Sudheer; Gautam, Ankur; Raghava, Gajendra P. S.

    2014-02-01

    Pancreatic cancer is the fifth most aggressive malignancy and urgently requires new biomarkers to facilitate early detection. For providing impetus to the biomarker discovery, we have developed Pancreatic Cancer Methylation Database (PCMDB, http://crdd.osdd.net/raghava/pcmdb/), a comprehensive resource dedicated to methylation of genes in pancreatic cancer. Data was collected and compiled manually from published literature. PCMdb has 65907 entries for methylation status of 4342 unique genes. In PCMdb, data was compiled for both cancer cell lines (53565 entries for 88 cell lines) and cancer tissues (12342 entries for 3078 tissue samples). Among these entries, 47.22% entries reported a high level of methylation for the corresponding genes while 10.87% entries reported low level of methylation. PCMdb covers five major subtypes of pancreatic cancer; however, most of the entries were compiled for adenocarcinomas (88.38%) and mucinous neoplasms (5.76%). A user-friendly interface has been developed for data browsing, searching and analysis. We anticipate that PCMdb will be helpful for pancreatic cancer biomarker discovery.

  15. DNA methylation and cognitive aging

    PubMed Central

    Xu, Xiangru

    2015-01-01

    With ever-increasing elder population, the high incidence of age-related diseases such as neurodegenerative disorders has turned out to be a huge public concern. Especially the elders and their families dreadfully suffer from the learning, behavioral and cognitive impairments. The lack of effective therapies for such a horrible symptom makes a great demanding for biological mechanism study for cognitive aging. Epigenetics is an emerging field that broadens the dimensions of mammalian genome blueprint. It is, unlike genetics, not only inheritable but also reversible. Recent studies suggest that DNA methylation, one of major epigenetic mechanisms, plays a pivotal role in the pathogenesis of age-related neurodegenerations and cognitive defects. In this review, the evolving knowledge of age-related cognitive functions and the potential DNA methylation mechanism of cognitive aging are discussed. That indicates the impairment of DNA methylation may be a crucial but reversible mechanism of behavioral and cognitive related neurodegeneration. The methods to examine the dynamics of DNA methylation patterns at tissue and single cell level and at the representative scale as well as the whole genome single base resolution are also briefly discussed. Importantly, the challenges of DNA methylation mechanism of cognitive aging research are brought up, and the possible solutions to tackle these difficulties are put forward. PMID:26015403

  16. DNA Methylation Assessed by SMRT Sequencing Is Linked to Mutations in Neisseria meningitidis Isolates

    PubMed Central

    Sater, Mohamad R. Abdul; Lamelas, Araceli; Wang, Guilin; Clark, Tyson A.; Röltgen, Katharina; Mane, Shrikant; Korlach, Jonas; Pluschke, Gerd; Schmid, Christoph D.

    2015-01-01

    The Gram-negative bacterium Neisseria meningitidis features extensive genetic variability. To present, proposed virulence genotypes are also detected in isolates from asymptomatic carriers, indicating more complex mechanisms underlying variable colonization modes of N. meningitidis. We applied the Single Molecule, Real-Time (SMRT) sequencing method from Pacific Biosciences to assess the genome-wide DNA modification profiles of two genetically related N. meningitidis strains, both of serogroup A. The resulting DNA methylomes revealed clear divergences, represented by the detection of shared and of strain-specific DNA methylation target motifs. The positional distribution of these methylated target sites within the genomic sequences displayed clear biases, which suggest a functional role of DNA methylation related to the regulation of genes. DNA methylation in N. meningitidis has a likely underestimated potential for variability, as evidenced by a careful analysis of the ORF status of a panel of confirmed and predicted DNA methyltransferase genes in an extended collection of N. meningitidis strains of serogroup A. Based on high coverage short sequence reads, we find phase variability as a major contributor to the variability in DNA methylation. Taking into account the phase variable loci, the inferred functional status of DNA methyltransferase genes matched the observed methylation profiles. Towards an elucidation of presently incompletely characterized functional consequences of DNA methylation in N. meningitidis, we reveal a prominent colocalization of methylated bases with Single Nucleotide Polymorphisms (SNPs) detected within our genomic sequence collection. As a novel observation we report increased mutability also at 6mA methylated nucleotides, complementing mutational hotspots previously described at 5mC methylated nucleotides. These findings suggest a more diverse role of DNA methylation and Restriction-Modification (RM) systems in the evolution of prokaryotic genomes. PMID:26656597

  17. The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach

    PubMed Central

    Gonzalez, Diego; Kozdon, Jennifer B.; McAdams, Harley H.; Shapiro, Lucy; Collier, Justine

    2014-01-01

    DNA methylation is involved in a diversity of processes in bacteria, including maintenance of genome integrity and regulation of gene expression. Here, using Caulobacter crescentus as a model, we exploit genome-wide experimental methods to uncover the functions of CcrM, a DNA methyltransferase conserved in most Alphaproteobacteria. Using single molecule sequencing, we provide evidence that most CcrM target motifs (GANTC) switch from a fully methylated to a hemi-methylated state when they are replicated, and back to a fully methylated state at the onset of cell division. We show that DNA methylation by CcrM is not required for the control of the initiation of chromosome replication or for DNA mismatch repair. By contrast, our transcriptome analysis shows that >10% of the genes are misexpressed in cells lacking or constitutively over-expressing CcrM. Strikingly, GANTC methylation is needed for the efficient transcription of dozens of genes that are essential for cell cycle progression, in particular for DNA metabolism and cell division. Many of them are controlled by promoters methylated by CcrM and co-regulated by other global cell cycle regulators, demonstrating an extensive cross talk between DNA methylation and the complex regulatory network that controls the cell cycle of C. crescentus and, presumably, of many other Alphaproteobacteria. PMID:24398711

  18. Methyl chloroform and the atmosphere

    SciTech Connect

    Ravishankara, A.R.; Albritton, D.L.

    1995-07-14

    The atmospheric abundance of methyl chloroform, CH{sub 3}CCl{sub 3}, a compound of only anthropogenic origin, is actually decreasing because of emission reductions in compliance with the United Nations Montreal Protocol and its subsequent amendments. This observation, reported by Prinn and co-workers elsewhere in this issue, is based on data from surface-level monitoring stations. The observed trends in methyl chloroform abundance have a few straightforward scientific consequences and substantial policy relevance as discussed in this article. 6 refs., 1 fig.

  19. METHYLATION OF MERCURY IN AGRICULTURAL SOILS

    EPA Science Inventory

    Methylation of applied divalent mercury ion was found to occur in agricultural soils. The production of methylmercury was affected by soil texture, soil moisture content, soil temperature, concentration of the ionic mercury amendment, and time. Methylation was directly proportion...

  20. 75 FR 19272 - Thifensulfuron methyl; Pesticide Tolerances

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-14

    ...residues of thifensulfuron methyl in or on safflower, seed. Interregional Research Project...2-thiophenecarboxylate), in or on safflower, seed at 0.05 parts per million...residues of thifensulfuron methyl on safflower seed at 0.05ppm. EPA's...

  1. Electronic transport in methylated fragments of DNA

    NASA Astrophysics Data System (ADS)

    de Almeida, M. L.; Oliveira, J. I. N.; Lima Neto, J. X.; Gomes, C. E. M.; Fulco, U. L.; Albuquerque, E. L.; Freire, V. N.; Caetano, E. W. S.; de Moura, F. A. B. F.; Lyra, M. L.

    2015-11-01

    We investigate the electronic transport properties of methylated deoxyribonucleic-acid (DNA) strands, a biological system in which methyl groups are added to DNA (a major epigenetic modification in gene expression), sandwiched between two metallic platinum electrodes. Our theoretical simulations apply an effective Hamiltonian based on a tight-binding model to obtain current-voltage curves related to the non-methylated/methylated DNA strands. The results suggest potential applications in the development of novel biosensors for molecular diagnostics.

  2. From trans-methylation to cytosine methylation: evolution of the methylation hypothesis of schizophrenia.

    PubMed

    Grayson, Dennis R; Chen, Ying; Dong, Erbo; Kundakovic, Marija; Guidotti, Alessandro

    2009-04-01

    The role of methylation in the history of psychiatry has traversed a storied path. The original trans-methylation hypothesis was proposed at a time when chlorpromazine had been synthesized but not yet marketed as an antipsychotic (Thorazine). The premise was that abnormal metabolism led to the methylation of biogenic amines in the brains of schizophrenia patients and that these hallucinogenic compounds produced positive symptoms of the disease. At the time, some psychiatrists were interested in drugs such as mescaline and lysergic acid diethylamide that replicated clinical symptoms. They understood that these compounds might provide a biological basis for psychosis. The amino acid methionine (MET) was given to patients in the hopes of confiriming the transmethylation hypothesis. However with time, many realized that the hunt for an endogenous psychotropic compound would remain elusive. We now believe that the MET studies may have produced a toxic reaction in susceptible patients by disrupting epigenetic regulation in the brain. The focus of the current review is on the coordinate regulation of multiple promoters expressed in neurons that may be modulated through methylation. While certainly the identification of genes and promoters regulated epigenetically has been steadily increasing over the years, there have been few studies that examine methylation changes as a consequence of increased levels of a dietary amino acid such as methionine (MET). We suggest that the MET mouse model may provide information regarding the identification of genes that are regulated by epigenetic perturbations. In addition to our studies with the reelin and GAD67 promoters, we also have evidence that additional promoters expressed in select neurons of the brain are similarly affected by MET administration. We suggest that to expand our knowledge of epigenetically-responsive promoters using MET might allow for a better appreciation of global methylation changes occurring in selected brain regions. PMID:19395859

  3. De novo DNA methylation activity of METHYLTRANSFERASE 1 (MET1) partially restores body methylation in Arabidopsis

    E-print Network

    Meyer, Peter

    and central body regions of active genes. If MET1 is removed in a mutant background, CG methylation is lost; Zhang et al., 2008). In contrast to repeats and transposable elements, these body methylation regionsDe novo DNA methylation activity of METHYLTRANSFERASE 1 (MET1) partially restores body methylation

  4. 40 CFR 721.6920 - Butyl acrylate, polymer with substituted methyl styrene, methyl methacrylate, and substituted...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Butyl acrylate, polymer with... acrylate, polymer with substituted methyl styrene, methyl methacrylate, and substituted silane. (a... butyl acrylate, polymer with substituted methyl styrene, methyl methacrylate, and substituted...

  5. 40 CFR 721.6920 - Butyl acrylate, polymer with substituted methyl styrene, methyl methacrylate, and substituted...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Butyl acrylate, polymer with... acrylate, polymer with substituted methyl styrene, methyl methacrylate, and substituted silane. (a... butyl acrylate, polymer with substituted methyl styrene, methyl methacrylate, and substituted...

  6. 40 CFR 721.6920 - Butyl acrylate, polymer with substituted methyl styrene, methyl methacrylate, and substituted...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Butyl acrylate, polymer with... acrylate, polymer with substituted methyl styrene, methyl methacrylate, and substituted silane. (a... butyl acrylate, polymer with substituted methyl styrene, methyl methacrylate, and substituted...

  7. 40 CFR 721.6920 - Butyl acrylate, polymer with substituted methyl styrene, methyl methacrylate, and substituted...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Butyl acrylate, polymer with... acrylate, polymer with substituted methyl styrene, methyl methacrylate, and substituted silane. (a... butyl acrylate, polymer with substituted methyl styrene, methyl methacrylate, and substituted...

  8. 40 CFR 721.6920 - Butyl acrylate, polymer with substituted methyl styrene, methyl methacrylate, and substituted...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Butyl acrylate, polymer with... acrylate, polymer with substituted methyl styrene, methyl methacrylate, and substituted silane. (a... butyl acrylate, polymer with substituted methyl styrene, methyl methacrylate, and substituted...

  9. PUBLISHED ONLINE: 11 JANUARY 2009 DOI: 10.1038/NGEO412 High methylation rates of mercury bound to

    E-print Network

    Morel, François M. M.

    concentrations of the amino acid cysteine. The formation of a mercury­cysteine complex promotes both the uptake fumarate-reducing conditions so that sulphide was not produced in the medium. Mercury methylation

  10. Pancancer analysis of DNA methylation-driven genes using MethylMix | Office of Cancer Genomics

    Cancer.gov

    Aberrant DNA methylation is an important mechanism that contributes to oncogenesis. Yet, few algorithms exist that exploit this vast dataset to identify hypo- and hyper-methylated genes in cancer. We developed a novel computational algorithm called MethylMix to identify differentially methylated genes that are also predictive of transcription. We apply MethylMix to twelve individual cancer sites, and additionally combine all cancer sites in a pancancer analysis. We discover pancancer hypo- and hyper-methylated genes and identify novel methylation-driven subgroups with clinical implications.

  11. Pancancer analysis of DNA methylation-driven genes using MethylMix

    Cancer.gov

    Aberrant DNA methylation is an important mechanism that contributes to oncogenesis. Yet, few algorithms exist that exploit this vast dataset to identify hypo- and hyper-methylated genes in cancer. We developed a novel computational algorithm called MethylMix to identify differentially methylated genes that are also predictive of transcription. We apply MethylMix to twelve individual cancer sites, and additionally combine all cancer sites in a pancancer analysis. We discover pancancer hypo- and hyper-methylated genes and identify novel methylation-driven subgroups with clinical implications.

  12. Protein methylation in pea chloroplasts. [Pisum sativum

    SciTech Connect

    Niemi, K.J.; Adler, J.; Selman, B.R. )

    1990-07-01

    The methylation of chloroplast proteins has been investigated by incubating intact pea (Pisum sativum) chloroplasts with ({sup 3}H-methyl)-S-adenosylmethionine. Incubation in the light increases the amount of methylation in both the thylakoid and stromal fractions. Numerous thylakoid proteins serve as substrates for the methyltransfer reactions. Three of these thylakoid proteins are methylated to a significantly greater extent in the light than in the dark. The primary stromal polypeptide methylated is the large subunit of ribulose bisphosphate carboxylase/oxygenase. One other stromal polypeptide is also methylated much more in the light than in the dark. Two distinct types of protein methylation occur. One methylinkage is stable to basic conditions whereas a second type is base labile. The base-stable linkage is indicative of N-methylation of amino acid residues while base-lability is suggestive of carboxymethylation of amino acid residues. Labeling in the light increases the percentage of methylation that is base labile in the thylakoid fraction while no difference is observed in the amount of base-labile methylations in light-labeled and dark-labeled stromal proteins. Also suggestive of carboxymethylation is the detection of volatile ({sup 3}H)methyl radioactivity which increases during the labeling period and is greater in chloroplasts labeled in the light as opposed to being labeled in the dark; this implies in vivo turnover of the ({sup 3}H)methyl group.

  13. GENE-NUTRIENT INTERACTIONS AND DNA METHYLATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many micronutrients and vitamins are critical for DNA synthesis/repair and maintenance of DNA methylation patterns. Folate has been most extensively investigated in this regard because of its unique function as methyl donor for nucleotide synthesis and biological methylation. Cell culture, animal, a...

  14. p-Chlorophenyl methyl sulfoxide

    Integrated Risk Information System (IRIS)

    p - Chlorophenyl methyl sulfoxide ; CASRN 934 - 73 - 6 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for

  15. p-Chlorophenyl methyl sulfone

    Integrated Risk Information System (IRIS)

    p - Chlorophenyl methyl sulfone ; CASRN 98 - 57 - 7 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for No

  16. Isopropyl methyl phosphonic acid (IMPA)

    Integrated Risk Information System (IRIS)

    Isopropyl methyl phosphonic acid ( IMPA ) ; CASRN 1832 - 54 - 8 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assess

  17. p-Chlorophenyl methyl sulfide

    Integrated Risk Information System (IRIS)

    p - Chlorophenyl methyl sulfide ; CASRN 123 - 09 - 1 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for N

  18. Lacinilene C 7-methyl ether

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lacinilene C 7-methyl ether is an antimicrobial compound produced by the cotton plant in response to attack by pathogens. For the first time, we now report the crystal structure of this compound. This may prove useful in studies on the interaction of the compound with pathogenic fungal cells....

  19. Methods of DNA methylation analysis.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The purpose of this review was to provide guidance for investigators who are new to the field of DNA methylation analysis. Epigenetics is the study of mitotically heritable alterations in gene expression potential that are not mediated by changes in DNA sequence. Recently, it has become clear that n...

  20. Gene methylation in gastric cancer.

    PubMed

    Qu, Yiping; Dang, Siwen; Hou, Peng

    2013-09-23

    Gastric cancer is one of the most common malignancies and remains the second leading cause of cancer-related death worldwide. Over 70% of new cases and deaths occur in developing countries. In the early years of the molecular biology revolution, cancer research mainly focuses on genetic alterations, including gastric cancer. Epigenetic mechanisms are essential for normal development and maintenance of tissue-specific gene expression patterns in mammals. Disruption of epigenetic processes can lead to altered gene function and malignant cellular transformation. Recent advancements in the rapidly evolving field of cancer epigenetics have shown extensive reprogramming of every component of the epigenetic machinery in cancer, including DNA methylation, histone modifications, nucleosome positioning, noncoding RNAs, and microRNAs. Aberrant DNA methylation in the promoter regions of gene, which leads to inactivation of tumor suppressor and other cancer-related genes in cancer cells, is the most well-defined epigenetic hallmark in gastric cancer. The advantages of gene methylation as a target for detection and diagnosis of cancer in biopsy specimens and non-invasive body fluids such as serum and gastric washes have led to many studies of application in gastric cancer. This review focuses on the most common and important phenomenon of epigenetics, DNA methylation, in gastric cancer and illustrates the impact epigenetics has had on this field. PMID:23669186

  1. METHYL BROMIDE - ALTERNATIVES FOR CALIFORNIA.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Preplant soil fumigation with methyl bromide (MeBr) has been a standard practice for several California high value crops such as strawberry, sweet potato, and certified nursery stock, common practice for replant of several tree and vine crops, and has also been widely used for pepper, melon, tomato,...

  2. Water Column Methylation in Estuaries

    NASA Astrophysics Data System (ADS)

    Schartup, A. T.; Calder, R.; Soerensen, A. L.; Mason, R. P.; Balcom, P. H.; Sunderland, E. M.

    2014-12-01

    Methylmercury (MeHg) is a neurotoxin that bioaccumulates in aquatic food webs and affects humans and wildlife through fish consumption. Many studies have measured active methylation/demethylation in ocean margin sediments but few have reported similar rates for the marine water column. This presentation will review available evidence for water column methylation in estuaries, including new experimental measurements of methylation/demethylation rates from a deep subarctic fjord in Labrador Canada collected in Spring and Fall of 2012-2013. We used these and other data to construct a mass budget for MeHg in the estuary and show that water column methylation (with rates ranging from 1.5 to 2.8 % day-1), is the largest contributor, followed by inputs from rivers (4.9 mol year-1), to the in situ pool of MeHg available for uptake by biota. By contrast, the sediment in this system is a net sink for MeHg (-1.5 mol year-1). We discuss the relationship between observed MeHg and other ancillary environmental factors (organic carbon, sulfur and nutrients) as well as implications for the response time of fish to future changes in mercury inputs.

  3. Desoxyhemigossypol-6-methyl-ether

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Desoxyhemigossypol-6-methyl ether is an antimicrobial compound produced by the cotton plant in response to attack by pathogens. For the first time, we now report the crystal structure of this compound. This may prove useful in studies on the interaction of the compound with pathogenic fungal cells...

  4. 40 CFR 180.437 - Methyl 2-(4-isopropyl-4-methyl-5-oxo-2-imidazolin-2-yl)-p-toluate and methyl 6-(4-isopropyl-4...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Methyl 2-(4-isopropyl-4-methyl-5-oxo-2-imidazolin-2-yl)-p-toluate and methyl 6-(4-isopropyl-4-methyl-5-oxo-2-imidazolin-2-yl)-m-toluate; tolerances... Tolerances § 180.437 Methyl 2-(4-isopropyl-4-methyl-5-oxo-2-imidazolin-2-yl)-p-toluate and methyl...

  5. Structural consequences of two methyl additions in the E. coli trp repressor L-tryptophan binding pocket

    SciTech Connect

    Lawson, C.L.

    1995-12-01

    The flexibility and specificity of the L-tryptophan corepressor binding pocket of E coli trp repressor are being investigated by high-resolution crystallographic examination of aporepressor/corepressor analog complexes. While addition of a methyl group on the corepressor indole (5-methyl-tryptophan) results in a small but measurable shift in the position of that functional group introduction of a methyl group on a nearby residue in the binding pocket (Val 58 {yields} Ile) leaves the indole position of L-tryptophan essentially unchanged. Careful alignment of these structures with aporepressor/L-tryptophan/operator-DNA complexes reveal why 5-methyltryptophan is a better corepressor than L-tryptophan.

  6. 40 CFR 721.10326 - 2-Propenoic acid, 2-methyl-, methyl ester, polymer with butyl 2-propenoate, ethyl 2-propenoate...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...2-Propenoic acid, 2-methyl-, methyl ester, polymer with butyl 2-propenoate, ethyl 2-propenoate...2-Propenoic acid, 2-methyl-, methyl ester, polymer with butyl 2-propenoate, ethyl 2-propenoate...2-propenoic acid, 2-methyl-, methyl ester, polymer with butyl 2-propenoate, ethyl...

  7. 40 CFR 721.10326 - 2-Propenoic acid, 2-methyl-, methyl ester, polymer with butyl 2-propenoate, ethyl 2-propenoate...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...2-Propenoic acid, 2-methyl-, methyl ester, polymer with butyl 2-propenoate, ethyl 2-propenoate...2-Propenoic acid, 2-methyl-, methyl ester, polymer with butyl 2-propenoate, ethyl 2-propenoate...2-propenoic acid, 2-methyl-, methyl ester, polymer with butyl 2-propenoate, ethyl...

  8. Global Analysis Reveals the Crucial Roles of DNA Methylation during Rice Seed Development1[OPEN

    PubMed Central

    Xing, Mei-Qing; Zhang, Yi-Jing; Zhou, Shi-Rong; Hu, Wen-Yan; Wu, Xue-Ting; Ye, Ya-Jin; Wu, Xiao-Xia; Xiao, Yun-Ping; Li, Xuan; Xue, Hong-Wei

    2015-01-01

    Seed development is an important process of reproductive development and consists of embryo and endosperm development; both comprise several key processes. To determine and investigate the functions of the dynamic DNA methylome during seed development, we profiled the DNA methylation genome wide in a series of developmental stages of rice (Oryza sativa) embryo and endosperm by methylcytosine immunoprecipitation followed by Illumina sequencing. The results showed that embryo is hypermethylated predominantly around non-transposable element (TE) genes, short DNA-TEs, and short interspersed TEs compared with endosperm, and non-TE genes have the most diverse methylation status across seed development. In addition, lowly expressed genes are significantly enriched in hypermethylated genes, but not vice versa, confirming the crucial role of DNA methylation in suppressing gene transcription. Further analysis revealed the significantly decreased methylation at early developing stages (from 2 to 3 d after pollination), indicating a predominant role of demethylation during early endosperm development and that genes with a consistent negative correlation between DNA methylation change and expression change may be potentially directly regulated by DNA methylation. Interestingly, comparative analysis of the DNA methylation profiles revealed that both rice indica and japonica subspecies showed robust fluctuant profiles of DNA methylation levels in embryo and endosperm across seed development, with the highest methylation level at 6 d after pollination (2 d after pollination of endosperm in japonica as well), indicating that a complex and finely controlled methylation pattern is closely associated with seed development regulation. The systemic characterization of the dynamic DNA methylome in developing rice seeds will help us understand the effects and mechanism of epigenetic regulation in seed development. PMID:26145151

  9. The superiority of asymmetric alkyl methyl carbonates

    SciTech Connect

    Ein-Eli, Y.; McDevitt, S.F.; Laura, R.

    1998-01-01

    The electrochemical behavior of graphite electrodes cycled galvanostatically versus Li metal in electrolyte solutions containing LiPF{sub 6}, LiC(SO{sub 2}CF{sub 3}){sub 3}, and LiN(SO{sub 2}C{sub 2}F{sub 5}){sub 2} in ethyl and methyl alkyl carbonates was studied. The solvents include ethyl methyl, ethyl propyl, methyl propyl, isopropyl methyl, and isopropyl ethyl carbonates. The use of asymmetric, aliphatic alkyl methyl carbonates is shown to be essential to achieve both high capacity and long cycle life with graphite electrodes in Li-ion batteries.

  10. Increased DNA methylation in the suicide brain

    PubMed Central

    Haghighi, Fatemeh; Xin, Yurong; Chanrion, Benjamin; O'Donnell, Anne H.; Ge, Yongchao; Dwork, Andrew J.; Arango, Victoria; Mann, J. John

    2014-01-01

    Clinical studies find that childhood adversity and stress-ful life events in adulthood increase the risk for major depression and for suicide. The predispositions to either major depression or suicide are thought to depend on genetic risk factors or epigenetic effects. We investigated DNA methylation signatures postmortem in brains of suicides with diagnosis of major depressive disorder. DNA methylation levels were determined at single C-phosphate-G (CpG) resolution sites within ventral prefrontal cortex of 53 suicides and nonpsychiatric controls, aged 16 to 89 years. We found that DNA methylation increases throughout the lifespan. Suicides showed an 8-fold greater number of methylated CpG sites relative to controls (P<2.2x10-16), with greater DNA methylation changes over and above the increased methylation observed in normal aging. This increased DNA methylation may be a significant contributor to the neuropathology and psychopathology underlying the risk of suicide in depression. PMID:25364291

  11. Gas phase methylation of methyl acetoacetate. Experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Morizur, J.-P.; Martigny, I.; Taphanel, M.-H.; Tortajada, J.; Geribaldi, S.; Decouzon, M.

    1992-04-01

    Fourier transform ion cyclotron resonance and tandem mass spectrometry, complemented by semiempirical molecular orbital calculations, have been used to study gas phase methylation of methyl acetoacetate as a mixture of the keto form 1 and the enol form 2. The daughter ion spectra of the ion/molecule reaction products were compared with those of model ions generated by electron impact or chemical ionization, in order to determine the site(s) of nucleophilic reaction for the mixture. The data indicate that the site of attachment in the keto form 1 is the keto-carbonyl oxygen. For the enol form 2, no C-methylation occurs in the gas phase; the only product corresponds to O-alkylation. The results derived from D- and 13C-labelled precursors have been used to study the fragmentation mechanisms of model ions a, CH3C+ (OCH3)CH2CO2CH3; and b, CH3COCH2C+(OCH3)2. Experimental results indicate that an irreversible isomerization a --> b occurs under collisional conditions. Unimolecularly both a and b ions eliminate a neutral molecule of ketene but by different pathways. Calculations of charge distributions in 1 and 2 as well as the enthalpies of the neutral and the adduct ions are discussed.

  12. Aberrant Methylation of Gene Associated CpG Sites Occurs in Borderline Personality Disorder

    PubMed Central

    Künzel, Natascha; Schmidt, Christian; Kiehl, Steffen; Dammann, Gerhard; Dammann, Reinhard

    2013-01-01

    Borderline personality disorder (BPD) is a complex psychiatric disease with an increased impact in the last years. While the diagnosis and therapy are well established, little is known on the pathogenesis of borderline personality disorder. Previously, a significant increase in DNA methylation of relevant neuropsychiatric genes in BPD patients has been reported. In our study we performed genome wide methylation analysis and revealed specific CpG sites that exhibited increased methylation in 24 female BPD patients compared to 11 female healthy controls. Bead chip technology and quantitative bisulfite pyrosequencing showed a significantly increased methylation at CpG sites of APBA2 (1.1 fold) and APBA3 (1.1 fold), KCNQ1 (1.5 fold), MCF2 (1.1 fold) and NINJ2 (1.2 fold) in BPD patients. For the CpG sites of GATA4 and HLCS an increase in DNA methylation was observed, but was only significant in the bead chip assay. Moreover genome wide methylation levels of blood samples of BPD patients and control samples are similar. In summary, our results show a significant 1.26 fold average increase in methylation at the analyzed gene associated CpG sites in the blood of BPD patients compared to controls samples (p<0.001). This data may provide new insights into epigenetic mechanisms underlying the pathogenesis of BPD. PMID:24367640

  13. Identification of mercury methylation product by tert-butyl compounds in aqueous solution under light irradiation.

    PubMed

    Chen, Baowei; Chen, Ping; He, Bin; Yin, Yongguang; Fang, Linchuan; Wang, Xiaowei; Liu, Hongtao; Yang, Lihua; Luan, Tiangang

    2015-09-15

    The methylation of mercury (Hg) is of great concern as methylmercury (MeHg), the most toxic species, is produced. This study examined the possibilities of tert-butyl compounds (tert-butyl alcohol (TBA) and tert-butyl hydroperoxide (TBH)) and other alcohols serving as methyl donors for Hg photo-methylation under light irradiation. The yield of MeHg varied among the methyl donors, and it was also significantly influenced by salinity and pH. MeHg could be generated in the presence of TBH under visible light irradiation. The hydroxyl radical (OH) was found to promote MeHg production at low levels, but degrade MeHg in excess. The photo-production of MeHg was tentatively proposed via the complexation of Hg and methyl donors, the formation of an intermediate (O(Hg)C(CH3)3), and the intramolecular methyl transfer from methyl donors to Hg. This study implicates photoreactions between Hg and organic pollutants in understanding the fate and transformation of Hg in the aquatic environment. PMID:26165936

  14. Fibrillarin methylates H2A in RNA polymerase I trans-active promoters in Brassica oleracea

    PubMed Central

    Loza-Muller, Lloyd; Rodríguez-Corona, Ulises; Sobol, Margarita; Rodríguez-Zapata, Luis C.; Hozak, Pavel; Castano, Enrique

    2015-01-01

    Fibrillarin is a well conserved methyltransferase involved in several if not all of the more than 100 methylations sites in rRNA which are essential for proper ribosome function. It is mainly localized in the nucleoli and Cajal bodies inside the cell nucleus where it exerts most of its functions. In plants, fibrillarin binds directly the guide RNA together with Nop56, Nop58, and 15.5ka proteins to form a snoRNP complex that selects the sites to be methylated in pre-processing of ribosomal RNA. Recently, the yeast counterpart NOP1 was found to methylate histone H2A in the nucleolar regions. Here we show that plant fibrillarin can also methylate histone H2A. In Brassica floral meristem cells the methylated histone H2A is mainly localized in the nucleolus but unlike yeast or human cells it also localize in the periphery of the nucleus. In specialized transport cells the pattern is altered and it exhibits a more diffuse staining in the nucleus for methylated histone H2A as well as for fibrillarin. Here we also show that plant fibrillarin is capable of interacting with H2A and carry out its methylation in the rDNA promoter. PMID:26594224

  15. An Epigenetic Regulator: Methyl-CpG-Binding Domain Protein 1 (MBD1)

    PubMed Central

    Li, Lu; Chen, Bi-Feng; Chan, Wai-Yee

    2015-01-01

    DNA methylation is an important form of epigenetic regulation in both normal development and cancer. Methyl-CpG-binding domain protein 1 (MBD1) is highly related to DNA methylation. Its MBD domain recognizes and binds to methylated CpGs. This binding allows it to trigger methylation of H3K9 and results in transcriptional repression. The CXXC3 domain of MBD1 makes it a unique member of the MBD family due to its affinity to unmethylated DNA. MBD1 acts as an epigenetic regulator via different mechanisms, such as the formation of the MCAF1/MBD1/SETDB1 complex or the MBD1-HDAC3 complex. As methylation status always changes along with carcinogenesis or neurogenesis, MBD1 with its interacting partners, including proteins and non-coding RNAs, participates in normal or pathological processes and functions in different regulatory systems. Because of the important role of MBD1 in epigenetic regulation, it is a good candidate as a therapeutic target for diseases. PMID:25751725

  16. Comprehensive and quantitative multilocus methylation analysis reveals the susceptibility of specific imprinted differentially methylated regions to aberrant methylation in Beckwith–Wiedemann syndrome with epimutations

    PubMed Central

    Maeda, Toshiyuki; Higashimoto, Ken; Jozaki, Kosuke; Yatsuki, Hitomi; Nakabayashi, Kazuhiko; Makita, Yoshio; Tonoki, Hidefumi; Okamoto, Nobuhiko; Takada, Fumio; Ohashi, Hirofumi; Migita, Makoto; Kosaki, Rika; Matsubara, Keiko; Ogata, Tsutomu; Matsuo, Muneaki; Hamasaki, Yuhei; Ohtsuka, Yasufumi; Nishioka, Kenichi; Joh, Keiichiro; Mukai, Tsunehiro; Hata, Kenichiro; Soejima, Hidenobu

    2014-01-01

    Purpose: Expression of imprinted genes is regulated by DNA methylation of differentially methylated regions (DMRs). Beckwith–Wiedemann syndrome is an imprinting disorder caused by epimutations of DMRs at 11p15.5. To date, multiple methylation defects have been reported in Beckwith–Wiedemann syndrome patients with epimutations; however, limited numbers of DMRs have been analyzed. The susceptibility of DMRs to aberrant methylation, alteration of gene expression due to aberrant methylation, and causative factors for multiple methylation defects remain undetermined. Methods: Comprehensive methylation analysis with two quantitative methods, matrix-assisted laser desorption/ionization mass spectrometry and bisulfite pyrosequencing, was conducted across 29 DMRs in 54 Beckwith–Wiedemann syndrome patients with epimutations. Allelic expressions of three genes with aberrant methylation were analyzed. All DMRs with aberrant methylation were sequenced. Results: Thirty-four percent of KvDMR1–loss of methylation patients and 30% of H19DMR–gain of methylation patients showed multiple methylation defects. Maternally methylated DMRs were susceptible to aberrant hypomethylation in KvDMR1–loss of methylation patients. Biallelic expression of the genes was associated with aberrant methylation. Cis-acting pathological variations were not found in any aberrantly methylated DMR. Conclusion: Maternally methylated DMRs may be vulnerable to DNA demethylation during the preimplantation stage, when hypomethylation of KvDMR1 occurs, and aberrant methylation of DMRs affects imprinted gene expression. Cis-acting variations of the DMRs are not involved in the multiple methylation defects. PMID:24810686

  17. Combustion characterization of methylal in reciprocating engines

    SciTech Connect

    Dodge, L.; Naegeli, D.

    1994-06-01

    Methylal, CH{sub 3}OCH{sub 2}OCH{sub 3}, also known as dimethoxy-methane, is unique among oxygenates in that it has a low autoignition temperature, no carbon-carbon bonds, and is soluble in middle distillate fuels. Because of these properties, methylal has been shown to be a favorable fuel additive for reducing smoke in diesel engines. Recent measurements of ignition delay times indicate that methylal has a cetane number in the range of 45-50, which is compatible with diesel fuels. Engine tests have shown that adding methylal to diesel fuel significantly reduces smoke emissions. Gaseous emissions and combustion efficiencies obtained with methylal/diesel fuel blends remain essentially the same as those measured using neat diesel fuel. Lubricity measurements of methylal/diesel fuel blends with a ball on cylinder lubrication evaluator (BOCLE) show that methylal improves the lubricity of diesel fuel. Even though additions of methylal lower the fuel viscosity, the results of the BOCLE tests indicate that the methylal/diesel fuel blends cause less pump wear than neat diesel fuel. The one drawback is that methylal has a low boiling point (42{degrees}C) and a relatively high vapor pressure. As a result, it lowers the flash point of diesel fuel and causes a potential fuel tank flammability hazard. One solution to this increased volatility is to make polyoxymethylenes with the general formula of CH{sub 3}O(CH{sub 2}O){sub x}CH{sub 3} where x > 2. The molecules are similar to methylal, but have higher molecular weights and thus higher viscosities and substantially lower vapor pressures. Therefore, their flash points will be compatible with regular diesel fuel. The polyoxymethylenes are expected to have combustion properties similar to methylal. It is theorized that by analogy with hydrocarbons, the ignition quality (i.e., cetane number) of the polyoxymethylenes will be better than that of methylal.

  18. A study of methyl formate in astrochemical environments

    NASA Astrophysics Data System (ADS)

    Occhiogrosso, A.; Viti, S.; Modica, P.; Palumbo, M. E.

    2011-12-01

    Several complex organic molecules are routinely detected in high abundances towards hot cores and hot corinos. For many of them, their paths of formation in space are uncertain, as gas-phase reactions alone seem to be insufficient. In this paper, we investigate a possible solid-phase route of formation for methyl formate (HCOOCH3). We use a chemical model updated with recent results from an experiment where simulated grain surfaces were irradiated with 200-keV protons at 16 K, to simulate the effects of cosmic ray irradiation on grain surfaces. We find that this model may be sufficient to reproduce the observed methyl formate in dark clouds, but not that found in hot cores and corinos.

  19. Diet, methyl donors and DNA methylation: interactions between dietary folate, methionine and choline.

    PubMed

    Niculescu, Mihai D; Zeisel, Steven H

    2002-08-01

    DNA methylation influences the expression of some genes and depends upon the availability of methyl groups from S-adenosylmethionine (SAM). Dietary methyl groups derive from foods that contain methionine, one-carbon units and choline (or the choline metabolite betaine). Humans ingest approximately 50 mmol of methyl groups per day; 60% of them are derived from choline. Transmethylation metabolic pathways closely interconnect choline, methionine, methyltetrahydrofolate (methyl-THF) and vitamins B-6 and B-12. The pathways intersect at the formation of methionine from homocysteine. Perturbing the metabolism of one of these pathways results in compensatory changes in the others. For example, methionine can be formed from homocysteine using methyl groups from methyl-THF, or using methyl groups from betaine that are derived from choline. Similarly, methyl-THF can be formed from one-carbon units derived from serine or from the methyl groups of choline via dimethylglycine, and choline can be synthesized de novo using methyl groups derived from methionine (via SAM). When animals and humans are deprived of choline, they use more methyl-THF to remethylate homocysteine in the liver and increase dietary folate requirements. Conversely, when they are deprived of folate, they use more methyl groups from choline, increasing the dietary requirement for choline. The availability of transgenic and knockout mice has made possible additional studies that demonstrate the interrelationship of these methyl sources. In summary, as we consider dietary requirements and possible effects on DNA methylation, it is important to realize that methionine, methyl-THF and choline can be fungible sources of methyl groups, and the design of our studies should reflect this. PMID:12163687

  20. Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome

    PubMed Central

    Ji, Lexiang; Eichten, Steven R.; Song, Jawon; Vaughn, Matthew W.; Schmitz, Robert J.; Springer, Nathan M.

    2014-01-01

    DNA methylation and dimethylation of lysine 9 of histone H3 (H3K9me2) are two chromatin modifications that can be associated with gene expression or recombination rate. The maize genome provides a complex landscape of interspersed genes and transposons. The genome-wide distribution of DNA methylation and H3K9me2 were investigated in seedling tissue for the maize inbred B73 and compared to patterns of these modifications observed in Arabidopsis thaliana. Most maize transposons are highly enriched for DNA methylation in CG and CHG contexts and for H3K9me2. In contrast to findings in Arabidopsis, maize CHH levels in transposons are generally low but some sub-families of transposons are enriched for CHH methylation and these families exhibit low levels of H3K9me2. The profile of modifications over genes reveals that DNA methylation and H3K9me2 is quite low near the beginning and end of genes. Although elevated CG and CHG methylation are found within gene bodies, CHH and H3K9me2 remain low. Maize has much higher levels of CHG methylation within gene bodies than observed in Arabidopsis and this is partially attributable to the presence of transposons within introns for some maize genes. These transposons are associated with high levels of CHG methylation and H3K9me2 but do not appear to prevent transcriptional elongation. Although the general trend is for a strong depletion of H3K9me2 and CHG near the transcription start site there are some putative genes that have high levels of these chromatin modifications. This study provides a clear view of the relationship between DNA methylation and H3K9me2 in the maize genome and how the distribution of these modifications is shaped by the interplay of genes and transposons. PMID:25122127

  1. Catechol-O-methyltransferase gene methylation and substance use in adolescents: the TRAILS study.

    PubMed

    van der Knaap, L J; Schaefer, J M; Franken, I H A; Verhulst, F C; van Oort, F V A; Riese, H

    2014-09-01

    Substance use often starts in adolescence and poses a major problem for society and individual health. The dopamine system plays a role in substance use, and catechol-O-methyltransferase (COMT) is an important enzyme that degrades dopamine. The Val(108/158) Met polymorphism modulates COMT activity and thus dopamine levels, and has been linked to substance use. COMT gene methylation, on the other hand, may affect expression and thus indirectly COMT activity. We investigated whether methylation of the COMT gene was associated with adolescents' substance use. Furthermore, we explored whether the COMT Val(108/158) Met polymorphism interacts with COMT gene methylation in association with substance use. In 463 adolescents (mean age=16, 50.8% girls), substance use (cigarette smoking, alcohol and cannabis use) was assessed with self-report questionnaires. From blood samples, COMT Val(108/158) Met genotype and methylation rates of membrane bound (MB) and soluble (S) COMT promoters were assessed. MB-COMT promoter methylation was associated with non-daily smoking [odds ratio (OR)=1.82, P=0.03], but not with daily smoking (OR=1.20, P=0.34), MB-COMT promoter methylation was not associated with alcohol use. Adolescents with the Met/Met genotype and high rates of MB-COMT promoter methylation were less likely to be high-frequent cannabis users than adolescents with the Val/Val or Val/Met genotype. S-COMT promoter methylation was not associated with substance use. These results indicate that there is an association between substance use and COMT gene methylation. Although this association is complex, combining genetic and epigenetic variation of the COMT gene may be helpful in further elucidating the influence of the dopamine system on substance use in adolescence. PMID:24902721

  2. Wp specific methylation of highly proliferated LCLs

    SciTech Connect

    Park, Jung-Hoon; Jeon, Jae-Pil; Shim, Sung-Mi; Nam, Hye-Young; Kim, Joon-Woo; Han, Bok-Ghee; Lee, Suman . E-mail: suman@cha.ac.kr

    2007-06-29

    The epigenetic regulation of viral genes may be important for the life cycle of EBV. We determined the methylation status of three viral promoters (Wp, Cp, Qp) from EBV B-lymphoblastoid cell lines (LCLs) by pyrosequencing. Our pyrosequencing data showed that the CpG region of Wp was methylated, but the others were not. Interestingly, Wp methylation was increased with proliferation of LCLs. Wp methylation was as high as 74.9% in late-passage LCLs, but 25.6% in early-passage LCLs. From two Burkitt's lymphoma cell lines, Wp specific hypermethylation was also found (>80%). Interestingly, the expression of EBNA2 gene which located directly next to Wp was associated with its methylation. Our data suggested that Wp specific methylation may be important for the indicator of the proliferation status of LCLs, and the epigenetic viral gene regulation of EBNA2 gene by Wp should be further defined possibly with other biological processes.

  3. The Role of the Ocean in the Atmospheric Budgets of Methyl Bromide, Methyl Chloride and Methane 

    E-print Network

    Hu, Lei

    2012-10-19

    The ocean is both a source and a sink for atmospheric methyl bromide (CH3Br) and methyl chloride (CH3Cl). It plays a significant role in their global biogeochemical cycling. In response to the Montreal Protocol, the ...

  4. Detailed Chemical Kinetic Reaction Mechanism for Biodiesel Components Methyl Stearate and Methyl Oleate

    SciTech Connect

    Naik, C; Westbrook, C K; Herbinet, O; Pitz, W J; Mehl, M

    2010-01-22

    New chemical kinetic reaction mechanisms are developed for two of the five major components of biodiesel fuel, methyl stearate and methyl oleate. The mechanisms are produced using existing reaction classes and rules for reaction rates, with additional reaction classes to describe other reactions unique to methyl ester species. Mechanism capabilities were examined by computing fuel/air autoignition delay times and comparing the results with more conventional hydrocarbon fuels for which experimental results are available. Additional comparisons were carried out with measured results taken from jet-stirred reactor experiments for rapeseed methyl ester fuels. In both sets of computational tests, methyl oleate was found to be slightly less reactive than methyl stearate, and an explanation of this observation is made showing that the double bond in methyl oleate inhibits certain low temperature chain branching reaction pathways important in methyl stearate. The resulting detailed chemical kinetic reaction mechanism includes more approximately 3500 chemical species and more than 17,000 chemical reactions.

  5. Quantitative DNA Methylation Profiling in Cancer.

    PubMed

    Ammerpohl, Ole; Haake, Andrea; Kolarova, Julia; Siebert, Reiner

    2016-01-01

    Epigenetic mechanisms including DNA methylation are fundamental for the regulation of gene expression. Epigenetic alterations can lead to the development and the evolution of malignant tumors as well as the emergence of phenotypically different cancer cells or metastasis from one single tumor cell. Here we describe bisulfite pyrosequencing, a technology to perform quantitative DNA methylation analyses, to detect aberrant DNA methylation in malignant tumors. PMID:26667456

  6. Direct synthesis of methyl phosphoramidates in carbohydrates.

    PubMed

    Dhurandhare, Vijay M; Mishra, Girija Prasad; Lam, Sarah; Wang, Cheng-Chung

    2015-09-28

    A direct installation of a methyl phosphoramidate group by using methyl benzylphosphoramidochloridate into carbohydrates and amino acid is described. This one-step synthesis is efficient for both primary and secondary alcohols and exhibited excellent regioselectivity and functional group compatibility. Formation of a single diastereomer is observed in certain cases. The N-benzyl protecting group on methyl phosphoramidates is easily removed under mild conditions. PMID:26247390

  7. 40 CFR 180.445 - Bensulfuron methyl; tolerances for residues.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Bensulfuron methyl; tolerances for... § 180.445 Bensulfuron methyl; tolerances for residues. (a) General. Tolerances are established for residues of the herbicide bensulfuron methyl (methyl-2 carbonyl] amino] sulfonyl] methyl] benzoate) in...

  8. RNA-directed DNA methylation in Arabidopsis

    PubMed Central

    Aufsatz, Werner; Mette, M. Florian; van der Winden, Johannes; Matzke, Antonius J. M.; Matzke, Marjori

    2002-01-01

    In plants, double-stranded RNA that is processed to short RNAs ?21–24 nt in length can trigger two types of epigenetic gene silencing. Posttranscriptional gene silencing, which is related to RNA interference in animals and quelling in fungi, involves targeted elimination of homologous mRNA in the cytoplasm. RNA-directed DNA methylation involves de novo methylation of almost all cytosine residues within a region of RNA–DNA sequence identity. RNA-directed DNA methylation is presumed to be responsible for the methylation observed in protein coding regions of posttranscriptionally silenced genes. Moreover, a type of transcriptional gene silencing and de novo methylation of homologous promoters in trans can occur if a double-stranded RNA contains promoter sequences. Although RNA-directed DNA methylation has been described so far only in plants, there is increasing evidence that RNA can also target genome modifications in other organisms. To understand how RNA directs methylation to identical DNA sequences and how changes in chromatin configuration contribute to initiating or maintaining DNA methylation induced by RNA, a promoter double-stranded RNA-mediated transcriptional gene silencing system has been established in Arabidopsis. A genetic analysis of this system is helping to unravel the relationships among RNA signals, DNA methylation, and chromatin structure. PMID:12169664

  9. DNA Methylation Landscapes of Human Fetal Development

    PubMed Central

    van Iperen, Liesbeth; Suchiman, H. Eka D.; Tobi, Elmar W.; Carlotti, Françoise; de Koning, Eelco J. P.; Slagboom, P. Eline; Heijmans, Bastiaan T.; Chuva de Sousa Lopes, Susana M.

    2015-01-01

    Remodelling the methylome is a hallmark of mammalian development and cell differentiation. However, current knowledge of DNA methylation dynamics in human tissue specification and organ development largely stems from the extrapolation of studies in vitro and animal models. Here, we report on the DNA methylation landscape using the 450k array of four human tissues (amnion, muscle, adrenal and pancreas) during the first and second trimester of gestation (9,18 and 22 weeks). We show that a tissue-specific signature, constituted by tissue-specific hypomethylated CpG sites, was already present at 9 weeks of gestation (W9). Furthermore, we report large-scale remodelling of DNA methylation from W9 to W22. Gain of DNA methylation preferentially occurred near genes involved in general developmental processes, whereas loss of DNA methylation mapped to genes with tissue-specific functions. Dynamic DNA methylation was associated with enhancers, but not promoters. Comparison of our data with external fetal adrenal, brain and liver revealed striking similarities in the trajectory of DNA methylation during fetal development. The analysis of gene expression data indicated that dynamic DNA methylation was associated with the progressive repression of developmental programs and the activation of genes involved in tissue-specific processes. The DNA methylation landscape of human fetal development provides insight into regulatory elements that guide tissue specification and lead to organ functionality. PMID:26492326

  10. Methylation – an uncommon modification of glycans*

    PubMed Central

    Staudacher, Erika

    2013-01-01

    A methyl group on a sugar residue is a rarely reported event. Until now this kind of modification has been found in the kingdom of animals only in worms and molluscs, whereas it is more frequently present in some species of bacteria, fungi, algae and plants, but not in mammals. The monosaccharides involved as well as the positions of the methyl groups on the sugar vary with the species. Methylation seems to play a role in some recognition events but details are still unknown. This review summarises the current knowledge on methylation of sugars in all kinds of organism. PMID:22944672

  11. MethylMix: an R package for identifying DNA methylation driven genes

    Cancer.gov

    DNA methylation is an important mechanism regulating gene transcription, and its role in carcinogenesis has been extensively studied. Hyper and hypomethylation of genes is an alternative mechanism to deregulate gene expression in a wide range of diseases. At the same time high throughput DNA methylation assays have been developed generating vast amounts of genome wide DNA methylation measurements.

  12. 21 CFR 177.2000 - Vinylidene chloride/methyl acrylate/methyl methacrylate polymers.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... methacrylate polymers. 177.2000 Section 177.2000 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF...: POLYMERS Substances for Use as Basic Components of Single and Repeated Use Food Contact Surfaces § 177.2000 Vinylidene chloride/methyl acrylate/methyl methacrylate polymers. The vinylidene chloride/methyl...

  13. 21 CFR 177.2000 - Vinylidene chloride/methyl acrylate/methyl methacrylate polymers.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... methacrylate polymers. 177.2000 Section 177.2000 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF...: POLYMERS Substances for Use as Basic Components of Single and Repeated Use Food Contact Surfaces § 177.2000 Vinylidene chloride/methyl acrylate/methyl methacrylate polymers. The vinylidene chloride/methyl...

  14. MethylMix: an R package for identifying DNA methylation driven genes | Office of Cancer Genomics

    Cancer.gov

    DNA methylation is an important mechanism regulating gene transcription, and its role in carcinogenesis has been extensively studied. Hyper and hypomethylation of genes is an alternative mechanism to deregulate gene expression in a wide range of diseases. At the same time high throughput DNA methylation assays have been developed generating vast amounts of genome wide DNA methylation measurements.

  15. 21 CFR 177.2000 - Vinylidene chloride/methyl acrylate/methyl methacrylate polymers.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... methacrylate polymers. 177.2000 Section 177.2000 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) INDIRECT FOOD ADDITIVES: POLYMERS Substances for Use as Basic.../methyl methacrylate polymers. The vinylidene chloride/methyl acrylate/methyl methacrylate polymers...

  16. Synthesis of both enantiomers of 12-methyl-13-tridecanolide and 14-methyl-15-pentadecanolide (muscolide).

    PubMed

    Noda, Yoshihiro; Mamiya, Natsuki; Kashin, Hitoshi

    2013-07-01

    Both enantiomers of 12-methyl-13-tridecanolide{(R)-(+)-1, (S)-(-)-1} and 14-methyl-15-pentadecanolide (muscolide) {(R)-(+)-2, (S)-(-)-2} were synthesized from either (S)-(+)- or (R)-(-)-3-bromo-2-methyl-1-propanol 8 as a chiral building block. PMID:23980425

  17. 21 CFR 177.2000 - Vinylidene chloride/methyl acrylate/methyl methacrylate polymers.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... methacrylate polymers. 177.2000 Section 177.2000 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF...: POLYMERS Substances for Use as Basic Components of Single and Repeated Use Food Contact Surfaces § 177.2000 Vinylidene chloride/methyl acrylate/methyl methacrylate polymers. The vinylidene chloride/methyl...

  18. 21 CFR 177.2000 - Vinylidene chloride/methyl acrylate/methyl methacrylate polymers.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... methacrylate polymers. 177.2000 Section 177.2000 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF...: POLYMERS Substances for Use as Basic Components of Single and Repeated Use Food Contact Surfaces § 177.2000 Vinylidene chloride/methyl acrylate/methyl methacrylate polymers. The vinylidene chloride/methyl...

  19. 40 CFR 721.1025 - Benzenamine, 4-chloro-2-methyl-; benzenamine, 4-chloro-2-methyl-, hydrochloride; and ben-zenamine...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Benzenamine, 4-chloro-2-methyl-; benzenamine, 4-chloro-2-methyl-, hydrochloride; and ben-zenamine, 2-chloro-6-methyl-. 721.1025 Section 721... Benzenamine, 4-chloro-2-methyl-; benzenamine, 4-chloro-2-methyl-, hydrochloride; and ben-zenamine,...

  20. Genome-Wide Binding of MBD2 Reveals Strong Preference for Highly Methylated Loci

    PubMed Central

    Menafra, Roberta; Brinkman, Arie B.; Matarese, Filomena; Franci, Gianluigi; Bartels, Stefanie J. J.; Nguyen, Luan; Shimbo, Takashi; Wade, Paul A.; Hubner, Nina C.; Stunnenberg, Hendrik G.

    2014-01-01

    MBD2 is a subunit of the NuRD complex that is postulated to mediate gene repression via recruitment of the complex to methylated DNA. In this study we adopted an MBD2 tagging-approach to study its genome wide binding characteristics. We show that in vivo MBD2 is mainly recruited to CpG island promoters that are highly methylated. Interestingly, MBD2 binds around 1 kb downstream of the transcription start site of a subset of ?400 CpG island promoters that are characterized by the presence of active histone marks, RNA polymerase II (Pol2) and low to medium gene expression levels and H3K36me3 deposition. These tagged-MBD2 binding sites in MCF-7 show increased methylation in a cohort of primary breast cancers but not in normal breast samples, suggesting a putative role for MBD2 in breast cancer. PMID:24927503

  1. Methylated DNA-binding protein is present in various mammalian cell types

    SciTech Connect

    Supakar, P.C.; Weist, D.; Zhang, D.; Inamdar, N.; Zhang, Xianyang; Khan, R.; Ehrlich, M. ); Ehrlich, K.C. )

    1988-08-25

    A DNA-binding protein from human placenta, methylated DNA-binding protein (MDBP), binds to certain DNA sequences only when they contain 5-methylcytosine (m{sup 5}C) residues at specific positions. The authors found a very similar DNA-binding activity in nuclear extracts of rat tissues, calf thymus, human embryonal carcinoma cells, HeLa cells, and mouse LTK cells. Like human placental MDBP, the analogous DNA-binding proteins from the above mammalian cell lines formed a number of different low-electrophoretic-mobility complexes with a 14-bp MDBP-specific oligonucleotide duplex. All of these complexes exhibited the same DNA methylation specificity and DNA sequence specificity. Although MDBP activity was found in various mammalian cell types, it was not detected in extracts of cultured mosquito cells and so may be associated only with cells with vertebrate-type DNA methylation.

  2. Aberrant TET1 Methylation Closely Associated with CpG Island Methylator Phenotype in Colorectal Cancer.

    PubMed

    Ichimura, Norihisa; Shinjo, Keiko; An, Byonggu; Shimizu, Yasuhiro; Yamao, Kenji; Ohka, Fumiharu; Katsushima, Keisuke; Hatanaka, Akira; Tojo, Masayuki; Yamamoto, Eiichiro; Suzuki, Hiromu; Ueda, Minoru; Kondo, Yutaka

    2015-08-01

    Inactivation of methylcytosine dioxygenase, ten-eleven translocation (TET) is known to be associated with aberrant DNA methylation in cancers. Tumors with a CpG island methylator phenotype (CIMP), a distinct subgroup with extensive DNA methylation, show characteristic features in the case of colorectal cancer. The relationship between TET inactivation and CIMP in colorectal cancers is not well understood. The expression level of TET family genes was compared between CIMP-positive (CIMP-P) and CIMP-negative (CIMP-N) colorectal cancers. Furthermore, DNA methylation profiling, including assessment of the TET1 gene, was assessed in colorectal cancers, as well as colon polyps. The TET1 was silenced by DNA methylation in a subset of colorectal cancers as well as cell lines, expression of which was reactivated by demethylating agent. TET1 methylation was more frequent in CIMP-P (23/55, 42%) than CIMP-N (2/113, 2%, P < 0.0001) colorectal cancers. This trend was also observed in colon polyps (CIMP-P, 16/40, 40%; CIMP-N, 2/24, 8%; P = 0.002), suggesting that TET1 methylation is an early event in CIMP tumorigenesis. TET1 methylation was significantly associated with BRAF mutation but not with hMLH1 methylation in the CIMP-P colorectal cancers. Colorectal cancers with TET1 methylation have a significantly greater number of DNA methylated genes and less pathological metastasis compared to those without TET1 methylation (P = 0.007 and 0.045, respectively). Our data suggest that TET1 methylation may contribute to the establishment of a unique pathway in respect to CIMP-mediated tumorigenesis, which may be incidental to hMLH1 methylation. In addition, our findings provide evidence that TET1 methylation may be a good biomarker for the prediction of metastasis in colorectal cancer. PMID:26063725

  3. Chiral methyl-branched pheromones.

    PubMed

    Ando, Tetsu; Yamakawa, Rei

    2015-07-01

    Insect pheromones are some of the most interesting natural products because they are utilized for interspecific communication between various insects, such as beetles, moths, ants, and cockroaches. A large number of compounds of many kinds have been identified as pheromone components, reflecting the diversity of insect species. While this review deals only with chiral methyl-branched pheromones, the chemical structures of more than one hundred non-terpene compounds have been determined by applying excellent analytical techniques. Furthermore, their stereoselective syntheses have been achieved by employing trustworthy chiral sources and ingenious enantioselective reactions. The information has been reviewed here not only to make them available for new research but also to understand the characteristic chemical structures of the chiral pheromones. Since biosynthetic studies are still limited, it might be meaningful to examine whether the structures, particularly the positions and configurations of the branched methyl groups, are correlated with the taxonomy of the pheromone producers and also with the function of the pheromones in communication systems. PMID:25849023

  4. 40 CFR 721.8660 - Propionic acid methyl ester (generic).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...2010-07-01 2010-07-01 false Propionic acid methyl ester (generic). 721...Chemical Substances § 721.8660 Propionic acid methyl ester (generic). ...substance identified generically as a propionic acid methyl ester (PMN...

  5. 40 CFR 721.8660 - Propionic acid methyl ester (generic).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...2011-07-01 2011-07-01 false Propionic acid methyl ester (generic). 721...Chemical Substances § 721.8660 Propionic acid methyl ester (generic). ...substance identified generically as a propionic acid methyl ester (PMN...

  6. 21 CFR 173.385 - Sodium methyl sulfate.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 3 2013-04-01 2013-04-01 false Sodium methyl sulfate. 173.385 Section 173.385...CONSUMPTION Specific Usage Additives § 173.385 Sodium methyl sulfate. Sodium methyl sulfate may be present in pectin in...

  7. 21 CFR 173.385 - Sodium methyl sulfate.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 3 2014-04-01 2014-04-01 false Sodium methyl sulfate. 173.385 Section 173.385...CONSUMPTION Specific Usage Additives § 173.385 Sodium methyl sulfate. Sodium methyl sulfate may be present in pectin in...

  8. 21 CFR 173.385 - Sodium methyl sulfate.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 3 2011-04-01 2011-04-01 false Sodium methyl sulfate. 173.385 Section 173.385...CONSUMPTION Specific Usage Additives § 173.385 Sodium methyl sulfate. Sodium methyl sulfate may be present in pectin in...

  9. 21 CFR 173.385 - Sodium methyl sulfate.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ...Drugs 3 2010-04-01 2009-04-01 true Sodium methyl sulfate. 173.385 Section 173.385...CONSUMPTION Specific Usage Additives § 173.385 Sodium methyl sulfate. Sodium methyl sulfate may be present in pectin in...

  10. 21 CFR 173.385 - Sodium methyl sulfate.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 3 2012-04-01 2012-04-01 false Sodium methyl sulfate. 173.385 Section 173.385...CONSUMPTION Specific Usage Additives § 173.385 Sodium methyl sulfate. Sodium methyl sulfate may be present in pectin in...

  11. The methylated component of the Neurospora crassa genome 

    E-print Network

    Selker, Eric U; Tountas, Nikolaos A; Cross, Sally H; Margolin, Brian S; Murphy, Jonathan G; Bird, Adrian P; Freitag, Michael

    2003-04-24

    Cytosine methylation is common, but not ubiquitous, in eukaryotes. Mammals (1) and the fungus Neurospora crassa (2,3) have about 2–3% of cytosines methylated. In mammals, methylation is almost exclusively in the ...

  12. Limiting dilution bisulfite (pyro)sequencing reveals parent-specific methylation patterns in single early mouse embryos and bovine oocytes

    PubMed Central

    El Hajj, Nady; Trapphoff, Tom; Linke, Matthias; May, Andreas; Hansmann, Tamara; Kuhtz, Juliane; Reifenberg, Kurt; Heinzmann, Julia; Niemann, Heiner; Daser, Angelika; Eichenlaub-Ritter, Ursula; Zechner, Ulrich

    2011-01-01

    To detect rare epigenetic effects associated with assisted reproduction, it is necessary to monitor methylation patterns of developmentally important genes in a few germ cells and individual embryos. Bisulfite treatment degrades DNA and reduces its complexity, rendering methylation analysis from small amounts of DNA extremely challenging. Here we describe a simple approach that allows determining the parent-specific methylation patterns of multiple genes in individual early embryos. Limiting dilution (LD) of bisulfite-treated DNA is combined with independent multiplex PCRs of single DNA target molecules to avoid amplification bias. Using this approach, we compared the methylation status of three imprinted (H19, Snrpn and Igf2r) and one pluripotency-related gene (Oct4) in three different groups of single mouse two-cell embryos. Standard in vitro fertilization of superovulated oocytes and the use of in vitro matured oocytes were not associated with significantly increased rates of stochastic single CpG methylation errors and epimutations (allele methylation errors), when compared with the in vivo produced controls. Similarly, we compared the methylation patterns of two imprinted genes (H19 and Snrpn) in individual mouse 16-cell embryos produced in vivo from superovulated and non-superovulated oocytes and did not observe major between-group differences. Using bovine oocytes and polar bodies as a model, we demonstrate that LD even allows the methylation analysis of multiple genes in single cells. PMID:21937882

  13. A GAS-PHASE FORMATION ROUTE TO INTERSTELLAR TRANS-METHYL FORMATE

    SciTech Connect

    Cole, Callie A.; Wehres, Nadine; Yang Zhibo; Thomsen, Ditte L.; Bierbaum, Veronica M.; Snow, Theodore P. E-mail: Nadine.Wehres@colorado.edu E-mail: Veronica.Bierbaum@colorado.edu E-mail: dlt@chem.ku.dk

    2012-07-20

    The abundance of methyl formate in the interstellar medium has previously been underpredicted by chemical models. Additionally, grain surface chemistry cannot account for the relative abundance of the cis- and trans-conformers of methyl formate, and the trans-conformer is not even formed at detectable abundance on these surfaces. This highlights the importance of studying formation pathways to methyl formate in the gas phase. The rate constant and branching fractions are reported for the gas-phase reaction between protonated methanol and formic acid to form protonated trans-methyl formate and water as well as adduct ion: Rate constants were experimentally determined using a flowing afterglow-selected ion flow tube apparatus at 300 K and a pressure of 530 mTorr helium. The results indicate a moderate overall rate constant of (3.19 {+-} 0.39) Multiplication-Sign 10{sup -10} cm{sup 3} s{sup -1} ({+-} 1{sigma}) and an average branching fraction of 0.05 {+-} 0.04 for protonated trans-methyl formate and 0.95 {+-} 0.04 for the adduct ion. These experimental results are reinforced by ab initio calculations at the MP2(full)/aug-cc-pVTZ level of theory to examine the reaction coordinate and complement previous density functional theory calculations. This study underscores the need for continued observational studies of trans-methyl formate and for the exploration of other gas-phase formation routes to complex organic molecules.

  14. Methylation quantitative trait locus analysis of osteoarthritis links epigenetics with genetic risk.

    PubMed

    Rushton, Michael D; Reynard, Louise N; Young, David A; Shepherd, Colin; Aubourg, Guillaume; Gee, Fiona; Darlay, Rebecca; Deehan, David; Cordell, Heather J; Loughlin, John

    2015-12-20

    Osteoarthritis (OA) is a common, painful and debilitating disease of articulating joints resulting from the age-associated loss of cartilage. Well-powered genetic studies have identified a number of DNA polymorphisms that are associated with OA susceptibility. Like most complex trait loci, these OA loci are thought to influence disease susceptibility through the regulation of gene expression, so-called expression quantitative loci, or eQTLs. One mechanism through which eQTLs act is epigenetic, by modulating DNA methylation. In such cases, there are quantitative differences in DNA methylation between the two alleles of the causal polymorphism, with the association signal referred to as a methylation quantitative trait locus, or meQTL. In this study, we aimed to investigate whether the OA susceptibility loci identified to date are functioning as meQTLs by integrating genotype data with whole genome methylation data of cartilage DNA. We investigated potential genotype-methylation correlations within a 1.0-1.5 Mb region surrounding each of 16 OA-associated single-nucleotide polymorphisms (SNPs) in 99 cartilage samples and identified four that function as meQTLs. Three of these replicated in an additional cohort of up to 62 OA patients. These observations suggest that OA susceptibility loci regulate the level of DNA methylation in cis and provide a mechanistic explanation as to how these loci impact upon OA susceptibility, further increasing our understanding of the role of genetics and epigenetics in this common disease. PMID:26464490

  15. Methylation quantitative trait locus analysis of osteoarthritis links epigenetics with genetic risk

    PubMed Central

    Rushton, Michael D.; Reynard, Louise N.; Young, David A.; Shepherd, Colin; Aubourg, Guillaume; Gee, Fiona; Darlay, Rebecca; Deehan, David; Cordell, Heather J.; Loughlin, John

    2015-01-01

    Osteoarthritis (OA) is a common, painful and debilitating disease of articulating joints resulting from the age-associated loss of cartilage. Well-powered genetic studies have identified a number of DNA polymorphisms that are associated with OA susceptibility. Like most complex trait loci, these OA loci are thought to influence disease susceptibility through the regulation of gene expression, so-called expression quantitative loci, or eQTLs. One mechanism through which eQTLs act is epigenetic, by modulating DNA methylation. In such cases, there are quantitative differences in DNA methylation between the two alleles of the causal polymorphism, with the association signal referred to as a methylation quantitative trait locus, or meQTL. In this study, we aimed to investigate whether the OA susceptibility loci identified to date are functioning as meQTLs by integrating genotype data with whole genome methylation data of cartilage DNA. We investigated potential genotype–methylation correlations within a 1.0–1.5 Mb region surrounding each of 16 OA-associated single-nucleotide polymorphisms (SNPs) in 99 cartilage samples and identified four that function as meQTLs. Three of these replicated in an additional cohort of up to 62 OA patients. These observations suggest that OA susceptibility loci regulate the level of DNA methylation in cis and provide a mechanistic explanation as to how these loci impact upon OA susceptibility, further increasing our understanding of the role of genetics and epigenetics in this common disease. PMID:26464490

  16. A Gas-phase Formation Route to Interstellar Trans-methyl Formate

    NASA Astrophysics Data System (ADS)

    Cole, Callie A.; Wehres, Nadine; Yang, Zhibo; Thomsen, Ditte L.; Snow, Theodore P.; Bierbaum, Veronica M.

    2012-07-01

    The abundance of methyl formate in the interstellar medium has previously been underpredicted by chemical models. Additionally, grain surface chemistry cannot account for the relative abundance of the cis- and trans-conformers of methyl formate, and the trans-conformer is not even formed at detectable abundance on these surfaces. This highlights the importance of studying formation pathways to methyl formate in the gas phase. The rate constant and branching fractions are reported for the gas-phase reaction between protonated methanol and formic acid to form protonated trans-methyl formate and water as well as adduct ion: Rate constants were experimentally determined using a flowing afterglow-selected ion flow tube apparatus at 300 K and a pressure of 530 mTorr helium. The results indicate a moderate overall rate constant of (3.19 ± 0.39) × 10-10 cm3 s-1 (± 1?) and an average branching fraction of 0.05 ± 0.04 for protonated trans-methyl formate and 0.95 ± 0.04 for the adduct ion. These experimental results are reinforced by ab initio calculations at the MP2(full)/aug-cc-pVTZ level of theory to examine the reaction coordinate and complement previous density functional theory calculations. This study underscores the need for continued observational studies of trans-methyl formate and for the exploration of other gas-phase formation routes to complex organic molecules.

  17. Polycomb binding precedes early-life stress responsive DNA methylation at the Avp enhancer.

    PubMed

    Murgatroyd, Chris; Spengler, Dietmar

    2014-01-01

    Early-life stress (ELS) in mice causes sustained hypomethylation at the downstream Avp enhancer, subsequent overexpression of hypothalamic Avp and increased stress responsivity. The sequence of events leading to Avp enhancer methylation is presently unknown. Here, we used an embryonic stem cell-derived model of hypothalamic-like differentiation together with in vivo experiments to show that binding of polycomb complexes (PcG) preceded the emergence of ELS-responsive DNA methylation and correlated with gene silencing. At the same time, PcG occupancy associated with the presence of Tet proteins preventing DNA methylation. Early hypothalamic-like differentiation triggered PcG eviction, DNA-methyltransferase recruitment and enhancer methylation. Concurrently, binding of the Methyl-CpG-binding and repressor protein MeCP2 increased at the enhancer although Avp expression during later stages of differentiation and the perinatal period continued to increase. Overall, we provide evidence of a new role of PcG proteins in priming ELS-responsive DNA methylation at the Avp enhancer prior to epigenetic programming consistent with the idea that PcG proteins are part of a flexible silencing system during neuronal development. PMID:24599304

  18. Examining the Causes and Consequences of Context-Specific Differential DNA Methylation in Maize1[OPEN

    PubMed Central

    Li, Qing; Song, Jawon; West, Patrick T.; Zynda, Greg; Eichten, Steven R.; Vaughn, Matthew W.; Springer, Nathan M.

    2015-01-01

    DNA methylation is a stable modification of chromatin that can contribute to epigenetic variation through the regulation of genes or transposons. Profiling of DNA methylation in five maize (Zea mays) inbred lines found that while DNA methylation levels for more than 99% of the analyzed genomic regions are similar, there are still 5,000 to 20,000 context-specific differentially methylated regions (DMRs) between any two genotypes. The analysis of identical-by-state genomic regions that have limited genetic variation provided evidence that DMRs can occur without local sequence variation, but they are less common than in regions with genetic variation. Characterization of the sequence specificity of DMRs, location of DMRs relative to genes and transposons, and patterns of DNA methylation in regions flanking DMRs reveals a distinct subset of DMRs. Transcriptome profiling of the same tissue revealed that only approximately 20% of genes with qualitative (on-off) differences in gene expression are associated with DMRs, and there is little evidence for association of DMRs with genes that show quantitative differences in gene expression. We also identify a set of genes that may represent cryptic information that is silenced by DNA methylation in the reference B73 genome. Many of these genes exhibit natural variation in other genotypes, suggesting the potential for selection to act upon existing epigenetic natural variation. This study provides insights into the origin and influences of DMRs in a crop species with a complex genome organization. PMID:25869653

  19. The Stem Cell Population of the Human Colon Crypt: Analysis via Methylation Patterns

    PubMed Central

    Nicolas, Pierre; Kim, Kyoung-Mee; Shibata, Darryl; Tavaré, Simon

    2007-01-01

    The analysis of methylation patterns is a promising approach to investigate the genealogy of cell populations in an organism. In a stem cell–niche scenario, sampled methylation patterns are the stochastic outcome of a complex interplay between niche structural features such as the number of stem cells within a niche and the niche succession time, the methylation/demethylation process, and the randomness due to sampling. As a consequence, methylation pattern studies can reveal niche characteristics but also require appropriate statistical methods. The analysis of methylation patterns sampled from colon crypts is a prototype of such a study. Previous analyses were based on forward simulation of the cell content of the whole crypt and subsequent comparisons between simulated and experimental data using a few statistics as a proxy to summarize the data. In this paper we develop a more powerful method to analyze these data based on coalescent modelling and Bayesian inference. Results support a scenario where the colon crypt is maintained by a high number of stem cells; the posterior indicates a number greater than eight and the posterior mode is between 15 and 20. The results also provide further evidence for synergistic effects in the methylation/demethylation process that could for the first time be quantitatively assessed through their long-term consequences such as the coexistence of hypermethylated and hypomethylated patterns in the same colon crypt. PMID:17335343

  20. Evolving insights on how cytosine methylation affects protein–DNA binding

    PubMed Central

    Dantas Machado, Ana Carolina; Zhou, Tianyin; Rao, Satyanarayan; Goel, Pragya; Rastogi, Chaitanya; Lazarovici, Allan; Bussemaker, Harmen J.

    2015-01-01

    Many anecdotal observations exist of a regulatory effect of DNA methylation on gene expression. However, in general, the underlying mechanisms of this effect are poorly understood. In this review, we summarize what is currently known about how this important, but mysterious, epigenetic mark impacts cellular functions. Cytosine methylation can abrogate or enhance interactions with DNA-binding proteins, or it may have no effect, depending on the context. Despite being only a small chemical change, the addition of a methyl group to cytosine can affect base readout via hydrophobic contacts in the major groove and shape readout via electrostatic contacts in the minor groove. We discuss the recent discovery that CpG methylation increases DNase I cleavage at adjacent positions by an order of magnitude through altering the local 3D DNA shape and the possible implications of this structural insight for understanding the methylation sensitivity of transcription factors (TFs). Additionally, 5-methylcytosines change the stability of nucleosomes and, thus, affect the local chromatin structure and access of TFs to genomic DNA. Given these complexities, it seems unlikely that the influence of DNA methylation on protein–DNA binding can be captured in a small set of general rules. Hence, data-driven approaches may be essential to gain a better understanding of these mechanisms. PMID:25319759

  1. Power and sample size estimation for epigenome-wide association scans to detect differential DNA methylation

    PubMed Central

    Tsai, Pei-Chien; Bell, Jordana T

    2015-01-01

    Background: Epigenome-wide association scans (EWAS) are under way for many complex human traits, but EWAS power has not been fully assessed. We investigate power of EWAS to detect differential methylation using case-control and disease-discordant monozygotic (MZ) twin designs with genome-wide DNA methylation arrays. Methods and Results: We performed simulations to estimate power under the case-control and discordant MZ twin EWAS study designs, under a range of epigenetic risk effect sizes and conditions. For example, to detect a 10% mean methylation difference between affected and unaffected subjects at a genome-wide significance threshold of P?=?1?×?10?6, 98?MZ twin pairs were required to reach 80% EWAS power, and 112 cases and 112 controls pairs were needed in the case-control design. We also estimated the minimum sample size required to reach 80% EWAS power under both study designs. Our analyses highlighted several factors that significantly influenced EWAS power, including sample size, epigenetic risk effect size, the variance of DNA methylation at the locus of interest and the correlation in DNA methylation patterns within the twin sample. Conclusions: We provide power estimates for array-based DNA methylation EWAS under case-control and disease-discordant MZ twin designs, and explore multiple factors that impact on EWAS power. Our results can help guide EWAS experimental design and interpretation for future epigenetic studies. PMID:25972603

  2. Leisingera methylohalidivorans gen. nov., sp. nov., a marine methylotroph that grows on methyl bromide

    USGS Publications Warehouse

    Schaefer, J.K.; Goodwin, K.D.; McDonald, I.R.; Murrell, J.C.; Oremland, R.S.

    2002-01-01

    A marine methylotroph, designated strain MB2T, was isolated for its ability to grow on methyl bromide as a sole carbon and energy source. Methyl chloride and methyl iodide also supported growth, as did methionine and glycine betaine. A limited amount of growth was observed with dimethyl sulfide. Growth was also noted with unidentified components of the complex media marine broth 2216, yeast extract and Casamino acids. No growth was observed on methylated amines, methanol, formate, acetate, glucose or a variety of other substrates. Growth on methyl bromide and methyl iodide resulted in their oxidation to CO2 with stoichiometric release of bromide and iodide, respectively. Strain MB2T exhibited growth optima at NaCl and Mg2+ concentrations similar to that of seawater. Phylogenetic analysis of the 16S rDNA sequence placed this strain in the ??-Proteobacteria in proximity to the genera Ruegeria and Roseobacter. It is proposed that strain MB2T (= ATCC BAA-92T = DSM 14336T) be designated Leisingera methylohalidivorans gen. nov., sp. nov.

  3. The Impact of Nutrition on Differential Methylated Regions of the Genome1

    PubMed Central

    Parle-McDermott, Anne; Ozaki, Mari

    2011-01-01

    Nutrition has always played an important role in health and disease, ranging from common diseases to its likely contribution to the fetal origins of adult disease. However, deciphering the molecular details of this role is much more challenging. The impact of nutrition on the methylome, i.e., DNA methylation, has received particular attention in more recent years. Our understanding of the complexity of the methylome is evolving as efforts to catalog the DNA methylation differences that exist between different tissues and individuals continue. We review selected examples of animal and human studies that provide evidence that, in fact, specific genes and DNA methylation sites are subject to change during development and during a lifetime as a direct response to nutrition. Investigation of the methyl donors folate, choline, and methionine provide the most compelling evidence of a role in mediating DNA methylation changes. Although a number of candidate regions/genes have been identified to date, we are just at the beginning in terms of cataloging so-called nutrient-sensitive methylation variable positions in humans. PMID:22332089

  4. DNA Methylation Modulates Nociceptive Sensitization after Incision.

    PubMed

    Sun, Yuan; Sahbaie, Peyman; Liang, DeYong; Li, Wenwu; Shi, Xiaoyou; Kingery, Paige; Clark, J David

    2015-01-01

    DNA methylation is a key epigenetic mechanism controlling DNA accessibility and gene expression. Blockade of DNA methylation can significantly affect pain behaviors implicated in neuropathic and inflammatory pain. However, the role of DNA methylation with regard to postoperative pain has not yet been explored. In this study we sought to investigate the role of DNA methylation in modulating incisional pain and identify possible targets under DNA methylation and contributing to incisional pain. DNA methyltranferase (DNMT) inhibitor 5-Aza-2'-deoxycytidine significantly reduced incision-induced mechanical allodynia and thermal sensitivity. Aza-2'-deoxycytidine also reduced hindpaw swelling after incision, suggesting an anti-inflammatory effect. Global DNA methylation and DNMT3b expression were increased in skin after incision, but none of DNMT1, DNMT3a or DNMT3b was altered in spinal cord or DRG. The expression of proopiomelanocortin Pomc encoding ?-endorphin and Oprm1 encoding the mu-opioid receptor were upregulated peripherally after incision; moreover, Oprm1 expression was further increased under DNMT inhibitor treatment. Finally, local peripheral injection of the opioid receptor antagonist naloxone significantly exacerbated incision-induced mechanical hypersensitivity. These results suggest that DNA methylation is functionally relevant to incisional nociceptive sensitization, and that mu-opioid receptor signaling might be one methylation regulated pathway controlling sensitization after incision. PMID:26535894

  5. METHYL BROMIDE ALTERNATIVES FOR VINEYARD REPLANT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil fumigation with methyl bromide is needed by grape growers in central California to control soilborne pests. However, use of methyl bromide is banned and soil fumigation with other chemicals subjects to strict regulations to protect human health and air quality. The objective was to determine,...

  6. ABIOLOGICAL METHYLATION OF MERCURY IN SOIL

    EPA Science Inventory

    This work defines several factors influencing the methylation of mercuric ion in soil. Two of the most important findings were that it is possible to extract the mercury methylating factor from soil with a solution of 0.5N sodium hydroxide and that this factor is responsible for ...

  7. Molecular Cell Protein Arginine Methylation in Mammals

    E-print Network

    Clarke, Steven

    Molecular Cell Review Protein Arginine Methylation in Mammals: Who, What, and Why Mark T. Bedford1.12.013 The covalent marking of proteins by methyl group addition to arginine residues can promote their recognition, it is unclear to what extent protein arginine demethylation occurs. Physiological roles for protein arginine

  8. Infraspecific DNA Methylation Polymorphism in Cotton (Gossypium

    E-print Network

    Wendel, Jonathan F.

    Infraspecific DNA Methylation Polymorphism in Cotton (Gossypium hirsutum L.) ANNA L. KEYTE, RYAN-polymorphism diversity at CCGG sites within allotetraploid cotton, Gossypium hirsutum, using a methylation in cotton may be a consequence of polyploidy and the attendant doubling of all genes. The information

  9. Methyl bromide alternatives for grape replant

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The project is part of the USDA-ARS Pacific Area-Wide Pest Management Program for Methyl Bromide Alternatives. The Critical Use Exemption (CUE) for methyl bromide (MB) on all grapes (wine, raisin, and table) is a short term solution until alternatives to MB are identified, and active research on MB ...

  10. DNA Methylation Modulates Nociceptive Sensitization after Incision

    PubMed Central

    Sun, Yuan; Sahbaie, Peyman; Liang, DeYong; Li, Wenwu; Shi, Xiaoyou; Kingery, Paige; Clark, J. David

    2015-01-01

    DNA methylation is a key epigenetic mechanism controlling DNA accessibility and gene expression. Blockade of DNA methylation can significantly affect pain behaviors implicated in neuropathic and inflammatory pain. However, the role of DNA methylation with regard to postoperative pain has not yet been explored. In this study we sought to investigate the role of DNA methylation in modulating incisional pain and identify possible targets under DNA methylation and contributing to incisional pain. DNA methyltranferase (DNMT) inhibitor 5-Aza-2?-deoxycytidine significantly reduced incision-induced mechanical allodynia and thermal sensitivity. Aza-2?-deoxycytidine also reduced hindpaw swelling after incision, suggesting an anti-inflammatory effect. Global DNA methylation and DNMT3b expression were increased in skin after incision, but none of DNMT1, DNMT3a or DNMT3b was altered in spinal cord or DRG. The expression of proopiomelanocortin Pomc encoding ?-endorphin and Oprm1 encoding the mu-opioid receptor were upregulated peripherally after incision; moreover, Oprm1 expression was further increased under DNMT inhibitor treatment. Finally, local peripheral injection of the opioid receptor antagonist naloxone significantly exacerbated incision-induced mechanical hypersensitivity. These results suggest that DNA methylation is functionally relevant to incisional nociceptive sensitization, and that mu-opioid receptor signaling might be one methylation regulated pathway controlling sensitization after incision. PMID:26535894

  11. Alternatives to Methyl Bromide for Raspberry Nursery

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Raspberry nurseries use preplant soil fumigation with Methyl Bromide:chloropicrin (MB:pic) to produce disease- and nematode-free plants. The use of Methyl Bromide has been largely phased out, and exemptions for continued use are becoming more difficult to obtain. Successful alternatives to MB:pic ...

  12. DNA methylation contributes to natural human variation

    PubMed Central

    Heyn, Holger; Moran, Sebastian; Hernando-Herraez, Irene; Sayols, Sergi; Gomez, Antonio; Sandoval, Juan; Monk, Dave; Hata, Kenichiro; Marques-Bonet, Tomas; Wang, Liewei; Esteller, Manel

    2013-01-01

    DNA methylation patterns are important for establishing cell, tissue, and organism phenotypes, but little is known about their contribution to natural human variation. To determine their contribution to variability, we have generated genome-scale DNA methylation profiles of three human populations (Caucasian-American, African-American, and Han Chinese-American) and examined the differentially methylated CpG sites. The distinctly methylated genes identified suggest an influence of DNA methylation on phenotype differences, such as susceptibility to certain diseases and pathogens, and response to drugs and environmental agents. DNA methylation differences can be partially traced back to genetic variation, suggesting that differentially methylated CpG sites serve as evolutionarily established mediators between the genetic code and phenotypic variability. Notably, one-third of the DNA methylation differences were not associated with any genetic variation, suggesting that variation in population-specific sites takes place at the genetic and epigenetic levels, highlighting the contribution of epigenetic modification to natural human variation. PMID:23908385

  13. The Synthesis of Methyl Salicylate: Amine Diazotization.

    ERIC Educational Resources Information Center

    Zanger, Murray; McKee, James R.

    1988-01-01

    Notes that this experiment takes safety and noncarcinogenic reactants into account. Demonstrates the use of diazonium salts for the replacement of an aromatic amine group by a phenolic hydroxyl. Involves two pleasant-smelling organic compounds, methyl anthranilate (grape) and methyl salicylate (oil of wintergreen). (MVL)

  14. Green exciplex emission from a bilayer light-emitting diode containing a rare earth ternary complex

    E-print Network

    Huang, Yanyi

    form 18 October 2001 Abstract A bilayer organic light-emitting diode using a blue-fluorescent yttrium complex, tris(1-phenyl-3-methyl-4-isobutyryl- 5-pyrazolone)-(2,20 -dipyridyl) yttrium [Y(PMIP)3(Bipy and does not emit visible light [7]; however the titled yttrium ternary complex, tris(1-phenyl-3-methyl-4

  15. A lifelong exposure to a Western-style diet, but not aging, alters global DNA methylation in mouse colon

    PubMed Central

    Tammen, Stephanie A; Liu, Zhenhua; Friso, Simonetta

    2015-01-01

    BACKGROUND/OBJECTIVES Previous studies have indicated that when compared to young mice, old mice have lower global DNA methylation and higher p16 promoter methylation in colonic mucosa, which is a common finding in colon cancer. It is also known that a Western-style diet (WSD) high in fat and calories, and low in calcium, vitamin D, fiber, methionine and choline (based on the AIN 76A diet) is tumorigenic in colons of mice. Because DNA methylation is modifiable by diet, we investigate whether a WSD disrupts DNA methylation patterns, creating a tumorigenic environment. SUBJECTVIES/METHODS We investigated the effects of a WSD and aging on global and p16 promoter DNA methylation in the colon. Two month old male C57BL/6 mice were fed either a WSD or a control diet (AIN76A) for 6, 12 or 17 months. Global DNA methylation, p16 promoter methylation and p16 expression were determined by LC/MS, methyl-specific PCR and real time RT-PCR, respectively. RESULTS The WSD group demonstrated significantly decreased global DNA methylation compared with the control at 17 months (4.05 vs 4.31%, P = 0.019). While both diets did not change global DNA methylation over time, mice fed the WSD had lower global methylation relative to controls when comparing all animals (4.13 vs 4.30%, P = 0.0005). There was an increase in p16 promoter methylation from 6 to 17 months in both diet groups (P < 0.05) but no differences were observed between diet groups. Expression of p16 increased with age in both control and WSD groups. CONCLUSIONS In this model a WSD reduces global DNA methylation, whereas aging itself has no affect. Although the epigenetic effect of aging was not strong enough to alter global DNA methylation, changes in promoter-specific methylation and gene expression occurred with aging regardless of diet, demonstrating the complexity of epigenetic patterns. PMID:26244073

  16. Structure-function properties of starch graft poly(methyl acrylate)copolymers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Spherulites, produced by steam jet-cooking high-amylose starch and oleic acid, were grafted with methyl acrylate, both before and after removal of un-complexed amylopectin. For comparison, granular high-amylose corn starch was graft polymerized in a similar manner. The amount of grafted and ungrafte...

  17. Structure-function properties of starch spherulites grafted with poly(methyl acrylate)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Spherulites, produced by steam jet-cooking high-amylose starch and oleic acid, were grafted with methyl acrylate, both before and after removal of un-complexed amylopectin. For comparison, granular high-amylose corn starch was graft polymerized in a similar manner. The amount of grafted and ungrafte...

  18. LABORATORY ECOSYSTEMS FOR STUDYING CHEMICAL FATE: AN EVALUATION USING METHYL PARATHION

    EPA Science Inventory

    The use of complex microcosms as tools for testing mathematical models of pollutant fate was evaluated by determining the transport and transformation of methyl parathion in two-8-compartment, continuous flow microcosms designed to enhance the effects of different degradation pro...

  19. Prediction of Plant Height in Arabidopsis thaliana Using DNA Methylation Data

    PubMed Central

    Hu, Yaodong; Morota, Gota; Rosa, Guilherme J. M.; Gianola, Daniel

    2015-01-01

    Prediction of complex traits using molecular genetic information is an active area in quantitative genetics research. In the postgenomic era, many types of -omic (e.g., transcriptomic, epigenomic, methylomic, and proteomic) data are becoming increasingly available. Therefore, evaluating the utility of this massive amount of information in prediction of complex traits is of interest. DNA methylation, the covalent change of a DNA molecule without affecting its underlying sequence, is one quantifiable form of epigenetic modification. We used methylation information for predicting plant height (PH) in Arabidopsis thaliana nonparametrically, using reproducing kernel Hilbert spaces (RKHS) regression. Also, we used different criteria for selecting smaller sets of probes, to assess how representative probes could be used in prediction instead of using all probes, which may lessen computational burden and lower experimental costs. Methylation information was used for describing epigenetic similarities between individuals through a kernel matrix, and the performance of predicting PH using this similarity matrix was reasonably good. The predictive correlation reached 0.53 and the same value was attained when only preselected probes were used for prediction. We created a kernel that mimics the genomic relationship matrix in genomic best linear unbiased prediction (G-BLUP) and estimated that, in this particular data set, epigenetic variation accounted for 65% of the phenotypic variance. Our results suggest that methylation information can be useful in whole-genome prediction of complex traits and that it may help to enhance understanding of complex traits when epigenetics is under examination. PMID:26253546

  20. DNA Methylation and Demethylation in Mammals*

    PubMed Central

    Chen, Zhao-xia; Riggs, Arthur D.

    2011-01-01

    Cell type-specific DNA methylation patterns are established during mammalian development and maintained in adult somatic cells. Understanding how these patterns of 5-methylcytosine are established and maintained requires the elucidation of mechanisms for both DNA methylation and demethylation. The enzymes involved in the de novo methylation of DNA and the maintenance of the resulting methylation patterns have been fairly well characterized. However, important remaining challenges are to understand how DNA methylation systems function in vivo and in the context of chromatin. In addition, the enzymes and mechanisms for demethylation remain to be elucidated. There is still no consensus as to how active enzymatic demethylation is achieved in mammalian cells, but recent studies implicate base excision repair for genome-wide DNA demethylation in germ cells and early embryos. PMID:21454628

  1. DNA methylation and hydroxymethylation in stem cells

    PubMed Central

    Cheng, Ying; Xie, Nina; Jin, Peng; Wang, Tao

    2015-01-01

    In mammals, DNA methylation and hydroxymethylation are specific epigenetic mechanisms that can contribute to the regulation of gene expression and cellular functions. DNA methylation is important for the function of embryonic stem cells and adult stem cells (such as haematopoietic stem cells, neural stem cells and germline stem cells), and changes in DNA methylation patterns are essential for successful nuclear reprogramming. In the past several years, the rediscovery of hydroxymethylation and the TET enzymes expanded our insights tremendously and uncovered more dynamic aspects of cytosine methylation regulation. Here, we review the current knowledge and highlight the most recent advances in DNA methylation and hydroxymethylation in embryonic stem cells, induced pluripotent stem cells and several well-studied adult stems cells. Our current understanding of stem cell epigenetics and new advances in the field will undoubtedly stimulate further clinical applications of regenerative medicine in the future. PMID:25776144

  2. Protein methylation reactions in intact pea chloroplasts

    SciTech Connect

    Niemi, K.J. )

    1989-04-01

    Post-translational protein methylation was investigated in Pisum sativum chloroplasts. Intact pea chloroplasts were incubated with ({sup 3}H-methyl)-S-adenosylmethionine under various conditions. The chloroplasts were then separated into stromal and thylakoid fractions and analyzed for radioactivity transferred to protein. Light enhanced the magnitude of labeling in both fractions. One thylakoid polypeptide with an apparent molecular mass of 43 kDa was labeled only in the light. Several other thylakoid and stromal proteins were labeled in both light and dark-labeling conditions. Both base-labile methylation, carboxy-methylesters and base-stable groups, N-methylations were found. Further characterization of the methyl-transfer reactions will be presented.

  3. Histone methylation modifiers in cellular signaling pathways.

    PubMed

    Alam, Hunain; Gu, Bingnan; Lee, Min Gyu

    2015-12-01

    Histone methyltransferases and demethylases epigenetically regulate gene expression by modifying histone methylation status in numerous cellular processes, including cell differentiation and proliferation. These modifiers also control methylation levels of various non-histone proteins, such as effector proteins that play critical roles in cellular signaling networks. Dysregulated histone methylation modifiers alter expression of oncogenes and tumor suppressor genes and change methylation states of effector proteins, frequently resulting in aberrant cellular signaling cascades and cellular transformation. In this review, we summarize the role of histone methylation modifiers in regulating the following signaling pathways: NF-?B, RAS/RAF/MEK/MAPK, PI3K/Akt, Wnt/?-catenin, p53, and ER?. PMID:26305020

  4. Turning over DNA methylation in the mind

    PubMed Central

    Lister, Ryan; Mukamel, Eran A.

    2015-01-01

    Cytosine DNA methylation is a stable epigenetic modification with established roles in regulating transcription, imprinting, female X-chromosome inactivation, and silencing of transposons. Dynamic gain or loss of DNA methylation reshapes the genomic landscape of cells during early differentiation, and in post-mitotic mammalian brain cells these changes continue to accumulate throughout the phases of cortical maturation in childhood and adolescence. There is also evidence for dynamic changes in the methylation status of specific genomic loci during the encoding of new memories, and these epigenome dynamics could play a causal role in memory formation. However, the mechanisms that may dynamically regulate DNA methylation in neurons during memory formation and expression, and the function of such epigenomic changes in this context, are unclear. Here we discuss the possible roles of DNA methylation in encoding and retrieval of memory. PMID:26283895

  5. Comparative methylome analysis in solid tumors reveals aberrant methylation at chromosome 6p in nasopharyngeal carcinoma

    PubMed Central

    Dai, Wei; Cheung, Arthur Kwok Leung; Ko, Josephine Mun Yee; Cheng, Yue; Zheng, Hong; Ngan, Roger Kai Cheong; Ng, Wai Tong; Lee, Anne Wing Mui; Yau, Chun Chung; Lee, Victor Ho Fu; Lung, Maria Li

    2015-01-01

    Altered patterns of DNA methylation are key features of cancer. Nasopharyngeal carcinoma (NPC) has the highest incidence in Southern China. Aberrant methylation at the promoter region of tumor suppressors is frequently reported in NPC; however, genome-wide methylation changes have not been comprehensively investigated. Therefore, we systematically analyzed methylome data in 25 primary NPC tumors and nontumor counterparts using a high-throughput approach with the Illumina HumanMethylation450 BeadChip. Comparatively, we examined the methylome data of 11 types of solid tumors collected by The Cancer Genome Atlas (TCGA). In NPC, the hypermethylation pattern was more dominant than hypomethylation and the majority of de novo methylated loci were within or close to CpG islands in tumors. The comparative methylome analysis reveals hypermethylation at chromosome 6p21.3 frequently occurred in NPC (false discovery rate; FDR=1.33 × 10?9), but was less obvious in other types of solid tumors except for prostate and Epstein–Barr virus (EBV)-positive gastric cancer (FDR<10?3). Bisulfite pyrosequencing results further confirmed the aberrant methylation at 6p in an additional patient cohort. Evident enrichment of the repressive mark H3K27me3 and active mark H3K4me3 derived from human embryonic stem cells were found at these regions, indicating both DNA methylation and histone modification function together, leading to epigenetic deregulation in NPC. Our study highlights the importance of epigenetic deregulation in NPC. Polycomb Complex 2 (PRC2), responsible for H3K27 trimethylation, is a promising therapeutic target. A key genomic region on 6p with aberrant methylation was identified. This region contains several important genes having potential use as biomarkers for NPC detection. PMID:25924914

  6. Methyltransferase expression and tumor suppressor gene methylation in sporadic and familial colorectal cancer.

    PubMed

    Joensuu, Emmi I; Nieminen, Taina T; Lotsari, Johanna E; Pavicic, Walter; Abdel-Rahman, Wael M; Peltomäki, Päivi

    2015-12-01

    Molecular mechanisms underlying coordinated hypermethylation of multiple CpG islands in cancer remain unclear and studies of methyltransferase enzymes have arrived at conflicting results. We focused on DNMT1 and DNMT3B, DNA methyltransferases responsible for (de novo) methylation, and EZH2, histone (H3K27) methyltransferase, and examined their roles in tumor suppressor gene (TSG) methylation patterns we have previously established in sporadic and familial cancers. Our investigation comprised 165 tumors, stratified by tissue of origin (117 colorectal and 48 endometrial carcinomas) and sporadic vs. familial disease (57 sporadic vs. 60 familial, mainly Lynch syndrome, colorectal carcinomas). By immunohistochemical evaluation, EZH2 protein expression was associated with a TSG methylator phenotype. DNMT1, DNMT3B, and EZH2 were expressed at significantly higher levels in tumor vs. normal tissues. DNMT1 and EZH2 expression were positively correlated and higher in microsatellite-unstable vs. microsatellite-stable tumors, whether sporadic or hereditary. Ki-67 expression mirrored the same pattern. Promoter methylation of the methyltransferase genes themselves was addressed as a possible cause behind their altered expression. While DNMT1 or EZH2 did not show differential methylation between normal and tumor tissues, DNMT3B analysis corroborated the regulatory role of a distal promoter region. Our study shows that methyltransferase expression in cancer depends on the tissue of origin, microsatellite-instability status, cellular proliferation, and-in the case of DNMT3B-promoter methylation of the respective gene. Translation of methyltransferase expression into DNA methylation appears complex as suggested by the fact that except for EZH2, no clear association between methyltransferase protein expression and TSG methylation was observed. © 2015 Wiley Periodicals, Inc. PMID:26305882

  7. Is the fungus Magnaporthe losing DNA methylation?

    PubMed

    Ikeda, Ken-ichi; Van Vu, Ba; Kadotani, Naoki; Tanaka, Masaki; Murata, Toshiki; Shiina, Kohta; Chuma, Izumi; Tosa, Yukio; Nakayashiki, Hitoshi

    2013-11-01

    The long terminal repeat retrotransposon, Magnaporthe gypsy-like element (MAGGY), has been shown to be targeted for cytosine methylation in a subset of Magnaporthe oryzae field isolates. Analysis of the F1 progeny from a genetic cross between methylation-proficient (Br48) and methylation-deficient (GFSI1-7-2) isolates revealed that methylation of the MAGGY element was governed by a single dominant gene. Positional cloning followed by gene disruption and complementation experiments revealed that the responsible gene was the DNA methyltransferase, MoDMT1, an ortholog of Neurospora crassa Dim-2. A survey of MAGGY methylation in 60 Magnaporthe field isolates revealed that 42 isolates from rice, common millet, wheat, finger millet, and buffelgrass were methylation proficient while 18 isolates from foxtail millet, green bristlegrass, Japanese panicgrass, torpedo grass, Guinea grass, and crabgrass were methylation deficient. Phenotypic analyses showed that MoDMT1 plays no major role in development and pathogenicity of the fungus. Quantitative polymerase chain reaction analysis showed that the average copy number of genomic MAGGY elements was not significantly different between methylation-deficient and -proficient field isolates even though the levels of MAGGY transcript were generally higher in the former group. MoDMT1 gene sequences in the methylation-deficient isolates suggested that at least three independent mutations were responsible for the loss of MoDMT1 function. Overall, our data suggest that MoDMT1 is not essential for the natural life cycle of the fungus and raise the possibility that the genus Magnaporthe may be losing the mechanism of DNA methylation on the evolutionary time scale. PMID:23979580

  8. Effect of Methylation on the Properties of the H-Bridges in DNA. A Systematic Theoretical Study on the Couples of Base Pairs.

    PubMed

    Villani, Giovanni

    2015-06-25

    The effects of the addition of one (hemimethylation) or two (methylation) methyl groups on the 10 different couples of base pairs of DNA (three dimers of A-T, three of C-G, and four mixed A-T and C-G complexes) has been studied. Changes in the main static properties (energy, structure, atomic charges) and dynamics (movement of hydrogen atoms from one base to the other) have been considered and analyzed. The results of this study support the idea that the quantitative effects of the methylation of these complexes depend on the specific system under consideration and on the H-bridge studied. In any case, some general behavior can be highlighted. In particular, the relationship between the transfer of hydrogen atoms between the bases (with the possible generation of mutation points) and the methylation can be schematized in the two most important methylated bases: adenine and cytosine. A different behavior has been found in these two cases, and we suggest that this could be related to the different amounts of these methylated systems in prokaryotes and eukaryotes. In particular, this different behavior could explain why adenine methylation is present mainly in the bacteria and cytosine methylation is present in more complex organisms. PMID:26051549

  9. The effect of a methyl-deficient diet on the global DNA methylation and the DNA methylation regulatory pathways.

    PubMed

    Takumi, Shota; Okamura, Kazuyuki; Yanagisawa, Hiroyuki; Sano, Tomoharu; Kobayashi, Yayoi; Nohara, Keiko

    2015-12-01

    Methyl-deficient diets are known to induce various liver disorders, in which DNA methylation changes are implicated. Recent studies have clarified the existence of the active DNA demethylation pathways that start with oxidization of 5-methylcytosine (5meC) to 5-hydroxymethylcytosine by ten-eleven translocation (Tet) enzymes, followed by the action of base-excision-repair pathways. Here, we investigated the effects of a methionine-choline-deficient (MCD) diet on the hepatic DNA methylation of mice by precisely quantifying 5meC using a liquid chromatography-electrospray ionization-mass spectrometry and by investigating the regulatory pathways, including DNA demethylation. Although feeding the MCD diet for 1 week induced hepatic steatosis and lower level of the methyl donor S-adenosylmethionine, it did not cause a significant reduction in the 5meC content. On the other hand, the MCD diet significantly upregulated the gene expression of the Tet enzymes, Tet2 and Tet3, and the base-excision-repair enzymes, thymine DNA glycosylase and apurinic/apyrimidinic-endonuclease 1. At the same time, the gene expression of DNA methyltransferase 1 and a, was also significantly increased by the MCD diet. These results suggest that the DNA methylation level is precisely regulated even when dietary methyl donors are restricted. Methyl-deficient diets are well known to induce oxidative stress and the oxidative-stress-induced DNA damage, 8-hydroxy-2'-deoxyguanosine (8OHdG), is reported to inhibit DNA methylation. In this study, we also clarified that the increase in 8OHdG number per DNA by the MCD diet is approximately 10 000 times smaller than the reduction in 5meC number, suggesting the contribution of 8OHdG formation to DNA methylation would not be significant. Copyright © 2015 John Wiley & Sons, Ltd. PMID:25690533

  10. Temporal augmentation with methyl methacrylate.

    PubMed

    Gordon, Chad R; Yaremchuk, Michael J

    2011-09-01

    Concavity in the temporal area reflects a deficiency in the bulk of the temporalis muscle or overlying temporal fat pad. It may be a reflection of senescence, low body fat, exaggerated adjacent skeletal or soft-tissue contours, idiopathic progressive atrophy, or postsurgical deformities. The authors describe the application of methyl methacrylate (MMA) to fill depressions in the temporal area. In instances in which no previous surgery has been performed or when the temporal area has served as a dissection plane for surgery in adjacent areas (eg, a subperiosteal facelift), the implant material is placed beneath the temporal muscle through a limited incision in the hair-bearing scalp. When previous reconstructive surgery has been performed in the temporal area, the area of depression is accessed through existing surgical incision scars to place MMA over the temporal muscle. These operative techniques have been reliable, durable, and relatively free of complications. PMID:21908815

  11. Formation of methyl formate after cosmic ion irradiation of icy grain mantles

    NASA Astrophysics Data System (ADS)

    Modica, P.; Palumbo, M. E.

    2010-09-01

    Context. Methyl formate (HCOOCH3) is a complex organic molecule detected in hot cores and hot corinos. Gas-phase chemistry fails to reproduce its observed abundance, which usually varies between 10-7 and 10-9 with respect to H2. Aims: Laboratory experiments were performed in order to investigate a solid-state route of methyl formate formation, to obtain an estimate of the amount that can be formed, and to verify whether it can account for the observed abundances. Methods: Several solid samples (16 K) of astrophysical interest were analyzed by infrared spectroscopy in the 4400-400 cm-1 range. The infrared spectral characteristics of frozen methyl formate were studied by deriving their band strength values. The effects produced upon warm-up of the samples were analyzed comparing the spectra taken at different temperatures. In order to study the formation and destruction mechanism of methyl formate in the interstellar ices, a binary mixture of methanol (CH3OH) and carbon monoxide (CO) ice and a sample of pure methanol were irradiated at 16 K with 200 keV protons. Methyl formate was identified through its fundamental mode (CH3 rocking) at about 1160 cm-1. Results: We present the mid-infrared methyl formate ice spectrum showing both the amorphous (16 K) and the crystalline (110 K) structure. We report novel measurements of the band strength values of the six main methyl formate bands. We prove the formation and the destruction of methyl formate after irradiation of CH3OH and a CO:CH3OH mixture. Extrapolating our results to the interstellar medium conditions we found that the production timescale of methyl formate agrees well with the evolutionary time of molecular clouds. The comparison with the observational data indicates that the amount of methyl formate formed after irradiation can account for the observed abundances. Conclusions: The present results allow us to suggest that gas phase methyl formate observed in dense molecular clouds is formed in the solid state after cosmic ion irradiation of icy grain mantles containing CO and CH3OH and released to the gas phase after desorption of icy mantles.

  12. Characterization of HPV DNA methylation of contiguous CpG sites by bisulfite treatment and massively parallel sequencing—the FRAGMENT approach

    PubMed Central

    Sun, Chang; McAndrew, Thomas; Smith, Benjamin C.; Chen, Zigui; Frimer, Marina; Burk, Robert D.

    2014-01-01

    Invasive cervix cancer (ICC) is the third most common malignant tumor in women and human papillomavirus 16 (HPV16) causes more than 50% of ICC. DNA methylation is a covalent modification predominantly occurring at CpG dinucleotides and increased methylation across the HPV16 genome is strongly associated with ICC development. Next generation (Next Gen) sequencing has been proposed as a novel approach to determine DNA methylation. However, utilization of this method to survey CpG methylation in the HPV16 genome is not well described. Moreover, it provides additional information on methylation “haplotypes.” In the current study, we chose 12 random samples, amplified multiple segments in the HPV16 bisulfite treated genome with specific barcodes, inspected the methylation ratio at 31 CpG sites for all samples using Illumina sequencing, and compared the results with quantitative pyrosequencing. Most of the CpG sites were highly consistent between the two approaches (overall correlation, r = 0.92), thus verifying that Next Gen sequencing is an accurate and convenient method to survey HPV16 methylation and thus can be used in clinical samples for risk assessment. Moreover, the CpG methylation patterns (methylation haplotypes) in single molecules identified an excess of complete-and non-methylated molecules and a substantial amount of partial-methylated ones, thus indicating a complex dynamic for the mechanisms of HPV16 CpG methylation. In summary, the advantages of Next Gen sequencing compared to pyrosequencing for HPV genome methylation analyses include higher throughput, increased resolution, and improved efficiency of time and resources. PMID:24917876

  13. Effects of sulforaphane and 3,3'-diindolylmethane on genome-wide promoter methylation in normal prostate epithelial cells and prostate cancer cells.

    PubMed

    Wong, Carmen P; Hsu, Anna; Buchanan, Alex; Palomera-Sanchez, Zoraya; Beaver, Laura M; Houseman, E Andres; Williams, David E; Dashwood, Roderick H; Ho, Emily

    2014-01-01

    Epigenetic changes, including aberrant DNA methylation, result in altered gene expression and play an important role in carcinogenesis. Phytochemicals such as sulforaphane (SFN) and 3,3'-diindolylmethane (DIM) are promising chemopreventive agents for the treatment of prostate cancer. Both have been shown to induce re-expression of genes, including tumor suppressor genes silenced in cancer cells, via modulation of epigenetic marks including DNA methylation. However, it remained unclear the effects SFN and DIM on DNA methylation at a genomic scale. The goal of this study was to determine the genome-wide effects of SFN and DIM on promoter methylation in normal prostate epithelial cells and prostate cancer cells. Both SFN and DIM treatment decreased DNA methyltransferase expression in normal prostate epithelial cells (PrEC), and androgen-dependent (LnCAP) and androgen-independent (PC3) prostate cancer cells. The effects of SFN and DIM on promoter methylation profiles in normal PrEC, LnCAP and PC3 prostate cancer cells were determined using methyl-DNA immunoprecipitation followed by genome-wide DNA methylation array. We showed widespread changes in promoter methylation patterns, including both increased and decreased methylation, in all three prostate cell lines in response to SFN or DIM treatments. In particular, SFN and DIM altered promoter methylation in distinct sets of genes in PrEC, LnCAP, and PC3 cells, but shared similar gene targets within a single cell line. We further showed that SFN and DIM reversed many of the cancer-associated methylation alterations, including aberrantly methylated genes that are dysregulated or are highly involved in cancer progression. Overall, our data suggested that both SFN and DIM are epigenetic modulators that have broad and complex effects on DNA methylation profiles in both normal and cancerous prostate epithelial cells. Results from our study may provide new insights into the epigenetic mechanisms by which SFN and DIM exert their cancer chemopreventive effects. PMID:24466240

  14. Integrated Genetic and Epigenetic Analysis Identifies Haplotype-Specific Methylation in the FTO Type 2 Diabetes and Obesity Susceptibility Locus

    PubMed Central

    Wilson, Gareth A.; Rakyan, Vardhman K.; Teschendorff, Andrew E.; Akan, Pelin; Stupka, Elia; Down, Thomas A.; Prokopenko, Inga; Morison, Ian M.; Mill, Jonathan; Pidsley, Ruth; Deloukas, Panos; Frayling, Timothy M.; Hattersley, Andrew T.; McCarthy, Mark I.; Beck, Stephan; Hitman, Graham A.

    2010-01-01

    Recent multi-dimensional approaches to the study of complex disease have revealed powerful insights into how genetic and epigenetic factors may underlie their aetiopathogenesis. We examined genotype-epigenotype interactions in the context of Type 2 Diabetes (T2D), focussing on known regions of genomic susceptibility. We assayed DNA methylation in 60 females, stratified according to disease susceptibility haplotype using previously identified association loci. CpG methylation was assessed using methylated DNA immunoprecipitation on a targeted array (MeDIP-chip) and absolute methylation values were estimated using a Bayesian algorithm (BATMAN). Absolute methylation levels were quantified across LD blocks, and we identified increased DNA methylation on the FTO obesity susceptibility haplotype, tagged by the rs8050136 risk allele A (p?=?9.40×10?4, permutation p?=?1.0×10?3). Further analysis across the 46 kb LD block using sliding windows localised the most significant difference to be within a 7.7 kb region (p?=?1.13×10?7). Sequence level analysis, followed by pyrosequencing validation, revealed that the methylation difference was driven by the co-ordinated phase of CpG-creating SNPs across the risk haplotype. This 7.7 kb region of haplotype-specific methylation (HSM), encapsulates a Highly Conserved Non-Coding Element (HCNE) that has previously been validated as a long-range enhancer, supported by the histone H3K4me1 enhancer signature. This study demonstrates that integration of Genome-Wide Association (GWA) SNP and epigenomic DNA methylation data can identify potential novel genotype-epigenotype interactions within disease-associated loci, thus providing a novel route to aid unravelling common complex diseases. PMID:21124985

  15. The DNA methylation landscape of human melanoma.

    PubMed

    Jin, Seung-Gi; Xiong, Wenying; Wu, Xiwei; Yang, Lu; Pfeifer, Gerd P

    2015-12-01

    Using MIRA-seq, we have characterized the DNA methylome of metastatic melanoma and normal melanocytes. Individual tumors contained several thousand hypermethylated regions. We discovered 179 tumor-specific methylation peaks present in all (27/27) melanomas that may be effective disease biomarkers, and 3113 methylation peaks were seen in >40% of the tumors. We found that 150 of the approximately 1200 tumor-associated methylation peaks near transcription start sites (TSSs) were marked by H3K27me3 in melanocytes. DNA methylation in melanoma was specific for distinct H3K27me3 peaks rather than for broadly covered regions. However, numerous H3K27me3 peak-associated TSS regions remained devoid of DNA methylation in tumors. There was no relationship between BRAF mutations and the number of methylation peaks. Gene expression analysis showed upregulated immune response genes in melanomas presumably as a result of lymphocyte infiltration. Down-regulated genes were enriched for melanocyte differentiation factors; e.g., KIT, PAX3 and SOX10 became methylated and downregulated in melanoma. PMID:26384656

  16. DNA methylation alterations exhibit intra-individual stability and inter-individual heterogeneity in prostate cancer metastases

    PubMed Central

    Aryee, Martin J; Liu, Wennuan; Engelmann, Julia C; Nuhn, Philipp; Gurel, Meltem; Haffner, Michael C; Esopi, David; Irizarry, Rafael A; Getzenberg, Robert H; Nelson, William G; Luo, Jun; Xu, Jianfeng; Isaacs, William B; Bova, G Steven; Yegnasubramanian, Srinivasan

    2013-01-01

    Human cancers nearly ubiquitously harbor epigenetic alterations. While such alterations in epigenetic marks, including DNA methylation, are potentially heritable, they can also be dynamically altered. Given this potential for plasticity, the degree to which epigenetic changes can be subject to selection and act as drivers of neoplasia has been questioned. Here, we carried out genome-scale analyses of DNA methylation alterations in lethal metastatic prostate cancer and created DNA methylation “cityscape” plots to visualize these complex data. We show that somatic DNA methylation alterations, despite showing marked inter-individual heterogeneity among men with lethal metastatic prostate cancer, were maintained across all metastases within the same individual. The overall extent of maintenance in DNA methylation changes was comparable to that of genetic copy number alterations. Regions that were frequently hypermethylated across individuals were markedly enriched for cancer and development/differentiation related genes. Additionally, regions exhibiting high consistency of hypermethylation across metastases within individuals, even if variably hypermethylated across individuals, showed enrichment of cancer-related genes. Interestingly, whereas some regions showed intra-individual metastatic tumor heterogeneity in promoter methylation, such methylation alterations were generally not correlated with gene expression. This was despite a general tendency for promoter methylation patterns to be strongly correlated with gene expression, particularly at regions that were variably methylated across individuals. These findings suggest that DNA methylation alterations have the potential for producing selectable driver events in carcinogenesis and disease progression and highlight the possibility of targeting such epigenome alterations for development of longitudinal markers and therapeutic strategies. PMID:23345608

  17. A genetic sensor for strong methylating compounds

    PubMed Central

    Moser, Felix; Horwitz, Andrew; Chen, Jacinto; Lim, Wendell A.; Voigt, Christopher A.

    2013-01-01

    Methylating chemicals are common in industry and agriculture and are often toxic, partly due to their propensity to methylate DNA. The Escherichia coli Ada protein detects methylating compounds by sensing aberrant methyl adducts on the phosphoester backbone of DNA. We characterize this system as a genetic sensor and engineer it to lower the detection threshold. By overexpressing Ada from a plasmid, we improve the sensor’s dynamic range to 350-fold induction and lower its detection threshold to 40 µM for methyl iodide. In eukaryotes, there is no known sensor of methyl adducts on the phosphoester backbone of DNA. By fusing the N-terminal domain of Ada to the Gal4 transcriptional activation domain, we built a functional sensor for methyl phosphotriester adducts in Saccharomyces cerevisiae. This sensor can be tuned to variable specifications by altering the expression level of the chimeric sensor and changing the number of Ada operators upstream of the Gal4-sensitive reporter promoter. These changes result in a detection threshold of 28 µM and 5.2-fold induction in response to methyl iodide. When the yeast sensor is exposed to different SN1 and SN2 alkylating compounds, its response profile is similar to that observed for the native Ada protein in E. coli, indicating that its native function is retained in yeast. Finally, we demonstrate that the specifications achieved for the yeast sensor are suitable for detecting methylating compounds at relevant concentrations in environmental samples. This work demonstrates the movement of a sensor from a prokaryotic to eukaryotic system and its rational tuning to achieve desired specifications. PMID:24032656

  18. Dietary and lifestyle factors of DNA methylation.

    PubMed

    Lim, Unhee; Song, Min-Ae

    2012-01-01

    Lifestyle factors, such as diet, smoking, physical activity, and body weight management, are known to constitute the majority of cancer causes. Epigenetics has been widely proposed as a main mechanism that mediates the reversible effects of dietary and lifestyle factors on carcinogenesis. This chapter reviews human studies on potential dietary and lifestyle determinants of DNA methylation. Apart from a few prospective investigations and interventions of limited size and duration, evidence mostly comes from cross-sectional observational studies and supports some associations. Studies to date suggest that certain dietary components may alter genomic and gene-specific DNA methylation levels in systemic and target tissues, affecting genomic stability and transcription of tumor suppressors and oncogenes. Most data and supportive evidence exist for folate, a key nutritional factor in one-carbon metabolism that supplies the methyl units for DNA methylation. Other candidate bioactive food components include alcohol and other key nutritional factors of one-carbon metabolism, polyphenols and flavonoids in green tea, phytoestrogen, and lycopene. Some data also support a link of DNA methylation with physical activity and energy balance. Effects of dietary and lifestyle exposures on DNA methylation may be additionally modified by common genetic variants, environmental carcinogens, and infectious agents, an aspect that remains largely unexplored. In addition, growing literature supports that the environmental conditions during critical developmental stages may influence later risk of metabolic disorders in part through persistent programming of DNA methylation. Further research of these modifiable determinants of DNA methylation will improve our understanding of cancer etiology and may present certain DNA methylation markers as attractive surrogate endpoints for prevention research. Considering the plasticity of epigenetic marks and correlated nature of lifestyle factors, more longitudinal studies of healthy individuals of varying age, sex, and ethnic groups are warranted, ideally with comprehensive data collection on various lifestyle factors. PMID:22359306

  19. Infrared spectra and chemical abundance of methyl propionate in icy astrochemical conditions

    NASA Astrophysics Data System (ADS)

    Sivaraman, B.; Radhika, N.; Das, A.; Gopakumar, G.; Majumdar, L.; Chakrabarti, S. K.; Subramanian, K. P.; Raja Sekhar, B. N.; Hada, M.

    2015-04-01

    We carried out an experiment in order to obtain the infrared (IR) spectra of methyl propionate (CH3CH2COOCH3) in astrochemical conditions and present the IR spectra for future identification of this molecule in the interstellar medium (ISM). The experimental IR spectrum is compared with the theoretical spectrum, and an attempt was made to assign the observed peak positions to their corresponding molecular vibrations in condensed phase. Moreover, our calculations suggest that methyl propionate must be synthesized efficiently within the complex chemical network of the ISM and therefore be present in cold dust grains, awaiting identification.

  20. Sunflower oil methyl ester as diesel fuel

    SciTech Connect

    Hassett, D.J.; Hasan, R.A.

    1982-01-01

    Methyl ester formation represents one approach to overcome the problems associated with the relatively high viscosity of sunflower oil when used as a diesel fuel replacement. Sunflower oil methyl ester is being prepared at the University of North Dakota Engieering Experiment Station. Physical and chemical properties of this material at varying levels of refinement and purity will be used to define fuel properties. Engine testing is being carried out to determine if the fouling characteristics of methyl ester are significantly less than those of sunflower oil. 1 figure, 1 table.

  1. Methyl-CpG island-associated genome signature tags

    DOEpatents

    Dunn, John J

    2014-05-20

    Disclosed is a method for analyzing the organismic complexity of a sample through analysis of the nucleic acid in the sample. In the disclosed method, through a series of steps, including digestion with a type II restriction enzyme, ligation of capture adapters and linkers and digestion with a type IIS restriction enzyme, genome signature tags are produced. The sequences of a statistically significant number of the signature tags are determined and the sequences are used to identify and quantify the organisms in the sample. Various embodiments of the invention described herein include methods for using single point genome signature tags to analyze the related families present in a sample, methods for analyzing sequences associated with hyper- and hypo-methylated CpG islands, methods for visualizing organismic complexity change in a sampling location over time and methods for generating the genome signature tag profile of a sample of fragmented DNA.

  2. Conformations and Barriers to Methyl Group Internal Rotation in Two Asymmetric Ethers: Propyl Methyl Ether and Butyl Methyl Ether

    NASA Astrophysics Data System (ADS)

    Long, B. E.; Dechirico, F.; Cooke, S. A.

    2012-06-01

    The conformational preferences of the O-C-C-C unit are important in many biological systems with the unit generally preferring a gauche configuration compared to an anti configuration. Butyl methyl ether and propyl methyl ether provide very simple systems for this phenomenom to manifest. Pure rotational spectra of the title molecules have been recorded using chirped pulse Fourier transform microwave spectroscopy (CP-FTMW). In the case of butyl methyl ether, only one conformer has been observed. This conformer has torsional angles of COCC = 180°, OCCC = 62° and CCCC = 180° (anti-gauche-anti) and rotational constants of A = 10259.4591(33) MHz, B = 1445.6470(13) MHz, and C = 1356.2944(14) MHz. The rotational spectrum was doubled and has been analyzed to produce an effective barrier to methyl group internal rotation of 780(35) cm-1. A prior rotational spectroscopic study on propyl methyl ether had focused only on the high energy anti-anti conformer. We have analyzed spectra from the lowest energy anti-gauche conformer and the spectroscopic constants will be presented. A summary of the differences in conformational energies and methyl group internal rotation barriers for the class of aliphatic asymmetric ethers will be presented. K. N. Houk, J. E. Eksterowicz, Y.-D. Wu, C. D. Fuglesang, D. B. Mitchell. J. Am. Chem. Soc. 115 (4170), 1993. Hiroshi Kato, Jun Nakagawa, Michiro Hayashi. J. Mol. Spectrosc. 80 (272), 1980.

  3. 21 CFR 173.385 - Sodium methyl sulfate.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Sodium methyl sulfate. 173.385 Section 173.385 Food... Specific Usage Additives § 173.385 Sodium methyl sulfate. Sodium methyl sulfate may be present in pectin in... sulfuric acid and methyl alcohol and subsequent treatment with sodium bicarbonate. (b) It does not exceed...

  4. 21 CFR 173.385 - Sodium methyl sulfate.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Sodium methyl sulfate. 173.385 Section 173.385... CONSUMPTION Specific Usage Additives § 173.385 Sodium methyl sulfate. Sodium methyl sulfate may be present in... pectin by sulfuric acid and methyl alcohol and subsequent treatment with sodium bicarbonate. (b) It...

  5. 21 CFR 172.872 - Methyl ethyl cellulose.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Methyl ethyl cellulose. 172.872 Section 172.872... CONSUMPTION Multipurpose Additives § 172.872 Methyl ethyl cellulose. The food additive methyl ethyl cellulose... of methyl groups and y is the number of ethyl groups. The average value of x is 0.3 and the...

  6. 21 CFR 173.250 - Methyl alcohol residues.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Methyl alcohol residues. 173.250 Section 173.250... and Related Substances § 173.250 Methyl alcohol residues. Methyl alcohol may be present in the... specifies the presence of methyl alcohol and provides for the use of the hops extract only as prescribed...

  7. 21 CFR 173.385 - Sodium methyl sulfate.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... pectin by sulfuric acid and methyl alcohol and subsequent treatment with sodium bicarbonate. (b) It does... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Sodium methyl sulfate. 173.385 Section 173.385... CONSUMPTION Specific Usage Additives § 173.385 Sodium methyl sulfate. Sodium methyl sulfate may be present...

  8. 21 CFR 173.385 - Sodium methyl sulfate.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... pectin by sulfuric acid and methyl alcohol and subsequent treatment with sodium bicarbonate. (b) It does... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Sodium methyl sulfate. 173.385 Section 173.385... CONSUMPTION Specific Usage Additives § 173.385 Sodium methyl sulfate. Sodium methyl sulfate may be present...

  9. Brain G protein gamma subunits contain an all-trans-geranylgeranylcysteine methyl ester at their carboxyl termini

    SciTech Connect

    Yamane, H.K.; Farnsworth, C.C.; Xie, H.Y.; Howald, W.; Fung, B.K.; Clarke, S.; Gelb, M.H.; Glomset, J.A. )

    1990-08-01

    We have shown previously that guanine nucleotide-binding protein (G protein) beta gamma complexes purified from bovine brain membranes are methyl esterified on a C-terminal cysteine residue of the gamma polypeptide. In the present study, 3H-methylated G beta gamma complexes cleaved to their constituent amino acids by exhaustive proteolysis were shown to contain radiolabeled material that coeluted with geranylgeranylcysteine methyl ester on reversed-phase HPLC and two TLC systems. Further treatment by performic acid oxidation yielded radiolabeled material that coeluted with L-cysteic acid methyl ester, verifying that the prenyl modification occurs on a C-terminal cysteine residue. Analysis by gas chromatography-coupled mass spectrometry of material released from purified G beta gamma by treatment with Raney nickel positively identified the covalently bound lipid as an all-trans-geranylgeranyl (C20) isoprenoid moiety. To delineate the distribution of this modification among gamma subunits, purified G beta gamma complexes were separated into 5-kDa (gamma 5) and 6-kDa (gamma 6) forms of the gamma polypeptide by reversed-phase HPLC. Gas chromatography-coupled mass spectrometry analyses of Raney nickel-treated purified gamma 5 and gamma 6 subunits showed that both polypeptides were modified by geranylgeranylation. These results demonstrate that at least two forms of brain gamma subunit are posttranslationally modified by geranylgeranylation and carboxyl methylation. These modifications may be important for targeting G beta gamma complexes to membranes.

  10. Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers

    PubMed Central

    2012-01-01

    Background Accurate outcome prediction in neuroblastoma, which is necessary to enable the optimal choice of risk-related therapy, remains a challenge. To improve neuroblastoma patient stratification, this study aimed to identify prognostic tumor DNA methylation biomarkers. Results To identify genes silenced by promoter methylation, we first applied two independent genome-wide methylation screening methodologies to eight neuroblastoma cell lines. Specifically, we used re-expression profiling upon 5-aza-2'-deoxycytidine (DAC) treatment and massively parallel sequencing after capturing with a methyl-CpG-binding domain (MBD-seq). Putative methylation markers were selected from DAC-upregulated genes through a literature search and an upfront methylation-specific PCR on 20 primary neuroblastoma tumors, as well as through MBD- seq in combination with publicly available neuroblastoma tumor gene expression data. This yielded 43 candidate biomarkers that were subsequently tested by high-throughput methylation-specific PCR on an independent cohort of 89 primary neuroblastoma tumors that had been selected for risk classification and survival. Based on this analysis, methylation of KRT19, FAS, PRPH, CNR1, QPCT, HIST1H3C, ACSS3 and GRB10 was found to be associated with at least one of the classical risk factors, namely age, stage or MYCN status. Importantly, HIST1H3C and GNAS methylation was associated with overall and/or event-free survival. Conclusions This study combines two genome-wide methylation discovery methodologies and is the most extensive validation study in neuroblastoma performed thus far. We identified several novel prognostic DNA methylation markers and provide a basis for the development of a DNA methylation-based prognostic classifier in neuroblastoma. PMID:23034519

  11. Intramolecular, photoinduced electron transfer in ruthenium(II) bipyridine-quinone complexes

    SciTech Connect

    Opperman, K.A.; Mecklenburg, S.L.; Meyer, T.J.

    1994-11-09

    Adsorption spectroscopy and transient emission spectroscopy were used to follow intramolecular electron transfer quenching after metal-to-ligand charge transfer (MLCT) excitation of Ru(II)bipyridine-quinone complexes. Studies of various N-((4{prime}methyl-2-2{prime}-bipyridyl)-4-methyl)-9,10-anthraquinone-2-carboxamide (bpy-AQ) complexes, revealed that these complexes quench by rapid electron transfer from ligand radical excited states to the metal center. A donor-chromophore-acceptor complex with the bpy-AQ ligand and the (10-[4({prime}-methyl-2,2{prime}-bipyridin-4-yl)methylphenothiazine)] (bpy-PTZ) ligand displays redox separation on excitation.

  12. Emission of methyl bromide from biomass burning

    SciTech Connect

    Manoe, S.; Andreae, M.O. )

    1994-03-04

    Bromine is, per atom, far more efficient than chlorine in destroying stratospheric ozone, and methyl bromide is the single largest source of stratospheric bromine. The two main previously known sources of this compound are emissions from the ocean and from the compound's use as an agricultural pesticide. Laboratory biomass combustion experiments showed that methyl bromide was emitted in the smoke from various fuels tested. Methyl bromide was also found in smoke plumes from wildfires in savannas, chaparral, and boreal forest. Global emissions of methyl bromide from biomass burning are estimated to be in the range of 10 to 50 gigagrams per year, which is comparable to the amount produced by ocean emission and pesticide use and represents a major contribution ([approximately]30 percent) to the stratospheric bromine budget.

  13. Incorporating DNA Methylation Dynamics Into Epigenetic Codes

    PubMed Central

    Szulwach, Keith E.; Jin, Peng

    2014-01-01

    Summary Genomic function is dictated by a combination of DNA sequence and the molecular mechanisms controlling access to genetic information. Access to DNA can be determined by the interpretation of covalent modifications that influence the packaging of DNA into chromatin, including DNA methylation and histone modifications. These modifications are believed to be forms of “epigenetic codes” that exist in discernable combinations that reflect cellular phenotype. Although DNA methylation is known to play important roles in gene regulation and genomic function, its contribution to the encoding of epigenetic information is just beginning to emerge. Here we discuss paradigms associated with the various components of DNA methylation/demethylation and recent advances in the understanding of its dynamic regulation in the genome, integrating these mechanisms into a framework to explain how DNA methylation could contribute to epigenetic codes. PMID:24242211

  14. Degradation of methyl bromide in anaerobic sediments

    USGS Publications Warehouse

    Oremland, R.S.; Miller, L.G.; Strohmaler, F.E.

    1994-01-01

    Methyl bromide (MeBr) was anaerobically degraded in saltmarsh sediments after reaction with sulfide. The product of this nucleophilic substitution reaction was methanethiol, which underwent further chemical and bacterial reactions to form dimethyl sulfide. These two gases appeared transiently during sediment incubations because they were metabolized by methanogenic and sulfate-reducing bacteria. A second, less significant reaction of MeBr was the exchange with chloride, forming methyl chloride, which was also susceptible to attack by sulfide. Incubation of 14C-labeled methyl iodide as an analogue of MeBr resulted in the formation of 14CH4 and 14CO2 and also indicated that sulfate-reducing bacteria as well as methanogens metabolized the methylated sulfur intermediates. These results suggest that exposed sediments with abundant free sulfide, such as coastal salt-marshes, may constitute a sink for atmospheric MeBr.

  15. DNA methylation of developmental genes in pediatric medulloblastomas identified by denaturation analysis of methylation differences.

    PubMed

    Diede, Scott J; Guenthoer, Jamie; Geng, Linda N; Mahoney, Sarah E; Marotta, Michael; Olson, James M; Tanaka, Hisashi; Tapscott, Stephen J

    2010-01-01

    DNA methylation might have a significant role in preventing normal differentiation in pediatric cancers. We used a genomewide method for detecting regions of CpG methylation on the basis of the increased melting temperature of methylated DNA, termed denaturation analysis of methylation differences (DAMD). Using the DAMD assay, we find common regions of cancer-specific methylation changes in primary medulloblastomas in critical developmental regulatory pathways, including Sonic hedgehog (Shh), Wingless (Wnt), retinoic acid receptor (RAR), and bone morphogenetic protein (BMP). One of the commonly methylated loci is the PTCH1-1C promoter, a negative regulator of the Shh pathway that is methylated in both primary patient samples and human medulloblastoma cell lines. Treatment with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5-aza-dC) increases the expression of PTCH1 and other methylated loci. Whereas genetic mutations in PTCH1 have previously been shown to lead to medulloblastoma, our study indicates that epigenetic silencing of PTCH1, and other critical developmental loci, by DNA methylation is a fundamental process of pediatric medulloblastoma formation. This finding warrants strong consideration for DNA demethylating agents in future clinical trials for children with this disease. PMID:19966297

  16. Hidden among the crowd: differential DNA methylation-expression correlations in cancer occur at important oncogenic pathways

    PubMed Central

    Mosquera Orgueira, Adrián

    2015-01-01

    DNA methylation is a frequent epigenetic mechanism that participates in transcriptional repression. Variations in DNA methylation with respect to gene expression are constant, and, for unknown reasons, some genes with highly methylated promoters are sometimes overexpressed. In this study we have analyzed the expression and methylation patterns of thousands of genes in five groups of cancer and normal tissue samples in order to determine local and genome-wide differences. We observed significant changes in global methylation-expression correlation in all the neoplasms, which suggests that differential correlation events are frequent in cancer. A focused analysis in the breast cancer cohort identified 1662 genes whose correlation varies significantly between normal and cancerous breast, but whose DNA methylation and gene expression patterns do not change substantially. These genes were enriched in cancer-related pathways and repressive chromatin features across various model cell lines, such as PRC2 binding and H3K27me3 marks. Substantial changes in methylation-expression correlation indicate that these genes are subject to epigenetic remodeling, where the differential activity of other factors break the expected relationship between both variables. Our findings suggest a complex regulatory landscape where a redistribution of local and large-scale chromatin repressive domains at differentially correlated genes (DCGs) creates epigenetic hotspots that modulate cancer-specific gene expression. PMID:26029238

  17. Formation of methyl formate in comets by irradiation of methanol-bearing ices

    NASA Astrophysics Data System (ADS)

    Modica, P.; Palumbo, M. E.; Strazzulla, G.

    2012-12-01

    Methyl formate is a complex organic molecule considered potentially relevant as precursor of biologically active molecules. It has been observed in several astrophysical environments, such as hot cores, hot corinos, and comets. The processes that drive the formation of molecules in cometary ices are poorly understood. In particular it is not yet clear if molecules are directly accreted from the pre-solar nebula to form comets or are formed after accretion. The present work analyzes the possible role of cosmic ion irradiation and radioactive decay in methyl formate formation in methanol-bearing ices. The results indicate that cosmic ion irradiation can account for about 12% of the methyl formate observed in comet Hale-Bopp, while radioactive decay can account for about 6% of this amount. The need of new data coming from earth based and space observational projects as well as from laboratory experiments is outlined.

  18. A Prototypic Lysine Methyltransferase 4 from Archaea with Degenerate Sequence Specificity Methylates Chromatin Proteins Sul7d and Cren7 in Different Patterns*

    PubMed Central

    Niu, Yanling; Xia, Yisui; Wang, Sishuo; Li, Jiani; Niu, Caoyuan; Li, Xiao; Zhao, Yuehui; Xiong, Huiyang; Li, Zhen; Lou, Huiqiang; Cao, Qinhong

    2013-01-01

    Histone methylation is one of the major epigenetic modifications even in early diverging unicellular eukaryotes. We show that a widespread lysine methyltransferase from Archaea (aKMT4), bears striking structural and functional resemblance to the core of distantly related eukaryotic KMT4/Dot1. aKMT4 methylates a set of various proteins, including the chromatin proteins Sul7d and Cren7, and RNA exosome components. Csl4- and Rrp4-exosome complexes are methylated in different patterns. aKMT4 can self-methylate intramolecularly and compete with other proteins for the methyl group. Automethylation is inhibited by suitable substrates or DNA in a concentration-dependent manner. The automethylated enzyme shows relatively compromised activity. aKMT4-8A mutant with abrogated automethylation shows a more than 150% increase in methylation of substrates, suggesting a possible mechanism to regulate methyltransferase activity. More interestingly, methylation of Sul7d, but not Cren7, by aKMT4 is significantly enhanced by DNA. MS/MS and kinetic analysis further suggest that aKMT4 methylates Sul7d in the chromatin context. These data provide a clue to the possible regulation of aKMT4 activity by the local chromatin environment, albeit as a promiscuous enzyme required for extensive and variegated lysine methylation in Sulfolobus. This study supports the prokaryotic origin model of eukaryotic histone modification enzymes and sheds light on regulation of archaeal chromatin. PMID:23530048

  19. REVERSIBLE METAL-TO-METAL METHYL TRANSFER IN n5-CYCLOPENTADIENYL(TRIPHENYLPHOSPHINE)DIMETHYLCOBALT(III)

    SciTech Connect

    Bryndza, Henry E.; Evitt, Eric R.; Bergman, Robert G.

    1980-05-01

    Labeling techniques have been used to demonstrate that {eta}{sup 5} cyclopentadienyl(triphenylphosphine)dimethylcobalt(III) (1) undergoes intermolecular cobalt-to-cobalt methyl group exchange. The reaction follows second order kinetics; rate constants for methyl exchange between complexes 1 and its methylcyclopentadienyl analog 4 show decreasing magnitude with increasing bulk of cyclopentadienyl substituents. Studies of the reaction with excess triphenylphosphine and complexes labeled with the non-dissociating trimethylphosphine ligand indicate the reaction requires dissociation of phosphine from one of the two partners in the exchange before scrambling can take place. Further studies with other complexes (e.g., Cp{sub 2}Zr(CH{sub 3}){sub 2}) suggest that alkyl exchange between two transition metal centers may be a more general reaction than has heretofore been suspected.

  20. Efficient acquisition of high-resolution 4-D diagonal-suppressed methyl-methyl NOESY for large proteins

    NASA Astrophysics Data System (ADS)

    Wen, Jie; Zhou, Pei; Wu, Jihui

    2012-05-01

    The methyl-methyl NOESY experiment plays an important role in determining the global folds of large proteins. Despite the high sensitivity of this experiment, the analysis of methyl-methyl NOEs is frequently hindered by the limited chemical shift dispersion of methyl groups, particularly methyl protons. This makes it difficult to unambiguously assign all of the methyl-methyl NOE crosspeaks using 3-D spectroscopy. The recent development of sparse sampling methods enables highly efficient acquisition of high-resolution 4-D spectra, which provides an excellent solution to resolving the degeneracy of methyl signals. However, many reconstruction algorithms for processing sparsely-sampled NMR data do not provide adequate suppression of aliasing artifacts in the presence of strong NOE diagonal signals. In order to overcome this limitation, we present a 4-D diagonal-suppressed methyl-methyl NOESY experiment specifically optimized for ultrasparse sampling and evaluate it using a deuterated, ILV methyl-protonated sample of the 42 kDa Escherichia coli maltose binding protein (MBP). Suppression of diagonal signals removes the dynamic range barrier of the methyl-methyl NOESY experiment such that residual aliasing artifacts in the CLEAN-reconstructed high-resolution 4-D spectrum can be further reduced. At an ultrasparse sampling rate of less than 1%, we were able to identify and unambiguously assign the vast majority of expected NOE crosspeaks between methyl groups separated by less than 5 Å and to detect very weak NOE crosspeaks from methyl groups that are over 7 Å apart.

  1. 40 CFR 721.10326 - 2-Propenoic acid, 2-methyl-, methyl ester, polymer with butyl 2-propenoate, ethyl 2-propenoate...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... ester, polymer with butyl 2-propenoate, ethyl 2-propenoate, zinc 2-methyl-2-propenoate (1:2) and zinc 2... 2-Propenoic acid, 2-methyl-, methyl ester, polymer with butyl 2-propenoate, ethyl 2-propenoate, zinc 2-methyl-2-propenoate (1:2) and zinc 2-propenoate (1:2), 2,2'-(1,2-diazenediyl)bis - and...

  2. Notes on the role of dynamic DNA methylation in mammalian development

    PubMed Central

    Bestor, Timothy H.; Edwards, John R.; Boulard, Mathieu

    2015-01-01

    It has been nearly 40 y since it was suggested that genomic methylation patterns could be transmitted via maintenance methylation during S phase and might play a role in the dynamic regulation of gene expression during development [Holliday R, Pugh JE (1975) Science 187(4173):226–232; Riggs AD (1975) Cytogenet Cell Genet 14(1):9–25]. This revolutionary proposal was justified by “... our almost complete ignorance of the mechanism for the unfolding of the genetic program during development” that prevailed at the time. Many correlations between transcriptional activation and demethylation have since been reported, but causation has not been demonstrated and to date there is no reasonable proof of the existence of a complex biochemical system that activates and represses genes via reversible DNA methylation. Such a system would supplement or replace the conserved web of transcription factors that regulate cellular differentiation in organisms that have unmethylated genomes (such as Caenorhaditis elegans and the Dipteran insects) and those that methylate their genomes. DNA methylation does have essential roles in irreversible promoter silencing, as in the monoallelic expression of imprinted genes, in the silencing of transposons, and in X chromosome inactivation in female mammals. Rather than reinforcing or replacing regulatory pathways that are conserved between organisms that have either methylated or unmethylated genomes, DNA methylation endows genomes with the ability to subject specific sequences to irreversible transcriptional silencing even in the presence of all of the factors required for their expression, an ability that is generally unavailable to organisms that have unmethylated genomes. PMID:25368180

  3. DNA methylation analysis of murine hematopoietic side population cells during aging

    PubMed Central

    Taiwo, Oluwatosin; Wilson, Gareth A; Emmett, Warren; Morris, Tiffany; Bonnet, Dominique; Schuster, Eugene; Adejumo, Tomas; Beck, Stephan; Pearce, Daniel J

    2013-01-01

    Stem cells have been found in most tissues/organs. These somatic stem cells produce replacements for lost and damaged cells, and it is not completely understood how this regenerative capacity becomes diminished during aging. To study the possible involvement of epigenetic changes in somatic stem cell aging, we used murine hematopoiesis as a model system. Hematopoietic stem cells (HSCs) were enriched for via Hoechst exclusion activity (SP-HSC) from young, medium-aged and old mice and subjected to comprehensive, global methylome (MeDIP-seq) analysis. With age, we observed a global loss of DNA methylation of approximately 5%, but an increase in methylation at some CpG islands. Just over 100 significant (FDR < 0.2) aging-specific differentially methylated regions (aDMRs) were identified, which are surprisingly few considering the profound age-based changes that occur in HSC biology. Interestingly, the polycomb repressive complex -2 (PCRC2) target genes Kiss1r, Nav2 and Hsf4 were hypermethylated with age. The promoter for the Sdpr gene was determined to be progressively hypomethylated with age. This occurred concurrently with an increase in gene expression with age. To explore this relationship further, we cultured isolated SP-HSC in the presence of 5-aza-deoxycytdine and demonstrated a negative correlation between Sdpr promoter methylation and gene expression. We report that DNA methylation patterns are well preserved during hematopoietic stem cell aging, confirm that PCRC2 targets are increasingly methylated with age, and suggest that SDPR expression changes with age in HSCs may be regulated via age-based alterations in DNA methylation. PMID:23949429

  4. DNA methylation analysis of murine hematopoietic side population cells during aging.

    PubMed

    Taiwo, Oluwatosin; Wilson, Gareth A; Emmett, Warren; Morris, Tiffany; Bonnet, Dominique; Schuster, Eugene; Adejumo, Tomas; Beck, Stephan; Pearce, Daniel J

    2013-10-01

    Stem cells have been found in most tissues/organs. These somatic stem cells produce replacements for lost and damaged cells, and it is not completely understood how this regenerative capacity becomes diminished during aging. To study the possible involvement of epigenetic changes in somatic stem cell aging, we used murine hematopoiesis as a model system. Hematopoietic stem cells (HSCs) were enriched for via Hoechst exclusion activity (SP-HSC) from young, medium-aged and old mice and subjected to comprehensive, global methylome (MeDIP-seq) analysis. With age, we observed a global loss of DNA methylation of approximately 5%, but an increase in methylation at some CpG islands. Just over 100 significant (FDR<0.2) aging-specific differentially methylated regions (aDMRs) were identified, which are surprisingly few considering the profound age-based changes that occur in HSC biology. Interestingly, the polycomb repressive complex -2 (PCRC2) target genes Kiss1r, Nav2 and Hsf4 were hypermethylated with age. The promoter for the Sdpr gene was determined to be progressively hypomethylated with age. This occurred concurrently with an increase in gene expression with age. To explore this relationship further, we cultured isolated SP-HSC in the presence of 5-aza-deoxycytdine and demonstrated a negative correlation between Sdpr promoter methylation and gene expression. We report that DNA methylation patterns are well preserved during hematopoietic stem cell aging, confirm that PCRC2 targets are increasingly methylated with age, and suggest that SDPR expression changes with age in HSCs may be regulated via age-based alterations in DNA methylation. PMID:23949429

  5. Solubility improvement of drugs using N-methyl pyrrolidone.

    PubMed

    Sanghvi, Ritesh; Narazaki, Ryuichi; Machatha, Stephen G; Yalkowsky, Samuel H

    2008-01-01

    The solubilization efficiency of N-methyl pyrrolidone (NMP) has been determined and compared to that of ethanol and propylene glycol for 13 poorly soluble drugs. NMP is found to be a more efficient solubilizer for all the drugs studied. The solubility enhancement as high as about 800-fold is obtained in 20% v/v NMP solution as compared to water. The mechanism of drug solubilization by NMP has also been investigated. It is proposed that NMP enhances drug solubility by simultaneously acting as a cosolvent and a complexing agent. A mathematical model is used to estimate the drug solubility in NMP-water mixture, according to which the total solubility enhancement is a sum of the two effects. This model describes the experimental data well and is more accurate than other models. A large and uniform reduction in the surface tension of water as a function of NMP concentration demonstrates its cosolvent effect. The complexation is supported by the fact that it's strength is affected by the temperature and the polarity of the medium. A strong correlation exists between log K (ow) of the drugs and the cosolvency coefficients. The correlation between log K (ow) and the complexation coefficients is weak suggesting that factors such as molecular shape and aromaticity of the drug molecule are significant in determining the complexation strength. This has been confirmed by the absence of a significant complexation between NMP and linear drug-like solutes. PMID:18431671

  6. PTEN methylation and expression in glioblastomas.

    PubMed

    Baeza, Nathalie; Weller, Michael; Yonekawa, Yasuhiro; Kleihues, Paul; Ohgaki, Hiroko

    2003-11-01

    The tumor suppressor gene PTEN on chromosome 10q23.3 regulates the Akt signaling pathway and modulates cell growth and apoptosis. The PTEN gene is mutated in 20-40% of glioblastomas. In this study, we assessed whether loss of PTEN expression is also caused epigenetically. Methylation-specific PCR revealed that CpG islands of the PTEN promoter were methylated in 27 of 77 (35%) glioblastomas and in 4 of 11 (36%) glioblastoma cell lines. Only two glioblastomas showed loss of PTEN immunoreactivity in the entire biopsy; both had a missense PTEN mutation and LOH at the PTEN locus, but lacked PTEN methylation. In biopsy specimens with focal loss of PTEN expression, DNA samples extracted from microdissected foci showed PTEN methylation only in areas with loss of PTEN expression. These results suggest that PTEN methylation occurs frequently in glioblastomas and may be associated with focal loss of PTEN expression. However, the correlation between PTEN methylation, PTEN mutations, LOH at the PTEN locus, and loss of PTEN protein expression was inconsistent. Possible reasons for discrepancies between gene status and protein expression include differences in the biological effect of specific PTEN mutations and the possibility that the processed PTEN pseudogene on 9p21 is expressed in glioblastomas and co-reacts with the PTEN antibody. PMID:12904991

  7. DNA methylation and application in forensic sciences.

    PubMed

    Kader, Farzeen; Ghai, Meenu

    2015-04-01

    DNA methylation of cytosine residues is a stable epigenetic alteration, beginning as early as foetal development in the uterus and continuously evolving throughout life. DNA methylation as well as other epigenetic modifications such as chromatin remodelling and histone modifications are indispensable in mammalian development. Methylation is to a large extent influenced by the ageing process, diets and lifestyle choices. Our understanding of this crucial modification may even contribute to the treatment and prevention of age-related illnesses in the very near future. Genome-wide methylation analysis using high throughput DNA technologies has discovered numerous differentially methylated regions (tDMRs) which differ in levels of methylation in various cell types and tissues. TDMRs have been useful in various applications, particularly medicine and forensic sciences. Forensic scientists are constantly seeking exciting and novel methods to aid in the reconstruction of crime scenes, and the analysis of tDMRs represents a new and reliable technique to identify biological fluids and tissues found at the scene of a violent act. Not only has research been able to unequivocally identify various fluids and tissues, but methods to determine the sex, age and phenotype of donors has been developed. New tDMRs in genes are being searched for consistently to serve as novel markers in forensic DNA analysis. PMID:25732744

  8. Non-reversible solvatochromism in N-methyl-2-pyrrolidone/toluene mixed solutions of fullerene C60

    NASA Astrophysics Data System (ADS)

    Kyzyma, O. A.; Kyrey, T. ?.; Avdeev, M. V.; Korobov, M. V.; Bulavin, L. A.; Aksenov, V. L.

    2013-01-01

    Non-reversible changes in the UV-Vis spectra (solvatochromism) of C60 fullerene in the binary solvent N-methyl-2-pyrrolidone/toluene are observed when varying the mixture composition. The solvatochromism strongly depends on the order of the mixture preparation. We attribute the effect to a great difference in the polarity of the liquid components, which determines different solvent-solute interaction with respect to the formation of charge-transfer complexes and, thus, provides conditions for selective solvation. The effect is also dependent on the temporal changes in the complexes C60-N-methyl-2-pyrrolidone and C60 cluster formation.

  9. 13C-METHYL Formate in Orion-Kl Alma Observations and Spectroscopic Characterization

    NASA Astrophysics Data System (ADS)

    Favre, Cécile; Carvajal, Miguel; Field, David; Bergin, Edwin; Neill, Justin; Crockett, Nathan; Jørgensen, Jes; Bisschop, Suzanne; Brouillet, Nathalie; Despois, Didier; Baudry, Alain; Kleiner, Isabelle; Margulès, L.; Huet, T. R.; Demaison, Jean

    2014-06-01

    Determination of elemental isotopic ratios is valuable for understanding the chemical evolution of interstellar material. Until now the 12C/13C ratio has predominantly been measured in simple species such as CO, CN and H2CO and, becomes larger with increasing distance from the Galactic Center. We have investigated the carbon isotopic ratio for methyl formate HCOOCH3, and its isotopologues H13COOCH3 and HCOO13CH3 addressing the issue whether the 12C/13C ratio is the same for both simple and large molecules. Using ALMA science verification observations of Orion-KL and the spectroscopic characterization of the complex H13COOCH3 and HCOO13CH3 species that we have performed, we have 1) confirmed the detection of the 13C-methyl formate species in Orion-KL and, 2) image for the first time their spatial distribution. I will present some of these results. In particular, our analysis shows that the 12C/13C isotope ratio in methyl formate toward the Compact Ridge and Hot Core-SW components that are associated with Orion-KL are, for both the 13C-methyl formate isotopologues, commensurate with the well-known 12C/13C ratio of the simple species CO. Our findings suggest that grain surface chemistry very likely prevails in the formation of methyl formate main and 13C isotopologues.

  10. Conceptual links between DNA methylation reprogramming in the early embryo and primordial germ cells.

    PubMed

    Seisenberger, Stefanie; Peat, Julian R; Reik, Wolf

    2013-06-01

    DNA methylation is a carrier of important regulatory information that undergoes global reprogramming in the mammalian germ line, including pre-implantation embryos and primordial germ cells (PGCs). A flurry of recent studies have employed technical advances to generate global profiles of methylation and hydroxymethylation in these cells, unravelling the dynamics of methylation erasure at single locus resolution. Active demethylation in the zygote, involving extensive oxidation, is followed by passive loss over early cell divisions. Certain gamete-contributed methylation marks appear to have evolved non-canonical mechanisms for targeted maintenance of methylation in the face of these processes. These protected sequences include the imprinting control regions (ICRs) required for parental imprinting but also a surprising number of other regions. Such targeted maintenance mechanisms may also operate at certain sequences during early PGC migration when global passive demethylation occurs. In later gonadal PGCs, imprints must be reset and this may be achieved through the targeting of active mechanisms including oxidation. Thus, emerging evidence paints a complex picture whereby active and passive demethylation pathways operate synergistically and in parallel to ensure robust erasure in the early embryo and PGCs. PMID:23510682

  11. Abnormalities of the DNA Methylation Mark and Its Machinery: An Emerging Cause of Neurologic Dysfunction

    PubMed Central

    Weissman, Jacqueline; Naidu, Sakkubai; Bjornsson, Hans T.

    2015-01-01

    Recently, Mendelian disorders of the DNA methylation machinery have been described which demonstrate the complex roles of epigenetics in neurodevelopment and disease. For example, defects of DNMT1, the maintenance methyltransferase, lead to adult-onset progressive neurologic disorders, whereas defects of the de novo methyltransferases DNMT3A and DNMT3B lead to nonprogressive neurodevelopmental conditions. Furthermore, patients with DNMT3A deficiency demonstrate overgrowth, a feature common to disorders of histone machinery and imprinting disorders, highlighting the interconnectedness of the many epigenetic layers. Disorders of the DNA methylation machinery include both the aforementioned “writers” and also the “readers” of the methyl mark, such as MeCP2, the cause of Rett syndrome. Any dosage disruption, either haploinsufficiency or overexpression of DNA methylation machinery leads to wide-spread gene expression changes in trans, disrupting expression of a subset of target genes that contribute to individual disease phenotypes. In contrast, classical imprinting disorders such as Angelman syndrome have been thought generally to cause epigenetic dysregulation in cis. However, the recent description of multilocus methylation disorders challenges this generalization. Here, in addition to summarizing recent developments in identifying the pathogenesis of these diseases, we highlight clinical considerations and some unexpected therapeutic opportunities, such as to poisomerase inhibitors for classical imprinting disorders. PMID:25192503

  12. MED12 methylation by CARM1 sensitizes human breast cancer cells to chemotherapy drugs

    PubMed Central

    Wang, Lu; Zeng, Hao; Wang, Qiang; Zhao, Zibo; Boyer, Thomas G.; Bian, Xiuwu; Xu, Wei

    2015-01-01

    The RNA polymerase II mediator complex subunit 12 (MED12) is frequently mutated in human cancers, and loss of MED12 has been shown to induce drug resistance through activation of transforming growth factor–? receptor (TGF-?R) signaling. We identified MED12 as a substrate for coactivator-associated arginine methyltransferase 1 (CARM1). Not only are the expression levels of CARM1 and MED12 positively correlated, but their high expression also predicts better prognosis in human breast cancers after chemotherapy. MED12 was methylated at R1862 and R1912 by CARM1, and mutation of these sites in cell lines resulted in resistance to chemotherapy drugs. Furthermore, we showed that the methylation-dependent drug response mechanism is distinct from activation of TGF-?R signaling, because methylated MED12 potently suppresses p21/WAF1 transcription. Cells defective in MED12 methylation have up-regulated p21 protein, which correlates with poor prognosis in breast cancer patients treated with chemotherapy. Collectively, this study identifies MED12 methylation as a sensor for predicting response to commonly used chemotherapy drugs in human cancers. PMID:26601288

  13. Regulators Associated with Clinical Outcomes Revealed by DNA Methylation Data in Breast Cancer

    PubMed Central

    Ung, Matthew H.; Varn, Frederick S.; Lou, Shaoke; Cheng, Chao

    2015-01-01

    The regulatory architecture of breast cancer is extraordinarily complex and gene misregulation can occur at many levels, with transcriptional malfunction being a major cause. This dysfunctional process typically involves additional regulatory modulators including DNA methylation. Thus, the interplay between transcription factor (TF) binding and DNA methylation are two components of a cancer regulatory interactome presumed to display correlated signals. As proof of concept, we performed a systematic motif-based in silico analysis to infer all potential TFs that are involved in breast cancer prognosis through an association with DNA methylation changes. Using breast cancer DNA methylation and clinical data derived from The Cancer Genome Atlas (TCGA), we carried out a systematic inference of TFs whose misregulation underlie different clinical subtypes of breast cancer. Our analysis identified TFs known to be associated with clinical outcomes of p53 and ER (estrogen receptor) subtypes of breast cancer, while also predicting new TFs that may also be involved. Furthermore, our results suggest that misregulation in breast cancer can be caused by the binding of alternative factors to the binding sites of TFs whose activity has been ablated. Overall, this study provides a comprehensive analysis that links DNA methylation to TF binding to patient prognosis. PMID:25996148

  14. Role of Morphological Growth State and Gene Expression in Desulfovibrio africanus strain Walvis Bay Mercury Methylation

    SciTech Connect

    Moberly, James G; Miller, Carrie L; Brown, Steven D; Biswas, Abir; Brandt, Craig C; Palumbo, Anthony Vito; Elias, Dwayne A

    2012-01-01

    The biogeochemical transformations of mercury are a complex process, with the production of methylmercury, a potent human neurotoxin, repeatedly demonstrated in sulfate- and Fe(III)- reducing as well as methanogenic bacteria. However, little is known regarding the morphology, genes or proteins involved in methylmercury generation. Desulfovibrio africanus strain Walvis Bay is a Hg-methylating -proteobacterium with a sequenced genome and has unusual pleomorphic forms. In this study, a relationship between the pleomorphism and Hg methylation was investigated. Proportional increases in the sigmoidal (regular) cell form corresponded with increased net MeHg production, but decreased when the pinched cocci (persister) form became the major morphotype. D. africanus microarrays indicated that the ferrous iron transport genes (feoAB), as well as ribosomal genes and several genes whose products are predicted to have metal binding domains (CxxC), were up-regulated during exposure to Hg in the exponential phase. While no specific methylation pathways were identified, the finding that Hg may interfere with iron transport and the correlation of growth-phase dependent morphology with MeHg production are notable. The identification of these relationships between differential gene expression, morphology, and the growth phase dependence of Hg transformations suggests that actively growing cells are primarily responsible for methylation, and so areas with ample carbon and electron-acceptor concentrations may also generate a higher proportion of methylmercury than more oligotrophic environments. The observation of increased iron transporter expression also suggests that Hg methylation may interfere with iron biogeochemical cycles.

  15. Arginine methylation of DRBD18 differentially impacts its opposing effects on the trypanosome transcriptome

    PubMed Central

    Lott, Kaylen; Mukhopadhyay, Shreya; Li, Jun; Wang, Jie; Yao, Jin; Sun, Yijun; Qu, Jun; Read, Laurie K.

    2015-01-01

    Arginine methylation is a posttranslational modification that impacts wide-ranging cellular functions, including transcription, mRNA splicing and translation. RNA binding proteins (RBPs) represent one of the largest classes of arginine methylated proteins in both mammals and the early diverging parasitic protozoan, Trypanosoma brucei. Here, we report the effects of arginine methylation on the functions of the essential and previously uncharacterized T. brucei RBP, DRBD18. RNAseq analysis shows that DRBD18 depletion causes extensive rearrangement of the T. brucei transcriptome, with increases and decreases in hundreds of mRNAs. DRBD18 contains three methylated arginines, and we used complementation of DRBD18 knockdown cells with methylmimic or hypomethylated DRBD18 to assess the functions of these methylmarks. Methylmimic and hypomethylated DRBD18 associate with different ribonucleoprotein complexes. These altered macromolecular interactions translate into differential impacts on the T. brucei transcriptome. Methylmimic DRBD18 preferentially stabilizes target RNAs, while hypomethylated DRBD18 is more efficient at destabilizing RNA. The protein arginine methyltransferase, TbPRMT1, interacts with DRBD18 and knockdown of TbPRMT1 recapitulates the effects of hypomethylated DRBD18 on mRNA levels. Together, these data support a model in which arginine methylation acts as a switch that regulates T. brucei gene expression. PMID:25940618

  16. Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

    PubMed Central

    Kacmarczyk, Thadeous J.; Ishii, Jennifer; Betel, Doron; Alonso, Alicia; Mason, Christopher E.; Figueroa, Maria E.; Melnick, Ari M.

    2015-01-01

    DNA methylation pattern mapping is heavily studied in normal and diseased tissues. A variety of methods have been established to interrogate the cytosine methylation patterns in cells. Reduced representation of whole genome bisulfite sequencing was developed to detect quantitative base pair resolution cytosine methylation patterns at GC-rich genomic loci. This is accomplished by combining the use of a restriction enzyme followed by bisulfite conversion. Enhanced Reduced Representation Bisulfite Sequencing (ERRBS) increases the biologically relevant genomic loci covered and has been used to profile cytosine methylation in DNA from human, mouse and other organisms. ERRBS initiates with restriction enzyme digestion of DNA to generate low molecular weight fragments for use in library preparation. These fragments are subjected to standard library construction for next generation sequencing. Bisulfite conversion of unmethylated cytosines prior to the final amplification step allows for quantitative base resolution of cytosine methylation levels in covered genomic loci. The protocol can be completed within four days. Despite low complexity in the first three bases sequenced, ERRBS libraries yield high quality data when using a designated sequencing control lane. Mapping and bioinformatics analysis is then performed and yields data that can be easily integrated with a variety of genome-wide platforms. ERRBS can utilize small input material quantities making it feasible to process human clinical samples and applicable in a range of research applications. The video produced demonstrates critical steps of the ERRBS protocol. PMID:25742437

  17. Enhanced reduced representation bisulfite sequencing for assessment of DNA methylation at base pair resolution.

    PubMed

    Garrett-Bakelman, Francine E; Sheridan, Caroline K; Kacmarczyk, Thadeous J; Ishii, Jennifer; Betel, Doron; Alonso, Alicia; Mason, Christopher E; Figueroa, Maria E; Melnick, Ari M

    2015-01-01

    DNA methylation pattern mapping is heavily studied in normal and diseased tissues. A variety of methods have been established to interrogate the cytosine methylation patterns in cells. Reduced representation of whole genome bisulfite sequencing was developed to detect quantitative base pair resolution cytosine methylation patterns at GC-rich genomic loci. This is accomplished by combining the use of a restriction enzyme followed by bisulfite conversion. Enhanced Reduced Representation Bisulfite Sequencing (ERRBS) increases the biologically relevant genomic loci covered and has been used to profile cytosine methylation in DNA from human, mouse and other organisms. ERRBS initiates with restriction enzyme digestion of DNA to generate low molecular weight fragments for use in library preparation. These fragments are subjected to standard library construction for next generation sequencing. Bisulfite conversion of unmethylated cytosines prior to the final amplification step allows for quantitative base resolution of cytosine methylation levels in covered genomic loci. The protocol can be completed within four days. Despite low complexity in the first three bases sequenced, ERRBS libraries yield high quality data when using a designated sequencing control lane. Mapping and bioinformatics analysis is then performed and yields data that can be easily integrated with a variety of genome-wide platforms. ERRBS can utilize small input material quantities making it feasible to process human clinical samples and applicable in a range of research applications. The video produced demonstrates critical steps of the ERRBS protocol. PMID:25742437

  18. PRMT1 mediated methylation of TAF15 is required for its positive gene regulatory function

    SciTech Connect

    Jobert, Laure; Argentini, Manuela; Tora, Laszlo

    2009-04-15

    TAF15 (formerly TAF{sub II}68) is a nuclear RNA-binding protein that is associated with a distinct population of TFIID and RNA polymerase II complexes. TAF15 harbours an N-terminal activation domain, an RNA recognition motif (RRM) and many Arg-Gly-Gly (RGG) repeats at its C-terminal end. The N-terminus of TAF15 serves as an essential transforming domain in the fusion oncoprotein created by chromosomal translocation in certain human chondrosarcomas. Post-transcriptional modifications (PTMs) of proteins are known to regulate their activity, however, nothing is known on how PTMs affect TAF15 function. Here we demonstrate that endogenous human TAF15 is methylated in vivo at its numerous RGG repeats. Furthermore, we identify protein arginine N-methyltransferase 1 (PRMT1) as a TAF15 interactor and the major PRMT responsible for its methylation. In addition, the RGG repeat-containing C-terminus of TAF15 is responsible for the shuttling between the nucleus and the cytoplasm and the methylation of RGG repeats affects the subcellular localization of TAF15. The methylation of TAF15 by PRMT1 is required for the ability of TAF15 to positively regulate the expression of the studied endogenous TAF15-target genes. Our findings demonstrate that arginine methylation of TAF15 by PRMT1 is a crucial event determining its proper localization and gene regulatory function.

  19. Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1.

    SciTech Connect

    Avvakumov, George V.; Walker, John R.; Xue, Sheng; Li, Yanjun; Duan, Shili; Bronner, Christian; Arrowsmith, Cheryl H.; Dhe-Paganon, Sirano

    2008-11-17

    Epigenetic inheritance in mammals is characterized by high-fidelity replication of CpG methylation patterns during development. UHRF1 (also known as ICBP90 in humans and Np95 in mouse) is an E3 ligase important for the maintenance of global and local DNA methylation in vivo. The preferential affinity of UHRF1 for hemi-methylated DNA over symmetrically methylated DNA by means of its SET and RING-associated (SRA) domain and its association with the maintenance DNA methyltransferase 1 (DNMT1) suggests a role in replication of the epigenetic code. Here we report the 1.7 {angstrom} crystal structure of the apo SRA domain of human UHRF1 and a 2.2 {angstrom} structure of its complex with hemi-methylated DNA, revealing a previously unknown reading mechanism for methylated CpG sites (mCpG). The SRA-DNA complex has several notable structural features including a binding pocket that accommodates the 5-methylcytosine that is flipped out of the duplex DNA. Two specialized loops reach through the resulting gap in the DNA from both the major and the minor grooves to read the other three bases of the CpG duplex. The major groove loop confers both specificity for the CpG dinucleotide and discrimination against methylation of deoxycytidine of the complementary strand. The structure, along with mutagenesis data, suggests how UHRF1 acts as a key factor for DNMT1 maintenance methylation through recognition of a fundamental unit of epigenetic inheritance, mCpG.

  20. Symmetrical Dose-Dependent DNA-Methylation Profiles in Children with Deletion or Duplication of 7q11.23.

    PubMed

    Strong, Emma; Butcher, Darci T; Singhania, Rajat; Mervis, Carolyn B; Morris, Colleen A; De Carvalho, Daniel; Weksberg, Rosanna; Osborne, Lucy R

    2015-08-01

    Epigenetic dysfunction has been implicated in a growing list of disorders that include cancer, neurodevelopmental disorders, and neurodegeneration. Williams syndrome (WS) and 7q11.23 duplication syndrome (Dup7) are rare neurodevelopmental disorders with broad phenotypic spectra caused by deletion and duplication, respectively, of a 1.5-Mb region that includes several genes with a role in epigenetic regulation. We have identified striking differences in DNA methylation across the genome between blood cells from children with WS or Dup7 and blood cells from typically developing (TD) children. Notably, regions that were differentially methylated in both WS and Dup7 displayed a significant and symmetrical gene-dose-dependent effect, such that WS typically showed increased and Dup7 showed decreased DNA methylation. Differentially methylated genes were significantly enriched with genes in pathways involved in neurodevelopment, autism spectrum disorder (ASD) candidate genes, and imprinted genes. Using alignment with ENCODE data, we also found the differentially methylated regions to be enriched with CCCTC-binding factor (CTCF) binding sites. These findings suggest that gene(s) within 7q11.23 alter DNA methylation at specific sites across the genome and result in dose-dependent DNA-methylation profiles in WS and Dup7. Given the extent of DNA-methylation changes and the potential impact on CTCF binding and chromatin regulation, epigenetic mechanisms most likely contribute to the complex neurological phenotypes of WS and Dup7. Our findings highlight the importance of DNA methylation in the pathogenesis of WS and Dup7 and provide molecular mechanisms that are potentially shared by WS, Dup7, and ASD. PMID:26166478

  1. DNA methylation at hepatitis B viral integrants is associated with methylation at flanking human genomic sequences

    PubMed Central

    Watanabe, Yoshiyuki; Yamamoto, Hiroyuki; Oikawa, Ritsuko; Toyota, Minoru; Yamamoto, Masakazu; Kokudo, Norihiro; Tanaka, Shinji; Arii, Shigeki; Yotsuyanagi, Hiroshi; Koike, Kazuhiko; Itoh, Fumio

    2015-01-01

    Integration of DNA viruses into the human genome plays an important role in various types of tumors, including hepatitis B virus (HBV)–related hepatocellular carcinoma. However, the molecular details and clinical impact of HBV integration on either human or HBV epigenomes are unknown. Here, we show that methylation of the integrated HBV DNA is related to the methylation status of the flanking human genome. We developed a next-generation sequencing-based method for structural methylation analysis of integrated viral genomes (denoted G-NaVI). This method is a novel approach that enables enrichment of viral fragments for sequencing using unique baits based on the sequence of the HBV genome. We detected integrated HBV sequences in the genome of the PLC/PRF/5 cell line and found variable levels of methylation within the integrated HBV genomes. Allele-specific methylation analysis revealed that the HBV genome often became significantly methylated when integrated into highly methylated host sites. After integration into unmethylated human genome regions such as promoters, however, the HBV DNA remains unmethylated and may eventually play an important role in tumorigenesis. The observed dynamic changes in DNA methylation of the host and viral genomes may functionally affect the biological behavior of HBV. These findings may impact public health given that millions of people worldwide are carriers of HBV. We also believe our assay will be a powerful tool to increase our understanding of the various types of DNA virus-associated tumorigenesis. PMID:25653310

  2. Evidence for methyl group transfer between the methyl-accepting chemotaxis proteins in Bacillus subtilis

    SciTech Connect

    Bedale, W.A.; Nettleton, D.O.; Sopata, C.S.; Thoelke, M.S.; Ordal, G.W.

    1988-01-01

    The authors present evidence for methyl (as methyl or methoxy) transfer from the methyl-accepting chemotaxis proteins H1 and possibly H3 of Bacillus subtilis to the methyl-accepting chemotaxis protein H2. This methyl transfer, which has been observed in vitro was strongly stimulated by the chemoattractant aspartate and thus may plan an important role in the sensory processing system of this organism. Although radiolabeling of H1 and H3 began at once after the addition of (/sup 3/H) methionine, radiolabeling of H2 showed a lag. Furthermore, the addition of excess nonradioactive methionine caused immediate exponential delabeling of H1 and H3 while labeling of H2 continued to increase. Methylation of H2 required the chemotactic methyltransferase, probably to first methylate H1 and H3. Aspartate caused increased labeling of H2 and strongly decreased labeling of H1 and H3 after the addition of nonradioactive methionine. Without the addition of nonradioactive methionine, aspartate caused demethylation of H1 and to a lesser extent H3, with an approximately equal increase of methylation of H2.

  3. Methyl N-phenyl carbamate synthesis from aniline and methyl formate: carbon recycling to chemical products.

    PubMed

    Yalfani, Mohammad S; Lolli, Giulio; Müller, Thomas E; Wolf, Aurel; Mleczko, Leslaw

    2015-02-01

    Methyl N-phenyl carbamate was synthesized from aniline by using methyl formate as a green and efficient carbonylating agent. High yields were obtained at milder reaction conditions compared to the conventional CO/CH3 OH route. Studies on the reaction sequence led to suggest an alternative and more efficient route to the carbamate via formanilide as intermediate. PMID:25504838

  4. Methyl esters from vegetable oils with hydroxy fatty acids: Comparison of lesquerella and castor methyl esters

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The search for alternative feedstocks for biodiesel as partial replacement for petrodiesel has recently extended to castor oil. In this work, the castor oil methyl esters were prepared and their properties determined in comparison to the methyl esters of lesquerella oil, which in turn is seen as alt...

  5. Methylal and Methylal-Diesel Blended Fuels from Use In Compression-Ignition Engines

    SciTech Connect

    Keith D. Vertin; James M. Ohi; David W. Naegeli; Kenneth H. Childress; Gary P. Hagen; Chris I. McCarthy; Adelbert S. Cheng; Robert W. Dibble

    1999-05-05

    Gas-to-liquids catalytic conversion technologies show promise for liberating stranded natural gas reserves and for achieving energy diversity worldwide. Some gas-to-liquids products are used as transportation fuels and as blendstocks for upgrading crude derived fuels. Methylal (CH{sub 3}-O-CH{sub 2}-O-CH{sub 3}) also known as dimethoxymethane or DMM, is a gas-to-liquid chemical that has been evaluated for use as a diesel fuel component. Methylal contains 42% oxygen by weight and is soluble in diesel fuel. The physical and chemical properties of neat methylal and for blends of methylal in conventional diesel fuel are presented. Methylal was found to be more volatile than diesel fuel, and special precautions for distribution and fuel tank storage are discussed. Steady state engine tests were also performed using an unmodified Cummins 85.9 turbocharged diesel engine to examine the effect of methylal blend concentration on performance and emissions. Substantial reductions of particulate matter emissions h ave been demonstrated 3r IO to 30% blends of methylal in diesel fuel. This research indicates that methylal may be an effective blendstock for diesel fuel provided design changes are made to vehicle fuel handling systems.

  6. Chromatin and DNA methylation dynamics during retinoic acid-induced RET gene transcriptional activation in neuroblastoma cells

    PubMed Central

    Angrisano, T.; Sacchetti, S.; Natale, F.; Cerrato, A.; Pero, R.; Keller, S.; Peluso, S.; Perillo, B.; Avvedimento, V. E.; Fusco, A.; Bruni, C. B.; Lembo, F.; Santoro, M.; Chiariotti, L.

    2011-01-01

    Although it is well known that RET gene is strongly activated by retinoic acid (RA) in neuroblastoma cells, the mechanisms underlying such activation are still poorly understood. Here we show that a complex series of molecular events, that include modifications of both chromatin and DNA methylation state, accompany RA-mediated RET activation. Our results indicate that the primary epigenetic determinants of RA-induced RET activation differ between enhancer and promoter regions. At promoter region, the main mark of RET activation was the increase of H3K4me3 levels while no significant changes of the methylation state of H3K27 and H3K9 were observed. At RET enhancer region a bipartite chromatin domain was detected in unstimulated cells and a prompt demethylation of H3K27me3 marked RET gene activation upon RA exposure. Moreover, ChIP experiments demonstrated that EZH2 and MeCP2 repressor complexes were associated to the heavily methylated enhancer region in the absence of RA while both complexes were displaced during RA stimulation. Finally, our data show that a demethylation of a specific CpG site at the enhancer region could favor the displacement of MeCP2 from the heavily methylated RET enhancer region providing a novel potential mechanism for transcriptional regulation of methylated RA-regulated loci. PMID:20952403

  7. Ion/molecule reactions involving ionized toluene or ionized methyl benzoate and neutral methyl isocyanide

    NASA Astrophysics Data System (ADS)

    Dechamps, Noémie; Flammang, Robert; Boulvin, Michaël; Lamote, Luc; Gerbaux, Pascal; Nam, Pham Cam; Nguyen, Minh Tho

    2008-03-01

    Ion/molecule reactions involving toluene and methyl isocyanide have been performed in a new rf-only hexapole collision cell recently installed in a large-scale tandem mass spectrometer. Among the various ionized products identified, indole derivatives have been characterized by collisional activation and result from the intermediacy of hydrogen-bridged radical cations and covalently bound dimers. Quantum theoretical computations support these experimental findings. A covalently bound dimer is also proposed in the ion/molecule reaction between ionized methyl benzoate and methyl isocyanide; such a dimer is nevertheless not detected due to the large exothermicity of the reaction leading to the ultimate products ascribed to N-methyl benzonitrilium ion, carbon dioxide and a methyl radical.

  8. Active transport, substrate specificity, and methylation of Hg(II) in anaerobic bacteria

    SciTech Connect

    Schasfer, Jeffra; Rocks, Sara; Zheng, Wang; Liang, Liyuan; Gu, Baohua; Morel, Francois M

    2011-01-01

    The formation of methylmercury (MeHg), which is biomagnified in aquatic food chains and poses a risk to human health, is effected by some iron- and sulfate-reducing bacteria (FeRB and SRB) in anaerobic environments. However, very little is known regarding the mechanism of uptake of inorganic Hg by these organisms, in part because of the inherent difficulty in measuring the intracellular Hg concentration. By using the FeRB Geobacter sulfurreducens and the SRB Desulfovibrio desulfuricans ND132 as model organisms, we demonstrate that Hg(II) uptake occurs by active transport. We also establish that Hg(II) uptake by G. sulfurreducens is highly dependent on the characteristics of the thiols that bind Hg(II) in the external medium, with some thiols promoting uptake and methylation and others inhibiting both. The Hg(II) uptake system of D. desulfuricans has a higher affinity than that of G. sulfurreducens and promotes Hg methylation in the presence of stronger complexing thiols. We observed a tight coupling between Hg methylation and MeHg export from the cell, suggesting that these two processes may serve to avoid the build up and toxicity of cellular Hg. Our results bring up the question of whether cellular Hg uptake is specific for Hg(II) or accidental, occurring via some essential metal importer. Our data also point at Hg(II) complexation by thiols as an important factor controlling Hg methylation in anaerobic environments.

  9. PRMT1 promotes mitosis of cancer cells through arginine methylation of INCENP.

    PubMed

    Deng, Xiaolan; Von Keudell, Gottfried; Suzuki, Takehiro; Dohmae, Naoshi; Nakakido, Makoto; Piao, Lianhua; Yoshioka, Yuichiro; Nakamura, Yusuke; Hamamoto, Ryuji

    2015-11-01

    Inner centromere protein (INCENP) is a part of a protein complex known as the chromosomal passenger complex (CPC) that is essential for correcting non-bipolar chromosome attachments and for cytokinesis. We here demonstrate that a protein arginine methyltransferase PRMT1, which are overexpressed in various types of cancer including lung and bladder cancer, methylates arginine 887 in an Aurora Kinase B (AURKB)-binding region of INCENP both in vitro and in vivo. R887-substituted INCENP revealed lower binding-affinity to AURKB than wild-type INCENP in the presence of PRMT1. Knockdown of PRMT1 as well as overexpression of methylation-inactive INCENP attenuated the AURKB activity in cancer cells, and resulted in abnormal chromosomal alignment and segregation. Furthermore, introduction of methylation-inactive INCENP into cancer cells reduced the growth rate, compared with those introduced wild-type INCENP or Mock. Our data unveils a novel mechanism of PRMT1-mediated CPC regulation through methylation of INCENP. PMID:26460953

  10. Glutamine methylation in histone H2A is an RNA-polymerase-I-dedicated modification

    NASA Astrophysics Data System (ADS)

    Tessarz, Peter; Santos-Rosa, Helena; Robson, Sam C.; Sylvestersen, Kathrine B.; Nelson, Christopher J.; Nielsen, Michael L.; Kouzarides, Tony

    2014-01-01

    Nucleosomes are decorated with numerous post-translational modifications capable of influencing many DNA processes. Here we describe a new class of histone modification, methylation of glutamine, occurring on yeast histone H2A at position 105 (Q105) and human H2A at Q104. We identify Nop1 as the methyltransferase in yeast and demonstrate that fibrillarin is the orthologue enzyme in human cells. Glutamine methylation of H2A is restricted to the nucleolus. Global analysis in yeast, using an H2AQ105me-specific antibody, shows that this modification is exclusively enriched over the 35S ribosomal DNA transcriptional unit. We show that the Q105 residue is part of the binding site for the histone chaperone FACT (facilitator of chromatin transcription) complex. Methylation of Q105 or its substitution to alanine disrupts binding to FACT in vitro. A yeast strain mutated at Q105 shows reduced histone incorporation and increased transcription at the ribosomal DNA locus. These features are phenocopied by mutations in FACT complex components. Together these data identify glutamine methylation of H2A as the first histone epigenetic mark dedicated to a specific RNA polymerase and define its function as a regulator of FACT interaction with nucleosomes.

  11. The Chirped-Pulse and Cavity Based Ftmw Spectroscopy of the Methyl Lactate-Water and Methyl Lactate-Deuterium Oxide Dimers

    NASA Astrophysics Data System (ADS)

    Thomas, Javix; Sukhorukov, Oleksandr; Jäger, Wolfgang; Xu, Yunjie

    2011-06-01

    The delicate competition between the inter- and intramolecular hydrogen-bonding in the complex consisting of a chiral alpha-hydroxy ester, methyl lactate, and water, has been studied using rotational spectroscopy and high level ab initio calculations. Extensive ab initio calculations have been performed to locate all possible low energy conformers of the methyl lactate-water contact pair and five lowest energy conformers have been identified. The most stable conformer forms a seven membered ring with two intermolecular hydrogen bonds: one between the alcoholic hydroxy group of methyl lactate and the oxygen of the water molecule and the other between the hydrogen of water and the oxygen of the carbonyl group. Broadband scans for the rotational spectra of these conformers have been carried out using a newly built chirped-pulse FTMW instrument and the final frequency measurements with a cavity based FTMW instrument. Spectral assignments have been made for the lowest energy conformer of methyl lactate-H2O and D2O. The hyperfine splitting and the source of the splitting will be discussed.

  12. Inheritance of DNA methylation in microinjected eggs of Xenopus laevis.

    PubMed Central

    Harland, R M

    1982-01-01

    Plasmid DNA methylated at Hpa II sites was injected into eggs of Xenopus laevis. The methylated DNA replicates extrachromosomally, and the methylated state of the H pa II sites is inherited through replication. Unmethylated sites remain unmethylated in progeny molecules. To test whether replication is necessary for new methylation to occur, DNA methylated on one strand only was injected and unreplicated DNA was selected for analysis. Methylation was copied onto a previously unmethylated strand in the absence of replication but less efficiently than in its presence. These experiments show that the individual methylated site contains enough information for inheritance of the methylated state and that inheritance of methylation does not require integration of the DNA into the chromosome. Images PMID:6285378

  13. Developmental differences in posttranslational calmodulin methylation in pea plants

    SciTech Connect

    Oh, Sukheung; Roberts, D.M. )

    1990-05-01

    A calmodulin-N-methyltransferase was used to analyze the degree of lysine-115 methylation of pea calmodulin. Calmodulin was isolated from segments of developing roots of young etiolated and green pea plants and was tested for its ability to be methylated by the calmodulin methyltransferase in the presence of {sup 3}H-methyl-S-adenosylmethionine. Calmodulin methylation levels were lower in apical root segments and in the young lateral roots compared with the mature, differentiated root tissues. The methylation of these calmodulin samples occurs specifically at lysine 115 since site-directed mutants of calmodulin with substitutions at this position were not methylated and competitively inhibited methylation. The present findings, combined with previous data showing differences in NAD kinase activation by methylated and unmethylated calmodulins, raise the possibility that posttranslational methylation could affect calmodulin action.

  14. DNA methylation array analyses identified breast cancer-associated HYAL2 methylation in peripheral blood.

    PubMed

    Yang, Rongxi; Pfütze, Katrin; Zucknick, Manuela; Sutter, Christian; Wappenschmidt, Barbara; Marme, Frederik; Qu, Bin; Cuk, Katarina; Engel, Christoph; Schott, Sarah; Schneeweiss, Andreas; Brenner, Hermann; Claus, Rainer; Plass, Christoph; Bugert, Peter; Hoth, Markus; Sohn, Christof; Schmutzler, Rita; Bartram, Claus R; Burwinkel, Barbara

    2015-04-15

    Breast cancer (BC) is the leading cause of cancer-related mortality in women worldwide. Changes in DNA methylation in peripheral blood could be associated with malignancy at early stage. However, the BC-associated DNA methylation signatures in peripheral blood were largely unknown. Here, we performed a genome-wide methylation screening and identified a BC-associated differentially methylated CpG site cg27091787 in the hyaluronoglucosaminidase 2 gene (HYAL2) (discovery round with 72 BC case and 24 controls: p = 2.61 × 10(-9) adjusted for cell-type proportions). The substantially decreased methylation of cg27091787 in BC cases was confirmed in two validation rounds (first validation round with 338 BC case and 507 controls: p < 0.0001; second validation round with 189 BC case and 189 controls: p < 0.0001). In addition to cg27091787, the decreased methylation of a 650-bp CpG island shore of HYAL2 was also associated with increased risk of BC. Moreover, the expression and methylation of HYAL2 were inversely correlated with a p-value of 0.006. To note, the BC-associated decreased HYAL2 methylation was replicated in the T-cell fraction (p = 0.034). The cg27091787 methylation level enabled a powerful discrimination of early-stage BC cases (stages 0 and I) from healthy controls [area under curve (AUC) = 0.89], and was robust for the detection of BC in younger women as well (age < 50, AUC = 0.87). Our study reveals a strong association between decreased HYAL2 methylation in peripheral blood and BC, and provides a promising blood-based marker for the detection of early BC. PMID:25213452

  15. Methylation plotter: a web tool for dynamic visualization of DNA methylation data

    PubMed Central

    2014-01-01

    Methylation plotter is a Web tool that allows the visualization of methylation data in a user-friendly manner and with publication-ready quality. The user is asked to introduce a file containing the methylation status of a genomic region. This file can contain up to 100 samples and 100 CpGs. Optionally, the user can assign a group for each sample (i.e. whether a sample is a tumoral or normal tissue). After the data upload, the tool produces different graphical representations of the results following the most commonly used styles to display this type of data. They include an interactive plot that summarizes the status of every CpG site and for every sample in lollipop or grid styles. Methylation values ranging from 0 (unmethylated) to 1 (fully methylated) are represented using a gray color gradient. A practical feature of the tool allows the user to choose from different types of arrangement of the samples in the display: for instance, sorting by overall methylation level, by group, by unsupervised clustering or just following the order in which data were entered. In addition to the detailed plot, Methylation plotter produces a methylation profile plot that summarizes the status of the scrutinized region, a boxplot that sums up the differences between groups (if any) and a dendrogram that classifies the data by unsupervised clustering. Coupled with this analysis, descriptive statistics and testing for differences at both CpG and group levels are provided. The implementation is based in R/shiny, providing a highly dynamic user interface that generates quality graphics without the need of writing R code. Methylation plotter is freely available at http://gattaca.imppc.org:3838/methylation_plotter/. PMID:25260021

  16. Methylation plotter: a web tool for dynamic visualization of DNA methylation data.

    PubMed

    Mallona, Izaskun; Díez-Villanueva, Anna; Peinado, Miguel A

    2014-01-01

    Methylation plotter is a Web tool that allows the visualization of methylation data in a user-friendly manner and with publication-ready quality. The user is asked to introduce a file containing the methylation status of a genomic region. This file can contain up to 100 samples and 100 CpGs. Optionally, the user can assign a group for each sample (i.e. whether a sample is a tumoral or normal tissue). After the data upload, the tool produces different graphical representations of the results following the most commonly used styles to display this type of data. They include an interactive plot that summarizes the status of every CpG site and for every sample in lollipop or grid styles. Methylation values ranging from 0 (unmethylated) to 1 (fully methylated) are represented using a gray color gradient. A practical feature of the tool allows the user to choose from different types of arrangement of the samples in the display: for instance, sorting by overall methylation level, by group, by unsupervised clustering or just following the order in which data were entered. In addition to the detailed plot, Methylation plotter produces a methylation profile plot that summarizes the status of the scrutinized region, a boxplot that sums up the differences between groups (if any) and a dendrogram that classifies the data by unsupervised clustering. Coupled with this analysis, descriptive statistics and testing for differences at both CpG and group levels are provided. The implementation is based in R/shiny, providing a highly dynamic user interface that generates quality graphics without the need of writing R code. Methylation plotter is freely available at http://gattaca.imppc.org:3838/methylation_plotter/. PMID:25260021

  17. Binding of sulfamethazine to ?-cyclodextrin and methyl-?-cyclodextrin.

    PubMed

    Zoppi, Ariana; Delrivo, Alicia; Aiassa, Virginia; Longhi, Marcela Raquel

    2013-06-01

    ?-cyclodextrin (?CD) and methyl-?-cyclodextrin (M?CD) complexes with sulfamethazine (SMT) were prepared and characterized by different experimental techniques, and the effects of ?CD and M?CD on drug solubility were assessed via phase-solubility analysis. The phase-solubility diagram for the drug showed an increase in water solubility, with the following affinity constants calculated: 40.4±0.4 (pH 2.0) and 29.4±0.4 (pH 8.0) M(-1) with ?CD and 56±1 (water), 39±3 (pH 2.0) and 39±5 (pH 8.0) M(-1) with M?CD. According to (1)H NMR and 2D NMR spectroscopy, the complexation mode involved the aromatic ring of SMT included in the M?CD cavity. The complexes obtained in solid state by freeze drying were characterized by Fourier transform infrared spectroscopy, scanning electron microscopy, and thermal analysis. The amorphous complexes obtained in this study may be useful in the preparation of pharmaceutical dosage forms of SMT. PMID:23606009

  18. Selenophene transition metal complexes

    SciTech Connect

    White, C.J.

    1994-07-27

    This research shows that selenophene transition metal complexes have a chemistry that is similar to their thiophene analogs. Selenophene coordination has been demonstrated and confirmed by molecular structure in both the {eta}{sup 5}- and the {eta}{sup 1}(Se)-coordination modes. The reaction chemistry of selenophene complexes closely resembles that of the analogous thiophene complexes. One major difference, however, is that selenophene is a better donor ligand than thiophene making the selenophene complexes more stable than the corresponding thiophene complexes. The {sup 77}Se NMR chemical shift values for selenophene complexes fall within distinct regions primarily depending on the coordination mode of the selenophene ligand. In the final paper, the C-H bond activation of {eta}{sup 1}(S)-bound thiophenes, {eta}{sup 1}(S)-benzothiophene and {eta}{sup 1}(Se)-bound selenophenes has been demonstrated. The deprotonation and rearrangement of the {eta}{sup 1}(E)-bound ligand to the carbon bound L-yl complex readily occurs in the presence of base. Reprotonation with a strong acid gives a carbene complex that is unreactive towards nucleophilic attack at the carbene carbon and is stable towards exposure to air. The molecular structure of [Cp(NO)(PPh{sub 3})Re(2-benzothioenylcarbene)]O{sub 3}SCF{sub 3} was determined and contains a Re-C bond with substantial double bond character. Methyl substitution for the thienylcarbene or selenylcarbene gives a carbene that rearranges thermally to give back the {eta}{sup 1}(E)-bound complex. Based on these model reactions, a new mechanism for the H/D exchange of thiophene over the hydrodesulfurization catalyst has been proposed.

  19. DNA Methylation, Its Mediators and Genome Integrity

    PubMed Central

    Meng, Huan; Cao, Ying; Qin, Jinzhong; Song, Xiaoyu; Zhang, Qing; Shi, Yun; Cao, Liu

    2015-01-01

    DNA methylation regulates many cellular processes, including embryonic development, transcription, chromatin structure, X-chromosome inactivation, genomic imprinting and chromosome stability. DNA methyltransferases establish and maintain the presence of 5-methylcytosine (5mC), and ten-eleven translocation cytosine dioxygenases (TETs) oxidise 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), which can be removed by base excision repair (BER) proteins. Multiple forms of DNA methylation are recognised by methyl-CpG binding proteins (MeCPs), which play vital roles in chromatin-based transcriptional regulation, DNA repair and replication. Accordingly, defects in DNA methylation and its mediators may cause silencing of tumour suppressor genes and misregulation of multiple cell cycles, DNA repair and chromosome stability genes, and hence contribute to genome instability in various human diseases, including cancer. Thus, understanding functional genetic mutations and aberrant expression of these DNA methylation mediators is critical to deciphering the crosstalk between concurrent genetic and epigenetic alterations in specific cancer types and to the development of new therapeutic strategies. PMID:25892967

  20. Methyl Iodide Fumigation of Bacillus anthracis Spores.

    PubMed

    Sutton, Mark; Kane, Staci R; Wollard, Jessica R

    2015-09-01

    Fumigation techniques such as chlorine dioxide, vaporous hydrogen peroxide, and paraformaldehyde previously used to decontaminate items, rooms, and buildings following contamination with Bacillus anthracis spores are often incompatible with materials (e.g., porous surfaces, organics, and metals), causing damage or residue. Alternative fumigation with methyl bromide is subject to U.S. and international restrictions due to its ozone-depleting properties. Methyl iodide, however, does not pose a risk to the ozone layer and has previously been demonstrated as a fumigant for fungi, insects, and nematodes. Until now, methyl iodide has not been evaluated against Bacillus anthracis. Sterne strain Bacillus anthracis spores were subjected to methyl iodide fumigation at room temperature and at 550C. Efficacy was measured on a log-scale with a 6-log reduction in CFUs being considered successful compared to the U.S. Environmental Protection Agency biocide standard. Such efficacies were obtained after just one hour at 55 °C and after 12 hours at room temperature. No detrimental effects were observed on glassware, PTFE O-rings, or stainless steel. This is the first reported efficacy of methyl iodide in the reduction of Bacillus anthracis spore contamination at ambient and elevated temperatures. PMID:26502561

  1. DNA Methylation in Memory Formation: Emerging Insights.

    PubMed

    Heyward, Frankie D; Sweatt, J David

    2015-10-01

    The establishment of synaptic plasticity and long-term memory requires lasting cellular and molecular modifications that, as a whole, must endure despite the rapid turnover of their constituent parts. Such a molecular feat must be mediated by a stable, self-perpetuating, cellular information storage mechanism. DNA methylation, being the archetypal cellular information storage mechanism, has been heavily implicated as being necessary for stable activity-dependent transcriptional alterations within the CNS. This review details the foundational discoveries from both gene-targeted and whole-genome sequencing studies that have brought DNA methylation to our attention as a chief regulator of activity- and experience-dependent transcriptional alterations within the CNS. We present a hypothetical framework to resolve disparate experimental findings regarding distinct manipulations of DNA methylation and their effect on memory, taking into account the unique impact activity-dependent alterations in DNA methylation potentially have on both memory-promoting and memory-suppressing gene expression. And last, we discuss potential avenues for future inquiry into the role of DNA methylation during remote memory formation. PMID:25832671

  2. Formation of Methyl Mercury by Bacteria

    PubMed Central

    Hamdy, M. K.; Noyes, O. R.

    1975-01-01

    Twenty-three Hg2+ resistant cultures were isolated from sediment of the Savannah River in Georgia; of these, 14 were gram-negative short rods belonging to the genera Escherichia and Enterobacter, six were gram-positive cocci (three Staphylococcus sp. and three Streptococcus sp.) and three were Bacillus sp. All the Escherichia, Enterobacter, and the Bacillus strain were more resistant to Hg2+ than the strains of staphylococci and streptococci. Adaptation using serial dilutions and concentration gradient agar plate techniques showed that it was possible to select a Hg2+-resistant strain from a parent culture identified as Enterobacter aerogenes. This culture resisted 1,200 ?g of Hg2+ per ml of medium and produced methyl mercury from HgCl2, but was unable to convert Hg2+ to volatile elemental mercury (Hg0). Under constant aeration (i.e., submerged culture), slightly more methyl mercury was formed than in the absence of aeration. Production of methyl mercury was cyclic in nature and slightly decreased if DL-homocysteine was present in media, but increased with methyl-cobalamine. It is concluded that the bacterial production of methyl mercury may be a means of resistance and detoxification against mercurials in which inorganic Hg2+ is converted to organic form and secreted into the environment. PMID:1180551

  3. Prognostic DNA Methylation Markers for Prostate Cancer

    PubMed Central

    Strand, Siri H.; Orntoft, Torben F.; Sorensen, Karina D.

    2014-01-01

    Prostate cancer (PC) is the most commonly diagnosed neoplasm and the third most common cause of cancer-related death amongst men in the Western world. PC is a clinically highly heterogeneous disease, and distinction between aggressive and indolent disease is a major challenge for the management of PC. Currently, no biomarkers or prognostic tools are able to accurately predict tumor progression at the time of diagnosis. Thus, improved biomarkers for PC prognosis are urgently needed. This review focuses on the prognostic potential of DNA methylation biomarkers for PC. Epigenetic changes are hallmarks of PC and associated with malignant initiation as well as tumor progression. Moreover, DNA methylation is the most frequently studied epigenetic alteration in PC, and the prognostic potential of DNA methylation markers for PC has been demonstrated in multiple studies. The most promising methylation marker candidates identified so far include PITX2, C1orf114 (CCDC181) and the GABRE~miR-452~miR-224 locus, in addition to the three-gene signature AOX1/C1orf114/HAPLN3. Several other biomarker candidates have also been investigated, but with less stringent clinical validation and/or conflicting evidence regarding their possible prognostic value available at this time. Here, we review the current evidence for the prognostic potential of DNA methylation markers in PC. PMID:25238417

  4. Autism: A Redox/Methylation Disorder

    PubMed Central

    2013-01-01

    While autism is still a mysterious developmental disorder, expansion of research efforts over the past 10 to 15 years has yielded a number of important clues implicating both genetic and environmental factors. We can now assert with a measure of confidence that contemporary autism reflects the combined impact of multiple environmental factors on the processes that regulate development in genetically vulnerable individuals. Since epigenetic regulation of gene expression is acknowledged as the most critical factor in development and DNA methylation (the addition of a carbon atom at discrete locations) is the fundamental event for epigenetic regulation, dysfunctional methylation can be considered as a likely cause of autism. Since methylation activity is highly sensitive to oxidative stress (an abnormal redox state) and many environmental factors promote oxidative stress, we have proposed a redox/methylation hypothesis for autism causation. The narrative herein describes the evolution of this hypothesis, which is essentially a series of linked discoveries about how the brain uniquely relies on oxidation and methylation to guide its development and to carry out its cognitive functions. PMID:24416710

  5. DNA methylation and demethylation: a pathway to gametogenesis and development.

    PubMed

    Dean, Wendy

    2014-02-01

    The generation of gametes falls between two reprogramming phases. These phases are characterised by profound periods of transcriptional activity, which define and reinforce lineage decisions. The control of these transcriptional programs and the interpretation of the underlying genetic instruction is the task of the epigenome. As such, dynamic processes during reprogramming are critical for the development of the germ line and its resetting, which propels that developmental process forward and provides the transfer of genetic and epigenetic information between generations. Central in this reprogramming is the addition and subtraction of DNA methylation and its oxidative products, coupled to the mechanisms at play to achieve this goal. The activities competent to add DNA methylation, and identification of those enzymes able to modify it, have heralded a new chapter in our understanding of the complexities that dictate and direct cellular fates. How the early embryos makes use of these marks and how they are modulated will give us insight into cellular differentiation and reprogramming critical for health and into the process of aging. This review details some of these processes and the activities essential to achieve the immortality of the mammalian germ line. PMID:24214338

  6. Synthesis, characterization and catalytic activities towards epoxidation of olefins of dinuclear copper(II) complexes

    NASA Astrophysics Data System (ADS)

    Halder, Shibashis; Mukherjee, Aparajita; Ghosh, Koushik; Dey, Sudipto; Nandi, Mahasweta; Roy, Partha

    2015-12-01

    Two copper(II) complexes, [Cu2(L1)Cl3].2H2O (1) and [Cu2(L2)(N3)Cl2] (2) where HL1 = 4-methyl-2,6-bis((2-morpholinoethylimino)methyl)phenol and HL2 = 4-methyl-2,6-bis((3-morpholinopropylimino)methyl)phenol have been synthesized and characterized by elemental analysis, various spectroscopic methods, TGA and single crystal X-ray diffraction analysis. Single crystal X-ray diffraction analysis reveals that in both the complexes, two copper atoms are linked by phenoxo oxygen atom and a bridging ligand, namely chloride and azide, respectively. These complexes have been used as catalyst for the epoxidation of cyclohexene, styrene, ?-methyl styrene, trans-stilbene and norbornene using tert-butyl hydroperoxide as the oxidant in acetonitrile under mild conditions. All of the substrates undergo conversion to produce respective epoxide as the major product.

  7. Martian Methyl Chloride. A lesson in uncertainty

    E-print Network

    Bains, William

    2013-01-01

    The MSL Lander Curiosity has recently detected methyl halides coming from heated samples of Martian soil. This is reminiscent of similar findings in the Viking Lander spacecraft. In the 1970s a consensus developed quickly explaining the methyl halides as contamination originating from the spacecraft, and ignoring lines of evidence that the two compounds originated from Mars, and that they could not have originated from the proposed spacecraft chemistry. I discuss why this consensus developed from the understanding of biochemistry and geochemistry of 1976, despite its implausibility. Subsequent explanations for the Viking methyl halides are more plausible but still not proven. The Curiosity rover results are also being explained as a result of on-spacecraft chemistry. I urge caution in this interpretation, in light of the historical Viking example: it is better to leave unexplained data unexplained than to lock in an explanation that precludes future developments.

  8. Fragrance material review on methyl dihydrojasmonate.

    PubMed

    Scognamiglio, J; Jones, L; Letizia, C S; Api, A M

    2012-10-01

    A toxicologic and dermatologic review of methyl dihydrojasmonate when used as a fragrance ingredient is presented. Methyl dihydrojasmonate is a member of the fragrance structural group ketones cyclopentanones and cyclopentenones. The common characteristic structural element of the group members is a cyclopentanone or cyclopentenone ring with a straight or branched chain alkane or alkene substituent. This review contains a detailed summary of all available toxicology and dermatology papers that are related to this individual fragrance ingredient and is not intended as a stand-alone document. Available data for methyl dihydrojasmonate were evaluated then summarized and includes physical properties, acute toxicity, skin irritation, mucous membrane (eye) irritation, skin sensitization, elicitation, phototoxicity, photoallergy, toxicokinetics, repeated dose, reproductive toxicity, and genotoxicity data. A safety assessment of the entire ketones cyclopentanones and cyclopentenones will be published simultaneously with this document; please refer to Belsito et al. (this issue) for an overall assessment of the safe use of this material. PMID:22449534

  9. Fragrance material review on methyl jasmonate.

    PubMed

    Scognamiglio, J; Jones, L; Letizia, C S; Api, A M

    2012-10-01

    A toxicologic and dermatologic review of methyl jasmonate when used as a fragrance ingredient is presented. Methyl jasmonate is a member of the fragrance structural group Ketones Cyclopentanones and Cyclopentenones. The common characteristic structural element of the group members is a cyclopentanone or cyclopentenone ring with a straight or branched chain alkane or alkene substituent. This review contains a detailed summary of all available toxicology and dermatology papers that are related to this individual fragrance ingredient and is not intended as a stand-alone document. Available data for methyl jasmonate were evaluated then summarized and includes physical properties, acute toxicity, skin irritation, mucous membrane (eye) irritation, skin sensitization, phototoxicity, and photoallergy data. A safety assessment of the entire Ketones Cyclopentanones and Cyclopentenones will be published simultaneously with this document; please refer to Belsito et al. (2012) for an overall assessment of the safe use of this material and all Ketones Cyclopentanones and Cyclopentenones in fragrances. PMID:22449543

  10. Methyl 12-bromo­dehydro­abietate

    PubMed Central

    Gao, Hong; Song, Zhan-Qian; Shang, Shi-Bin

    2010-01-01

    The title compound [systematic name: (1R)-methyl 6-bromo-7-isopropyl-1,4a-dimethyl-1,2,3,4,4a,9,10,10a-octa­hydro­phen­anthrene-1-carboxyl­ate], C21H29BrO2, was synthesized from N-bromo­succinimide and methyl dehydro­abietate, which was prepared through an esterification reaction using dehydro­abietic acid and methanol as raw materials. The three six-membered rings adopt planar (mean deviation = 0.002?Å) half-chair and chair conformations. The two cyclo­hexane rings form a trans ring junction with the two methyl groups in axial positions. The crystal structure is stabilized by weak inter­molecular C—H?O contacts along the b axis. PMID:21579237

  11. Synthesis, characterization, structural and biological aspects of copper(II) dithiocarbamate complexes - Part II, [Cu{S2CN(Me)(R1)}2], [Cu{S2CN(Me)(R2)}2] and [Cu{S2CN(R3)(R4)}2] {R1 = CH2CH(OMe)2, R2 = 2-methyl-1,3-dioxolane, R3 = CH2(CH2)2NCHPhOCH2Ph and R4 = CH2CH2OH}

    NASA Astrophysics Data System (ADS)

    Ferreira, Isabella P.; de Lima, Geraldo M.; Paniago, Eucler B.; Takahashi, Jacqueline A.; Krambrock, Klaus; Pinheiro, Carlos B.; Wardell, James L.; Visentin, Lorenzo C.

    2013-09-01

    Three new copper(II) dithiocarbamates (DTC), [Cu{S2CN(Me)(R1)}2] (1), [Cu{S2CN(Me)(R2)}2] (2) and [Cu{S2CN(R3)(R4)}2] (3) with R1 = CH2CH(OMe)2, R2 = 2-methyl-1,3-dioxolane, R3 = CH2(CH2)2NCHPhOCH2Ph and R4 = CH2CH2OH, have been synthesized and characterized by different spectroscopic techniques. Complexes (1) and (2) display typical EPR spectra for separated Cu(II) centers, and the spectrum of (3) is characteristic of two magnetically coupled Cu(II) ions with S = 1. The X-ray crystallographic determination has shown that complexes (1) and (2) crystallise in the triclinic and monoclinic systems. In addition both complexes are monomers in which the geometry at each Cu(II) is square planar. The in vitro antimicrobial activity of the sodium salts of ligands, and of the Cu(II)-DTC complexes have been screened against Aspergillus flavus, Aspergillus niger, Aspergillus parasiticus, Penicillium citrinum and Curvularia senegalensis, as well as Gram positive and Gram negative bacteria. Finally, the toxic effects of complexes (1)-(3) were performed using Chlorella vulgaris.

  12. JMJD6 Regulates ER? Methylation on Arginine

    PubMed Central

    Poulard, Coralie; Rambaud, Juliette; Hussein, Nader; Corbo, Laura; Le Romancer, Muriel

    2014-01-01

    ER? functions are tightly controlled by numerous post-translational modifications including arginine methylation, which is required to mediate the extranuclear functions of the receptor. We report that upon oestrogenic stimulation, JMJD6, the only arginine demethylase described so far, interacts with and regulates methylated ER? (metER?) function. Moreover, by combining the silencing of JMJD6 with demethylation assays, we show that metER? is a new substrate for JMJD6. We propose that the demethylase activity of JMJD6 is a decisive regulator of the rapid physiological responses to oestrogen. PMID:24498420

  13. Direct and selective hydrogenolysis of arenols and aryl methyl ethers.

    PubMed

    Kusumoto, Shuhei; Nozaki, Kyoko

    2015-01-01

    For valorization of biomass, the conversion of lignin to deoxygenated bulk aromatic compounds is an emerging subject of interest. Because aromatic rings are susceptible to metal-catalysed hydrogenation, the selective hydrogenolysis of carbon-oxygen bonds still remains a great challenge. Herein we report direct and selective hydrogenolysis of sp(2) C-OH bonds in substituted phenols and naphthols catalysed by hydroxycyclopentadienyl iridium complexes. The corresponding arenes were obtained in up to 99% yields, indicating the possible production of arenes from lignin-derived bio-oils. Furthermore, the same catalysts were applied to the unprecedented selective hydrogenolysis of the sp(3) C-O bonds in aryl methyl ethers. Thus, the hydrodeoxygenation of vanillylacetone, a lignin model compound, afforded alkylbenzenes as the major products via triple deoxygenation. PMID:25704229

  14. LnOs H LnOs Synthesis and reactivity of the osmium methylidene complex

    E-print Network

    Girolami, Gregory S.

    LnOs H LnOs H CH3 LnOs CH2 + CH3 + ­H2 (1) + Synthesis and reactivity of the osmium methylidene, or by abstraction of a proton from a cationic methyl compound.13 We now describe the synthesis of an osmium methylidene complex from the reaction of an osmium hydride with methyl trifluoromethanesulfonate (Me

  15. SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation

    SciTech Connect

    Del Rizzo, Paul A.; Couture, Jean-François; Dirk, Lynnette M.A.; Strunk, Bethany S.; Roiko, Marijo S.; Brunzelle, Joseph S.; Houtz, Robert L.; Trievel, Raymond C.

    2010-11-15

    SET domain lysine methyltransferases (KMTs) methylate specific lysine residues in histone and non-histone substrates. These enzymes also display product specificity by catalyzing distinct degrees of methylation of the lysine {epsilon}-amino group. To elucidate the molecular mechanism underlying this specificity, we have characterized the Y245A and Y305F mutants of the human KMT SET7/9 (also known as KMT7) that alter its product specificity from a monomethyltransferase to a di- and a trimethyltransferase, respectively. Crystal structures of these mutants in complex with peptides bearing unmodified, mono-, di-, and trimethylated lysines illustrate the roles of active site water molecules in aligning the lysine {epsilon}-amino group for methyl transfer with S-adenosylmethionine. Displacement or dissociation of these solvent molecules enlarges the diameter of the active site, accommodating the increasing size of the methylated {epsilon}-amino group during successive methyl transfer reactions. Together, these results furnish new insights into the roles of active site water molecules in modulating lysine multiple methylation by SET domain KMTs and provide the first molecular snapshots of the mono-, di-, and trimethyl transfer reactions catalyzed by these enzymes.

  16. Lsh Is Essential for Maintaining Global DNA Methylation Levels in Amphibia and Fish and Interacts Directly with Dnmt1

    PubMed Central

    Dunican, Donncha S.; Pennings, Sari; Meehan, Richard R.

    2015-01-01

    Eukaryotic genomes are methylated at cytosine bases in the context of CpG dinucleotides, a pattern which is maintained through cell division by the DNA methyltransferase Dnmt1. Dramatic methylation losses are observed in plant and mouse cells lacking Lsh (lymphoid specific helicase), predominantly at repetitive sequences and gene promoters. However, the mechanism by which Lsh contributes to the maintenance of DNA methylation is unknown. Here we show that DNA methylation is lost in Lsh depleted frog and fish embryos, both of which exhibit developmental delay. Additionally, we show that both Lsh and Dnmt1 are associated with chromatin and that Lsh knockdown leads to a decreased Dnmt1-chromatin association. Coimmunoprecipitation experiments reveal that Lsh and Dnmt1 are found in the same protein complex, and pulldowns show this interaction is direct. Our data indicate that Lsh is usually diffuse in the nucleus but can be recruited to heterochromatin in a HP1?-dependent manner. These data together (a) show that the role of Lsh in DNA methylation is conserved in plants, amphibian, fish, and mice and (b) support a model in which Lsh contributes to Dnmt1 binding to chromatin, explaining how its loss can potentially lead to perturbations in DNA methylation maintenance. PMID:26491684

  17. Lsh Is Essential for Maintaining Global DNA Methylation Levels in Amphibia and Fish and Interacts Directly with Dnmt1.

    PubMed

    Dunican, Donncha S; Pennings, Sari; Meehan, Richard R

    2015-01-01

    Eukaryotic genomes are methylated at cytosine bases in the context of CpG dinucleotides, a pattern which is maintained through cell division by the DNA methyltransferase Dnmt1. Dramatic methylation losses are observed in plant and mouse cells lacking Lsh (lymphoid specific helicase), predominantly at repetitive sequences and gene promoters. However, the mechanism by which Lsh contributes to the maintenance of DNA methylation is unknown. Here we show that DNA methylation is lost in Lsh depleted frog and fish embryos, both of which exhibit developmental delay. Additionally, we show that both Lsh and Dnmt1 are associated with chromatin and that Lsh knockdown leads to a decreased Dnmt1-chromatin association. Coimmunoprecipitation experiments reveal that Lsh and Dnmt1 are found in the same protein complex, and pulldowns show this interaction is direct. Our data indicate that Lsh is usually diffuse in the nucleus but can be recruited to heterochromatin in a HP1?-dependent manner. These data together (a) show that the role of Lsh in DNA methylation is conserved in plants, amphibian, fish, and mice and (b) support a model in which Lsh contributes to Dnmt1 binding to chromatin, explaining how its loss can potentially lead to perturbations in DNA methylation maintenance. PMID:26491684

  18. A Transgenic Drosophila Model for Arsenic Methylation Suggests a Metabolic Rationale for Differential Dose-Dependent Toxicity Endpoints

    PubMed Central

    Muñiz Ortiz, Jorge G.; Shang, Junjun; Catron, Brittany; Landero, Julio; Caruso, Joseph A.; Cartwright, Iain L.

    2011-01-01

    The mechanisms by which exposure to arsenic induces its myriad pathological effects are undoubtedly complex, while individual susceptibility to their type and severity is likely to be strongly influenced by genetic factors. Human metabolism of arsenic into methylated derivatives, once presumed to result in detoxification, may actually produce species with significantly greater pathological potential. We introduce a transgenic Drosophila model of arsenic methylation, allowing its consequences to be studied in a higher eukaryote exhibiting conservation of many genes and pathways with those of human cells while providing an important opportunity to uncover mechanistic details via the sophisticated genetic analysis for which the system is particularly well suited. The gene for the human enzyme, arsenic (+3 oxidation state) methyltransferase, was introduced into nonmethylating Drosophila under inducible control. Transgenic flies were characterized for enzyme inducibility, production of methylated arsenic species, and the dose-dependent consequences for chromosomal integrity and organismal longevity. Upon enzyme induction, transgenic flies processed arsenite into mono and dimethylated derivatives identical to those found in human urine. When induced flies were exposed to 9 ppm arsenite, chromosomal stability was clearly reduced, whereas at much higher doses, adult life span was significantly increased, a seemingly paradoxical pair of outcomes. Measurement of arsenic body burden in the presence or absence of methylation suggested that enhanced clearance of methylated species might explain this greater longevity under acutely toxic conditions. Our study clearly demonstrates both the hazards and the benefits of arsenic methylation in vivo and suggests a resolution based on evolutionary grounds. PMID:21447609

  19. Experimental and chemical kinetic modeling study of small methyl esters oxidation: Methyl (E)-2-butenoate and methyl butanoate

    SciTech Connect

    Gail, S.; Sarathy, S.M.; Thomson, M.J.; Dievart, P.; Dagaut, P.

    2008-12-15

    This study examines the effect of unsaturation on the combustion of fatty acid methyl esters (FAME). New experimental results were obtained for the oxidation of methyl (E)-2-butenoate (MC, unsaturated C{sub 4} FAME) and methyl butanoate (MB, saturated C{sub 4} FAME) in a jet-stirred reactor (JSR) at atmospheric pressure under dilute conditions over the temperature range 850-1400 K, and two equivalence ratios ({phi}=0.375,0.75) with a residence time of 0.07 s. The results consist of concentration profiles of the reactants, stable intermediates, and final products, measured by probe sampling followed by on-line and off-line gas chromatography analyses. The oxidation of MC and MB in the JSR and under counterflow diffusion flame conditions was modeled using a new detailed chemical kinetic reaction mechanism (301 species and 1516 reactions) derived from previous schemes proposed in the literature. The laminar counterflow flame and JSR (for {phi}=1.13) experimental results used were from a previous study on the comparison of the combustion of both compounds. Sensitivity analyses and reaction path analyses, based on rates of reaction, were used to interpret the results. The data and the model show that MC has reaction pathways analogous to that of MB under the present conditions. The model of MC oxidation provides a better understanding of the effect of the ester function on combustion, and the effect of unsaturation on the combustion of fatty acid methyl ester compounds typically found in biodiesel. (author)

  20. DNA containing 4'-thio-2'-deoxycytidine inhibits methylation by HhaI methyltransferase.

    PubMed Central

    Kumar, S; Horton, J R; Jones, G D; Walker, R T; Roberts, R J; Cheng, X

    1997-01-01

    4'-Thio-2'-deoxycytidine was synthesized as a 5'- protected phosphoramidite compatible with solid phase DNA synthesis. When incorporated as the target cytosine (C*) in the GC*GC recognition sequence for the DNA methyltransferase M. HhaI, methyl transfer was strongly inhibited. In contrast, these same oligonucleotides were normal substrates for the cognate restriction endonuclease R. HhaI and its isoschizomer R. Hin P1I. M. HhaI was able to bind both 4'-thio-modified DNA and unmodified DNA to equivalent extents under equilibrium conditions. However, the presence of 4'-thio-2'-deoxycytidine decreased the half-life of the complex by >10-fold. The crystal structure of a ternary complex of M. HhaI, AdoMet and DNA containing 4'-thio-2'-deoxycytidine was solved at 2.05 A resolution with a crystallographic R-factor of 0.186 and R-free of 0.231. The structure is not grossly different from previously solved ternary complexes containing M. HhaI, DNA and AdoHcy. The difference electron density suggests partial methylation at C5 of the flipped target 4'-thio-2'-deoxycytidine. The inhibitory effect of the 4'sulfur atom on enzymatic activity may be traced to perturbation of a step in the methylation reaction after DNA binding but prior to methyl transfer. This inhibitory effect can be partially overcome after a considerably long time in the crystal environment where the packing prevents complex dissociation and the target is accurately positioned within the active site. PMID:9207024

  1. 40 CFR 180.580 - Iodosulfuron-Methyl-Sodium; tolerances for residues.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...2014-07-01 false Iodosulfuron-Methyl-Sodium; tolerances for residues. 180.580... § 180.580 Iodosulfuron-Methyl-Sodium; tolerances for residues. (a) General...of the herbicide Iodosulfuron-Methyl-Sodium (methyl...

  2. 40 CFR 180.580 - Iodosulfuron-Methyl-Sodium; tolerances for residues.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...2010-07-01 false Iodosulfuron-Methyl-Sodium; tolerances for residues. 180.580... § 180.580 Iodosulfuron-Methyl-Sodium; tolerances for residues. (a) General...of the herbicide Iodosulfuron-Methyl-Sodium (methyl...

  3. 40 CFR 180.580 - Iodosulfuron-Methyl-Sodium; tolerances for residues.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...2013-07-01 false Iodosulfuron-Methyl-Sodium; tolerances for residues. 180.580... § 180.580 Iodosulfuron-Methyl-Sodium; tolerances for residues. (a) General...of the herbicide Iodosulfuron-Methyl-Sodium (methyl...

  4. 40 CFR 180.580 - Iodosulfuron-Methyl-Sodium; tolerances for residues.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...2011-07-01 false Iodosulfuron-Methyl-Sodium; tolerances for residues. 180.580... § 180.580 Iodosulfuron-Methyl-Sodium; tolerances for residues. (a) General...of the herbicide Iodosulfuron-Methyl-Sodium (methyl...

  5. 40 CFR 180.580 - Iodosulfuron-Methyl-Sodium; tolerances for residues.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...2012-07-01 false Iodosulfuron-Methyl-Sodium; tolerances for residues. 180.580... § 180.580 Iodosulfuron-Methyl-Sodium; tolerances for residues. (a) General...of the herbicide Iodosulfuron-Methyl-Sodium (methyl...

  6. Establishment of DNA methylation patterns during mouse development 

    E-print Network

    Athanasiadou, Rodoniki

    2007-01-01

    Methylation is the only known modification of DNA and in animals it mainly occurs at cytosines in a CpG context. The pattern of DNA methylation varies among organisms; some invertebrates are totally devoid of it, while ...

  7. Consequences of dietary methyl donor supplements: Is more always better?

    PubMed

    Shorter, Kimberly R; Felder, Michael R; Vrana, Paul B

    2015-07-01

    Epigenetic mechanisms are now recognized to play roles in disease etiology. Several diseases increasing in frequency are associated with altered DNA methylation. DNA methylation is accomplished through metabolism of methyl donors such as folate, vitamin B12, methionine, betaine (trimethylglycine), and choline. Increased intake of these compounds correlates with decreased neural tube defects, although this mechanism is not well understood. Consumption of these methyl donor pathway components has increased in recent years due to fortification of grains and high supplemental levels of these compounds (e.g. vitamins, energy drinks). Additionally, people with mutations in one of the enzymes that assists in the methyl donor pathway (5-MTHFR) are directed to consume higher amounts of methyl donors to compensate. Recent evidence suggests that high levels of methyl donor intake may also have detrimental effects. Individualized medicine may be necessary to determine the appropriate amounts of methyl donors to be consumed, particularly in women of child bearing age. PMID:25841986

  8. 40 CFR 180.451 - Tribenuron methyl; tolerances for residues.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...General . Tolerances are established for residues of the herbicide tribenuron methyl and its metabolites and degradates...defined in § 180.1(l) are established for residues of the herbicide tribenuron methyl...

  9. 40 CFR 180.451 - Tribenuron methyl; tolerances for residues.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...General . Tolerances are established for residues of the herbicide tribenuron methyl and its metabolites and degradates...defined in § 180.1(n) are established for residues of the herbicide tribenuron methyl...

  10. ARSENIC (+3 OXIDATION STATE) METHYLTRANSFERASE AND THE METHYLATION OF ARSENICALS

    EPA Science Inventory

    Metabolic conversion of inorganic arsenic into methylated products is a multistep process that yields mono, di, and trimethylated arsenicals. In recent years, it has become apparent that formation of methylated metabolites of inorganic arsenic is not necessarily a detoxification...

  11. Nutrients Intake Is Associated with DNA Methylation of Candidate Inflammatory Genes in a Population of Obese Subjects

    PubMed Central

    Bollati, Valentina; Favero, Chiara; Albetti, Benedetta; Tarantini, Letizia; Moroni, Alice; Byun, Hyang-Min; Motta, Valeria; Conti, Diana Misaela; Tirelli, Amedea Silvia; Vigna, Luisella; Bertazzi, Pier Alberto; Pesatori, Angela Cecilia

    2014-01-01

    The aim of the present study was to evaluate the potential association between dietary nutrients and alterations in DNA methylation in a set of five candidate genes, including CD14, Et-1, iNOS, HERV-w and TNF?, in a population of overweight/obese subjects. We evaluated possible associations between gene methylation and clinical blood parameters, including total cholesterol (TC), low- and high-density lipoprotein cholesterol (LDL-C and HDL-C), triglyceride and homocysteine levels. We employed validated methods to assess anthropometric, clinical and dietary data, as well as pyrosequencing to evaluate DNA methylation of the five candidate genes in 165 overweight/obese subjects. There was no association between body mass index and DNA methylation of the five candidate genes in this group of subjects. Positive associations were observed between TNF? methylation and blood levels of LDL-C (? = 0.447, p = 0.002), TC/HDL-C (? = 0.467, p = 0.001) and LDL-C/HDL-C (? = 0.445, p = 0.002), as well as between HERV-w methylation and dietary intakes of ?-carotene (? = 0.088, p = 0.051) and carotenoids (? = 0.083, p = 0.029). TNF? methylation showed negative associations with dietary intakes of cholesterol (? = ?0.278, p = 0.048), folic acid (? = ?0.339, p = 0.012), ?-carotene (? = ?0.332, p = 0.045), carotenoids (? = ?0.331, p = 0.015) and retinol (? = ?0.360, p = 0.008). These results suggest a complex relationship among nutrient intake, oxidative stress and DNA methylation. PMID:25340371

  12. Spaceflight induces both transient and heritable alterations in DNA methylation and gene expression in rice (Oryza sativa L.).

    PubMed

    Ou, Xiufang; Long, Likun; Zhang, Yunhong; Xue, Yiqun; Liu, Jingchun; Lin, Xiuyun; Liu, Bao

    2009-03-01

    Spaceflight represents a complex environmental condition in which several interacting factors such as cosmic radiation, microgravity and space magnetic fields are involved, which may provoke stress responses and jeopardize genome integrity. Given the inherent property of epigenetic modifications to respond to intrinsic as well as external perturbations, it is conceivable that epigenetic markers like DNA methylation may undergo alterations in response to spaceflight. We report here that extensive alteration in both DNA methylation and gene expression occurred in rice plants subjected to a spaceflight, as revealed by a set of characterized sequences including 6 transposable elements (TEs) and 11 cellular genes. We found that several features characterize the alterations: (1) All detected alterations are hypermethylation events; (2) whereas alteration in both CG and CNG methylation occurred in the TEs, only alteration in CNG methylation occurred in the cellular genes; (3) alteration in expression includes both up- and down-regulations, which did not show a general correlation with alteration in methylation; (4) altered methylation patterns in both TEs and cellular genes are heritable to progenies at variable frequencies; however, stochastic reversion to wild-type patterns and further de novo changes in progenies are also apparent; and (5) the altered expression states in both TEs and cellular genes are also heritable to selfed progenies but with markedly lower transmission frequencies than altered DNA methylation states. Furthermore, we found that a set of genes encoding for the various putative DNA methyltransferases, 5-methylcytosine DNA glycosylases, the SWI/SNF chromatin remodeller (DDM1) and siRNA-related proteins are extremely sensitive to perturbation by spaceflight, which might be an underlying cause for the altered methylation patterns in the space-flown plants. We discuss implications of spaceflight-induced epigenetic variations with regard to health safety issues of spaceship crews and potentiality of spaceflight as a means for mutagenesis in crop breeding. PMID:19135069

  13. 40 CFR 721.10122 - 2-Propenoic acid, 2-methyl-, 1,1?-[2-ethyl-2-[[(2-methyl-1-oxo-2-propen-1-yl)oxy]methyl]- 1,3...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false 2-Propenoic acid, 2-methyl-, 1,1â²- methyl]- 1,3-propanediyl] ester, polymer with 1,3-butadiene, ethenylbenzene and 2-hydroxyethyl 2-methyl-2... Specific Chemical Substances § 721.10122 2-Propenoic acid, 2-methyl-, 1,1?- methyl]- 1,3-propanediyl]...

  14. 40 CFR 721.4925 - Methyl n-butyl ketone.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Methyl n-butyl ketone. 721.4925... Substances § 721.4925 Methyl n-butyl ketone. (a) Chemical substance and significant new use subject to reporting. (1) The chemical substance methyl n-butyl ketone, CAS Number 591-78-6, is subject to...

  15. 21 CFR 173.385 - Sodium methyl sulfate.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Sodium methyl sulfate. 173.385 Section 173.385... Sodium methyl sulfate. Sodium methyl sulfate may be present in pectin in accordance with the following... subsequent treatment with sodium bicarbonate. (b) It does not exceed 0.1 percent by weight of the pectin....

  16. METHYLATION OF SODIUM ARSENITE BY VARIOUS MAMMALIAN CELLS

    EPA Science Inventory


    Methylation of Sodium Arsenite by various Mammalian Cells

    Methylation of arsenite (As 3-1) is thought to play an important role in the carcinogenicity of arsenic. AIM: I. Characterization of methylation of arsenite in primary rodent and transformed human cell lines. ...

  17. Methyl substituted polyimides containing carbonyl and ether connecting groups

    NASA Technical Reports Server (NTRS)

    Hergenrother, Paul M. (inventor); Havens, Stephen J. (inventor)

    1992-01-01

    Polyimides were prepared from the reaction of aromatic dianhydrides with novel aromatic diamines having carbonyl and ether groups connecting aromatic rings containing pendant methyl groups. The methyl substituent polyimides exhibit good solubility and form tough, strong films. Upon exposure to ultraviolet irradiation and/or heat, the methyl substituted polyimides crosslink to become insoluble.

  18. 75 FR 3233 - Sulfometuron Methyl Amendment to Reregistration Eligibility Decision

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-20

    ...following the Sulfometuron Methyl RED. Based on the new information...modifications to the Sulfometuron Methyl RED. FOR FURTHER INFORMATION CONTACT...Yard (South Bldg.), 2777 S. Crystal Dr., Arlington, VA. The hours...standards. In 2008, EPA issued a RED for sulfometuron methyl...

  19. Sequential gene promoter methylation during HPV-induced cervical carcinogenesis.

    PubMed

    Henken, F E; Wilting, S M; Overmeer, R M; van Rietschoten, J G I; Nygren, A O H; Errami, A; Schouten, J P; Meijer, C J L M; Snijders, P J F; Steenbergen, R D M

    2007-11-19

    We aimed to link DNA methylation events occurring in cervical carcinomas to distinct stages of HPV-induced transformation. Methylation specific-multiplex ligation-dependent probe amplification (MS-MLPA) analysis of cervical carcinomas revealed promoter methylation of 12 out of 29 tumour suppressor genes analysed, with MGMT being most frequently methylated (92%). Subsequently, consecutive stages of HPV16/18-transfected keratinocytes (n=11), ranging from pre-immortal to anchorage-independent phenotypes, were analysed by MS-MLPA. Whereas no methylation was evident in pre-immortal cells, progression to anchorage independence was associated with an accumulation of frequent methylation events involving five genes, all of which were also methylated in cervical carcinomas. TP73 and ESR1 methylation became manifest in early immortal cells followed by RARbeta and DAPK1 methylation in late immortal passages. Complementary methylation of MGMT was related to anchorage independence. Analysis of nine cervical cancer cell lines, representing the tumorigenic phenotype, revealed in addition to these five genes frequent methylation of CADM1, CDH13 and CHFR. In conclusion, eight recurrent methylation events in cervical carcinomas could be assigned to different stages of HPV-induced transformation. Hence, our in vitro model system provides a valuable tool to further functionally address the epigenetic alterations that are common in cervical carcinomas. PMID:17971771

  20. Arginine methylation regulates mitochondrial gene expression in Trypanosoma brucei through

    E-print Network

    Hing, Huey

    Arginine methylation regulates mitochondrial gene expression in Trypanosoma brucei through multiple, Buffalo, New York 14214, USA ABSTRACT Arginine methylation is a post-translational modification that impacts gene expression in both the cytoplasm and nucleus. Here, we demonstrate that arginine methylation

  1. 21 CFR 177.1830 - Styrene-methyl methacrylate copolymers.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Styrene-methyl methacrylate copolymers. 177.1830... Basic Components of Single and Repeated Use Food Contact Surfaces § 177.1830 Styrene-methyl methacrylate copolymers. Styrene-methyl methacrylate copolymers identified in this section may be safely used...

  2. 40 CFR 721.8660 - Propionic acid methyl ester (generic).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Propionic acid methyl ester (generic... Substances § 721.8660 Propionic acid methyl ester (generic). (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified generically as a propionic acid methyl...

  3. 40 CFR 721.9080 - Nitro methyl quinoline.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Nitro methyl quinoline. 721.9080... Substances § 721.9080 Nitro methyl quinoline. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified generically as nitro methyl quinoline (PMN P-96-1319)...

  4. 75 FR 5582 - Methyl Bromide; Amendments to Terminate Uses

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-03

    ... AGENCY Methyl Bromide; Amendments to Terminate Uses AGENCY: Environmental Protection Agency (EPA). ACTION... requested by the registrants and accepted by the Agency, of products containing the pesticide methyl bromide... Requests from the registrants listed in Table 2 to amend to terminate post-harvest methyl bromide uses...

  5. 40 CFR 180.492 - Triflusulfuron methyl; tolerances for residues.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Triflusulfuron methyl; tolerances for... § 180.492 Triflusulfuron methyl; tolerances for residues. (a) General. Tolerances are established for residues of the herbicide, triflusulfuron methyl 2- amino]carbonyl]amino]sulfonyl]-3-methylbenzoate in...

  6. Cobalt Limitation of Growth and Mercury Methylation in

    E-print Network

    Morel, François M. M.

    Cobalt Limitation of Growth and Mercury Methylation in Sulfate-Reducing Bacteria E I L E E N B . E.Hereweexploretheroleofcorrinoid-containing methyltransferases, which contain a cobalt-reactive center, in Hg methylation. To this end, we performed cobalt methylation rates of D. africanus cultures remained nearly constant regardless of the inorganic cobalt

  7. WEED CONTROL IN THE LIFE AFTER METHYL BROMIDE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Vegetable growers are losing the soil fumigant methyl bromide. Efforts are on-going to extend the deadline for using methyl bromide until suitable alternatives are developed. Regardless of whether the deadline is extended or not, growers need to begin to study alternatives to methyl bromide and be...

  8. ASSESSING THE EFFECTS OF HIGH METHIONINE INTAKE ON DNA METHYLATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Methylation of DNA occurs at cytosines within CpG (cytosine-guanine) dinucleotides and is one of several epigenetic mechanisms that serve to establish and maintain tissue-specific patterns of gene expression. The methyl groups transferred in mammalian DNA methylation reactions are ultimately derived...

  9. 40 CFR 721.10491 - Benzenepropanal,.alpha.-methyl-.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Benzenepropanal,.alpha.-methyl-. 721... Substances § 721.10491 Benzenepropanal,.alpha.-methyl-. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as benzenepropanal,.alpha.-methyl- (PMN...

  10. 40 CFR 721.10491 - Benzenepropanal,.alpha.-methyl-.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Benzenepropanal,.alpha.-methyl-. 721... Substances § 721.10491 Benzenepropanal,.alpha.-methyl-. (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified as benzenepropanal,.alpha.-methyl- (PMN...

  11. 40 CFR 721.9080 - Nitro methyl quinoline.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...2011-07-01 false Nitro methyl quinoline. 721.9080 Section 721.9080...Substances § 721.9080 Nitro methyl quinoline. (a) Chemical substance and significant...identified generically as nitro methyl quinoline (PMN P-96-1319) is subject...

  12. 40 CFR 721.9080 - Nitro methyl quinoline.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...2010-07-01 false Nitro methyl quinoline. 721.9080 Section 721.9080...Substances § 721.9080 Nitro methyl quinoline. (a) Chemical substance and significant...identified generically as nitro methyl quinoline (PMN P-96-1319) is subject...

  13. 21 CFR 173.250 - Methyl alcohol residues.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Methyl alcohol residues. 173.250 Section 173.250... CONSUMPTION Solvents, Lubricants, Release Agents and Related Substances § 173.250 Methyl alcohol residues. Methyl alcohol may be present in the following foods under the conditions specified: (a) In...

  14. Histone deacetylase inhibitors decrease reelin promoter methylation in vitro

    E-print Network

    Champagne, Frances A.

    Histone deacetylase inhibitors decrease reelin promoter methylation in vitro Colin P. Mitchell that induce reelin mRNA expression in vitro on the methylation status of the human reelin promoter in neural drugs reduced the methylation profile of the reelin promoter relative to untreated cells

  15. 75 FR 3233 - Sulfometuron Methyl Amendment to Reregistration Eligibility Decision

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-20

    ... November 12, 2008 (73 FR 219) (FRL-8388-5), the Agency received comments and mitigation proposals submitted... herbicide sulfometuron methyl. EPA conducted this reassessment of the Sulfometuron Methyl RED in response to... methyl concludes EPA's reregistration eligibility decision making process for this herbicide....

  16. Assessing Global Terrestrial Sources of Methyl Halides - Ozone Regulating Gases 

    E-print Network

    Gancarczyk, Maciej

    2010-11-24

    Methyl bromide (CH3Br) and methyl chloride (CH3Cl) play significant roles in the depletion of the stratospheric ozone layer. The vast portion of methyl halide sources and sinks sources and sinks are natural in origin. The sources are poorly...

  17. Global and gene specific DNA methylation changes during zebrafish development

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA methylation is dynamic through the life of an organism. In this study, we measured the global and gene specific DNA methylation changes in zebrafish at different developmental stages. We found that the methylation percentage of cytosines was 11.75 ± 0.96% in 3.3 hour post fertilization (hpf) zeb...

  18. Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2

    PubMed Central

    Kinde, Benyam; Gabel, Harrison W.; Gilbert, Caitlin S.; Griffith, Eric C.; Greenberg, Michael E.

    2015-01-01

    DNA methylation at CpG dinucleotides is an important epigenetic regulator common to virtually all mammalian cell types, but recent evidence indicates that during early postnatal development neuronal genomes also accumulate uniquely high levels of two alternative forms of methylation, non-CpG methylation and hydroxymethylation. Here we discuss the distinct landscape of DNA methylation in neurons, how it is established, and how it might affect the binding and function of protein readers of DNA methylation. We review studies of one critical reader of DNA methylation in the brain, the Rett syndrome protein methyl CpG-binding protein 2 (MeCP2), and discuss how differential binding affinity of MeCP2 for non-CpG and hydroxymethylation may affect the function of this methyl-binding protein in the nervous system. PMID:25739960

  19. A KINETIC STUDY OF THE METHANOLYSIS OF THE SULFONYLUREAS BENSULFURON METHYL AND SULFOMETURON METHYL USING CAPILLARY ELECTROPHORESIS

    EPA Science Inventory

    The instability of sulfonylureas in solution in methanol has led us to a kinetic study of methanolysis of two sulfonylureas using capillary electrophoresis. In a preliminary experiment solutions of the seven compounds, bensulfuron methyl, sulfometuron methyl, nicosulfuron, chlori...

  20. Simultaneous Determination of Salicylic Acid, Jasmonic Acid, Methyl Salicylate, and Methyl Jasmonate from Ulmus pumila Leaves by GC-MS

    PubMed Central

    Huang, Zhi-hong; Wang, Zhi-li; Shi, Bao-lin; Wei, Dong; Chen, Jian-xin; Wang, Su-li; Gao, Bao-jia

    2015-01-01

    Salicylic acid, jasmonic acid, methyl salicylate, and methyl jasmonate are important phytohormones and defensive signaling compounds, so it is of great importance to determine their levels rapidly and accurately. The study uses Ulmus pumila leaves infected by Tetraneura akinire Sasaki at different stages as materials; after extraction with 80% methanol and ethyl acetate and purification with primary secondary amine (PSA) and graphitized carbon blacks (GCB), the contents of signal compounds salicylic acid, jasmonic acid, methyl salicylate, and methyl jasmonate were determined by GC-MS. The results showed that the level of salicylic acid, jasmonic acid, methyl salicylate, and methyl jasmonate increased remarkably in U. pumila once infected by T. akinire Sasaki, but the maximums of these four compounds occurred at different times. Salicylic acid level reached the highest at the early stage, and jasmonic acid level went to the maximum in the middle stage; by contrast, change of content of methyl salicylate and methyl jasmonate was the quite opposite. PMID:26457083

  1. METHYL TERT-BUTYLETHER-WATER INTERACTION

    EPA Science Inventory

    Methyl tert-butyl ether (MTBE) is a well-known environmental contaminant owing to its high solubility in water. Since the early 1990s, MTBE has been added to gasoline to improve air quality in some metropolitan areas of the United States. Improved air quality was, however, achiev...

  2. 77 FR 35295 - Methyl Bromide; Pesticide Tolerances

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-13

    .... Background In the Federal Register of April 6, 2012 (77 FR 20752) (FRL-9345- 1), EPA issued a proposed rule... methyl bromide in or on cotton, undelinted seed under the Federal Food, Drug, and Cosmetic Act (FFDCA... on cotton, undelinted seed at 150 parts per million (ppm). EPA issued a proposed rule that...

  3. Methyl tert-butyl ether (MTBE)

    Integrated Risk Information System (IRIS)

    Methyl tert - butyl ether ( MTBE ) ; CASRN 1634 - 04 - 4 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments f

  4. 2-Methyl-4-chlorophenoxyacetic acid (MCPA)

    Integrated Risk Information System (IRIS)

    2 - Methyl - 4 - chlorophenoxyacetic acid ( MCPA ) ; CASRN 94 - 74 - 6 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard

  5. Methyl bromide alternatives being identified in Georgia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    It has become clear that the price and availability of methyl bromide (MB) will soon limit its use on Georgia farms. MB alternatives for many diseases and nematodes do exist. Recent research has focused on nutsedge response to MB alternatives in conjunction with various types of mulch. A study was c...

  6. Histone methylation makes its mark on longevity

    E-print Network

    Brunet, Anne

    Histone methylation makes its mark on longevity Shuo Han and Anne Brunet Department of Genetics), in longevity. Regulation of longevity Longevity is regulated by both genetic and environmental factors. Genetic factors regulate longevity in a conserved manner (Table 1), and recent evidence in mammalian cells indi

  7. METHYL BROMIDE ALTERNATIVES FOR CALIFORNIA STRAWBERRY NURSERIES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The effects of methyl bromide (MB) alternative fumigants on soil pests, plant productivity in nursery and fruiting fields, as well as production costs, were evaluated in California strawberry nurseries by an interdisciplinary team. Our trials followed nursery stock through low and high elevation ph...

  8. Challenges in Weed Management Without Methyl Bromide

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Methyl bromide has been used for several decades for pre-plant soil fumigation in high value agricultural and horticultural crops because it can provide broad-spectrum control of insects, nematodes, pathogens, and weeds. However, MeBr has been identified as a powerful ozone-depleting chemical and i...

  9. Epoxidation of Methyl Oleate using Heterogeneous Catalyst

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this work we studied the catalytic activity of commercial alumina, and laboratory synthesized alumina doped with Lewis acid metals, in the epoxidation of methyl oleate with aqueous hydrogen peroxide. It was observed that the reaction yields increased when the amount of catalyst, the quantity of ...

  10. Can Georgia growers replace methyl bromide

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The price and availability of methyl bromide is limiting its use on Georgia farms; the need for an alternative is essential for sustainable vegetable production in GA. Three alternatives were evaluated in on-farm trials in the spring 2007 in Tift, Colquitt and Echols Counties. Treatments were replic...

  11. Low temperature synthesis of methyl formate

    DOEpatents

    Mahajan, Devinder (Selden, NY); Slegeir, William A. (Hampton Bays, NY); Sapienza, Richard S. (Shoreham, NY); O'Hare, Thomas E. (Huntington Station, NY)

    1986-01-01

    A gas reaction process for the preferential production of methyl formate over the co-production of methanol wherein the reactant ratio of CO/H.sub.2 is upgraded and this reaction takes place at low temperatures of 50.degree.-150.degree. C. and moderate pressures of .gtoreq.100 psi.

  12. 27 CFR 21.116 - Methyl alcohol.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Methyl alcohol. 21.116 Section 21.116 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS FORMULAS FOR DENATURED ALCOHOL AND RUM Specifications for Denaturants §...

  13. METHYLATED TRIVALENT ARSENIC SPECIES ARE GENOTOXIC

    EPA Science Inventory

    ABSTRACT

    The genotoxic effects of arsenic compounds are generally believed to result from other than direct interacton with DNA. The reactivties of methyloxarsine (MAsIII) and iododimethylarsine (DMAsIII), two methylated trivalent arsenicals, toward supercoiled X174 RFI ...

  14. Genetic Control and Evolution of Anthocyanin Methylation.

    PubMed

    Provenzano, Sofia; Spelt, Cornelis; Hosokawa, Satoko; Nakamura, Noriko; Brugliera, Filippa; Demelis, Linda; Geerke, Daan P; Schubert, Andrea; Tanaka, Yoshikazu; Quattrocchio, Francesca; Koes, Ronald

    2014-05-15

    Anthocyanins are a chemically diverse class of secondary metabolites that color most flowers and fruits. They consist of three aromatic rings that can be substituted with hydroxyl, sugar, acyl, and methyl groups in a variety of patterns depending on the plant species. To understand how such chemical diversity evolved, we isolated and characterized METHYLATION AT THREE2 (MT2) and the two METHYLATION AT FIVE (MF) loci from Petunia spp., which direct anthocyanin methylation in petals. The proteins encoded by MT2 and the duplicated MF1 and MF2 genes and a putative grape (Vitis vinifera) homolog Anthocyanin O-Methyltransferase1 (VvAOMT1) are highly similar to and apparently evolved from caffeoyl-Coenzyme A O-methyltransferases by relatively small alterations in the active site. Transgenic experiments showed that the Petunia spp. and grape enzymes have remarkably different substrate specificities, which explains part of the structural anthocyanin diversity in both species. Most strikingly, VvAOMT1 expression resulted in the accumulation of novel anthocyanins that are normally not found in Petunia spp., revealing how alterations in the last reaction can reshuffle the pathway and affect (normally) preceding decoration steps in an unanticipated way. Our data show how variations in gene expression patterns, loss-of-function mutations, and alterations in substrate specificities all contributed to the anthocyanins' structural diversity. PMID:24830298

  15. 27 CFR 21.116 - Methyl alcohol.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2014-04-01 2014-04-01 false Methyl alcohol. 21.116 Section 21.116 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY ALCOHOL FORMULAS FOR DENATURED ALCOHOL AND RUM Specifications for Denaturants §...

  16. 27 CFR 21.116 - Methyl alcohol.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2011-04-01 2011-04-01 false Methyl alcohol. 21.116 Section 21.116 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS FORMULAS FOR DENATURED ALCOHOL AND RUM Specifications for Denaturants §...

  17. 27 CFR 21.116 - Methyl alcohol.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2013-04-01 2013-04-01 false Methyl alcohol. 21.116 Section 21.116 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY ALCOHOL FORMULAS FOR DENATURED ALCOHOL AND RUM Specifications for Denaturants §...

  18. 27 CFR 21.116 - Methyl alcohol.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2012-04-01 2012-04-01 false Methyl alcohol. 21.116 Section 21.116 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS FORMULAS FOR DENATURED ALCOHOL AND RUM Specifications for Denaturants §...

  19. Methyl bromide alternatives for raspberry nurseries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Raspberry nurseries must produce plants free from disease to meet marketplace and export requirements. Minor disease infestations in nurseries can cause severe epidemics in production fields. Raspberry nurseries presently qualify for critical use and quarantine/preshipment exemptions to use Methyl B...

  20. SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation

    PubMed Central

    Varshney, Dhaval; Vavrova-Anderson, Jana; Oler, Andrew J.; Cowling, Victoria H.; Cairns, Bradley R.; White, Robert J.

    2015-01-01

    Short interspersed nuclear elements (SINEs), such as Alu, spread by retrotransposition, which requires their transcripts to be copied into DNA and then inserted into new chromosomal sites. This can lead to genetic damage through insertional mutagenesis and chromosomal rearrangements between non-allelic SINEs at distinct loci. SINE DNA is heavily methylated and this was thought to suppress its accessibility and transcription, thereby protecting against retrotransposition. Here we provide several lines of evidence that methylated SINE DNA is occupied by RNA polymerase III, including the use of high-throughput bisulphite sequencing of ChIP DNA. We find that loss of DNA methylation has little effect on accessibility of SINEs to transcription machinery or their expression in vivo. In contrast, a histone methyltransferase inhibitor selectively promotes SINE expression and occupancy by RNA polymerase III. The data suggest that methylation of histones rather than DNA plays a dominant role in suppressing SINE transcription. PMID:25798578