Science.gov

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-1:2κ(8)N,N',O:O;3:2κ(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. Epigenome-wide association of liver methylation patterns and complex metabolic traits in mice.

    PubMed

    Orozco, Luz D; Morselli, Marco; Rubbi, Liudmilla; Guo, Weilong; Go, James; Shi, Huwenbo; Lopez, David; Furlotte, Nicholas A; Bennett, Brian J; Farber, Charles R; Ghazalpour, Anatole; Zhang, Michael Q; Bahous, Renata; Rozen, Rima; Lusis, Aldons J; Pellegrini, Matteo

    2015-06-01

    Heritable epigenetic factors can contribute to complex disease etiology. Here we examine the contribution of DNA methylation to complex traits that are precursors to heart disease, diabetes, and osteoporosis. We profiled DNA methylation in the liver using bisulfite sequencing in 90 mouse inbred strains, genome-wide expression levels, proteomics, metabolomics, and 68 clinical traits and performed epigenome-wide association studies (EWAS). We found associations with numerous clinical traits including bone density, insulin resistance, expression, and protein and metabolite levels. A large proportion of associations were unique to EWAS and were not identified using GWAS. Methylation levels were regulated by genetics largely in cis, but we also found evidence of trans regulation, and we demonstrate that genetic variation in the methionine synthase reductase gene Mtrr affects methylation of hundreds of CpGs throughout the genome. Our results indicate that natural variation in methylation levels contributes to the etiology of complex clinical traits. PMID:26039453

  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. Physical properties and biological activities of hesperetin and naringenin in complex with methylated β-cyclodextrin

    PubMed Central

    Sangpheak, Waratchada; Kicuntod, Jintawee; Schuster, Roswitha; Rungrotmongkol, Thanyada; Wolschann, Peter; Kungwan, Nawee; Viernstein, Helmut

    2015-01-01

    Summary The aim of this work is to improve physical properties and biological activities of the two flavanones hesperetin and naringenin by complexation with β-cyclodextrin (β-CD) and its methylated derivatives (2,6-di-O-methyl-β-cyclodextrin, DM-β-CD and randomly methylated-β-CD, RAMEB). The free energies of inclusion complexes between hesperetin with cyclodextrins (β-CD and DM-β-CD) were theoretically investigated by molecular dynamics simulation. The free energy values obtained suggested a more stable inclusion complex with DM-β-CD. The vdW force is the main guest–host interaction when hesperetin binds with CDs. The phase solubility diagram showed the formation of a soluble complex of AL type, with higher increase in solubility and stability when hesperetin and naringenin were complexed with RAMEB. Solid complexes were prepared by freeze-drying, and the data from differential scanning calorimetry (DSC) confirmed the formation of inclusion complexes. The data obtained by the dissolution method showed that complexation with RAMEB resulted in a better release of both flavanones to aqueous solution. The flavanones-β-CD/DM-β-CD complexes demonstrated a similar or a slight increase in anti-inflammatory activity and cytotoxicity towards three different cancer cell lines. The overall results suggested that solubilities and bioactivities of both flavanones were increased by complexation with methylated β-CDs. PMID:26877798

  5. Complex reaction dynamics in the cerium-bromate-2-methyl-1,4-hydroquinone photoreaction.

    PubMed

    Bell, Jeffrey G; Green, James R; Wang, Jichang

    2014-10-23

    Spontaneous oscillations with a long induction time were observed in the bromate-2-methyl-1,4-hydroquinone photoreaction in a batch reactor, where removal of illumination effectively quenched any reactivity. A substantial lengthening of the oscillatory window and a dramatic increase in the complexity of the reaction behavior arose upon the addition of cerium ions, in which separate bifurcation regions and mixed mode oscillations were present. The complexity has a strong dependence on the intensity of illumination supplied to the system and on the initial concentrations of the reactants. (1)H NMR spectroscopy measurements show that the photoreduction of 2-methyl-1,4-benzoquinone leads to the formation of 2-methyl-1,4-hydroquinone and the compound 2-hydroxy-3-methyl-1,4-benzoquinone. Spectroscopic investigation also indicates that the presence of methyl group hinders the bromination of the studied organic substrate 2-methyl-1,4-hydroquinone, resulting in the formation of 2-methyl-1,4-benzoquinone. PMID:25279948

  6. 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; Espaola, 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.

  7. Kinetics of DNA methylation inheritance by the Dnmt1-including complexes during the cell cycle

    PubMed Central

    2012-01-01

    Background The clonal transmission of lineage-specific DNA methylation patterns in a mammalian genome during the cellular division is a crucial biological process controlled by the DNA methyltransferase Dnmt1, mainly. To investigate possible dynamic mechanisms of DNA methylation inheritance during the cell cycle, we used a Proximity Ligation In Situ Assay (P-LISA) to analyze the kinetic of formation and DNA recruitment of Dnmt1-including complexes. Results P-LISA, sequential chromatin immunoprecipitation and quantitative methylation specific PCR revealed that the Dnmt1/PCNA/UHRF1-including complexes are mainly formed and recruited on DNA during the S-phase of cell cycle, while the formation and the DNA recruitment of several Dnmt1/transcription factors-including complexes are not S-phase dependent but are G0/G1 and/or G2/M phases dependent. Conclusion Our data confirm that DNA methylation inheritance occurs in S-phase, and demonstrate that DNA methylation inheritance can also occur in G0/G1 and G2/M phases of the cell cycle. PMID:22348533

  8. A protein complex required for polymerase V transcripts and RNA-directed DNA methylation in plants

    PubMed Central

    Law, Julie A.; Ausin, Israel; Johnson, Lianna M.; Vashisht, Ajay A.; Zhu, Jian-Kang; Wohlschlegel, James A.; Jacobsen, Steven E.

    2010-01-01

    Summary DNA methylation is an epigenetic modification associated with gene silencing. In Arabidopsis, DNA methylation is established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), which is targeted by small interfering RNAs through a pathway termed RNA-directed DNA methylation (RdDM)[1, 2]. Recently, RdDM was shown to require intergenic noncoding (IGN) transcripts that are dependent on the Pol V polymerase. These transcripts are proposed to function as scaffolds for the recruitment of downstream RdDM proteins, including DRM2, to loci that produce both siRNAs and IGN transcripts[3]. However, the mechanism(s) through which Pol V is targeted to specific genomic loci remains largely unknown. Through affinity purification of two known RdDM components, DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 1 (DRD1)[4] and DEFECTIVE IN MERISTEM SILENCING 3 (DMS3)[5, 6], we found that they copurify with each other and with a novel protein, RNA-DIRECTED DNA METHYLATION 1 (RDM1), forming a complex we term DDR. We also found that DRD1 copurified with Pol V subunits and that, RDM1, like DRD1[3] and DMS3[7], is required for the production of Pol V-dependent transcripts. These results suggest that the DDR complex acts in RdDM at a step upstream of the recruitment or activation of Pol V. PMID:20409711

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

    PubMed

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

    2016-03-13

    We perform a statistical study of the distances between successive occurrences of a given dinucleotide in the DNA sequence for a number of organisms of different complexity. Our analysis highlights peculiar features of the CG dinucleotide 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 CG dinucleotides provides useful insights into characterizing and classifying organisms in terms of methylation functionalities. PMID:26857665

  10. 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.

  11. 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

    2015-12-14

    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

  12. 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...

  13. 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.

  14. Decoding of Methylated Histone H3 Tail by the Pygo-BCL9 Wnt Signaling Complex

    PubMed Central

    Fiedler, Marc; Snchez-Barrena, Mara Jos; Nekrasov, Maxim; Mieszczanek, Juliusz; Rybin, Vladimir; Mller, Jrg; Evans, Phil; Bienz, Mariann

    2008-01-01

    Summary Pygo and BCL9/Legless transduce the Wnt signal by promoting the transcriptional activity of ?-catenin/Armadillo in normal and malignant cells. We show that human and Drosophila Pygo PHD fingers associate with their cognate HD1 domains from BCL9/Legless to bind specifically to the histone H3 tail methylated at lysine 4 (H3K4me). The crystal structures of ternary complexes between PHD, HD1, and two different H3K4me peptides reveal a unique mode of histone tail recognition: efficient histone binding requires HD1 association, and the PHD-HD1 complex binds preferentially to H3K4me2 while displaying insensitivity to methylation of H3R2. Therefore, this is a prime example of histone tail binding by a PHD finger (of Pygo) being modulated by a cofactor (BCL9/Legless). Rescue experiments in Drosophila indicate that Wnt signaling outputs depend on histone decoding. The specificity of this process provided by the Pygo-BCL9/Legless complex suggests that this complex facilitates an early step in the transition from gene silence to Wnt-induced transcription. PMID:18498752

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

    PubMed

    Schdle, Dorothea; Maichle-Mssmer, Ccilia; Schdle, 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

  16. Structure and Electronic Spectra of Purine-Methyl Viologen Charge Transfer Complexes

    PubMed Central

    Jalilov, Almaz S.; Patwardhan, Sameer; Singh, Arunoday; Simeon, Tomekia; Sarjeant, Amy A.; Schatz, George C.; Lewis, Frederick D.

    2014-01-01

    The structure and properties of the electron donor-acceptor complexes formed between methyl viologen (MV) and purine nucleosides and nucleotides in water and the solid state have been investigated using a combination of experimental and theoretical methods. Solution studies were performed using UV-vis and 1H NMR spectroscopy. Theoretical calculations were performed within the framework of density functional theory (DFT). Energy decomposition analysis indicates that dispersion and induction (charge-transfer) interactions dominate the total binding energy, whereas electrostatic interactions are largely repulsive. The appearance of charge transfer bands in the absorption spectra of the complexes are well described by time-dependent (TD) DFT and are further explained in terms of the redox properties of purine monomers and solvation effects. Crystal structures are reported for complexes of methyl viologen with the purines 2?-deoxyguanosine 3?-monophosphate GMP (DAD?DAD? type) and 7-deazaguanosine zG (DAD?ADAD? type). Comparison of the structures determined in the solid state and by theoretical methods in solution provides valuable insights into the nature of charge-transfer interactions involving purine bases as electron donors. PMID:24294996

  17. 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.

  18. Antifungal activity of α-methyl trans cinnamaldehyde, its ligand and metal complexes: promising growth and ergosterol inhibitors.

    PubMed

    Shreaz, Sheikh; Sheikh, Rayees A; Bhatia, Rimple; Neelofar, Khan; Imran, Sheikh; Hashmi, Athar A; Manzoor, Nikhat; Basir, Seemi F; Khan, Luqman A

    2011-10-01

    Antifungal effectivity and utility of cinnamaldehyde is limited because of its high MIC and skin sensitivity. In this study, α-methyl trans cinnamaldehyde, a less irritating derivative, have been self coupled and complexed with Co(II) and Ni(II) to generate N, N'-Bis (α-methyl trans cinnamadehyde) ethylenediimine [C(22)H(24)N(2)], [Co(C(44)H(48)N(4))Cl(2)] and [Ni(C(44)H(48)N(4))Cl(2)]. Ligand and complexes were characterized on the basis of FTIR, ESI-MS, IR and (1)HNMR techniques. Synthesized ligand [L] and complexes were investigated for their MICs, inhibition of ergosterol biosynthesis and H(+) extrusion against three strains of Candida: C. albicans 44829, C. tropicalis 750 and C. krusei 6258. Average of three species MIC of methyl cinnamaldehyde is 317 μg/ml (2168 μM). Compared to methyl cinnamaldehyde ligand [L], Co(II) and Ni(II) complex are found to be 4.48, 17.78 and 21.46 times more effective in liquid medium and 2.73, 8.93 and 10.38 times more effective in solid medium. At their respective MIC(90) average inhibition of ergosterol biosynthesis caused by methyl cinnamaldehyde, ligand [L], Co(II) and Ni(II) complex, respectively was 80, 78, 90 and 93%. H(+) extrusion was also significantly inhibited but did not co-relate well with MIC(90). Results indicate ergosterol biosynthesis as site of action of α-methyl cinnamaldehyde, synthesized ligand and complexes. α-methyl cinnamaldehyde and ligand did not show any toxicity against H9c2 rat cardiac myoblast cell, whereas Co(II) and Ni(II) complexes on an average produced 19% cellular toxicity. PMID:21476019

  19. Synthesis, structural features, and methyl methacrylate polymerisation of binuclear zinc(II) complexes with tetradentate pyrazolyl ligands

    NASA Astrophysics Data System (ADS)

    Kim, Sunghoon; Kim, Dongil; Lee, Ha-Jin; Lee, Hyosun

    2014-04-01

    The reaction of ZnCl2 with ancillary ligands, including 1,4-bis-(N,N-di-(1H-pyrazolyl-1-methyl)amine)benzene (L1) and 4,4?-bis-(N,N-di(1H-pyrazolyl-1-methyl)phenyl)methane (L2), in ethanol yields Zn(II) chloride complexes, i.e., 1,4-bis-(N,N-di-(1H-pyrazolyl-1-methyl)amine)benzene(dichloro)Zn(II) [L1Zn2Cl4] and 4,4?-bis-(N,N-di-(1H-pyrazolyl-1-methyl)phenyl)methane(dichloro)Zn(II) [L2Zn2Cl4]. The X-ray crystal structures of Zn(II) complexes revealed that they are binuclear, and each zinc atom has a distorted tetrahedral geometry which involves a nitrogen atom from two pyrazole groups and two chloro ligands. The catalytic activity of [L1Zn2Cl4] and [L2Zn2Cl4] for the polymerisation of methyl methacrylate (MMA) in the presence of modified methylaluminoxane (MMAO) increased by twofold compared to the corresponding monomeric Zn(II) complex, N,N-bis(1H-pyrazolyl-1-methyl)aniline(dichloro)Zn(II) [LZnCl2], at 60 C.

  20. 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.

  1. Reaction time dependent formation of Pd(II) and Pt(II) complexes of bis(methyl)thiasalen podand.

    PubMed

    Dutta, Pradip Kr; Panda, Snigdha; Krishna, G Rama; Reddy, C Malla; Zade, Sanjio S

    2013-01-14

    Thiasalen podand 9 having S2N2 donor set has been synthesized by the condensation of 2-methylthiobenzaldehyde with ethylenediamine. The reaction of the thiasalen podand ligand with Pd(II) afforded two complexes depending on the reaction time. Shorter reaction time (5 min) afforded thioether complex 10; whereas with increase in reaction time (4 h) thioether-thiolate complex 11 was obtained via cleavage of one of the two S-C(Me) bonds of bis(methyl)thiasalen podand upon complexation. The reaction of 9 with Pt(II) afforded only thiolate-thioether complex 12 independent of the reaction time. The cleavage of both the S-C(Me) bonds of bis(methyl)thiasalen to afford bisthiolate complexes has never been observed. The structures of thiasalen podands and all three complexes have been determined by single crystal X-ray diffraction analysis. All three complexes possess a square planar geometry around the metal centres. Weak van der Waals interactions through C-HF interactions are present in all three complexes leading to the formation of supramolecular synthons and the supramolecular structures are stabilized by aromatic ?? interactions, which leads to the formation of 3D pseudo-double helical network packing. Under similar conditions bis(methyl)salen did not form any complexes with Pd(II) and Pt(II). PMID:23073301

  2. 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

  3. 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.

  4. 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.

  5. Whole-genome DNA methylation patterns and complex associations with gene structure and expression during flower development in Arabidopsis.

    PubMed

    Yang, Hongxing; Chang, Fang; You, Chenjiang; Cui, Jie; Zhu, Genfeng; Wang, Lei; Zheng, Yu; Qi, Ji; Ma, Hong

    2015-01-01

    Flower development is a complex process requiring proper spatiotemporal expression of numerous genes. Accumulating evidence indicates that epigenetic mechanisms, including DNA methylation, play essential roles in modulating gene expression. However, few studies have examined the relationship between DNA methylation and floral gene expression on a genomic scale. Here we present detailed analyses of DNA methylomes at single-base resolution for three Arabidopsis floral periods: meristems, early flowers and late flowers. We detected 1.5 million methylcytosines, and estimated the methylation levels for 24 035 genes. We found that many cytosine sites were methylated de novo from the meristem to the early flower stage, and many sites were demethylated from early to late flowers. A comparison of the transcriptome data of the same three periods revealed that the methylation and demethylation processes were correlated with expression changes of >3000 genes, many of which are important for normal flower development. We also found different methylation patterns for three sequence contexts ((m) CG, (m) CHG and (m) CHH) and in different genic regions, potentially with different roles in gene expression. PMID:25404462

  6. 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...

  7. 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).

  8. 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- 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

  9. Cytotoxic and Antitumour Studies of Acetoacetanilide N(4)-methyl(phenyl)thiosemicarbazone and its Transition Metal Complexes

    PubMed Central

    Priya, N. P.; Firdous, A. P.; Jeevana, R.; Aravindakshan, K. K.

    2015-01-01

    Cytotoxic activities of acetoacetanilide N(4)-methyl(phenyl)thiosemicarbazone (L2H) and its seven different metal complexes were studied. Of these, IC50 value of the copper complex was found to be 46 μg/ml. Antitumour studies of this copper complex was carried out using Daltons Lymphoma Ascites cell-induced solid tumour model and Ehrlich's Ascites Carcinoma cell-induced ascites tumour model. Administration of the copper complex at different concentrations (10, 5 and 1 mg/kg b. wt) inhibited the solid tumour development in mice and increased the mean survival rate and the life span of Ascites tumour bearing mice in a concentration dependent manner.

  10. 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 to 3.61 . Our results provide a dynamic process concerning the motion of methyl group above the benzene ring.

  11. Theory of electronic structure and nuclear quadrupole interactions in the BF3-NH3 complex and methyl derivatives

    NASA Astrophysics Data System (ADS)

    Pink, R. H.; Dubey, Archana; Mahato, Dip N.; Badu, S. R.; Scheicher, R. H.; Mahanti, Mahendra K.; Huang, M. B.; Saha, H. P.; Chow, Lee; Das, T. P.

    Magnetic Hyperfine and Nuclear Quadrupole Interactions (HPI and NQI) are now important tools for characterization of systems of interest in materials research and industry. Boron-Trifluoride is an inorganic compound that is very important in this respect as a catalyst in chemical physics research and industry, forming complexes in the process with compounds like ammonia, water and methyl alcohol. The present paper deals with the BP3-NH3 complex and methyl derivatives BP3NHx(CH3)3-x for which we have studied the electronic structures, binding energies, and 19F* (I=5/2) nuclear quadrupole interactions using the first-principles Hartree-Fock-Roothaan procedure combined with electron correlation effects. Our results for the 19F* nuclear quadrupole coupling constant (e 2qQ/h) in units of MHz compare well with experiment. Trends in the binding energies and NQI parameters between the complexes are discussed.

  12. Theory of electronic structure and nuclear quadrupole interactions in the BF3 NH3 complex and methyl derivatives

    NASA Astrophysics Data System (ADS)

    Pink, R. H.; Dubey, Archana; Mahato, Dip N.; Badu, S. R.; Scheicher, R. H.; Mahanti, Mahendra K.; Huang, M. B.; Saha, H. P.; Chow, Lee; Das, T. P.

    2007-04-01

    Magnetic Hyperfine and Nuclear Quadrupole Interactions (HFI and NQI) are now important tools for characterization of systems of interest in materials research and industry. Boron-Trifluoride is an inorganic compound that is very important in this respect as a catalyst in chemical physics research and industry, forming complexes in the process with compounds like ammonia, water and methyl alcohol. The present paper deals with the BF3 NH3 complex and methyl derivatives BF3NHx(CH3)3-x for which we have studied the electronic structures, binding energies, and 19F* ( I = 5/2) nuclear quadrupole interactions using the first-principles Hartree Fock Roothaan procedure combined with electron correlation effects. Our results for the 19F* nuclear quadrupole coupling constant ( e 2 qQ/ h) in units of MHz compare well with experiment. Trends in the binding energies and NQI parameters between the complexes are discussed.

  13. N-methyl-D-aspartate/phencyclidine receptor complex of rat forebrain: Purification and biochemical characterization

    SciTech Connect

    Ikin, A.F.; Kloog, Y.; Sokolovsky, M. )

    1990-03-06

    The N-methyl-D-aspartate NMDA/phencyclidine (PCP) receptor from rat forebrain was solubilized with sodium cholate and purified by affinity chromatography on amino-PCP-agarose. A 3,700-fold purification was achieved. Polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate and dithiothreitol revealed four major bands of M{sub r} 67,000, 57,000, 46,000, and 33,000. ({sup 3}H)Azido-PCP was irreversibly incorporated into each of these bands after UV irradiation. The dissociation constant (K{sub d}) of (1-(2-thienyl)cyclohexyl)piperidine (({sup 3}H)TCP) binding to the purified NMDA/PCP receptor was 120 nM. The maximum specific binding (B{sub max}) for ({sup 3}H)TCP binding was 3.3 nmol/mg of protein. The pharmacological profile of the purified receptor complex was similar to that of the membranal and soluble receptors. The binding of ({sup 3}H)TCP to the purified receptor was modulated by the NMDA receptor ligands glutamate, glycine, and NMDA.

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

    PubMed Central

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

    2015-01-01

    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 pre-treatment with Escherichia coli AlkB to demethylate 1-methyladenosine, 3-methylcytidine, and 1-methylguanosine, all commonly found in transfer RNAs. 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-derived small RNAs accurately recapitulate the m1A 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-derived RNAs as biomarkers or signaling molecules. PMID:26237225

  15. 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

  16. ?-[11C]-Methyl-l-tryptophanPET in 191 patients with tuberous sclerosis complex

    PubMed Central

    Luat, Aimee F.; Kumar, Ajay; Govindan, Rajkumar; Pawlik, Kathy; Asano, Eishi

    2013-01-01

    Objectives: This was an observational study done on a large cohort of patients with tuberous sclerosis complex (TSC) to determine whether i) the presence of ?-[11C]-methyl-l-tryptophan (AMT) hotspots is related to the duration of seizure intractability, ii) the presence of AMT hotspots is related to specific TSC gene mutations, and iii) there is concordance between areas with an AMT hotspot and seizure lateralization/localization on scalp EEG. Methods: One hundred ninety-one patients (mean age: 6.7 years; median: 5 years; range: 3 months to 37 years) with TSC and intractable epilepsy were included. All patients underwent AMT-PET scan. AMT uptake in each tuber and normal-appearing cortex was measured and correlated with clinical, scalp EEG, and, if available, electrocorticographic data. Results: The longer the duration of seizure intractability, the greater the number of AMT hotspots (r = 0.2; p = 0.03). AMT hotspots were seen in both TSC1 and TSC2. There was excellent agreement in seizure focus lateralization between ictal scalp EEG and AMT-PET (Cohen ? 0.94) in 68 of 95 patients in whom both ictal video-EEG and AMT-PET showed lateralizing findings; in 28 of 68 patients (41%), AMT was more localizing. Furthermore, AMT-PET was localizing in 10 of 17 patients (58%) with nonlateralized ictal EEG. Conclusion: AMT-PET, when used together with video-EEG, provides additional lateralization/localization data, regardless of TSC mutation. The duration of seizure intractability may predict the multiplicity of areas with AMT hotspots. PMID:23851963

  17. Influence of the preparation method on the physicochemical properties of indomethacin and methyl-β-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-β-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-β-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

  18. 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 π-methyl- L-histidine (π-methis) and τ-methyl- L-histidine (τ-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 π-methis or τ-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 π-methis or τ-methis) with respect to the UV charge transfer process to copper(II) ion.

  19. 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.

  20. 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.

  1. Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis

    PubMed Central

    Tomazou, Eleni M; Rakyan, Vardhman K; Lefebvre, Gregory; Andrews, Robert; Ellis, Peter; Jackson, David K; Langford, Cordelia; Francis, Matthew D; Bckdahl, Liselotte; Miretti, Marcos; Coggill, Penny; Ottaviani, Diego; Sheer, Denise; Murrell, Adele; Beck, Stephan

    2008-01-01

    Background The major histocompatibility complex (MHC) is essential for human immunity and is highly associated with common diseases, including cancer. While the genetics of the MHC has been studied intensively for many decades, very little is known about the epigenetics of this most polymorphic and disease-associated region of the genome. Methods To facilitate comprehensive epigenetic analyses of this region, we have generated a genomic tiling array of 2 Kb resolution covering the entire 4 Mb MHC region. The array has been designed to be compatible with chromatin immunoprecipitation (ChIP), methylated DNA immunoprecipitation (MeDIP), array comparative genomic hybridization (aCGH) and expression profiling, including of non-coding RNAs. The array comprises 7832 features, consisting of two replicates of both forward and reverse strands of MHC amplicons and appropriate controls. Results Using MeDIP, we demonstrate the application of the MHC array for DNA methylation profiling and the identification of tissue-specific differentially methylated regions (tDMRs). Based on the analysis of two tissues and two cell types, we identified 90 tDMRs within the MHC and describe their characterisation. Conclusion A tiling array covering the MHC region was developed and validated. Its successful application for DNA methylation profiling indicates that this array represents a useful tool for molecular analyses of the MHC in the context of medical genomics. PMID:18513384

  2. Jarid2 Methylation via the PRC2 Complex Regulates H3K27me3 Deposition during Cell Differentiation.

    PubMed

    Sanulli, Serena; Justin, Neil; Teissandier, Aurlie; Ancelin, Katia; Portoso, Manuela; Caron, Matthieu; Michaud, Audrey; Lombard, Berangre; da Rocha, Simao T; Offer, John; Loew, Damarys; Servant, Nicolas; Wassef, Michel; Burlina, Fabienne; Gamblin, Steve J; Heard, Edith; Margueron, Raphal

    2015-03-01

    Polycomb Group (PcG) proteins maintain transcriptional repression throughout development, mostly by regulating chromatin structure. Polycomb Repressive Complex 2 (PRC2), a component of the Polycomb machinery, is responsible for the methylation of histone H3 lysine 27 (H3K27me2/3). Jarid2 was previously identified as a cofactor of PRC2, regulating PRC2 targeting to chromatin and its enzymatic activity. Deletion of Jarid2 leads to impaired orchestration of gene expression during cell lineage commitment. Here, we reveal an unexpected crosstalk between Jarid2 and PRC2, with Jarid2 being methylated by PRC2. This modification is recognized by the Eed core component of PRC2 and triggers an allosteric activation of PRC2's enzymatic activity. We show that Jarid2 methylation is important to promote PRC2 activity at a locus devoid of H3K27me3 and forthe correct deposition of this mark during cell differentiation. Our results uncover a regulation loop where Jarid2 methylation fine-tunes PRC2 activity depending on the chromatin context. PMID:25620564

  3. G9a-mediated methylation of ERα links the PHF20/MOF histone acetyltransferase complex to hormonal gene expression

    PubMed Central

    Zhang, Xi; Peng, Danni; Xi, Yuanxin; Yuan, Chao; Sagum, Cari A.; Klein, Brianna J.; Tanaka, Kaori; Wen, Hong; Kutateladze, Tatiana G.; Li, Wei; Bedford, Mark T.; Shi, Xiaobing

    2016-01-01

    The euchromatin histone methyltransferase 2 (also known as G9a) methylates histone H3K9 to repress gene expression, but it also acts as a coactivator for some nuclear receptors. The molecular mechanisms underlying this activation remain elusive. Here we show that G9a functions as a coactivator of the endogenous oestrogen receptor α (ERα) in breast cancer cells in a histone methylation-independent manner. G9a dimethylates ERα at K235 both in vitro and in cells. Dimethylation of ERαK235 is recognized by the Tudor domain of PHF20, which recruits the MOF histone acetyltransferase (HAT) complex to ERα target gene promoters to deposit histone H4K16 acetylation promoting active transcription. Together, our data suggest the molecular mechanism by which G9a functions as an ERα coactivator. Along with the PHF20/MOF complex, G9a links the crosstalk between ERα methylation and histone acetylation that governs the epigenetic regulation of hormonal gene expression. PMID:26960573

  4. 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 CXXCBAH1 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

  5. 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.

  6. 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.

  7. 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...

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

    NASA Astrophysics Data System (ADS)

    Lazarowska, Agata; Jzefowicz, Marek; Heldt, Janina R.; Heldt, Jzef

    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.

  9. A TDG/CBP/RAR? ternary complex mediates the retinoic acid-dependent expression of DNA methylation-sensitive genes.

    PubMed

    Lger, Hlne; Smet-Nocca, Caroline; Attmane-Elakeb, Amel; Morley-Fletcher, Sara; Benecke, Arndt G; Eilebrecht, Sebastian

    2014-02-01

    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

  10. Comparison of DNA Methylation and Expression Pattern of S100 and Other Epidermal Differentiation Complex Genes in Differentiating Keratinocytes.

    PubMed

    Sobiak, Barbara; Graczyk-Jarzynka, Agnieszka; Leśniak, Wiesława

    2016-05-01

    Epidermal Differentiation Complex (EDC) is a gene cluster on human chromosome 1 q21, which comprises genes encoding four protein families: S100, S100 fused (SFTP), small proline-rich region (SPRR) and late cornified envelope (LCE) proteins. Contrary to the latter three families, which group proteins important for skin barrier formation, the role of S100 proteins has not been well defined and there are no systematic comparative data concerning their expression in the epidermis. Furthermore, little is known about epigenetic mechanisms controlling changes in S100 and other EDC genes expression in differentiating epidermis. In our study, using real-time PCR, we followed the expression of nine S100 genes at subsequent stages of differentiation of primary human keratinocytes and found that they exhibited different expression patterns. Then, we confronted the expression level in undifferentiated and differentiated keratinocytes with the extent of DNA methylation within their promoter or intragenic regions assessed by bisulfite sequencing. Methylation analysis was also performed for three other EDC genes of known expression pattern (involucrin, loricrin, and NICE-1) and a recently identified evolutionary conserved region with defined enhancer properties. The results indicate that altered EDC genes expression is not accompanied by major changes in DNA methylation. J. Cell. Biochem. 117: 1092-1098, 2016. © 2015 Wiley Periodicals, Inc. PMID:26443750

  11. 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

  12. Bis( N-methyl)-dithioformamidinium dihalides and their complexes with copper(I), silver(I) and gold(I)

    NASA Astrophysics Data System (ADS)

    Malavasi, Wanda; Peyronel, Giorgio; Pignedoli, Anna

    The bis( N-methyl)-dithioformamidinium dihalides (Me 2Tu 2X 2, X = Cl, Br, I), obtained by oxidation of N-methyl-thiourea (MeTu), and their complexes: 2 MX. 1.5 Me 2Tu 2X 2 (M = Cu, X = Cl, Br; M = Ag, X = Cl), MX.Me 2Tu 2X 2 (M = Cu, X = Br, I; M = Ag, X = I), 5CuCl.3Me 2Tu 2Cl 2, 4AgBr.Me 2Tu 2Br 2, AuCl. 1.5 Me 2Tu 2Cl 2, AuBr.2Me 2Tu 2Br 2, AuI. 4.5 Me 2Tu 2I 2 were prepared and studied by i.r. spectroscopy. Some i.r. bands of the Me 2Tu 2X 2 compounds and their complexes are assigned by comparison with those of MeTu. The Me 2Tu 2+2 cation is N-coordinated to the metal ions. Some ?MN and ?MX bands are tentatively assigned.

  13. Corrigendum to "Synthesis, structural features, and methyl methacrylate polymerisation of binuclear zinc(II) complexes with tetradentate pyrazolyl ligands" [J. Mol. Struct. 1063 (2014) 70-76

    NASA Astrophysics Data System (ADS)

    Kim, Sunghoon; Kim, Dongil; Lee, Ha-Jin; Lee, Hyosun

    2015-05-01

    The authors regret to inform that 4,4?-bis-(N,N-di(1H-pyrazolyl-1-methyl)phenyl)methane (L2) and its binuclear 4,4?-bis-(N,N-di-(1H-pyrazolyl-1-methyl)phenyl)methane(dichloro)Zn(II) complex, namely, [L2Zn2Cl4] in the paper were published as the thesis for the degree of master in the Department of Chemistry at Kyungpook National University in 2003.

  14. 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

  15. Reaction of a polydentate cysteine-based ligand and its nickel(ii) complex with electrophilic and nucleophilic methyl-transfer reagents - from S-methylation to acetyl coenzyme A synthase reactivity.

    PubMed

    Warner, D S; Limberg, C; Oldenburg, F J; Braun, B

    2015-11-14

    The L-cysteine derived N2S2 ligand precursor H2L and its nickel(ii) complex L2Ni2 were investigated with respect to their behaviour in contact with electrophilic and nucleophilic methylation reagents (H2L = (N,N'-dimethyl-(2R,5R)-bis-(sulfanylmethyl)-piperazine). Treatment of deprotonated L(2-) with MeI led to the selective methylation of the thiolate groups thus generating a novel potential ligand, Me2L, which is neutral and contains two thioether donors. The coordinating properties of Me2L were demonstrated by the synthesis of a first nickel(ii) complex: reaction with NiBr2 led to a mononuclear complex 2 where all donor atoms coordinate to the nickel ion, which completes its octahedral coordination sphere by the two bromide ligands. If, however, the complex [LNi]2 (1) is treated with MeI only one thiolate function per ligand moiety is methylated, while the other one remains a thiolate. This leads to [MeLNi](+) complex metal fragments, which trimerize including a ?3-bridging iodide ion to give the compound 3 that was tested with regards to ACS reactivity. While it behaved inert towards CO, attempts to replace the bridging iodide ligand by methyl units in reactions with nucleophilic methylation reagents led to a product, which could not be identified but reacted with CO. Work-up showed that this protocol had converted the thiolate function of MeL(-) into a thioester function, which corresponds to an ACS-like reactivity. PMID:26390049

  16. Highly selective methyl transfer from methylsilanes to phenylthallium(III) crown ether complexes

    SciTech Connect

    Kakiuchi, Fumitoshi; Furuta, Kiyonori; Murai, Shinji ); Kawasaki, Yoshikane )

    1993-01-01

    Reactions of (18-crown-6)phenylthallium(III) diperchlorate monohydrate (1a) with Me[sub 3]SiR (R = PhCH[sub 2], Et, Ph, CH[double bond]CH[sub 2], SiMe[sub 3], OSiMe[sub 3]) proceeded at 60[degrees]C to provide (18-crown-6)phenylmethylthallium(III) perchlorate (3) in good to excellent yields. Cleavage of the Me-Si bond in tetramethylsilane using 1a also occurred at 25[degrees]C, albeit for a long reaction time. The silicon-containing products of the reaction of 1a with benzyltrimethylsilane were siloxanes. Intramolecular trapping of the silyl fragments by a hydroxy group using (1,7-DTC)phenylthallium(III) bis(trifluoromethanesulfonate) (1b) was employed with trans-2-((trimethylsilyl)methyl)-1-cyclohexanol, affording a bicyclic silyl ether in 92% yield. 18 refs., 1 tab.

  17. 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 15patients with SLE and 15healthy 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 6loci in the MHC segment of SLE. We found 4single-nucleotide polymorphisms(SNPs) in the CpG promoter of human leukocyte antigen-B(HLA-B) and 2SNPs 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

  18. Synthesis and photophysics of a new deep red soluble phosphorescent iridium(III) complex based on chlorine-methyl-substituted 2,4 diphenyl quinoline

    NASA Astrophysics Data System (ADS)

    Dahule, H. K.; Dhoble, S. J.; Ahn, J.-S.; Pode, Ramchandra

    2011-12-01

    A new iridium complex with a chlorine-methyl-substituted 2,4 diphenyl quinoline, (Cl-MDPQ) ligand has been synthesized. The synthesized iridium metal complex, Ir(Cl-MDPQ)2(acac) where Cl-MDPQ=chlorine-methyl substituted, 2,4 diphenyl quinoline, acac=acetyl acetone is characterized by employing different techniques such as mass spectrometry, 1H NMR, DTA/TGA, XRD, and FTIR. The molecular structures of Cl-MDPQ and Ir(Cl-MDPQ)2(acac) complexes are confirmed by the FTIR spectra. Strong singlet metal-to-ligand charge-transfer (1MLCT) and triplet metal-to-ligand charge-transfer (3MLCT) absorption peaks at 353 and 437 nm in tetrahydrofuran (THF) are reported in the synthesized complex, respectively. A deep red emitting Ir(Cl-MDPQ)2(acac) complex at 662 nm is promising for flexible organic devices.

  19. 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.

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

    PubMed

    Curado, Natalia; Carrasco, Mario; lvarez, Eleuterio; Maya, Celia; Peloso, Riccardo; Rodrguez, Amor; Lpez-Serrano, Joaqun; 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-CH3Li 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 CH3Li interactions. PMID:26305709

  1. Twin-based DNA methylation analysis takes the center stage of studies of human complex diseases.

    PubMed

    Zhang, Dongfeng; Li, Shuxia; Tan, Qihua; Pang, Zengchang

    2012-11-20

    The etiology of complex diseases is characterized by the interaction between the genome and environmental conditions and the interface of epigenetics may be a central mechanism. Current technologies already allow us high-throughput profiling of epigenetic patterns at genome level. However, our understanding of the epigenetic processes remains limited. Twins are special samples in genetic studies due to their genetic similarity and rearing-environment sharing. In the past decades, twins have made a great contribution in dissecting the genetic and environmental contributions to human diseases and complex traits. In the era of functional genomics, the valuable samples of twins are helping to bridge the gap between gene activity and environmental conditions through epigenetic mechanisms unlimited to DNA sequence variations. We review the recent progresses in using twins to study disease-related molecular epigenetic phenotypes and link them with environmental exposures especially early life events. Various study designs and application issues will be highlighted and discussed with aim at making uses of twins in assessing the environmental impact on epigenetic changes during the development of complex diseases. PMID:23177145

  2. 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

  3. 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

  4. Zebularine: A Novel DNL Methylation Inhibitor that Forms a Covalent Complex with DNA Methyltransferases

    SciTech Connect

    Zhou, L.; Cheng, X; Connolly, B; Dickman, M; Hurd, P; Hornby, D

    2009-01-01

    Mechanism-based inhibitors of enzymes, which mimic reactive intermediates in the reaction pathway, have been deployed extensively in the analysis of metabolic pathways and as candidate drugs. The inhibition of cytosine-[C5]-specific DNA methyltransferases (C5 MTases) by oligodeoxynucleotides containing 5-azadeoxycytidine (AzadC) and 5-fluorodeoxycytidine (FdC) provides a well-documented example of mechanism-based inhibition of enzymes central to nucleic acid metabolism. Here, we describe the interaction between the C5 MTase from Haemophilus haemolyticus (M.HhaI) and an oligodeoxynucleotide duplex containing 2-H pyrimidinone, an analogue often referred to as zebularine and known to give rise to high-affinity complexes with MTases. X-ray crystallography has demonstrated the formation of a covalent bond between M.HhaI and the 2-H pyrimidinone-containing oligodeoxynucleotide. This observation enables a comparison between the mechanisms of action of 2-H pyrimidinone with other mechanism-based inhibitors such as FdC. This novel complex provides a molecular explanation for the mechanism of action of the anti-cancer drug zebularine.

  5. 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 (), b = 11.6229 (), c = 27.983 (), ? = 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 (), b = 11.652 (), c = 24.887 (), ? = 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.

  6. Analytical studies of the interaction of Tb(III)-2-{[(4-methoxy benzoyl) oxy]} methyl benzoic acid binary complex with nucleosides

    NASA Astrophysics Data System (ADS)

    Shehata, A. M. A.; Azab, H. A.; El-assy, N. B.; Anwar, Z. M.; Mostafa, H. M.

    2016-01-01

    The interaction of Tb(III)-2-{[(4-methoxy benzoyl) oxy]} methyl benzoic acid binary complex with nucleosides (adenosine, cytidine, guanosine and inosine) was investigated using UV and fluorescence methods. The reaction of Tb-complex with cytidine, guanosine and adenosine is accompanied by shift to longer wavelength in the absorption band, while there is a blue shift in the absorption band with an enhancement in the molar absorptivity upon the reaction with inosine. The fluorescence intensity of Tb(III)-2-{[(4- methoxy benzoyl) oxy]} methyl benzoic acid binary complex at λ = 545 nm (5D4 → 7F5) was decreased with the addition of the nucleoside molecule following the order: cytidine > inosine > guanosine > adenosine.

  7. Crystal structures of copper(II) and nickel(II) nitrate and chloride complexes with 4-bromo-2-[(2-hydroxyethylimino)-methyl]phenol

    SciTech Connect

    Chumakov, Yu. M.; Tsapkov, V. I.; Filippova, I. G.; Bocelli, G.; Gulea, A. P.

    2008-07-15

    The crystal structures of {l_brace}4-bromo-2-[(2-hydroxyethylimino)-methyl]phenolo{r_brace}aquacopper(II) nitrate hemihydrate (I), chloro-{l_brace}4-bromo-2-[(2-hydroxyethylimino)-methyl]phenolo{r_brace}copper hemihydrate (II), and chloro-{l_brace}4-bromo-2-[(2-hydroxyethylimino)-methyl]phenolo{r_brace}aquanickel (III) are determined using X-ray diffraction. Crystals of compound I are formed by cationic complexes, nitrate ions, and solvate water molecules. In the cation, the copper atom coordinates the singly deprotonated molecule of tridentate azomethine and the water molecule. The copper complexes are joined into centrosymmetric dimers by the O{sub w}-H...O hydrogen bonds. The crystal structure of compound II is composed of binuclear copper complexes and solvate water molecules. The copper atom coordinates the O,N,O ligand molecule and the chlorine ion, which fulfills a bridging function. The coordination polyhedron of the metal atom is a distorted tetragonal bipyramid in which the vertex is occupied by the chlorine atom of the neighboring complex in the dimer. Compound III is a centrosymmetric dimer complex. The coordination polyhedra of two nickel atoms related via the inversion center are distorted octahedra shared by the edge.

  8. Synthesis and characterization of methylated poly(L-histidine) to control the stability of its siRNA polyion complexes for RNAi.

    PubMed

    Asayama, Shoichiro; Kumagai, Takao; Kawakami, Hiroyoshi

    2012-07-18

    Poly(L-histidine) (PLH) with dimethylimidazole groups has been synthesized as a pH-sensitive polypeptide to control the stability of its small interfering RNA (siRNA) polyion complexes for RNA interference (RNAi). The resulting methylated PLH (PLH-Me) was water-soluble despite deprotonation of the imidazole groups at physiological pH, as determined by acid-base titration and solution turbidity measurement. Agarose gel retardation assay proved that the quaternary dimethylimidazole groups worked as cationic groups to retain siRNA. The stability of the PLH-Me/siRNA complexes has depended on the content of hydrophobic groups, that is, ?/?-methylimidazole groups as well as deprotonated imidazole groups. PLH-Me exhibited no significant cytotoxicity despite the existence of cationic dimethylimidazole groups. By use of PLH-Me as a pH-sensitive siRNA carrier, the PLH-Me/siRNA complexes mediated efficient siRNA delivery attributed to the dimethylimidazole groups, and the gene silencing depended on the content balance among dimethyl, ?/?-methyl, and unmodified imidazole groups. These results suggest that PLH-Me controls the stability of siRNA polyion complexes by enhancing noncytotoxic siRNA delivery by optimizing the content balance of dimethyl, ?/?-methyl, and unmodified imidazole groups. PMID:22681572

  9. Crystal structures of copper(II) nitrate complexes containing 4,4'-bipyridyl and halogen-substituted 2-[(2-hydroxyethylimino)methyl]phenols

    SciTech Connect

    Chumakov, Yu. M.; Tsapkov, V. I.; Petrenko, P. A.; Popovski, L. G.; Simonov, Yu. A.; Bocelli, G.; Gulea, A. P.

    2009-03-15

    The crystal structures of ({mu}-4,4'-bipyridyl)-di{l_brace}nitrato-2,4-dibromo-6-[(2-hydroxyethylimino)methyl] phenolo (1-)copper{r_brace} (I), ({mu}-4,4'-bipyridyl)-di{l_brace}nitrato-2,4-dichloro-6-[(2-hydroxyethylimino)methyl] phenolo(1-)copper{r_brace} (II), and ({mu}-4,4'-bipyridyl)-{l_brace}4-chloro-2-[(2-hydroxyethylimino)methyl]phenolo(2-) copper-nitrato-4-chloro-2-[(2-hydroxyethylimino)methyl]phenolo(1-)copper{r_brace} tetrahydrate (III) are determined. The crystal structures of compounds I and II contain binuclear complexes, in which each copper atom is coordinated by the singly deprotonated tridentate molecule of the corresponding azomethine, the monodentate nitrate ion, and bipyridyl that plays the role of a bridge between the central atoms. In the structures of compounds I and II, the coordination polyhedra of the copper atoms are slightly distorted tetragonal pyramids. The pyramid base is formed by the imine and bipyridyl nitrogen atoms and the phenol and alcohol oxygen atoms. The axial vertices of the pyramids are occupied by the oxygen atoms of the monodentate nitrato groups. The crystal structure of compound III involves tetranuclear complexes in which the coordination polyhedra of the central copper atoms are (4 + 1 + 1) bipyramids. The base of these bipyramids is formed by the imine and bipyridyl nitrogen atoms and the phenol and alcohol oxygen atoms. One apical vertex is occupied by the bridging phenol oxygen atom of the nearest complex. The sixth coordination site of the first copper atom is occupied by the chlorine atom of the salicylidene fragment of the neighboring complex related to the initial complex through the center of symmetry. In turn, the sixth coordination site of the second copper atom is occupied by the oxygen atom of the monodentate nitrato group.

  10. Effect of complexation with randomly methylated beta-cyclodextrin on the aqueous solubility, photostability and antioxidant activity of an indolinonic nitroxide radical.

    PubMed

    Damiani, Elisabetta; Tursilli, Rosanna; Casolari, Alberto; Astolfi, Paola; Greci, Lucedio; Scalia, Santo

    2005-01-01

    The interaction between the hydrophobic indolinonic nitroxide radical, 1,2-dihydro-2-methyl-2-phenyl-3H-indole-3-one-1-oxyl and hydrophilic alpha-, beta- and gamma-cyclodextrin derivatives was investigated in water by phase-solubility analysis. Among the studied cyclodextrins, random methyl-beta-cyclodextrin (RM-beta-CD) had the greatest solubilizing activity (1312-fold increase in. the intrinsic aqueous solubility). Solid complexes were prepared by the freeze-drying method and characterized by powder X-ray diffractometry and thermal analysis. Complexation of the nitroxide with RM-beta-CD was also confirmed in solution by electron paramagnetic resonance (EPR) spectroscopy. Photodegradation of the nitroxide was reduced by complexation with RM-beta-CD, this effect being more pronounced in the solid-state (the extent of degradation was 28.0% for the complex vs. 78.8% for uncomplexed nitroxide) than in solution (41.2 vs. 69.1% for uncomplexed nitroxide). The antioxidant activity of the complex was also investigated on the peroxidation of methyl linoleate micelles and on protein oxidation induced by free radical generators, and in both systems the free form of the nitroxide as well as its complex with RM-beta-CD, showed essentially the same degree of protection. Moreover, EPR experiments showed a time-dependent decrease in the EPR signal of both the complexed and uncomplexed nitroxides with the free-radical generators. Therefore, RM-beta-CD complexation of the nitroxide represents an effective strategy to improve its aqueous solubility and photostability, which is essential for certain biological applications, while it does not interfere with its radical scavenging efficiency. PMID:15875810

  11. Inclusion complexes of cyclomaltoheptaose (beta-cyclodextrin) and its methylated derivatives with the main components of the pheromone of the olive fruit fly.

    PubMed

    Botsi, A; Yannakopoulou, K; Hadjoudis, E

    1993-03-17

    The inclusion complexes of cyclomaltoheptaose (beta CD) and heptakis(2,3,6-tri-O-methyl)cyclomaltoheptaose (TM-beta CD) with the four major components of the pheromone of the olive fruit fly (Dacus oleae), namely 1,7-dioxaspiro[5.5]undecane, (-)-alpha-pinene, nonanal, and ethyl dodecanoate, and the complex of heptakis(2,6-di-O-methyl)cyclomaltoheptaose (DM-beta CD) with 1,7-dioxaspiro[5.5]undecane were studied. The complexes were characterised in the solid state by differential scanning calorimetry and X-ray powder diffraction. In aqueous solution, the structure of the complexes was investigated by 1H NMR spectroscopy. In solution, 1,7-dioxaspiro[5.5]undecane, (-)-alpha-pinene, and nonanal enter the cavity of the cyclo-oligosaccharides. Association constants for some of these complexes were also measured. The complexes of ethyl dodecanoate did not provide evidence of their structure in solution. This was attributed to the existence of negligible amounts of these complexes in water due to the combined effects of low solubility and low association constant. PMID:8472260

  12. 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

  13. 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.

  14. Crystal structures of bis-ligand complexes of copper(II) with 2-[(2-hydroxyethylamino)-methyl]-4,6-dinitrophenol, 2,4-dichloro-6-[(2-hydroxyethylamino)-methyl]phenol, and 2,4-dibromo-6-[(2-hydroxyethylamino)-methyl]phenol

    SciTech Connect

    Chumakov, Yu. M. Tsapkov, V. I.; Bocelli, G.; Palomares-Sanchez, S. A.; Ortiz, R. S.; Gulea, A. P.

    2007-02-15

    The crystal structures of bis{l_brace}2,4-dibromo-6-[(2-hydroxyethylamino)-methyl]phenolato{r_brace}copper (I), bis{l_brace}2,4-dichloro-6-[(2-hydroxyethylamino)-methyl]phenolato{r_brace}copper (II), and bis{l_brace}2-[(2-hydroxyethylamino)-methyl]-4,6-dinitrophenolato{r_brace}copper (III) in which the metal atom is located at the center of symmetry are determined using X-ray diffraction. Crystals of compounds I and II are isostructural. The copper atom in the structures of compounds I and I coordinates two singly deprotonated bidentate molecules of the ligand through the phenol oxygen atoms and the azomethine nitrogen atoms with the formation of a distorted planar square. In the crystals, complexes I and II form one-dimensional infinite chains along the b axis. In the structure of compound III, the coordination polyhedron of the central atom is an elongated tetragonal bipyramid with the base formed by the azomethine nitrogen atoms and the phenol oxygen atoms. Both vertices of the bipyramid are occupied by the oxygen atoms of the amino alcohol groups of the neighboring complexes, which are related to the initial complex through the center of symmetry. In turn, the oxygen atoms of the alcohol groups of the initial complex are located at the vertices of the coordination bipyramids of the metal atoms of the neighboring centrosymmetric complexes, thus forming infinite polymer chains along the a axis.

  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. Synthesis of Fischer carbene complexes of iridium by C-H bond activation of methyl and cyclic ethers: Evidence for reversible {alpha}-hydrogen migration

    SciTech Connect

    Luecke, H.F.; Arndtsen, B.A.; Burger, P.; Bergman, R.G.

    1996-03-13

    We report here a mild and versatile route to Fischer carbene complexes of iridium via the activation of C-H bonds of methyl and cyclic ethers, along with our preliminary studies of this rare family of carbene complexes. Theoretical studies suggest that {alpha}-hydrogen migrations can be kinetically favorable if a coordinatively unsaturated species can be accessed. Thus, the lability of the triflate ligand presumably facilitates this process. Further evidence for the rapidity, as well as reversibility, of this rearrangement was obtained by NMR analysis. 20 refs.

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

    PubMed

    Atria, Ana Mara; 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-HO 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

  18. Hydrogen-bonded complexes of phenylacetylene with water, methanol, ammonia, and methylamine. The origin of methyl group-induced hydrogen bond switching.

    PubMed

    Sedlak, Robert; Hobza, Pavel; Patwari, G Naresh

    2009-06-18

    The infrared spectra in the acetylenic C-H stretching region for the complexes of phenylacetylene with water, methanol, ammonia, and methylamine are indicative of change in the intermolecular structure upon substitution with a methyl group. High-level ab initio calculations at CCSD(T)/aug-cc-pVDZ level indicate that the observed complexes of water and ammonia are energetically the most favored structures, and electrostatics play a dominant role in stabilizing these structures. The ability of the pi electron density of the benzene ring to offer a larger cross-section for the interaction and the increased polarizability of the O-H and N-H groups in methanol and methylamine favor the formation of pi hydrogen-bonded complexes, in which dispersion is the dominant force. Further, the observed phenylacetylene-methylamine complex can be tentatively assigned to a kinetically trapped higher energy structure. The observed methyl group-induced hydrogen bond switching in the phenylacetylene complexes can be attributed to the switching of the dominant interaction from electrostatic to dispersion. PMID:19514784

  19. 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.

  20. 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 .; 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.

  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 μ3-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 μ2-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. SODs, DNA binding and cleavage studies of new Mn(III) complexes with 2-((3-(benzyloxy)pyridin-2-ylimino)methyl)phenol

    NASA Astrophysics Data System (ADS)

    Shivakumar, L.; Shivaprasad, K.; Revanasiddappa, Hosakere D.

    2013-04-01

    Newly synthesized ligand [2-((3-(benzyloxy)pyridin-2-ylimino)methyl)phenol] (Bpmp) react with manganese(II) to form mononuclear complexes [Mn(phen)(Bpmp)(CH3COO)(H2O)]4H2O (1), (phen = 1,10-phenanthroline) and [Mn(Bpmp)2(CH3COO)(H2O)]5H2O (2). These complexes were characterized by elemental analysis, IR, 1H NMR, Mass, UV-vis spectral studies. Molar conductance and thermogravimetric analysis of these complexes were also recorded. The in vitro SOD mimic activity of Mn(III) complexes were carried out and obtained with good result. The DNA-binding properties of the complexes 1 and 2 were investigated by UV-spectroscopy, fluorescence spectroscopy and viscosity measurements. The spectral results suggest that the complexes 1 and 2 can bind to Calf thymus DNA by intercalation mode. The cleavage properties of these complexes with super coiled pUC19 have been studied using the gel electrophoresis method, wherein both complexes 1 and 2 displayed chemical nuclease activity in the absence and presence of H2O2via an oxidative mechanism. All the complexes inhibit the growth of both Gram positive and Gram negative bacteria to competent level. The MIC was determined by microtiter method.

  4. Oxidative addition of methyl iodide to monosubstituted and disubstituted derivatives of ruthenium pentacarbonyl: Preparation of neutral and ionic complexes of ruthenium

    SciTech Connect

    Bellachioma, G.; Cardaci, G.; Macchioni, A.; Madami, A. )

    1993-03-03

    The oxidative addition of CH[sub 3]I to Ru(CO)[sub 4]PMe[sub 3] (1) gives the methyl complex Ru(CO)[sub 3]PMe[sub 3](CH[sub 3])I (3); with PMe[sub 3] complex 3 gives the acetyl complexes Ru(CO)[sub 2](PMe[sub 3])[sub 2](COCH[sub 3])I (isomers 10a and 10b), which, by decarbonylation, give Ru(CO)[sub 2](PMe[sub 3])[sub 2](CH[sub 3])I (4). Complex 4 can also be obtained by oxidative addition of CH[sub 3]I to Ru(CO)[sub 3](PMe[sub 3])[sub 2] (2). Complex 4 reacts at room temperature with the nucelotphiles CO, PMe[sub 3], and P(OMe)[sub 3] giving the acetyl complexes (structures 7, 15, and 18, respectively), which at higher temperatures isomerize to 8, 16, and 19, respectively. Decarbonylation of these complexes gives complex 4 (in the case of CO), complex 12 (in the case of PMe[sub 3]) and complex 13 (in the case of P(OMe)[sub 3]). This last complex reacts with different nucleophiles (PMe[sub 3], P(OMe)[sub 3]) and gives the ionic tetraphosphine complexes [Ru(CO)(PMe[sub 3])[sub 3]P(OMe)[sub 3](CH[sub 3])]I (22) and [Ru-(CO)(PMe[sub 3])[sub 2](P(OMe)[sub 3])[sub 2](CH[sub 3])]BPh[sub 4] (24), respectively. The trisubstituted cyano derivative Ru(CO)(PMe[sub 3])[sub 2]P(OMe)[sub 3](CH[sub 3])CN (14) is obtained by the reaction of complex 22 with KCN in acetone. The structures of the various complexes were assigned, in most cases, on the basis of spectroscopic (IR, [sup 1]H, [sup 31]P, [sup 13]C) information. 45 refs., 1 fig., 3 tabs.

  5. "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

  6. 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.

  7. Synthesis of conducting polyelectrolyte complexes of polyaniline and poly(2-acrylamido-3-methyl-1-propanesulfonic acid) catalyzed by pH-stable palm tree peroxidase.

    PubMed

    Caramyshev, Alexei V; Evtushenko, Evgeny G; Ivanov, Viktor F; Barceló, Alfonso Ros; Roig, Manuel G; Shnyrov, Valery L; van Huystee, Robert B; Kurochkin, Iliya N; Vorobiev, Andrey Kh; Sakharov, Ivan Yu

    2005-01-01

    Comparison of the stability of five plant peroxidases (horseradish, royal palm tree leaf, soybean, and cationic and anionic peanut peroxidases) was carried out under acidic conditions favorable for synthesis of polyelectrolyte complexes of polyaniline (PANI). It demonstrates that palm tree peroxidase has the highest stability. Using this peroxidase as a catalyst, the enzymatic synthesis of polyelectrolyte complexes of PANI and poly(2-acrylamido-3-methyl-1-propanesulfonic acid) (PAMPS) was developed. The template polymerization of aniline was carried out in aqueous buffer at pH 2.8. Varying the concentrations of aniline, PAMPS, and hydrogen peroxide as reagents, favorable conditions for production of PANI were determined. UV-vis-NIR absorption and EPR demonstrated that PAMPS and PANI formed the electroactive complex similar to PANI doped traditionally using low molecular weight sulfonic acids. The effect of pH on conformational variability of the complex was evaluated by UV-vis spectroscopy. Atomic force microscopy showed that a size of the particles of the PANI-PAMPS complexes varied between 10 and 25 nm, depending on a concentration of PAMPS in the complex. The dc conductivity of the complexes depends also on the content of PAMPS, the higher conductivity being for the complexes containing the lower content of the polymeric template. PMID:15877353

  8. 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, Şevki

    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.

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

    PubMed

    Alyar, Saliha; Adem, ?evki

    2014-10-15

    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. (1)H and (13)C 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. PMID:24835932

  10. Synthesis and characterization of terbium(III) complexes with the biscoumarin derivative 3,3?-[(4-hydroxyphenyl)methyl]bis-(4-hydroxy-2H-chromen-2-one)

    NASA Astrophysics Data System (ADS)

    Elenkova, D.; Monov, R.; Tadjer, A.; Manolov, I.; Milanova, M.

    2016-02-01

    Complexes of Tb(III) with the biscoumarin derivative 3,3?-[(4-hydroxyphenyl)methyl]bis-(4-hydroxy-2H-chromen-2-one) are synthesized by using a solution of tetraethylammonium hydroxide, [(C2H5)4N]OH, in water as deprotonating base. Elemental analysis, IR- and fluorescence spectroscopy are used to characterize the samples obtained. The complexes have good fluorescent properties and show the characteristic emission bands of the Tb(III) ion. The triplet state of the mono-deprotonated ligand H2L- was determined. The optimised geometries of the ligand and the complexes were obtained by means of molecular modelling with first principles (DFT) methods.

  11. Dimeric and polymeric mercury(II) complexes of 1-methyl-1,2,3,4-tetrazole-5-thiol: Synthesis, crystal structure, spectroscopic characterization, and thermal analyses

    NASA Astrophysics Data System (ADS)

    Taheriha, Mohammad; Ghadermazi, Mohammad; Amani, Vahid

    2016-03-01

    Two-dimensional coordination polymer of [Hg(μ3-mmtz)2]n (1) and centrosymmetric dinuclear complexes of {[H2en][Hg2(mmtz)4(μ-Br)2]} (2) and {[H2en][Hg2(mmtz)4(μ-I)2]} (3) (where Hmmtz is 1-methyl-1,2,3,4-tetrazole-5-thiol and en is ethylene diamine) were synthesized from the reaction of Hmmtz and en with HgCl2, HgBr2 and HgI2, respectively, in CH3OH. Complex 1 was also synthesized from the reaction of Hmmtz and en with HgX2 (X = OAc and SCN) in CH3OH. These three complexes were thoroughly characterized by elemental analysis (CHN), thermal gravimetric analysis (TGA), differential thermal analyses (DTA), infrared, UV-vis, 1H NMR, and luminescence spectroscopy, and their structures were determined by single-crystal X-ray diffraction.

  12. Growth of tantalum nitride film as a Cu diffusion barrier by plasma-enhanced atomic layer deposition from bis((2-(dimethylamino)ethyl)(methyl)amido)methyl(tert-butylimido)tantalum complex

    NASA Astrophysics Data System (ADS)

    Han, Jeong Hwan; Kim, Hyo Yeon; Lee, Sang Chan; Kim, Da Hye; Park, Bo Keun; Park, Jin-Seong; Jeon, Dong Ju; Chung, Taek-Mo; Kim, Chang Gyoun

    2016-01-01

    A new bis((2-(dimethylamino)ethyl)(methyl)amido)methyl(tert-butylimido)tantalum complex was synthesized for plasma-enhanced atomic layer deposition (PEALD) of tantalum nitride (TaN) film. Using the synthesized Ta compound, PEALD of TaN was conducted at growth temperatures of 150-250 °C in combination with NH3 plasma. The TaN PEALD showed a saturated growth rate of 0.062 nm/cycle and a high film density of 9.1-10.3 g/cm3 at 200-250 °C. Auger depth profiling revealed that the deposited TaN film contained low carbon and oxygen impurity levels of approximately 3-4%. N-rich amorphous TaN films were grown at all growth temperatures and showed highly resistive characteristic. The Cu barrier performance of the TaN film was evaluated by annealing of Cu/TaN (0-6 nm)/Si stacks at 400-800 °C, and excellent Cu diffusion barrier properties were observed even with ultrathin 2 nm-thick TaN film.

  13. New ethanol and propylene glycol free gel formulations containing a minoxidil-methyl-β-cyclodextrin complex as promising tools for alopecia treatment.

    PubMed

    Lopedota, Angela; Cutrignelli, Annalisa; Denora, Nunzio; Laquintana, Valentino; Lopalco, Antonio; Selva, Stefano; Ragni, Lorella; Tongiani, Serena; Franco, Massimo

    2015-05-01

    New topical totally aqueous formulations that improve the low water solubility of minoxidil and realize an adequate permeability of drug in the skin are proposed. These formulations are lacking in propylene glycol and alcohol that are the principal irritant ingredients present in minoxidil commercial solutions. In order to enhance poor water solubility of minoxidil randomly methyl-β-cyclodextrin was used, and four hydrogels such as, calcium alginate, sodium alginate, carbopol 934 and hydroxyethylcellulose were utilized to ensure a prolonged time of contact with the scalp. The inclusion complex minoxidil/methyl-β-cyclodextrin with a molar ratio 1:1 was obtained by freeze drying and evaluated by NMR, FT-IR and DSC analysis. An apparent stability constant of formed inclusion complex was calculated by phase solubility diagram and its value was 400 M(-1). The solid inclusion complex was used to prepare gel formulations with similar dose to minoxidil commercial solution. The gels were evaluated for various technological parameters including rheological behavior, in vitro drug release and ex vivo permeation through pig skin. The best performance was observed for the calcium alginate formulation. PMID:24650036

  14. 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-Franois

    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

  15. 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-Franois; 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

  16. 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 γ-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

  17. 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 γ-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.

  18. 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 γ-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

  19. 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.

  20. 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.

  1. The toluene-Ar complex: S0 and S1 van der Waals modes, changes to methyl rotation, and torsion-van der Waals vibration coupling

    NASA Astrophysics Data System (ADS)

    Gascooke, Jason R.; Lawrance, Warren D.

    2013-02-01

    The methyl rotor and van der Waals vibrational levels in the S1 and S0 states of toluene-Ar have been investigated by the technique of two-dimensional laser induced fluorescence (2D-LIF). The S0 van der Waals and methyl rotor levels are reported for the first time, while improved S1 values are presented. The correlations seen in the 2D-LIF images between the S0 and S1 states lead to a reassignment of key features in the S1 ← S0 excitation spectrum. This reassignment reveals that there are significant changes in the methyl rotor levels in the complex compared with those in bare toluene, particularly at low m. The observed rotor energies are explained by the introduction of a three-fold, V3, term in the torsion potential (this term is zero in toluene) and a reduction in the height of the six-fold, V6, barriers in S0 and S1 from their values in bare toluene. The V3 term is larger in magnitude than the V6 term in both S0 and S1. The constants determined are |V3(S1)| = 33.4 ± 1.0 cm-1, |V3(S0)| = 20.0 ± 1.0 cm-1, V6(S1) = -10.7 ± 1.0 cm-1, and V6(S0) = -1.7 ± 1.0 cm-1. The methyl rotor is also found to couple with van der Waals vibration; specifically, the m″ = 2 rotor state couples with the combination level involving one quantum of the long axis bend and m″ = 1. The coupling constant is determined to be 1.9 cm-1, which is small compared with the values typically reported for torsion-vibration coupling involving ring modes.

  2. In situ synthesis of mononuclear copper(II) complexes of the new tridentate ligand bis[(3,5-dimethyl-1H-pyrazol-1-yl)methyl]amine.

    PubMed

    Yu, Fan

    2011-10-01

    Two mononuclear copper complexes, {bis[(3,5-dimethyl-1H-pyrazol-1-yl-?N(2))methyl]amine-?N}(3,5-dimethyl-1H-pyrazole-?N(2))(perchlorato-?O)copper(II) perchlorate, [Cu(ClO(4))(C(5)H(8)N(2))(C(12)H(19)N(5))]ClO(4), (I), and {bis[(3,5-dimethyl-1H-pyrazol-1-yl-?N(2))methyl]amine-?N}bis(3,5-dimethyl-1H-pyrazole-?N(2))copper(II) bis(hexafluoridophosphate), [Cu(C(5)H(8)N(2))(2)(C(12)H(19)N(5))](PF(6))(2), (II), have been synthesized by the reactions of different copper salts with the tripodal ligand tris[(3,5-dimethyl-1H-pyrazol-1-yl)methyl]amine (TDPA) in acetone-water solutions at room temperature. Single-crystal X-ray diffraction analysis revealed that they contain the new tridentate ligand bis[(3,5-dimethyl-1H-pyrazol-1-yl)methyl]amine (BDPA), which cannot be obtained by normal organic reactions and has thus been captured in the solid state by in situ synthesis. The coordination of the Cu(II) ion is distorted square pyramidal in (I) and distorted trigonal bipyramidal in (II). The new in situ generated tridentate BDPA ligand can act as a meridional or facial ligand during the process of coordination. The crystal structures of these two compounds are stabilized by classical hydrogen bonding as well as intricate nonclassical hydrogen-bond interactions. PMID:21979969

  3. 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.

  4. Ir(2-phenylpyridine)2(benzene-1,2-dithiolate) anion as a diastereoselective metalloligand and nucleophile: stereoelectronic effect, spectroscopy, and computational study of the methylated and aurated complexes and their oxygenation products.

    PubMed

    Nguyen, Van Ha; Khoo, Rebecca Shu Hui; Yip, John H K

    2015-03-01

    The anionic complex [Ir(2-phenylpyridine)2(benzene-1,2-dithiolate)](-) ([IrSS](-)) is a nucleophile and metalloligand that reacts with methyl iodide and AuPR3(+) (R = Ph or Et) to form S-methylated complexes (thiother-thiolate and dithiother complexes) and S-aurated complexes, respectively. The reactions are completely diastereselective, producing only the enantiomers ?S and ?R or ?SS and ?RR. The diastereoselectivity is stereoelectronically controlled by the orientation of the highest occupied molecular orbital (HOMO) of [IrSS](-) arising from filled d?-p? antibonding interactions, and the chirality of the iridium ion. Methylation or auration removes the high-energy lone pair of the thiolate S atom, leading to low-lying HOMOs composed mainly of the Ir d-orbital and the 2-phenylpyridine ? (ppy?) orbital. The methylated and aurated complexes can be oxidized by H2O2 or peracid to give sulfinate-thiother, disulfoxide, and sulfinate-sulfoxide complexes, and the oxygenation further stabilizes the HOMO. All the complexes are luminescent, and their electronic spectra are interpreted with the aid of time-dependent density functional theory calculations. The thiother-thiolate complex exhibits ligand(S)-to-ligand(?* of ppy)-charge-transfer/metal-to-ligand-charge-transfer absorption (LLCT/MLCT) and a relatively low-energy (3)LLCT/MLCT emission, while the other complexes display (3)??*/MLCT emissions. PMID:25692396

  5. Stereospecific ligands and their complexes. Part VII. Synthesis, characterization and in vitro antitumoral activity of platinum(II) complexes with O,O'-dialkyl esters of (S,S)-ethylenediamine-N,N'-di-2-(4-methyl)pentanoic acid.

    PubMed

    Vuji?, Jelena M; Kalu?erovi?, Goran N; Milovanovi?, Marija; Zmejkovski, Bojana B; Volarevi?, Vladislav; ivi?, Danijela; ?ur?evi?e, Predrag; Arsenijevi?, Neboja; Trifunovi?, Sre?ko R

    2011-09-01

    Platinum(II) complexes (1-4) with bidentate N,N'-ligands, O,O'-dialkyl esters (alkyl = ethyl, n-propyl, n-butyl and n-pentyl), of (S,S)-ethylenediamine-N,N'-di-2-(4-methyl)pentanoic acid were synthesized and characterized by IR, (1)H NMR and (13)C NMR spectroscopy and elemental analysis. DFT calculations were performed for the complexes and it was found that only one diastereoisomer could be formed. Cytotoxic activity of complexes 1-4 was determined against chronic lymphocytic leukemia cells (CLL) and compared to the activity of ligand precursors L1 2HCl-L42HCl and corresponding palladium(II) complexes, [PdCl(2)L] (L = L1-L4). The complexes were found to exhibit significantly higher antitumor activities than cisplatin on CLL cells. Cytotoxic effect of platinum(II) complexes on CLL cells was higher compared to corresponding palladium(II) complexes. In addition the mode of cell death induced by platinum(II) complexes was determined. PMID:21840630

  6. Bis(3-methyl-2-pyridyl)ditelluride and pyridyl tellurolate complexes of zinc, cadmium, mercury: Synthesis, characterization and their conversion to metal telluride nanoparticles.

    PubMed

    Kedarnath, G; Jain, Vimal K; Wadawale, Amey; Dey, Gautam K

    2009-10-21

    Treatment of an acetonitrile solution of metal chloride with bis(3-methyl-2-pyridyl)ditelluride, [Te(2)(pyMe)(2)], in the same solvent yielded complexes of composition [MCl(2){Te(2)(pyMe)(2)}] (M = Zn or Cd) whereas reactions of [MCl(2)(tmeda)] with NaTepyR (R = H or Me) gave tellurolate complexes of the general formula [M(TepyR)(2)] (M = Cd or Hg). When the cadmium complex [Cd(Tepy)(2)] was crystallized in the presence of excess tmeda, [Cd(Tepy)(2)(tmeda)] was formed exclusively. These complexes were characterized by elemental analyses, uv-vis, (1)H NMR data. The crystal structures of [ZnCl(2){Te(2)(pyMe)(2)}] and [Cd(Tepy)(2)(tmeda)] were established by single crystal X-ray diffraction. In the former zinc is coordinated to nitrogen atoms of the pyridyl group, while in the latter the coordination environment around tetrahedral cadmium is defined by the two neutral nitrogen atoms of tmeda, and two pyridyl tellurolate ligands. Thermal behavior of some of these complexes was studied by thermogravimetric analysis. Pyrolysis of [M(Tepy)(2)] in a furnace or in coordinating solvents such as hexadecylamine/tri-n-octylphosphine oxide (HDA/TOPO) at 350 and 160 degrees C, respectively gave MTe nanoparticles, which were characterized by uv-vis, photoluminiscence, XRD, EDAX and TEM. PMID:19789791

  7. 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

  8. 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

  9. The role of thiol and nitrosothiol compounds in the nitric oxide-forming reactions of the iron-N-methyl-d-glucamine dithiocarbamate complex.

    PubMed Central

    Tsuchiya, Koichiro; Kirima, Kazuyoshi; Yoshizumi, Masanori; Houchi, Hitoshi; Tamaki, Toshiaki; Mason, Ronald P

    2002-01-01

    The object of the present study is to investigate whether the physiologically dominant thiol compounds such as GSH and cysteine or their nitrosothiol compounds affect the formation of the iron- N -methyl-D-glucamine dithiocarbamate [(MGD)(2)Fe(2+)]-nitric oxide complex. The present study provided experimental evidence that physiological concentrations of GSH (approx. 5 mM) and L-cysteine (approx. 0.5 mM) accelerated the formation of the (MGD)(2)Fe(2+)-NO complex from nitrite by two and three times respectively. The rate constants for the reduction of (MGD)(3)Fe(3+) to (MGD)(2)Fe(2+) by GSH and cysteine were calculated as 1.3 and 2.0x10(2) M(-1).s(-1) respectively. Furthermore, depletion of GSH was demonstrated in PC12 cells, and thiol compounds enhanced the formation of reactive oxygen species by the (MGD)(2)Fe(2+) complex by accelerating its redox turnover. The main effect of the physiological concentration of thiols was the reduction of (MGD)(3)Fe(3+). S -nitrosoglutathione spontaneously reacted with (MGD)(2)Fe(2+) to produce the (MGD)(2)Fe(2+)-NO complex with a 1:2 stoichiometry. In fact, (MGD)(2)Fe(2+) was as good an indicator of nitrosothiols as it was of NO itself. The present study elucidates the difficulties of utilizing the (MGD)(2)Fe(2+) complex for the quantification of NO in biological samples, especially in vivo. PMID:12141947

  10. Hydrolysis Mechanism of the NAMI-A-type Antitumor Complex (HL)[trans-RuCl4L(dmso-S)] (L=1-methyl-1,2,4-triazole)

    NASA Astrophysics Data System (ADS)

    Chen, Lan-mei; Chen, Jin-can; Liao, Si-yan; Liu, Jiang-qin; Luo, Hui; Zheng, Kang-cheng

    2011-08-01

    The hydrolysis process of Ru(III) complex (HL)[trans-RuCl4L(dmso-S)] (L=1-methyl-1,2,4-triazole and dmso-S=S-dimethyl sulfoxide) (1), a potential antitumor complex similar to the well-known antitumor agent (Him)[trans-RuCl4(dmso-S)(im)] (NAMI-A, im=imidazole), was investigated using density functional theory combined with the conductor-like polarizable continuum model approach. The structural characteristics and the detailed energy profiles for the hydrolysis processes of this complex were obtained. For the first hydrolysis step, complex 1 has slightly higher barrier energies than the reported anticancer drug NAMI-A, and the result is in accordance with the experimental evidence indicating larger half-life for complex 1. For the second hydrolysis step, the formation of cis-diaqua species is thermodynamic preferred to that of trans isomers. In addition, on the basis of the analysis of electronic characteristics of species in the hydrolysis process, the trend in nucleophilic attack abilities of hydrolysis products by pertinent biomolecules is revealed and predicted.

  11. Synthesis, spectral characterization, molecular modeling, biological activity and potentiometric studies of 4-amino-5-mercapto-3-methyl-S-triazole Schiff's base complexes

    NASA Astrophysics Data System (ADS)

    Alaghaz, Abdel-Nasser M. A.; Zayed, Mohamed E.; Alharbi, Suliman A.

    2015-03-01

    The Schiff's base derived from condensation of s-triazole (4-amino-5-mercapto-3-methyl-S-triazole) with pyridine-2-aldehyde and their corresponding Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) complexes have been synthesized. The isolated solid complexes were characterized by elemental analyses, molar conductance, spectral (IR, UV-Vis, 1H NMR, mass), magnetic moment and thermal measurements. The IR spectral data suggest that the ligand coordinate in a tridentate manner (SNN) via the one thiol (SH), one pyridine ring and the azomethine (Cdbnd N) groups. The data show that the complexes have composition of ML2 type. The activation of thermodynamic parameters are calculated using Coats-Redfern, Horowitz-Metzger (HM), and Piloyan-Novikova (PN). The octahedral geometry of the complexes is confirmed using DFT method from DMOL3 calculations and ligand field parameters. Protonation constants of Schiff base and stability constants of their binary metal complexes have been determined potentiometrically in 50% DMSO-water media at 25 C and ionic strength 0.10 M potassium nitrate. The biological activity of these compounds against various fungi has been investigated.

  12. 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

  13. 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.

  14. 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

    Budzk, imon; 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

  15. 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

  16. Paramagnetic metal effect on the ligand localized S/sub 1/. -->. T/sub 1/ intersystem crossing in the rare-earth-metal complexes and methyl salicylate

    SciTech Connect

    Tobita, S.; Arakawa, M.; Tanaka, I.

    1985-01-01

    The electronic relaxation processes in the chelates of La/sup 3 +/, Gd/sup 3 +/, Tb/sup 3 +/, and Lu/sup 3 +/ with methyl salicylate have been investigated by measurements of picosecond fluorescence, nanosecond transient absorptions, and quantum yields. The quantum yields of the S/sub 1/ ..-->.. T/sub 1/ intersystem crossing are not appreciably altered by a change in the central metal ions. However, the fluorescence lifetimes are decreased dramatically in the paramagnetic Gd/sup 3 +/ (240 ps) and Tb/sup 3 +/ (<10 ps) complexes compared with those in the diamagnetic La/sup 3 +/ (2.2 ns) and Lu/sup 3 +/ (2.4 ns) complexes. The rate constants derived from these results for the S/sub 1/ ..-->.. T/sub 1/ intersystem crossing, k/sub TM/, in ligands are 5.5 x 10/sup 7/, 7.5 x 10/sup 8/, and 7.9 x 10/sup 7/ s/sup -1/ for the La/sup 3 +/, Gd/sup 3 +/, and Lu/sup 3 +/ complexes, respectively. A large increase of k/sub TM/ is observed in the paramagnetic Gd/sup 3 +/ complexes, which can be attributed to the electron exchange mechanism with ligand ..pi.. electrons. 27 references, 8 figures, 3 tables.

  17. A new ?3-oxo-centered tri-nuclear carboxyl bridged iron (III) complex with thio-methyl groups in the periphery: Structural, spectroscopic and electrochemical studies

    NASA Astrophysics Data System (ADS)

    Lu, Maofeng; Chen, Tingting; Wang, Miao; Jiang, Guomin; Lu, Tianhong; Jiang, Guoqing; Du, Jiangyan

    2014-02-01

    A tri-nuclear iron (III) complex [Fe3(?3-O)(O2CC6H4SCH3)6(Py)3]FeCl4 has been synthesized and characterized by X-ray crystallography, Surface enhanced Raman Scattering (SERS), Fourier Transform Infra Red (FT-IR), Ultraviolet-Visible (UV-Vis) spectroscopy and Thermogravimetric analysis (TGA)/Differential scanning calorimetry (DSC). The functionalized thio-methyl groups around the periphery of the complex 1 may provide binding sites to the surface of some specific materials, such as noble metals. The Ag sols and complex 1-Ag sol had been characterized by SERS and UV-Vis spectroscopy. The complex 1 were also self-assembled on gold electrode by AuS bond, exhibiting an irreversible process at E1/2 = 0.967 V (?E = 0.525 V). Meanwhile the Raman spectra were compared with FT-IR, and the results indicated that the strong Raman lines either correspond to weak Infrared absorptions or are absent in the Infrared spectra.

  18. DFT study of the structure and spectral behavior of new pt(II) complexes with 5-methyl-5(4-pyridyl)hydantoin

    NASA Astrophysics Data System (ADS)

    Bakalova, Adriana; Varbanov, Hristo; Stanchev, Stancho; Ivanov, Darvin; Jensen, Frank

    Platinum complexes are a great interest of study, because of the antitumor activity and the clinical use of some of them in the recent anticancer chemotherapy. In many cases, computational studies can be very useful for predicting the structure and some physicochemical properties of metal complexes. Theoretical calculations can also be used for the rational design of new complexes with optimal ratio: antitumor activity/toxicity. The geometry of three new Pt(II) complexes with general formula cis-[PtL2X2] (where L is 5-methyl-5(4-pyridyl)hydantoin and X = Cl-, Br-, I-) and of the free organic ligand were optimized using the hybrid DFT method B3LYP with LAN2DZ basis sets. The results were in very good correlation with the data of similar compounds from the literature. The same DFT method was used for the study of their spectral behavior, by reproducing their IR and Raman spectra and comparing them with experimental data. In addition, the distribution of charges by ESP analysis was calculated.

  19. Protein Complex Interactor Analysis and Differential Activity of KDM3 Subfamily Members Towards H3K9 Methylation

    PubMed Central

    Brauchle, Michael; Yao, Zhiping; Arora, Rishi; Thigale, Sachin; Clay, Ieuan; Inverardi, Bruno; Fletcher, Joy; Taslimi, Paul; Acker, Michael G.; Gerrits, Bertran; Voshol, Johannes; Bauer, Andreas; Schbeler, Dirk; Bouwmeester, Tewis; Ruffner, Heinz

    2013-01-01

    Histone modifications play an important role in chromatin organization and gene regulation, and their interpretation is referred to as epigenetic control. The methylation levels of several lysine residues in histone tails are tightly controlled, and JmjC domain-containing proteins are one class of broadly expressed enzymes catalyzing methyl group removal. However, several JmjC proteins remain uncharacterized, gaps persist in understanding substrate recognition, and the integration of JmjC proteins into signaling pathways is just emerging. The KDM3 subfamily is an evolutionarily conserved group of histone demethylase proteins, thought to share lysine substrate specificity. Here we use a systematic approach to compare KDM3 subfamily members. We show that full-length KDM3A and KDM3B are H3K9me1/2 histone demethylases whereas we fail to observe histone demethylase activity for JMJD1C using immunocytochemical and biochemical approaches. Structure-function analyses revealed the importance of a single amino acid in KDM3A implicated in the catalytic activity towards H3K9me1/2 that is not conserved in JMJD1C. Moreover, we use quantitative proteomic analyses to identify subsets of the interactomes of the 3 proteins. Specific interactor candidates were identified for each of the three KDM3 subfamily members. Importantly, we find that SCAI, a known transcriptional repressor, interacts specifically with KDM3B. Taken together, we identify substantial differences in the biology of KDM3 histone demethylases, namely enzymatic activity and protein-protein interactions. Such comparative approaches pave the way to a better understanding of histone demethylase specificity and protein function at a systems level and are instrumental in identifying the more subtle differences between closely related proteins. PMID:23593242

  20. Ionic interactions and transport properties in methyl terminated poly(propylene glycol)(4000) complexed with LiCF{sub 3}SO{sub 3}

    SciTech Connect

    Ferry, A.

    1997-01-09

    Alternating current (ac) impedance, restricted diffusion, and vibrational spectroscopic (Raman and IR) measurements have been conducted on complexes of methyl capped poly(propylene glycol) of molecular weight 4000 and LiCF{sub 3}SO{sub 3} salt. The relative concentrations of anions in different chemical environments have been calculated from an analysis of the symmetric anion SO{sub 3} stretch (Raman) over a wide concentration range. Comparisons are made to previous studies on hydroxyl capped PPG systems, and we find that polar polymer end groups play an important role in the solvation of the salt. The relative fraction of anions interacting directly with lithium cations is considerably higher over the entire concentration range in the present study, and we infer the existence of negatively charged ionic aggregates in the solutions. We also note that the fraction of spectroscopically `free` anions increases with increasing salt concentration in the ether oxygen to alkali metal cation ratio (O:M) range 502:1 to 12:1, contrary to a decrease reported for the analogue hydroxyl terminated electrolytes. The ionic conductivity has a more pronounced concentration dependency in the methyl capped system; notably, the molar conductivity ({Lambda}) increases dramatically with increasing salt concentration passing through a relatively sharp maximum at O:M = 20:1 at room temperature. 71 refs., 8 figs., 1 tab.

  1. MBD5 and MBD6 interact with the human PR-DUB complex through their methyl-CpG-binding domain.

    PubMed

    Baymaz, H Irem; Fournier, Alexandra; Laget, Sophie; Ji, Zongling; Jansen, Pascal W T C; Smits, Arne H; Ferry, Laure; Mensinga, Anneloes; Poser, Ina; Sharrocks, Andrew; Defossez, Pierre-Antoine; Vermeulen, Michiel

    2014-10-01

    MBD5 and MBD6 are two members of the methyl-CpG-binding domain (MBD) family of proteins that are poorly characterized. Studies performed thus far have failed to show binding of the MBD5 and MBD6 MBD to methylated DNA. Here, we show that both MBD5 and MBD6 interact with the mammalian PR-DUB Polycomb protein complex in a mutually exclusive manner. Strikingly, the MBD of MBD5 and MBD6 is both necessary and sufficient to mediate this interaction. Chromatin immunoprecipitation analyses reveal that MBD6 and FOXK2/PR-DUB share a subset of genomic target genes, suggesting a functional interaction in vivo. Finally, we show that MBD6, but not MBD5, is recruited to sites of DNA damage in a PR-DUB independent manner. Our study thus implies a shared function for MBD5 and MBD6 through an interaction with PR-DUB, as well as an MBD6-specific recruitment to sites of DNA damage. PMID:24634419

  2. Synthesis and spectroscopy studies of the inclusion complex of 3-amino-5-methyl pyrazole with beta-cyclodextrin

    NASA Astrophysics Data System (ADS)

    Louiz, S.; Labiadh, H.; Abderrahim, R.

    2015-01-01

    Amino pyrazole belongs to anti-inflammatory class, and is characterized by a low solubility in water. (In order to increase its solubility in water, inclusion complex of amino pyrazole with ?-CD was obtained.) The inclusion complex obtained between AMP and ?-cyclodextrin, was characterized by FT-IR, 1H NMR, 1H-1H NOESY, 13C NMR, DEPT, XHCOR, spectra, through TG analysis, DTA, DSC and Scanning Electron Microscopy (SEM). The stoichiometry of inclusion complex is 1:1 (guest-host) and K stability is 1.1 104 M-1.

  3. Effects of methyl substituent on the charge-transfer complexations of dicarbazolylalkanes with p-chloranil, tetracyanoethylene and tetracyanoquinodimethane

    NASA Astrophysics Data System (ADS)

    Asker, Erol; Uzkara, Ece; Zeybek, Orhan

    2011-09-01

    Series of 1, n-dicarbazolylalkanes and 1, n-di(3-methylcarbazolyl)alkanes (where n = 1-5) were synthesized and the molar extinction coefficients, equilibrium constants, enthalpies, and entropies of their charge-transfer (CT) complexes with the ?-acceptors p-chloranil, tetracyanoethylene, and tetracyanoquinodimethane were investigated. 1, n-Di(3-methylcarbazolyl)alkanes formed CT complexes with higher equilibrium constants, more negative enthalpies and entropies than 1, n-dicarbazolylalkanes. Vibrational spectra of CT complexes of one of the donor molecules (1,4-dicarbazolylbutane) with all three acceptors were compared.

  4. Effects of methyl substituent on the charge-transfer complexations of dicarbazolylalkanes with p-chloranil, tetracyanoethylene and tetracyanoquinodimethane.

    PubMed

    Asker, Erol; Uzkara, Ece; Zeybek, Orhan

    2011-09-01

    Series of 1,n-dicarbazolylalkanes and 1,n-di(3-methylcarbazolyl)alkanes (where n=1-5) were synthesized and the molar extinction coefficients, equilibrium constants, enthalpies, and entropies of their charge-transfer (CT) complexes with the ?-acceptors p-chloranil, tetracyanoethylene, and tetracyanoquinodimethane were investigated. 1,n-Di(3-methylcarbazolyl)alkanes formed CT complexes with higher equilibrium constants, more negative enthalpies and entropies than 1,n-dicarbazolylalkanes. Vibrational spectra of CT complexes of one of the donor molecules (1,4-dicarbazolylbutane) with all three acceptors were compared. PMID:21700488

  5. 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])24(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

  6. Molecular recognition in cyclodextrin complexes of amino acid derivatives. 2. A new perturbation: the room-temperature crystallographic structure determination for the N-acetyl-p-methoxy-L-phenylalanine methyl ester/beta-cyclodextrin complex.

    PubMed

    Clark, J L; Booth, B R; Stezowski, J J

    2001-10-10

    Cyclodextrins (CDs) are cyclic oligosaccharides that encapsulate various small organic molecules, forming inclusion complexes. Because CD complexes are held together purely by noncovalent interactions, they function as excellent models for the study of chiral and molecular recognition mechanisms. Recently, room-temperature crystallographic studies of both the 2:2 N-acetyl-L-phenylalanine methyl ester/beta-CD and 2:2 N-acetyl-L-phenylalanine amide/beta-CD complexes were reported. The effect of changes in carboxyl backbone functional group on molecular recognition by the host CD molecule was examined for the nearly isomorphous supramolecular complexes. A new perturbation of the system is now examined, specifically perturbation of the aromatic side chain. We report a room-temperature crystal structure determination for the 2:2 N-acetyl-p-methoxy-L-phenylalanine methyl ester/beta-CD inclusion complex. The complex crystallizes isomorphously with the two previously reported examples in space group P1; the asymmetric unit consists of a hydrated head-to-head host dimer with two included guest molecules. The crystal packing provides both a nonconstraining extended hydrophobic pocket and an adjacent hydrophilic region, where hydrogen-bonding interactions can potentially occur with primary hydroxyl groups of neighboring CD molecules and waters of hydration. The rigid host molecules show no sign of conformational disorder, and water of hydration molecules exhibit the same type of disorder observed for the other two complexes, with a few significant differences in locations of water molecules in the hydrophilic region near guest molecules. There is evidence for modest disorder in the guest region of an electron density map. In comparing this system with the two previously reported complexes of phenylalanine derivatives, it is found that the packing of the guest molecules inside the torus of the CD changes upon substitution of a methoxy group at the para position of the aromatic phenyl ring. Backbone hydrogen-bonding interactions for the guest molecules with the CD primary hydroxyls and waters also change. This structure determination is a new and revealing addition to a small but growing database of amino acid and peptidomimetic interactions with carbohydrates. PMID:11583553

  7. 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

  8. 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.

  9. Enzyme Inhibitor Studies Reveal Complex Control of Methyl-D-Erythritol 4-Phosphate (MEP) Pathway Enzyme Expression in Catharanthus roseus

    PubMed Central

    Han, Mei; Heppel, Simon C.; Su, Tao; Bogs, Jochen; Zu, Yuangang; An, Zhigang; Rausch, Thomas

    2013-01-01

    In Catharanthus roseus, the monoterpene moiety exerts a strong flux control for monoterpene indole alkaloid (MIA) formation. Monoterpene synthesis depends on the methyl-D-erythritol 4-phosphate (MEP) pathway. Here, we have explored the regulation of this pathway in response to developmental and environmental cues and in response to specific enzyme inhibitors. For the MEP pathway entry enzyme 1-deoxy-D-xylulose 5-phosphate synthase (DXS), a new (type I) DXS isoform, CrDXS1, has been cloned, which, in contrast to previous reports on type II CrDXS, was not transcriptionally activated by the transcription factor ORCA3. Regulation of the MEP pathway in response to metabolic perturbations has been explored using the enzyme inhibitors clomazone (precursor of 5-ketochlomazone, inhibitor of DXS) and fosmidomycin (inhibitor of deoxyxylulose 5-phosphate reductoisomerase (DXR)), respectively. Young leaves of non-flowering plants were exposed to both inhibitors, adopting a non-invasive in vivo technique. Transcripts and proteins of DXS (3 isoforms), DXR, and hydroxymethylbutenyl diphosphate synthase (HDS) were monitored, and protein stability was followed in isolated chloroplasts. Transcripts for DXS1 were repressed by both inhibitors, whereas transcripts for DXS2A&B, DXR and HDS increased after clomazone treatment but were barely affected by fosmidomycin treatment. DXS protein accumulated in response to both inhibitors, whereas DXR and HDS proteins were less affected. Fosmidomycin-induced accumulation of DXS protein indicated substantial posttranscriptional regulation. Furthermore, fosmidomycin effectively protected DXR against degradation in planta and in isolated chloroplasts. Thus our results suggest that DXR protein stability may be affected by substrate binding. In summary, the present results provide novel insight into the regulation of DXS expression in C. roseus in response to MEP-pathway perturbation. PMID:23650515

  10. Methyl-, Ethenyl-, and Ethynyl-Bridged Cationic Digold Complexes Stabilized by Coordination to a Bulky Terphenylphosphine Ligand.

    PubMed

    Espada, María F; Campos, Jesús; López-Serrano, Joaquín; Poveda, Manuel L; Carmona, Ernesto

    2015-12-14

    Reactions of the gold(I) triflimide complex [Au(NTf2 )(PMe2 Ar${{^{{\\rm Dipp}{_{2}}}}}$)] (1) with the gold(I) hydrocarbyl species [AuR(PMe2 Ar${{^{{\\rm Dipp}{_{2}}}}}$)] (2 a-2 c) enable the isolation of hydrocarbyl-bridged cationic digold complexes with the general composition [Au2 (μ-R)(PMe2 Ar${{^{{\\rm Dipp}{_{2}}}}}$)2 ][NTf2 ], where Ar${{^{{\\rm Dipp}{_{2}}}}}$=C6 H3 -2,6-(C6 H3 -2,6-iPr2 )2 and R=Me (3), CHCH2 (4), or CCH (5). Compound 3 is the first alkyl-bridged digold complex to be reported and features a symmetric [Au(μ-CH3 )Au](+) core. Complexes 4 and 5 are the first species of their kind that contain simple, unsubstituted vinyl and acetylide units, respectively. In the series of complexes 3-5, the bridging carbon atom systematically changes its hybridization from sp(3) to sp(2) and sp. Concomitant with this change, and owing to variations in the nature of the bonding within the [Au(μ-R)Au](+) unit, there is a gradual decrease in aurophilicity, that is, the strength of the Au⋅⋅⋅Au bonding interaction decreases. This change is illustrated by a monotonic increase in the Au-Au distance by approximately 0.3 Å from R=CH3 (2.71 Å) to CHCH2 (3.07 Å) and CCH (3.31 Å). PMID:26555404

  11. IDENTIFICATION OF METHYL FARNESOATE FROM IN VITRO CULTURE OF THE RETROCEREBRAL COMPLEX OF ADULT FEMALES OF THE MOTH, HELIOTHIS VIRESCENS (LEPIDOPTERA: NOCTUIDAE) AND ITS CONVERSION TO JUVENILE HORMONE III

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Gas chromatographic-mass spectral analysis of extracts obtained from in vitro culture of isolated retrocerebral complexes obtained from adult females of the moth Heliothis virescens resulted in identification of methyl farnesoate as well as, juvenile hormone III (JH III) but not JH III acid. Inhibit...

  12. Structural, spectroscopic and theoretical studies of short OHO hydrogen bonds in 2:1 complexes of 1-methyl-6-oxyquinolinium betaine with mineral acids

    NASA Astrophysics Data System (ADS)

    Barczy?ski, P.; Komasa, A.; Ratajczak-Sitarz, M.; Katrusiak, A.; Dega-Szafran, Z.; Szafran, M.

    2010-12-01

    Bis(1-methyl-6-oxyquinolinium) hydroiodide, (6QB) 2HI ( 1), has been characterized by X-ray diffraction, B3LYP calculations, FTIR and NMR spectroscopy. The complex crystallizes in triclinic P1 space group. A pair of 6QB molecules is bridged by the OHO hydrogen bond of 2.450(2) . The anion I - electrostatically interacts with both positively charged nitrogen atoms of the neighboring 6QB molecules. The isolated entities of the complex were analyzed at the B3LYP/6-311G(d,p) level of theory in order to determine the influence of counter ions (X - = I -, Br -, Cl - and ClO4-) on the hydrogen bond in (6QB) 2HX ( 2- 5). The FTIR spectra of (6QB) 2HI and (6QB) 2HClO 4 show a broad and intense absorption in the 1500-400 cm -1 region, typical for short hydrogen bonds. Both 1H and 13C chemical shifts depend on the acid-base stoichiometry and counter ions.

  13. Pd(II) and Pd(IV) complexes with 5-methyl-5-(4-pyridyl)hydantoin: Synthesis, physicochemical, theoretical, and pharmacological investigation

    NASA Astrophysics Data System (ADS)

    Sabounchei, Seyyed Javad; Shahriary, Parisa; Salehzadeh, Sadegh; Gholiee, Yasin; Nematollahi, Davood; Chehregani, Abdolkarim; Amani, Ameneh; Afsartala, Zohreh

    2015-01-01

    The reaction of K2[PdCl4] and PdCl2 with 5-methyl-5-(4-pyridyl)-2,4-imidazolidenedione (L) proceeded with the formation of two different Pd complexes, PdL2Cl2 (1) and PdL2Cl4 (2c), corresponded to a substitution reaction and a substitution reaction along with unanticipated oxidation, respectively. The nature of the oxidizing agent is unknown. These compounds have been studied by elemental analysis, IR, 1H and 13CNMR, molar conductivity, and cyclic voltammetry. In addition, structural optimization by DFT calculations and simulation of NMR spectra have been performed and compared with the experimental data. NBO analysis, HOMO and LUMO, have been used to elucidate the information regarding charge transfer within the molecules. Theoretical studies confirmed that in 1 and 2c the trans structures are about 41 and 33 kJ mol-1 more stable than cis ones. Antibacterial activity and in vitro cytotoxicity of these compounds, as respectively assessed in six bacterial strains and two human tumor cell lines, have been investigated. Results showed the title complexes have the capacity of inhibiting the metabolic growth of bacteria and tumor cells to different extents.

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

    PubMed Central

    Garca, Agustina; Leonardi, Daro; Vasconi, Mara D.; Hinrichsen, Lucila I.; Lamas, Mara 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

  15. Separation of Enantiomers by Inclusion Gas Chromatography: On the Influence of Water in the Molecular Complexation of Methyl 2-Chloropropanoate Enantiomers and the Modified ?-Cyclodextrin Lipodex-E.

    PubMed

    Mandoli, Alessandro; Schurig, Volker

    2016-02-01

    A profound influence of water has previously been detected in the complexation of the enantiomers of methyl 2-chloropropanoate (MCP) and the chiral selector octakis(3-O-butanoyl-2,6-di-O-pentyl)-?-cyclodextrin (Lipodex-E) in NMR and sensor experiments. We therefore investigated the retention behavior of MCP enantiomers on Lipodex-E by gas chromatography (GC) under hydrous conditions. Addition of water to the N2 carrier gas modestly reduced the retention factors k of the enantiomers, notably for the second eluted enantiomer (S)-MCP. This resulted in an overall decrease of enantioselectivity -?S,R (?G) in the presence of water. The effect was fully reversible. Consequently, for a conditioned column in the absence of residual water, the determined thermodynamic data, i.e. ?S,R (?H) = -12.64 0.08 kJ mol(-1) and ?S,R (?S) = -28.18 0.23 J K(-1) mol(-1) , refer to a true 1:1 complexation process devoid of hydrophobic hydration. Chirality 28:124-131, 2015. 2015 Wiley Periodicals, Inc. PMID:26636659

  16. 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...

  17. 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).

  18. DNA methylation program during development

    PubMed Central

    ZHOU, Feng C.

    2013-01-01

    DNA methylation is a key epigenetic mark when occurring in the promoter and enhancer regions regulates the accessibility of the binding protein and gene transcription. DNA methylation is inheritable and can be de novo-synthesized, erased and reinstated, making it arguably one of the most dynamic upstream regulators for gene expression and the most influential pacer for development. Recent progress has demonstrated that two forms of cytosine methylation and two pathways for demethylation constitute ample complexity for an instructional program for orchestrated gene expression and development. The forum of the current discussion and review are whether there is such a program, if so what the DNA methylation program entails, and what environment can change the DNA methylation program. The translational implication of the DNA methylation program is also proposed. PMID:23687512

  19. Targeting the D1-N-methyl-d-aspartate receptor complex reduces l-dopa-induced dyskinesia in 6-hydroxydopamine-lesioned Parkinsons rats

    PubMed Central

    Song, Lu; Zhang, Zhanzhao; Hu, Rongguo; Cheng, Jie; Li, Lin; Fan, Qinyi; Wu, Na; Gan, Jing; Zhou, Mingzhu; Liu, Zhenguo

    2016-01-01

    L-3,4-dihydroxyphenylalanine (l-dopa) remains the most effective therapy for Parkinsons disease (PD), but its long-term administration is associated with the development of debilitating motor complications known as l-dopa-induced dyskinesia (LID). Enhanced function of dopamine D1 receptor (D1R) and N-methyl-d-aspartate receptor (NMDAR) is believed to participate in the pathogenesis of LID. Given the existence of physical and functional interactions between D1R and NMDAR, we explored the effects of uncoupling D1R and NMDA GluN1 (GluN1) interaction on LID by using the Tat-conjugated interfering peptide (Tat-D1-t2). In this study, we demonstrated in 6-hydroxydopamine (6-OHDA)-lesioned PD rat model that intrastriatal injection of Tat-D1-t2 alleviated dyskinetic behaviors and downregulated the phosphorylation of DARPP-32 at Thr34 induced by levodopa. Moreover, we also showed intrastriatal administration of Tat-D1-t2 elicited alterations in membranous GluN1 and D1R expression. These findings indicate that D1R/GluN1 complexes may be a molecular target with therapeutic potential for the treatment of dyskinesia in Parkinsons patients. PMID:26893543

  20. Targeting the D1-N-methyl-d-aspartate receptor complex reduces l-dopa-induced dyskinesia in 6-hydroxydopamine-lesioned Parkinson's rats.

    PubMed

    Song, Lu; Zhang, Zhanzhao; Hu, Rongguo; Cheng, Jie; Li, Lin; Fan, Qinyi; Wu, Na; Gan, Jing; Zhou, Mingzhu; Liu, Zhenguo

    2016-01-01

    L-3,4-dihydroxyphenylalanine (l-dopa) remains the most effective therapy for Parkinson's disease (PD), but its long-term administration is associated with the development of debilitating motor complications known as l-dopa-induced dyskinesia (LID). Enhanced function of dopamine D1 receptor (D1R) and N-methyl-d-aspartate receptor (NMDAR) is believed to participate in the pathogenesis of LID. Given the existence of physical and functional interactions between D1R and NMDAR, we explored the effects of uncoupling D1R and NMDA GluN1 (GluN1) interaction on LID by using the Tat-conjugated interfering peptide (Tat-D1-t2). In this study, we demonstrated in 6-hydroxydopamine (6-OHDA)-lesioned PD rat model that intrastriatal injection of Tat-D1-t2 alleviated dyskinetic behaviors and downregulated the phosphorylation of DARPP-32 at Thr34 induced by levodopa. Moreover, we also showed intrastriatal administration of Tat-D1-t2 elicited alterations in membranous GluN1 and D1R expression. These findings indicate that D1R/GluN1 complexes may be a molecular target with therapeutic potential for the treatment of dyskinesia in Parkinson's patients. PMID:26893543

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

    PubMed Central

    Resnik, Nataša; Repnik, Urška; Kreft, Mateja Erdani; Sepčić, Kristina; Maček, Peter; Turk, Boris; Veranič, 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-β-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

  2. 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.

  3. 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.

  4. [CuCl3(H2O)](-) complexes aggregated to form hydrate columns in methyl-substituted pyridinium or piperidinium salts.

    PubMed

    Nalla, Sowjanya; Bond, Marcus R

    2011-06-01

    1,2,3-Trimethylpyridinium aquatrichloridocuprate(II), (C(8)H(12)N)[CuCl(3)(H(2)O)], (I), 3,4-dimethylpyridinium aquatrichloridocuprate(II), (C(7)H(10)N)[CuCl(3)(H(2)O)], (II), and 2,3-dimethylpyridinium aquatrichloridocuprate(II), (C(7)H(10)N)[CuCl(3)(H(2)O)], (III), exhibit the same fundamental structure, with (I) and (II) isomorphous and with the unit-cell constants of (III) similar to the reduced unit-cell constants of (I) and (II). The distorted square-planar [CuCl(3)(H(2)O)](-) complex [mirror symmetric in (I) and (II)] forms two semicoordinate CuCl bonds to a neighboring complex to produce a dimer with 2/m symmetry [only inversion symmetry in (III)]. The semicoordinate Cu...Cl bond length of the dimer shows significant elongation at 295 K compared with that at 100 K, while the coordinate Cu-Cl bond lengths are slightly contracted at 295 K compared with those at 100 K. The inorganic dimers are linked by eight hydrogen bonds to four neighboring dimers to establish a checkerboard network layer in the ab plane, with voids between the dimers that accommodate, on both sides, inversion-related organic cation pairs. The organic cations are required by mirror-plane symmetry to be disordered in (I) and (II). The organic cations and [CuCl(3)(H(2)O)](-) complexes are nearly coplanar and tilted out of the layer plane to establish a hybrid organic-inorganic layer structure parallel to (202) [(11-2) in (III)], with hydrate columns (defined by water molecules) and hydrophobic columns (defined by methyl groups) parallel to each other [and along the 2(1) axes in (I) and (II)]. In 1,1-dimethylpiperidinium aquatrichloridocuprate(II), (C(7)H(16)N)[CuCl(3)(H(2)O)], (IV), the bulkier organic cation prevents semicoordinate bonding between complexes, which are hydrogen bonded side-to-side in zigzag chains that place water molecules in columns along half of the 2(1) axes. PMID:21633151

  5. Theoretical and experimental studies on three new coordination complexes of Co(II), Ni(II), and Cu(II) with 2,4-dichloro-6-{(E)-[(5-chloro-2 sulfanylphenyl)imino]methyl}phenol Schiff base ligand.

    PubMed

    Kusmariya, Brajendra S; Mishra, A P

    2015-11-01

    Three mononuclear coordination complexes of Co(II), Ni(II), and Cu(II) have been synthesized from 2,4-dichloro-6-{(E)-[(5-chloro-2-sulfanylphenyl)imino]methyl}phenol ligand (H 2 L) obtained by simple condensation reaction of 3,5-dichloro-2-hydroxybenzaldehyde and 2-amino-4-chlorobenzenethiol and characterized by elemental analysis, spectral (FT-IR, electronic, and (1)H-NMR), molar conductance, thermal, SEM, PXRD, and fluorescence studies. The PXRD analysis and SEM-EDX micrographs show the crystalline nature of complexes. The domain size and the lattice strain of synthesized compounds have been determined according to Williamson-Hall plot. TG of the synthesized complexes illustrates the general decomposition pattern of the complexes. The ligand exhibits an interesting fluorescence property which is suppressed after complex formation. The Co(II) complex adopted a distorted octahedral configuration while Ni(II) and Cu(II) complexes showed square planar geometry around metal center. The geometry optimization, HOMO-LUMO, molecular electrostatic potential map (MEP), and spin density of synthesized compounds have been performed by density functional theory (DFT) method using B3LYP/6-31G and B3LYP/LANL2DZ as basis set. Graphical abstract Three new coordination complexes of Co(II), Ni(II) and Cu(II) with 2,4-dichloro-6-{(E)-[(5-chloro-2 sulfanylphenyl)imino]methyl}phenol Schiff base ligand. PMID:26438445

  6. Methyl methacrylate

    Integrated Risk Information System (IRIS)

    TOXICOLOGICAL REVIEW of METHYL METHACRYLATE ( CAS No . 80 - 62 - 6 ) In Support of Summary Information on the Integrated Risk Information System ( IRIS ) January 1998 U.S . Environmental Protection Agency Washington , DC TABLE OF CONTENTS DISCLAIMER . . . . . . . . . . . . . . . . . . . . . . . . .

  7. Infrared spectra of the CH3-MX, CH2=MHX, and CH[triple bond]MH2X- complexes formed by reaction of methyl halides with laser-ablated group 5 metal atoms.

    PubMed

    Cho, Han-Gook; Andrews, Lester

    2006-08-24

    Reactions of group 5 metal atoms and methyl halides give carbon-metal single, double, and triple bonded complexes that are identified from matrix IR spectra and vibrational frequencies computed by DFT. Two different pairs of complexes are prepared in reactions of methyl fluoride with laser-ablated vanadium and tantalum atoms. The two vanadium complexes (CH(3)-VF and CH(2)=VHF) are persistently photoreversible and show a kinetic isotope effect on the yield of CD(2)=VDF. Identification of CH(2)=TaHF and CH[triple bond]TaH(2)F(-), along with the similar anionic Nb complex, suggests that the anionic methylidyne complex is a general property of the heavy group 5 metals. Reactions of Nb and Ta with CH(3)Cl and CH(3)Br have also been carried out to understand the ligand effects on the calculated structures and the vibrational characteristics. The methylidene complexes become more distorted with increasing halogen size, while the calculated C=M bond lengths and stretching frequencies decrease and increase, respectively. The anionic methylidyne complexes are less favored with increasing halogen size. Infrared spectra show a dramatic increase of the Ta methylidenes upon annealing, suggesting that the formation of CH(3)-TaX and its conversion to CH(2)=TaHX require essentially no activation energy. PMID:16913680

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

    PubMed Central

    Do, Loi H.; Xue, Genqiang

    2012-01-01

    The composition of a (?-oxo)diiron(III) complex coordinated by tris((3,5-dimethy-4-methoxy)pyridyl-2-methyl)amine (R3TPA) ligands was investigated. Characterization using a variety of spectroscopic methods and X-ray crystallography indicated that the reaction of iron(III) perchlorate, sodium hydroxide, and R3TPA affords [Fe2(?-O)(?-OH)(R3TPA)2](ClO4)3 (2), rather than the previously reported species, [Fe2(?-O)(OH)(H2O)(R3TPA)2](ClO4)3 (1). Facile conversion of the (?-oxo)(?-hydroxo)diiron(III) core of 2 to the (?-oxo)(hydroxo)(aqua)diiron(III) core of 1 occurs in the presence of water and at low temperature. When 2 is exposed to wet acetonitrile at room temperature, the CH3CN adduct is hydrolyzed to CH3COO?, which forms the compound [Fe2(?-O)(?-CH3COO)(R3TPA)2](ClO4)3 (10). The identity of 10 was confirmed by comparison of its spectroscopic properties with those of an independently prepared sample. To evaluate whether or not 1 and 2 are capable of generating the diiron(IV) species [Fe2(?-O)(OH)(O)(R3TPA)2]3+ (4), which has previously been generated as a synthetic model for high-valent diiron protein oxygenated intermediates, studies were performed to investigate their reactivity with hydrogen peroxide. Because 2 reacts rapidly with hydrogen peroxide in CH3CN but not in CH3CN/H2O, conditions that favor conversion to 1, complex 1 is not a likely precursor to 4. Compound 4 also forms in the reaction of 2 with H2O2 in solvents lacking a nitrile, suggesting that hydrolysis of CH3CN is not involved in the H2O2 activation reaction. These findings shed light on the formation of several diiron complexes of electron-rich R3TPA ligands and elaborate on conditions required to generate synthetic models of diiron(IV) protein intermediates with this ligand framework. PMID:22264120

  9. Mssbauer and magnetic studies on the spin states of mono- and binuclear iron(III) complexes with quinquedentate ligand methyl-substituted pyridine and bridged by pyrazine or bis(pyridine) compounds

    NASA Astrophysics Data System (ADS)

    Wei, H. H.; Sheu, J. F.

    1992-04-01

    Mono- and binuclear iron(III) complexes with the general formula [FeXL] and [LFe-Y-FeL](BPh4)2 have been prepared and their spin states of the iron atom in the complexes has been investigated by means of the temperature-dependent Mssbauer spectroscopy and magnetic measurements, where X is a methyl-substituted pyridine, L denotes a quinquedentate Schiff-base derived from salicylaldehyde with N-(2-aminoethyl)-1,3-propanediamine and Y denotes bridged ligands such as pyrazine(pyr), 4,4'-pyridine(bpy), 4,4'-vinylenepyridine(vipy). On the basis of the Mssbauer and magnetic data, it was concluded that the spintransition characteristics depends on the methyl substituent of pyridine and the bridged ligand.

  10. 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

  11. DNA Methylation

    PubMed Central

    Marinus, M.G.; Lbner-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:26442938

  12. Comparative sensitivity to methyl eugenol of four putative Bactrocera dorsalis complex sibling species – further evidence that they belong to one and the same species B. dorsalis

    PubMed Central

    Hee, Alvin K.W.; Ooi, Yue-Shin; Wee, Suk-Ling; Tan, Keng-Hong

    2015-01-01

    Abstract Males of certain species belonging to the Bactrocera dorsalis complex are strongly attracted to, and readily feed on methyl eugenol (ME), a plant secondary compound that is found in over 480 plant species worldwide. Amongst those species is one of the world’s most severe fruit pests the Oriental fruit fly, Bactrocera dorsalis s.s., and the former taxonomic species Bactrocera invadens, Bactrocera papayae and Bactrocera philippinensis. The latter species have been recently synonymised with Bactrocera dorsalis based on their very similar morphology, mating compatibility, molecular genetics and identical sex pheromones following consumption of ME. Previous studies have shown that male fruit fly responsiveness to lures is a unique phenomenon that is dose species-specific, besides showing a close correlation to sexual maturity attainment. This led us to use ME sensitivity as a behavioural parameter to test if Bactrocera dorsalis and the three former taxonomic species had similar sensitivity towards odours of ME. Using Probit analysis, we estimated the median dose of ME required to elicit species’ positive response in 50% of each population tested (ED50). ED50 values were compared between Bactrocera dorsalis and the former species. Our results showed no significant differences between Bactrocera dorsalis s.s., and the former Bactrocera invadens, Bactrocera papayae and Bactrocera philippinensis in their response to ME. We consider that the Bactrocera males’ sensitivity to ME may be a useful behavioural parameter for species delimitation and, in addition to other integrative taxonomic tools used, provides further supportive evidence that the four taxa belong to one and the same biological species, Bactrocera dorsalis. PMID:26798265

  13. 7-Chlorokynurenic acid is a selective antagonist at the glycine modulatory site of the N-methyl-D-aspartate receptor complex.

    PubMed Central

    Kemp, J A; Foster, A C; Leeson, P D; Priestley, T; Tridgett, R; Iversen, L L; Woodruff, G N

    1988-01-01

    Glycine markedly potentiates N-methyl-D-aspartate (N-Me-D-Asp) responses in mammalian neurons by an action at a modulatory site on the N-Me-D-Asp receptor-ionophore complex. Here we present evidence that 7-chlorokynurenic acid (7-Cl KYNA) inhibits N-Me-D-Asp responses by a selective antagonism of glycine at this modulatory site. In rat cortical slices 7-Cl KYNA (10-100 microM) noncompetitively inhibited N-Me-D-Asp responses, and this effect could be reversed by the addition of glycine (100 microM) or D-serine (100 microM). Radioligand binding experiments showed that 7-Cl KYNA had a much higher affinity for the strychnine-insensitive [3H]glycine binding site (IC50 = 0.56 microM) than for the N-Me-D-Asp (IC50 169 microM), quisqualate (IC50 = 153 microM), or kainate (IC50 greater than 1000 microM) recognition sites. In whole-cell patch-clamp recordings from rat cortical neurones in culture, the inhibitory effects of 7-Cl KYNA on N-Me-D-Asp-induced currents could not be overcome by increasing the N-Me-D-Asp concentration but could be reversed by increasing the glycine concentration. 7-Cl KYNA could completely abolish N-Me-D-Asp responses, including basal responses in the absence of added glycine, suggesting that it may possess negative modulatory effects at the glycine site. These findings indicate that the glycine modulatory site is functional in intact adult tissue and that 7-Cl KYNA should prove to be a selective tool for elucidating the involvement of this site in physiological and pathological events mediated by N-Me-D-Asp receptors. PMID:2842779

  14. 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).

  15. 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

  16. Methyl chloride

    Integrated Risk Information System (IRIS)

    Methyl chloride ; CASRN 74 - 87 - 3 ( 07 / 17 / 2001 ) 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

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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).

  4. Methylation, memory and addiction

    PubMed Central

    Bali, Purva; Im, Heh-In

    2011-01-01

    Dynamic chromatin remodeling is at the heart of most biological processes including gene transcription, DNA replication and repair, cell differentiation and apoptosis. Chromatin remodeling as a result of covalent histone modifications, including histone acetylation, methylation or SUMOylation, play important roles in these processes. Similarly, direct chemical modification of DNA, most notably DNA methylation, also plays a key role in controlling gene expression and basic aspects of cell biology. Memory, one of the most fundamental of all brain functions, is a complex process involving diverse cellular signaling cascades and coordinated regulation of entire networks of genes. Synaptic plasticity, which is defined as activity-dependent changes in synaptic strength between neurons, provides the cellular basis of memory. The role for covalent histone modifications in synaptic plasticity and in learning and memory has been now been firmly established.13 In contrast, much less had been known concerning DNA methylation in memory formation and storage. Emerging evidence now suggests that DNA methylation plays a central role in these processes, likely by directly influencing the expression of genes involved in synaptic plasticity.4 PMID:21586900

  5. Synthesis, spectral characterization and antioxidant activity studies of a bidentate Schiff base, 5-methyl thiophene-2-carboxaldehyde-carbohydrazone and its Cd(II), Cu(II), Ni(II) and Zn(II) complexes

    NASA Astrophysics Data System (ADS)

    Harinath, Y.; Harikishore Kumar Reddy, D.; Naresh Kumar, B.; Apparao, Ch.; Seshaiah, K.

    2013-01-01

    A new Schiff base bidentate ligand (L), 5-methyl thiophene-2-carboxaldehyde-carbohydrazone and its metal (Cu(II), Cd(II), Ni(II) and Zn(II)) complexes with general stoichiometry [M(L)2X2] (where X = Cl) were synthesized. The ligand and its metal complexes were characterized by elemental analyses, IR, 1H NMR, ESR spectral analyses, and molar conductance studies. The molar conductance data revealed that all the metal chelates are non-electrolytes. IR spectra showed that ligand (L) is coordinated to the metal ions in a bidentate manner with N and O donor sites of the azomethine-N, and carbonyl-O. ESR and UV-Vis spectral data showed that the geometrical structure of the complexes are Orthorhombic. Furthermore, the antioxidant activity of the ligand and its complexes was determined by hydroxyl radical scavenging, DPPH, NO, reducing power methods in vitro. The obtained IC50 value of the DPPH activity for the copper complex (IC50 = 66.4 μm) was higher than other compounds. Microbial assay of the above complexes against Staphylococcus aureus, Escherichia coli, Rhizocotonia bataticola and Alternaria alternata showed that copper complex exhibited higher activity than the other complexes.

  6. 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.

  7. 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.

    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, τ=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

  8. 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; zmen, 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

  9. Spectral characterization, molecular modeling and antimicrobial studies on hydrazone metal complexes of 5-acetyl-4-hydroxy-2H-1,3-thiazine-2,6(3H)dione and S-methyl dithiocarbazate

    NASA Astrophysics Data System (ADS)

    Taha, Ali; Emara, Adel A. A.; Mashaly, Mahmoud M.; Adly, Omima M. I.

    2014-09-01

    Metal complexes of copper(II), nickel(II), cobalt(II), oxovanadium(IV), chromium(III) and cadmium(II) with a new bridged ONS dibasic tridentate hydrazone (H2L) derived from 5-acetyl-4-hydroxy-2H-1,3-thiazine-2,6(3H)-dione with S-methyl dithiocarbazate have been synthesized and characterized by elemental analysis, molar conductance, magnetic susceptibility measurements, spectral (infrared, electronic, mass, 1H NMR and ESR) studies as well as thermal gravimetric analysis (TGA). The synthesized complexes have dimeric structures with the general formula [ML(NO3)m(H2O)x]2nH2OzMeOH, L = dianion of the hydrazone, m = 0-1, x = 0-2, n = 0-4 and z = 0-1. The metal complexes exhibited square planar, tetrahedral and octahedral geometrical arrangements, the molar conductivity data indicates that all complexes are neutral. The Coats-Redfern equation was used to calculate the kinetic and thermodynamic parameters for the different thermal decomposition stages of some complexes. Structural parameters of the ligand and its metal complexes have been theoretically computed on the basis of semiempirical PM3 level and the results were correlated with their experimental data. Antibacterial activities of the free ligand and its metal complexes were screened against various organisms.

  10. Spectral characterization, molecular modeling and antimicrobial studies on hydrazone metal complexes of 5-acetyl-4-hydroxy-2H-1,3-thiazine-2,6(3H)dione and S-methyl dithiocarbazate.

    PubMed

    Taha, Ali; Emara, Adel A A; Mashaly, Mahmoud M; Adly, Omima M I

    2014-09-15

    Metal complexes of copper(II), nickel(II), cobalt(II), oxovanadium(IV), chromium(III) and cadmium(II) with a new bridged ONS dibasic tridentate hydrazone (H2L) derived from 5-acetyl-4-hydroxy-2H-1,3-thiazine-2,6(3H)-dione with S-methyl dithiocarbazate have been synthesized and characterized by elemental analysis, molar conductance, magnetic susceptibility measurements, spectral (infrared, electronic, mass, 1H NMR and ESR) studies as well as thermal gravimetric analysis (TGA). The synthesized complexes have dimeric structures with the general formula [ML(NO3)m(H2O)x]2nH2OzMeOH, L=dianion of the hydrazone, m=0-1, x=0-2, n=0-4 and z=0-1. The metal complexes exhibited square planar, tetrahedral and octahedral geometrical arrangements, the molar conductivity data indicates that all complexes are neutral. The Coats-Redfern equation was used to calculate the kinetic and thermodynamic parameters for the different thermal decomposition stages of some complexes. Structural parameters of the ligand and its metal complexes have been theoretically computed on the basis of semiempirical PM3 level and the results were correlated with their experimental data. Antibacterial activities of the free ligand and its metal complexes were screened against various organisms. PMID:24810030

  11. Unexpected metal-induced isomerisms and phosphoryl migrations in Pt(II) and Pd(II) complexes of the functional phosphine 2-(bis(diphenylphosphino)methyl)-oxazoline.

    PubMed

    Zhang, Shuanming; Pattacini, Roberto; Braunstein, Pierre

    2011-04-18

    The reaction of the functional diphosphine 1 [1 = 2-(bis(diphenylphosphino)methyl-oxazoline] with [PtCl(2)(NCPh)(2)] or [PdCl(2)(NCPh)(2)], in the presence of excess NEt(3), affords [Pt{(Ph(2)P)(2)CC(NCH(2)CH(2)O)}(2)] ([Pt(1(-H)-P,P)(2)], 3a) and [Pd{(Ph(2)P)(2)CC(NCH(2)CH(2)O)}(2)] ([Pd(1(-H)-P,P)(2)], 3b), respectively, in which 1(-H) is (oxazoline-2-yl)bis(diphenylphosphino)methanide. The reaction of 3b with 2 equiv of [AuCl(tht)] (tht = tetrahydrothiophene) afforded [Pd(1(-H)-P,N)(2)(AuCl)(2)] (4), as a result of the opening of the four-membered metal chelate since ligand 1(-H), which was P,P-chelating in 3b, behaves as a P,N-chelate toward the Pd(II) center in 4 and coordinates to Au(I) through the other P donor. In the absence of a base, the reaction of ligand 1 with [PtCl(2)(NCPh)(2)] in MeCN or CH(2)Cl(2) afforded the isomers [Pt{(Ph(2)P)(2)C?C(OCH(2)CH(2)NH)}(2)]Cl(2) ([Pt(1'-P,P)(2)]Cl(2) (5), 1' = 2-(bis(diphenylphosphino)methylene)-oxazolidine) and [Pt{(Ph(2)P)(2)C?C(OCH(2)CH(2)NH)}{Ph(2)PCH?C(OCH(2)CH(2)N(PPh(2))}]Cl(2) ([Pt(1'-P,P)(2'-P,P)]Cl(2) (6), 2' = (E)-3-(diphenylphosphino)-2-((diphenylphosphino)methylene)oxazolidine]. The P,P-chelating ligands in 5 result from a tautomeric shift of the C-H proton of 1 to the nitrogen atom, whereas the formation of one of the P,P-chelates in 6 involves a carbon to nitrogen phosphoryl migration. The reaction of 5 and 6 with a base occurred by deprotonation at the nitrogen to afford 3a and [Pt{(Ph(2)P)(2)CC(NCH(2)CH(2)O)}{Ph(2)PCH?COCH(2)CH(2)N(PPh(2))}]Cl ([Pt(1(-H)-P,P)(2'-P,P)]Cl (7)], respectively. In CH(2)Cl(2), an isomer of 3a, [Pt{Ph(2)P)(2)CC(NCH(2)CH(2)O)}{Ph(2)PC(PPh(2))?COCH(2)CH(2)N}] ([Pt(1(-H)-P,P)(1(-H)-P,N)] (8)), was obtained as a side product which contains ligand 1(-H) in two different coordination modes. Complexes 3b4CH(2)Cl(2), 4CHCl(3), 62.5CH(2)Cl(2), and 8CH(2)Cl(2) have been structurally characterized by X-ray diffraction. PMID:21405088

  12. Successive ratio subtraction coupled with constant multiplication spectrophotometric method for determination of hydroquinone in complex mixture with its degradation products, tretinoin and methyl paraben.

    PubMed

    Elghobashy, Mohamed R; Bebawy, Lories I; Shokry, Rafeek F; Abbas, Samah S

    2016-03-15

    A sensitive and selective stability-indicating successive ratio subtraction coupled with constant multiplication (SRS-CM) spectrophotometric method was studied and developed for the spectrum resolution of five component mixture without prior separation. The components were hydroquinone in combination with tretinoin, the polymer formed from hydroquinone alkali degradation, 1,4 benzoquinone and the preservative methyl paraben. The proposed method was used for their determination in their pure form and in pharmaceutical formulation. The zero order absorption spectra of hydroquinone, tretinoin, 1,4 benzoquinone and methyl paraben were determined at 293, 357.5, 245 and 255.2nm, respectively. The calibration curves were linear over the concentration ranges of 4.00-46.00, 1.00-7.00, 0.60-5.20, and 1.00-7.00?gmL(-1) for hydroquinone, tretinoin, 1,4 benzoquinone and methyl paraben, respectively. The pharmaceutical formulation was subjected to mild alkali condition and measured by this method resulting in the polymerization of hydroquinone and the formation of toxic 1,4 benzoquinone. The proposed method was validated according to ICH guidelines. The results obtained were statistically analyzed and compared with those obtained by applying the reported method. PMID:26745510

  13. Successive ratio subtraction coupled with constant multiplication spectrophotometric method for determination of hydroquinone in complex mixture with its degradation products, tretinoin and methyl paraben

    NASA Astrophysics Data System (ADS)

    Elghobashy, Mohamed R.; Bebawy, Lories I.; Shokry, Rafeek F.; Abbas, Samah S.

    2016-03-01

    A sensitive and selective stability-indicating successive ratio subtraction coupled with constant multiplication (SRS-CM) spectrophotometric method was studied and developed for the spectrum resolution of five component mixture without prior separation. The components were hydroquinone in combination with tretinoin, the polymer formed from hydroquinone alkali degradation, 1,4 benzoquinone and the preservative methyl paraben. The proposed method was used for their determination in their pure form and in pharmaceutical formulation. The zero order absorption spectra of hydroquinone, tretinoin, 1,4 benzoquinone and methyl paraben were determined at 293, 357.5, 245 and 255.2 nm, respectively. The calibration curves were linear over the concentration ranges of 4.00-46.00, 1.00-7.00, 0.60-5.20, and 1.00-7.00 μg mL- 1 for hydroquinone, tretinoin, 1,4 benzoquinone and methyl paraben, respectively. The pharmaceutical formulation was subjected to mild alkali condition and measured by this method resulting in the polymerization of hydroquinone and the formation of toxic 1,4 benzoquinone. The proposed method was validated according to ICH guidelines. The results obtained were statistically analyzed and compared with those obtained by applying the reported method.

  14. Synthesis, Characterization and Thermal Studies of Zn(II), Cd(II) and Hg(II) Complexes of N-Methyl-N-Phenyldithiocarbamate: The Single Crystal Structure of [(C6H5)(CH3)NCS2]4Hg2

    PubMed Central

    Onwudiwe, Damian C.; Ajibade, Peter A.

    2011-01-01

    Zn(II), Cd(II) and Hg(II) complexes of N-methyl-N-phenyl dithiocarbamate have been synthesized and characterized by elemental analysis and spectral studies (IR, 1H and 13C-NMR). The single crystal X-ray structure of the mercury complex revealed that the complex contains a Hg centre with a distorted tetrahedral coordination sphere in which the dinuclear Hg complex resides on a crystallographic inversion centre and each Hg atom is coordinated to four S atoms from the dithiocarbamate moiety. One dithiocarbamate ligand acts as chelating ligand while the other acts as chelating bridging ligand between two Hg atoms, resulting in a dinuclear eight-member ring. The course of the thermal degradation of the complexes has been investigated using thermogravimetric and differential thermal analyses techniques. Thermogravimetric analysis of the complexes show a single weight loss to give MS (M = Zn, Cd, Hg) indicating that they might be useful as single source precursors for the synthesis of MS nanoparticles and thin films. PMID:21673933

  15. 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.

  16. 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)26H2O 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 CH?F hydrogen bonds, forming a three-dimensional network. An intramolecular CH?F hydrogen bond is also observed. PMID:25484774

  17. 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.

  18. 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.

  19. Flavivirus RNA methylation.

    PubMed

    Dong, Hongping; Fink, Katja; Zst, Roland; Lim, Siew Pheng; Qin, Cheng-Feng; Shi, Pei-Yong

    2014-04-01

    The 5' end of eukaryotic mRNA contains the type-1 (m7GpppNm) or type-2 (m7GpppNmNm) cap structure. Many viruses have evolved various mechanisms to develop their own capping enzymes (e.g. flavivirus and coronavirus) or to 'steal' caps from host mRNAs (e.g. influenza virus). Other viruses have developed 'cap-mimicking' mechanisms by attaching a peptide to the 5' end of viral RNA (e.g. picornavirus and calicivirus) or by having a complex 5' RNA structure (internal ribosome entry site) for translation initiation (e.g. picornavirus, pestivirus and hepacivirus). Here we review the diverse viral RNA capping mechanisms. Using flavivirus as a model, we summarize how a single methyltransferase catalyses two distinct N-7 and 2'-O methylations of viral RNA cap in a sequential manner. For antiviral development, a structural feature unique to the flavivirus methyltransferase was successfully used to design selective inhibitors that block viral methyltransferase without affecting host methyltransferases. Functionally, capping is essential for prevention of triphosphate-triggered innate immune activation; N-7 methylation is critical for enhancement of viral translation; and 2'-O methylation is important for subversion of innate immune response during viral infection. Flaviviruses defective in 2'-O methyltransferase are replicative, but their viral RNAs lack 2'-O methylation and are recognized and eliminated by the host immune response. Such mutant viruses could be rationally designed as live attenuated vaccines. This concept has recently been proved with Japanese encephalitis virus and dengue virus. The findings obtained with flavivirus should be applicable to other RNA viruses. PMID:24486628

  20. The influence of counter ion and ligand methyl substitution on the solid-state structures and photophysical properties of mercury(II) complexes with (E)-N-(pyridin-2-ylmethylidene)arylamines.

    PubMed

    Basu Baul, Tushar S; Kundu, Sajal; Mitra, Sivaprasad; Hpfl, Herbert; Tiekink, Edward R T; Linden, Anthony

    2013-02-01

    Ten neutral monomeric, dimeric and polymeric mercury(II) complexes of compositions HgX(2)L (3, 8), [HgX(2)L](2) (1, 2, 4-6 and 7), [Hg(NO(3))(2)L](n) (9) and {[Hg(N(3))(2)L](2)}(n) (10) where X = chloride, bromide, iodide, nitrate and azide, and L = (E)-N-(pyridin-2-ylmethylidene)arylamine, are described. Compounds 1-10 were characterized by elemental analyses, and IR and (1)H NMR spectroscopic studies. The solution-state photophysical properties of the complexes are highly dependent on the anions as seen in the fluorescence emission features. Single-crystal X-ray crystallography showed that the molecular complexes can aggregate into larger entities depending upon the anion coordinated to the metal centre. Iodide gives discrete monomeric complexes, chloride and bromide generate binuclear complexes formed through Hg-X-Hg bridges, while nitrate and azide lead to 1D coordination polymers. The significant differences in the observed aggregation patterns of the compounds indicate that the anions exert a substantial influence on the formation of the compounds. A further influence upon supramolecular aggregation is the presence of methyl substituents in L(3) and L(4), which generally enhances the probability of forming supramolecular ?? interactions involving the five-membered C(2)N(2)Hg chelate rings in their crystal structures. PMID:23172550

  1. 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.

    PubMed

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

    2011-10-15

    Reactions of 2-hydroxy-benzoic acid [1-(4-hydroxy-6-methyl-2-oxo-2H-pyran-3-yl)-ethylidene]-hydrazide (H(2)L) 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, (1)H NMR and (13)C 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) ?, b=12.8627(12) ?, c=21.683(2) ?, ?=90.00, ?=114.626(2), ?=90.00 V=4721.8(8) ?, 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-HN 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. PMID:21763180

  2. Synthesis, characterization, and tyrosinase biomimetic catalytic activity of copper(II) complexes with schiff base ligands derived from α-diketones with 2-methyl-3-amino-(3 H)-quinazolin-4-one

    NASA Astrophysics Data System (ADS)

    Ramadan, Abd El-Motaleb M.; Ibrahim, Mohamed M.; Shaban, Shaban Y.

    2011-12-01

    A template condensation of α-diketones (biacetyl, benzile and 2,3-pentanedione) with 2-methyl-3-amino-(3 H)-quinazolin-4-one (AMQ) in the presence of CuX 2 (X = Cl -, Br -, NO3- or ClO4-) resulted in the formation of tetradentate Schiff base copper(II) complexes of the type [CuLX]X and [CuL]X 2. Structural characterization of the complex species was achieved by several physicochemical methods, namely elemental analysis, electronic spectra, IR, ESR, molar conductivity, thermal analysis (TAG & DTG), and magnetic moment measurements. The stereochemistry, the nature of the metal chelates, and the catalytic reactivity are markedly dependent upon the type of counter anions and the ligand substituent within the carbonyl moiety. A square planar monomeric structure is proposed for the perchlorate, nitrate, and bromide complexes, in which the counter anions are loosely bonded to copper(II) ion. For the chloride complexes, the molar conductivities and the spectral data indicated that they have square-pyramidal environments around copper(II) center. The reported copper(II) complexes exhibit promising tyrosinase catalytic activity towards the hydroxylation of phenol followed by the aerobic oxidation of the resulting catechol. A linear correlation almost exists between the catalytic reactivity and the Lewis-acidity of the central copper(II) ion created by the donating properties of the parent ligand. The steric considerations could be accounted to clarify the difference in the catalytic activity of these functional models.

  3. 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) , b = 12.8627(12) , c = 21.683(2) , ? = 90.00, ? = 114.626(2), ? = 90.00 V = 4721.8(8) , 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 OHN 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.

  4. Inhibition of cortical spreading depression by L-701,324, a novel antagonist at the glycine site of the N-methyl-D-aspartate receptor complex.

    PubMed Central

    Obrenovitch, T. P.; Zilkha, E.

    1996-01-01

    1. Spreading depression (SD) is a propagating transient suppression of electrical activity, associated with cellular depolarization, which probably underlies the migraine aura and may contribute to neuronal damage in focal ischaemia. The purpose of this study was to examine whether L-701,324 (7-chloro-4-hydroxy-3-(3-phenoxy)phenyl-2-(1H)-quinolone), a high affinity antagonist at the glycine site of the N-methyl-D-aspartate (NMDA) receptor complex, inhibits the initiation and propagation of K(+)-induced SD in the rat cerebral cortex in vivo. 2. Microdialysis probes incorporating a recording electrode were implanted in the cerebral cortex of anaesthetized rats and perfused with artificial cerebrospinal fluid (ACSF). Five episodes of repetitive SD were elicited by switching to a medium containing 130 mM K+ for 20 min, each separated by 40 min of recovery (i.e. perfusion with normal ACSF). The brief negative shifts of the extracellular direct current (d.c.) potential, characteristic of SD elicitation, were recorded with the microdialysis electrode and a reference electrode placed under the scalp. Propagation of SD was examined using glass capillary electrodes inserted about 3 mm posterior to the microdialysis electrode. L-701,324 (5 or 10 mg kg-1) or its vehicle were administered i.v. 10 min after the end of the second K(+)-stimulus. The effects of L-701,324 were compared to those of dizocilpine (MK-801; 1 mg kg-1 i.v.), a NMDA-channel blocker known to potently block SD elicitation. 3. Potassium-induced SD initiation was inhibited by 10 mg kg-1 (but not by 5 mg kg-1) of L-701,324. Thirty minutes after administration of 10 mg kg-1 L-701,324, the cumulative area of SD peaks elicited during 20 min was 15.3 +/- 2.1 mV min, versus 23.2 +/- 1.1 mV min in animals which received only the drug vehicle (P < 0.02; n = 6). The delay between application of 130 mM K+ and occurrence of the first SD was also significantly increased. It was approximately doubled in animals treated with 10 mg kg-1 of L-701,324. 4. SD propagation was more sensitive than SD elicitation to L-701,324, as both 5 and 10 mg kg-1 produced an effective inhibition. Even at the lower dose of 5 mg kg-1, L-701,324 completely blocked the propagation of SD elicited 30 min after drug administration. This differential sensitivity of SD elicitation and propagation is not specific to L-701,324 since it was previously observed with other drugs. At doses effective against SD, L-701,324 did not produce any marked alterations of the electroencephalogram. 5. L-701,324 (10 mg kg-1) and MK-801 (1 mg kg-1) had identical effects on the d.c. potential when administered during the recovery which followed the second K+ stimulus. Both drugs produced a positive shift of around 4.5 mV within 10 min of i.v. drug administration, indicating rapid drug penetration into the CNS. Paradoxically, L-701,324 (10 mg kg-1) was markedly less effective than MK-801 (1 mg kg-1) in blocking SD, since this dose of MK-801 was sufficient virtually to abolish SD initiation and completely block its propagation. The higher potency of MK-801 against SD may reflect its use-dependency, i.e. binding of MK-801 and channel blockade are enhanced when the NMDA-receptor ionophore is open. 6. Taken together, these data demonstrate that L-701,324 has an inhibitory effect on both SD initiation and propagation. This action may be beneficial in focal ischaemia, and possibly also against migraine, especially as this drug was shown to be active when administered orally. Images Figure 4 Figure 6 PMID:8851513

  5. Inhibition of cortical spreading depression by L-701,324, a novel antagonist at the glycine site of the N-methyl-D-aspartate receptor complex.

    PubMed

    Obrenovitch, T P; Zilkha, E

    1996-03-01

    1. Spreading depression (SD) is a propagating transient suppression of electrical activity, associated with cellular depolarization, which probably underlies the migraine aura and may contribute to neuronal damage in focal ischaemia. The purpose of this study was to examine whether L-701,324 (7-chloro-4-hydroxy-3-(3-phenoxy)phenyl-2-(1H)-quinolone), a high affinity antagonist at the glycine site of the N-methyl-D-aspartate (NMDA) receptor complex, inhibits the initiation and propagation of K(+)-induced SD in the rat cerebral cortex in vivo. 2. Microdialysis probes incorporating a recording electrode were implanted in the cerebral cortex of anaesthetized rats and perfused with artificial cerebrospinal fluid (ACSF). Five episodes of repetitive SD were elicited by switching to a medium containing 130 mM K+ for 20 min, each separated by 40 min of recovery (i.e. perfusion with normal ACSF). The brief negative shifts of the extracellular direct current (d.c.) potential, characteristic of SD elicitation, were recorded with the microdialysis electrode and a reference electrode placed under the scalp. Propagation of SD was examined using glass capillary electrodes inserted about 3 mm posterior to the microdialysis electrode. L-701,324 (5 or 10 mg kg-1) or its vehicle were administered i.v. 10 min after the end of the second K(+)-stimulus. The effects of L-701,324 were compared to those of dizocilpine (MK-801; 1 mg kg-1 i.v.), a NMDA-channel blocker known to potently block SD elicitation. 3. Potassium-induced SD initiation was inhibited by 10 mg kg-1 (but not by 5 mg kg-1) of L-701,324. Thirty minutes after administration of 10 mg kg-1 L-701,324, the cumulative area of SD peaks elicited during 20 min was 15.3 +/- 2.1 mV min, versus 23.2 +/- 1.1 mV min in animals which received only the drug vehicle (P < 0.02; n = 6). The delay between application of 130 mM K+ and occurrence of the first SD was also significantly increased. It was approximately doubled in animals treated with 10 mg kg-1 of L-701,324. 4. SD propagation was more sensitive than SD elicitation to L-701,324, as both 5 and 10 mg kg-1 produced an effective inhibition. Even at the lower dose of 5 mg kg-1, L-701,324 completely blocked the propagation of SD elicited 30 min after drug administration. This differential sensitivity of SD elicitation and propagation is not specific to L-701,324 since it was previously observed with other drugs. At doses effective against SD, L-701,324 did not produce any marked alterations of the electroencephalogram. 5. L-701,324 (10 mg kg-1) and MK-801 (1 mg kg-1) had identical effects on the d.c. potential when administered during the recovery which followed the second K+ stimulus. Both drugs produced a positive shift of around 4.5 mV within 10 min of i.v. drug administration, indicating rapid drug penetration into the CNS. Paradoxically, L-701,324 (10 mg kg-1) was markedly less effective than MK-801 (1 mg kg-1) in blocking SD, since this dose of MK-801 was sufficient virtually to abolish SD initiation and completely block its propagation. The higher potency of MK-801 against SD may reflect its use-dependency, i.e. binding of MK-801 and channel blockade are enhanced when the NMDA-receptor ionophore is open. 6. Taken together, these data demonstrate that L-701,324 has an inhibitory effect on both SD initiation and propagation. This action may be beneficial in focal ischaemia, and possibly also against migraine, especially as this drug was shown to be active when administered orally. PMID:8851513

  6. Novel square arrangements in tetranuclear and octanuclear iron(III) complexes with asymmetric iron environments created by the unsymmetric bridging ligand N,N,N{prime}-tris((N-methyl)-2-benzimidazolylmethyl)-N{prime}-methyl-1,3-diamino-2-propanol

    SciTech Connect

    Satcher, J.H. Jr.; Parkin, S.R.; Olmstead, M.M.; Noll, B.C.; Balch, A.L.; Droege, M.W.; May, L.

    1998-12-28

    The synthesis and characterization of novel tetranuclear and octanuclear iron(III) complexes with structures based on a nearly square arrangement of four iron ions are reported. Reaction of ferric nitrate, sodium acetate, and the unsymmetrical binucleating ligand HBMDP, where HBMDP is N,N,N{prime}-tris((N-methyl)-2-benzimidazolylmethyl)-N{prime}-methyl-1,3-diamino-2-propanol, in acetone/water yields the tetranuclear iron complex [Fe{sub 4}({mu}-O){sub 2}({mu}-BMDP){sub 2}-({mu}-OAc){sub 2}]{sup 4+}, which exhibits coordination number asymmetry. The structure of [Fe{sub 4}({mu}-O){sub 2}({mu}-BMDP){sub 2}({mu}-OAc){sub 2}](NO{sub 3}){sub 3}(OH){center_dot}12H{sub 2}O has been determined by single-crystal X-ray diffraction. Each ({mu}-BMDP) ligand spans two iron(III) ions and causes these ions to become structurally distinct. Within this binuclear unit one iron atom is five-coordinate with distorted square pyramidal geometry and an N{sub 2}O{sub 3} donor set, while the other iron is six-coordinate with distorted octahedral geometry and an N{sub 3}O{sub 3} donor set. Two of these binuclear units are linked through a pair of oxo and acetato bridges to form the centrosymmetric tetranuclear complex. Efforts to increase the solubility of [Fe{sub 4}({mu}-O){sub 2}({mu}-BMDP){sub 2}({mu}-OAc){sub 2}]{sup 4+} by metathesis with sodium tetrafluoroborate resulted in the isolation of crystals of a new octanuclear iron species, which has also been characterized by single-crystal X-ray diffraction.

  7. Hydrogen-bonding interaction of methyl-substituted pyridines with thioacetamide: steric hindrance of methyl group

    NASA Astrophysics Data System (ADS)

    Choi, Kee-Hyun; Lee, Ho-Jin; Karpfen, Alfred; Yoon, Chang-Ju; Park, Jeunghee; Choi, Young-Sang

    2001-09-01

    The hydrogen-bonding interaction between a series of methyl-substituted pyridines as proton acceptors and thioacetamide as a proton donor in CCl 4 has been investigated using near-infrared absorption spectroscopy. The stability of the 1:1 hydrogen-bonded complex increases with the number of methyl groups and depends on the position of methyl groups. The steric hindrance of ortho-methyl groups particularly reduces the stability of complex. The relative stability agrees with the ease of miscibility of pyridines with water for methyl and dimethyl homologs. The calculated proton affinities and the DFT association energies using 6-31+G(d, p) and 6-311++G(2d, 2p) basis sets reveal the steric hindrance of ortho-methyl groups.

  8. 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 π–π stacking of the benzene rings [centroid–centroid distance = 3.8602 (18) Å] result in a strongly linked, compact three-dimensional structure. PMID:25484753

  9. Synthesis, characterization, and biological activity of N-methyl-2-(1H-1,2,3-benzotriazol-1-y1)-3-oxobutan- ethioamide complexes with some divalent metal (II) ions.

    PubMed

    Al-Awadi, Nouria A; Shuaib, Nadia M; Abbas, Alaa; El-Sherif, Ahmed A; El-Dissouky, Ali; Al-Saleh, Esmaeil

    2008-01-01

    A new series of Zn(2+), Cu(2+), Ni(2+), and Co(2+) complexes of N(1)-methyl-2-(1H-1,2,3-benzotriazol-1-yl)-3-oxobutanethioamide (MBOBT), HL, has been synthesized and characterized by different spectral and magnetic measurements and elemental analysis. IR spectral data indicates that (MBOBT) exists only in the thione form in the solid state while 13C NMR spectrum indicates its existence in thione and thiole tautomeric forms. The IR spectra of all complexes indicate that (MBOBT) acts as a monobasic bidentate ligand coordinating to the metal(II) ions via the keto-oxygen and thiolato-sulphur atoms. The electronic spectral studies showed that (MBOBT) bonded to all metal ions through sulphur and nitrogen atoms based on the positions and intensity of their charge transfer bands. Furthermore, the spectra reflect four coordinate tetrahedral zinc(II), tetragonally distorted copper(II), square planar nickel(II), and cobalt(II) complexes. Thermal decomposition study of the complexes was monitored by TG and DTG analyses under N(2) atmosphere. The decomposition course and steps were analyzed and the activation parameters of the nonisothermal decomposition are determined. The isolated metal chelates have been screened for their antimicrobial activities and the findings have been reported and discussed in relation to their structures. PMID:18364993

  10. Spectrophotometric, conductometric and thermal studies of Co(II), Ni(II) and Cu(II) complexes with 2-(2-hydroxynaphthylazo)-4-hydroxy-6-methyl-1,3-pyrimidine

    NASA Astrophysics Data System (ADS)

    Gaber, Mohamed; Mansour, Ikhlas A.; El-Sayed, Yousif S. Y.

    2007-10-01

    The electronic absorption spectra of 2-(2-hydroxynaphthylazo)-4-hydroxy-6-methyl-1,3-pyrimidine in pure organic solvents of different polarities and in buffer solutions of varying pH are studied. The important bands in the IR and the main signals in the 1H NMR spectra are assigned. The observed UV-vis absorption bands are assigned to the corresponding electronic transitions. The molecular stoichiometry, stability constant, absorption maximum, molar absorptivity and Sandell's sensitivity of the complexes are calculated. Obeyence to Beer's law and Ringbom optimum concentration ranges are also determined. The ability of using the titled azodye as metalochromic indicator in complexometric titrations was also studied. The effect of Co(II), Ni(II) and Cu(II) ions on the fluorescence of the azodye is also considered. The solid Cu(II) complexes of the titled azodye have been prepared and characterized by elemental, IR, UV-vis spectra as well as by conductometric and magnetic measurements. The data suggest square planar geometry for 1:1 and 1:2 (M:L) complexes. The thermal behaviour of the complexes has been studied. The kinetic parameters ( n, E, A, Δ H, Δ S and Δ G) of the thermal decomposition steps are computed using Coats-Redfern equations.

  11. 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.

  12. Whole genome methylation profiling by immunoprecipitation of methylated DNA.

    PubMed

    Sharp, Andrew J

    2012-01-01

    I provide a protocol for DNA methylation profiling based on immunoprecipitation of methylated DNA using commercially available monoclonal antibodies that specifically recognize 5-methylcytosine. Quantification of the level of enrichment of the resulting DNA enables DNA methylation to be assayed for any genomic locus, including entire chromosomes or genomes if appropriate microarray or high-throughput sequencing platforms are used. In previous studies (1, 2), I have used hybridization to oligonucleotide arrays from Roche Nimblegen Inc, which allow any genomic region of interest to be interrogated, dependent on the array design. For example, using modern tiling arrays comprising millions of oligonucleotide probes, several complete human chromosomes can be assayed at densities of one probe per 100 bp or greater, sufficient to yield high-quality data. However, other methods such as quantitative real-time PCR or high-throughput sequencing can be used, giving either measurement of methylation at a single locus or across the entire genome, respectively. While the data produced by single locus assays is relatively simple to analyze and interpret, global assays such as microarrays or high-throughput sequencing require more complex statistical approaches in order to effectively identify regions of differential methylation, and a brief outline of some approaches is given. PMID:22907491

  13. Potentiometric study of binary complexes of methyl 2-pyridyl ketone oxime, phenyl 2-pyridyl ketone oxime and diacetyl monooxime with some transition and heavy metal ions in aqueous solution

    NASA Astrophysics Data System (ADS)

    Shokrollahi, Ardeshir; Ghaedi, Mehrorang; Rajabi, Hamid Reza; Niband, Marzieyeh Sadat.

    2008-11-01

    The complexation reaction between some oximes including methyl-2-pyridylketone oxime (MPKO), phenyl-2-pyridylketone oxime (PPKO) and diacetyl monooxime (DMO) with some transition and heavy metal ions Co 2+, Ni 2+, Zn 2+, Pb 2+, Fe 2+, Fe 3+, Cr 3+ and La 3+ has been studied potentiometrically in aqueous solution at 25 ± 0.1 °C and ionic strength ( μ) of 0.1 M supported by KCl. The overall stability constants log β's of respective species were obtained by computer refinement of pH-volume data using BEST program. The best model among the several proposed models was selected according to the lowest σfit value. The main species in binary systems are ML, ML 2, MLH, MLH 2, ML 2H, ML 2H 2, MOHL, M(OH) 2L, M(OH)L 2 and M(OH) 2L 2 (L = MPKO or PPKO or DMO).

  14. Novel light-conversion hybrids of SBA-16 functionalized with rare earth (Eu3+, Nd3+, Yb3+) complexes of modified 2-methyl-9-hydroxyphenalenone and 1,10-phenanthroline

    NASA Astrophysics Data System (ADS)

    Gu, Yan-Jing; Yan, Bing; Qiao, Xiao-Fei

    2013-03-01

    Novel rare earth complex-functionalized mesoporous SBA-16-type hybrid materials are synthesized by the co-condensation of modified 2-methyl-9-hydroxyphenalenone (MHPOSi), from modified 3-(triethoxysilyl)-propyl isocyanate (TEPIC), and tetraethoxysilane (TEOS) in the presence of Pluronic F127 as a template. These inorganic-organic mesoporous hybrids are characterized by FT-IR spectra, small-angle X-ray diffraction (SAXRD), N2 adsorption-desorption measurements, thermal analysis and spectroscopy. Their photophysical properties, which show novel light conversion properties, are discussed in detail. The Eu3+ hybrid system shows ultraviolet excitation and visible emission, and the Nd+ and Yb3+ hybrids exhibit visible excitation and NIR emission.

  15. Well-defined iron complexes as efficient catalysts for "green" atom-transfer radical polymerization of styrene, methyl methacrylate, and butyl acrylate with low catalyst loadings and catalyst recycling.

    PubMed

    Nakanishi, So-Ichiro; Kawamura, Mitsunobu; Kai, Hidetomo; Jin, Ren-Hua; Sunada, Yusuke; Nagashima, Hideo

    2014-05-01

    Environmentally friendly iron(II) catalysts for atom-transfer radical polymerization (ATRP) were synthesized by careful selection of the nitrogen substituents of N,N,N-trialkylated-1,4,9-triazacyclononane (R3 TACN) ligands. Two types of structures were confirmed by crystallography: "[(R3 TACN)FeX2 ]" complexes with relatively small R groups have ionic and dinuclear structures including a [(R3 TACN)Fe(?-X)3 Fe(R3 TACN)](+) moiety, whereas those with more bulky R groups are neutral and mononuclear. The twelve [(R3 TACN)FeX2 ]n complexes that were synthesized were subjected to bulk ATRP of styrene, methyl methacrylate (MMA), and butyl acrylate (BA). Among the iron complexes examined, [{(cyclopentyl)3 TACN}FeBr2 ] (4?b) was the best catalyst for the well-controlled ATRP of all three monomers. This species allowed easy catalyst separation and recycling, a lowering of the catalyst concentration needed for the reaction, and the absence of additional reducing reagents. The lowest catalyst loading was accomplished in the ATRP of MMA with 4?b (59?ppm of Fe based on the charged monomer). Catalyst recycling in ATRP with low catalyst loadings was also successful. The ATRP of styrene with 4?b (117?ppm Fe atom) was followed by precipitation from methanol to give polystyrene that contained residual iron below the calculated detection limit (0.28?ppm). Mechanisms that involve equilibria between the multinuclear and mononuclear species were also examined. PMID:24664500

  16. Strategy to enhance efficacy of doxorubicin in solid tumor cells by methyl-β-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-β-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-α (PFT-α) 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

  17. 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.

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

    NASA Astrophysics Data System (ADS)

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

    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, 1H NMR, 13C NMR, mass spectra and thermal analysis (TG/DTA). The elemental analysis suggests the stoichiometry to be 1:1 (metal:ligand). The IR, 1H NMR, 13C 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.

  19. 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

  20. 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; Kotliński, Maciej; Kroteń, Magdalena A.; Knizewski, Lukasz; Lange, Bartosz; Muszewska, Anna; Śniegowska-Świerk, Katarzyna; Kościelniak, Janusz; Iwanicka-Nowicka, Roksana; Buza, Krisztián; Janowiak, Franciszek; Żmuda, Katarzyna; Jõesaar, Indrek; Laskowska-Kaszub, Katarzyna; Fogtman, Anna; Kollist, Hannes; Zielenkiewicz, Piotr; Tiuryn, Jerzy; Siedlecki, Paweł; Swiezewski, Szymon; Ginalski, Krzysztof; Koblowska, Marta; Archacki, Rafał; 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

  1. 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, Krisztin; Janowiak, Franciszek; ?muda, Katarzyna; Jesaar, 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

  2. Anti-N-methyl-d-aspartate receptor encephalitis in a patient with a 7-year history of being diagnosed as schizophrenia: complexities in diagnosis and treatment

    PubMed Central

    Huang, Chaohua; Kang, Yukun; Zhang, Bo; Li, Bin; Qiu, Changjian; Liu, Shanming; Ren, Hongyan; Yang, Yanchun; Liu, Xiehe; Li, Tao; Guo, Wanjun

    2015-01-01

    Anti-N-methyl-d-aspartate receptor (NMDAR) encephalitis is a form of autoimmune encephalitis associated with antibodies against the NR1 subunits of NMDARs. Although new-onset acute prominent psychotic syndromes in patients with NMDAR encephalitis have been well documented, there is a lack of case studies on differential diagnosis and treatment of anti-NMDAR encephalitis after a long-term diagnostic history of functional psychotic disorders. The present study reports an unusual case of anti-NMDAR encephalitis. The patient had been diagnosed with schizophrenia 7 years earlier, and was currently hospitalized for acute-onset psychiatric symptoms. The diagnosis became unclear when the initial psychosis was confounded with considerations of other neurotoxicities (such as neuroleptic malignant syndrome). Finally, identification of specific immunoglobulin G NR1 autoantibodies in the cerebrospinal fluid and greater effectiveness of immunotherapy over antipsychotics alone (which has been well documented in anti-NMDAR encephalitis) indicated the diagnosis of anti-NMDAR encephalitis in this case. Based on the available evidence, however, the relationship between the newly diagnosed anti-NMDAR encephalitis and the seemingly clear, long-term history of schizophrenia in the preceding 7 years is uncertain. This case report illustrates that psychiatrists should consider anti-NMDAR encephalitis and order tests for specific immunoglobulin G NR1 autoantibodies in patients presenting with disorientation, disturbance of consciousness, cognitive deficit, dyskinesia, autonomic disturbance, or rapid deterioration, even with a seemingly clear history of a psychiatric disorder and no specific findings on routine neuroimaging, electroencephalography, or cerebrospinal fluid tests in the early stage of the illness. PMID:26089673

  3. 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 ...

  4. 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 () 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

  5. Syntheses of monomeric (. eta. sup 5 -pentamethylcyclopentadienyl)platinum(IV) methyl and bromo complexes and of (hydrotris(3,5-dimethyl-1-pyrazolyl)borato)trimethylplatinum

    SciTech Connect

    Roth, S.; Ramamoorthy, V.; Sharp, P.R. )

    1990-09-05

    The reaction of Cp*MgCl{center dot}THF (Cp* = C{sub 5}Me{sub 5}) with 1 equiv of PtMe{sub 3}I and PtMe{sub 2}Br{sub 2} produces Cp*PtMe{sub 3} (1) and Cp*PtMe{sub 2}Br (2), respectively. Reaction of 2 with Br{sub 2} produces Cp*PtMeBr{sub 2} (3) in good yield. The structures of 2 and 3 have been determined by x-ray crystallography, and the crystal structure data are reported. Complex 2 crystallizes in the monoclinic space group, P2{sub 1}/m, and complex 3 crystallizes in the monoclinic space group, P2{sub 1}/m. The molecules reside on mirror planes and are monomeric pseudotetrahedral Pt(IV) complexes with piano stool type geometries and {eta}{sup 5}-Cp* groups. Both molecules have Br atoms on the mirror. This leads to a disorder of the Me and the second Br positions in complex 3. The average Pt-C(Cp*) bond length is 2.25 (7) {angstrom} in 2 and 2.22 (4) {angstrom} in 3. The Pt-C(Me) and Pt-Br bond lengths in 2 are 2.07 (2) and 2.498 (2) {angstrom}, respectively. The ordered Pt-Br bond length in 3 is 2.496 (2) {angstrom}. Treatment of 1 with halogens results in the cleavage of the Pt-Cp* bond. The reaction of PtMe{sub 3}I with KTp* (Tp* = (HB(3,5-dimethylpyrazolyl){sub 3}){sup {minus}}) in thf gives Tp*PtMe{sub 3} (4) in almost quantitative yield. The reaction of 4 with Br{sub 2} brominates the 4-position of the pyrazolyl ring only. 28 refs., 2 figs., 5 tabs.

  6. 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 ...

  7. Magnetic susceptibility and ground-state zero-field splitting in high-spin mononuclear manganese(III) of inverted N-methylated porphyrin complexes: Mn(2-NCH3NCTPP)Br.

    PubMed

    Hung, Sheng-Wei; Yang, Fuh-An; Chen, Jyh-Horung; Wang, Shin-Shin; Tung, Jo-Yu

    2008-08-18

    The crystal structures of diamagnetic dichloro(2-aza-2-methyl-5,10,15,20-tetraphenyl-21-carbaporphyrinato-N,N',N'')-tin(IV) methanol solvate [Sn(2-NCH 3NCTPP)Cl 2.2(0.2MeOH); 6.2(0.2MeOH)] and paramagnetic bromo(2-aza-2-methyl-5,10,15,20-tetraphenyl-21-carbaporphyrinato-N,N',N'')-manganese(III) [Mn(2-NCH 3NCTPP)Br; 5] were determined. The coordination sphere around Sn (4+) in 6.2(0.2MeOH) is described as six-coordinate octahedron ( OC-6) in which the apical site is occupied by two transoid Cl (-) ligands, whereas for the Mn (3+) ion in 5, it is a five-coordinate square pyramid ( SPY-5) in which the unidentate Br (-) ligand occupies the axial site. The g value of 9.19 (or 10.4) measured from the parallel polarization (or perpendicular polarization) of X-band EPR spectra at 4 K is consistent with a high spin mononuclear manganese(III) ( S = 2) in 5. The magnitude of axial ( D) and rhombic ( E) zero-field splitting (ZFS) for the mononuclear Mn(III) in 5 were determined approximately as -2.4 cm (-1) and -0.0013 cm (-1), respectively, by paramagnetic susceptibility measurements and conventional EPR spectroscopy. Owing to weak C(45)-H(45A)...Br(1) hydrogen bonds, the mononuclear Mn(III) neutral molecules of 5 are arranged in a one-dimensional network. A weak Mn(III)...Mn(III) ferromagnetic interaction ( J = 0.56 cm (-1)) operates via a [Mn(1)-C(2)-C(1)-N(4)-C(45)-H(45A)...Br(1)-Mn(1)] superexchange pathway in complex 5. PMID:18646843

  8. Maternal DNA Methylation Regulates Early Trophoblast Development.

    PubMed

    Branco, Miguel R; King, Michelle; Perez-Garcia, Vicente; Bogutz, Aaron B; Caley, Matthew; Fineberg, Elena; Lefebvre, Louis; Cook, Simon J; Dean, Wendy; Hemberger, Myriam; Reik, Wolf

    2016-01-25

    Critical roles for DNA methylation in embryonic development are well established, but less is known about its roles during trophoblast development, the extraembryonic lineage that gives rise to the placenta. We dissected the role of DNA methylation in trophoblast development by performing mRNA and DNA methylation profiling of Dnmt3a/3b mutants. We find that oocyte-derived methylation plays a major role in regulating trophoblast development but that imprinting of the key placental regulator Ascl2 is only partially responsible for these effects. We have identified several methylation-regulated genes associated with trophoblast differentiation that are involved in cell adhesion and migration, potentially affecting trophoblast invasion. Specifically, trophoblast-specific DNA methylation is linked to the silencing of Scml2, a Polycomb Repressive Complex 1 protein that drives loss of cell adhesion in methylation-deficient trophoblast. Our results reveal that maternal DNA methylation controls multiple differentiation-related and physiological processes in trophoblast via both imprinting-dependent and -independent mechanisms. PMID:26812015

  9. 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.

  10. Maternal DNA Methylation Regulates Early Trophoblast Development

    PubMed Central

    Branco, Miguel R.; King, Michelle; Perez-Garcia, Vicente; Bogutz, Aaron B.; Caley, Matthew; Fineberg, Elena; Lefebvre, Louis; Cook, Simon J.; Dean, Wendy; Hemberger, Myriam; Reik, Wolf

    2016-01-01

    Summary Critical roles for DNA methylation in embryonic development are well established, but less is known about its roles during trophoblast development, the extraembryonic lineage that gives rise to the placenta. We dissected the role of DNA methylation in trophoblast development by performing mRNA and DNA methylation profiling of Dnmt3a/3b mutants. We find that oocyte-derived methylation plays a major role in regulating trophoblast development but that imprinting of the key placental regulator Ascl2 is only partially responsible for these effects. We have identified several methylation-regulated genes associated with trophoblast differentiation that are involved in cell adhesion and migration, potentially affecting trophoblast invasion. Specifically, trophoblast-specific DNA methylation is linked to the silencing of Scml2, a Polycomb Repressive Complex 1 protein that drives loss of cell adhesion in methylation-deficient trophoblast. Our results reveal that maternal DNA methylation controls multiple differentiation-related and physiological processes in trophoblast via both imprinting-dependent and -independent mechanisms. PMID:26812015

  11. 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, Jrg; 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)), Mssbauer spectroscopy, and NMR spectroscopy. Structural parameters assessing redox noninnocence are discussed, as are structural and mechanistic consequences of the various electronic environments. PMID:25010819

  12. 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

  13. 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

    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? and two long C13?H13?O2 and C32?H32?O3 hydrogen bonds of 2.48?. 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

  14. 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

  15. A series of dinuclear Dy(iii) complexes bridged by 2-methyl-8-hydroxylquinoline: replacement on the periphery coordinated ?-diketonate terminal leads to different single-molecule magnetic properties.

    PubMed

    Zhang, Wan-Ying; Tian, Yong-Mei; Li, Hong-Feng; Chen, Peng; Sun, Wen-Bin; Zhang, Yi-Quan; Yan, Peng-Fei

    2016-03-01

    A series of HMq-bridged dinuclear dysprosium complexes, namely, [Dy(acac)2(CH3OH)]2(?-HMq)2 (1), [Dy(DBM)2]2(?-HMq)2(n-C6H14) (2), [Dy(hmac)2]2(?-HMq)2 (3) and [Dy(hfac)3]2(?-HMq)2 (4) (HMq = 2-methyl-8-hydroxyquinoline, acac = acetylacetone, DBM = dibenzoylmethane, hmac = hexamethylacetylacetonate and hfac = hexafluoroacetylacetonate), were structurally and magnetically characterized. X-ray crystallographic analyses of the structures reveal that HMq serves as the effective bridge to link two Dy(iii) centers by means of the phenoxyl oxygen and nitrogen atoms and the periphery ?-diketonate ligands complete the coordination sphere by bidentate oxygen atoms. The different substituents on the ?-diketonate terminal lead to different coordination models mostly due to the steric hindrance of these substituents, and the electron-withdrawing or donating effects likely influence the strength of the ligand fields and the Dy(iii) ion anisotropy. Measurements of alternating-current (ac) susceptibility on complexes 1-4 reveal that complexes 3 and 4 display significant zero-field single-molecule magnetic (SMM) behavior with barrier energy Ueff/kB = 14.8 K, ?0 = 1.8 10(-5) s and Ueff/kB = 9.2 K, ?0 = 1.7 10(-5) s, respectively, whereas 1 and 2 exhibit field-induced SMM behavior, and these differences are attributed to the alteration on the periphery ?-diketonate ligands. Their distinct slow magnetic relaxation behaviors were related to their different individual Dy(iii) ion magnetic anisotropy and intramolecular coupling, which were confirmed by ab initio calculations. PMID:26905041

  16. 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

  17. Influencing the coordination mode of tbta (tbta = tris[(1-benzyl-1H-1,2,3-triazol-4-yl)methyl]amine) in dicobalt complexes through changes in metal oxidation states.

    PubMed

    Schweinfurth, David; Klein, Johannes; Hohloch, Stephan; Dechert, Sebastian; Demeshko, Serhiy; Meyer, Franc; Sarkar, Biprajit

    2013-05-21

    The complexes [(tbta)Co(?-CA(-2H))Co(tbta)(CH3CN)](BF4)2 1 and [(tbta)Co(?-OH)2Co(tbta)](BF4)4 2 (tbta = tris[(1-benzyl-1H-1,2,3-triazol-4-yl)methyl]amine and CA = chloranilic acid) were synthesized and characterized by X-ray crystallography, SQUID magnetometry and NMR spectroscopy. The reactions to form these complexes deliver 1 as a paramagnetic species containing two high spin Co(II) centers, and 2 as a diamagnetic compound with two low spin Co(III) centers. Structural analysis shows that in 1 the capped-octahedral environment around the Co(II) centers is highly distorted with rather long bonds between the metal and donor atoms. The tbta ligand binds to the Co(II) centers through the three triazole nitrogen donor atoms in a facial form, with the Co-N(amine) distance of 2.494(2) acting as a capping bond to the octahedron. In the crystal an unusual observation of one acetonitrile molecule statistically occupying the coordination sites at both Co(II) centers is made. 1 displays a series of intermolecular C-HCl and ?-? interactions leading to extended three-dimensional structures in the solid state. These interactions lead to the formation of voids and explain why only one acetonitrile molecule can be bound to the dinuclear complexes. In contrast to 1, the cobalt centers in 2 display a more regular octahedral environment with shorter cobalt-donor atom distances, as would be expected for a low spin Co(III) situation. The tbta ligand acts as a perfect tetradentate ligand in this case with the cobalt-N(amine) distance of 2.012(3) falling in the range of a normal bond. Thus, we present the rare instances where the ligand tbta has been observed to bind in a perfectly tetradentate fashion in its metal complexes. The room temperature magnetic moment of 6.30 ?B for 1 shows values typical of two high spin Co(II) centers, and this value decreases at temperatures lower than 30 K indicating a weak antiferromagnetic coupling and zero field splitting. Mass spectrometric analysis of 2 provided evidence for the formation of an oxo-bridged dicobalt complex in the gas phase. PMID:23508268

  18. On how mammalian transcription factors recognize methylated DNA.

    PubMed

    Buck-Koehntop, Bethany A; Defossez, Pierre-Antoine

    2013-02-01

    DNA methylation is an epigenetic mark that is essential for the development of mammals; it is frequently altered in diseases ranging from cancer to psychiatric disorders. The presence of DNA methylation attracts specialized methyl-DNA binding factors that can then recruit chromatin modifiers. These methyl-CpG binding proteins (MBPs) have key biological roles and can be classified into three structural families: methyl-CpG binding domain (MBD), zinc finger, and SET and RING finger-associated (SRA) domain. The structures of MBD and SRA proteins bound to methylated DNA have been previously determined and shown to exhibit two very different modes of methylated DNA recognition. The last piece of the puzzle has been recently revealed by the structural resolution of two different zinc finger proteins, Kaiso and ZFP57, in complex with methylated DNA. These structures show that the two methyl-CpG binding zinc finger proteins adopt differential methyl-CpG binding modes. Nonetheless, there are similarities with the MBD proteins suggesting some commonalities in methyl-CpG recognition across the various MBP domains. These fresh insights have consequences for the analysis of the many other zinc finger proteins present in the genome, and for the biology of methyl-CpG binding zinc finger proteins. PMID:23324617

  19. 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.

  20. LC-MS and GC-MS metabolite profiling of nickel(II) complexes in the latex of the nickel-hyperaccumulating tree Sebertia acuminata and identification of methylated aldaric acid as a new nickel(II) ligand.

    PubMed

    Callahan, Damien L; Roessner, Ute; Dumontet, Vincent; Perrier, Nicolas; Wedd, Anthony G; O'Hair, Richard A J; Baker, Alan J M; Kolev, Spas D

    2008-01-01

    Targeted liquid chromatography-mass spectrometry (LC-MS) technology using size exclusion chromatography and metabolite profiling based on gas chromatography-mass spectrometry (GC-MS) were used to study the nickel-rich latex of the hyperaccumulating tree Sebertia acuminata. More than 120 compounds were detected, 57 of these were subsequently identified. A methylated aldaric acid (2,4,5-trihydroxy-3-methoxy-1,6-hexan-dioic acid) was identified for the first time in biological extracts and its structure was confirmed by 1D and 2D nuclear magnetic resonance (NMR) spectroscopy. After citric acid, it appears to be one of the most abundant small organic molecules present in the latex studied. Nickel(II) complexes of stoichiometry NiII:acid=1:2 were detected for these two acids as well as for malic, itaconic, erythronic, galacturonic, tartaric, aconitic and saccharic acids. These results provide further evidence that organic acids may play an important role in the transport and possibly in the storage of metal ions in hyperaccumulating plants. PMID:17765935

  1. 5-Hydroxytryptamine 5HT2C Receptors Form a Protein Complex with N-Methyl-d-aspartate GluN2A Subunits and Activate Phosphorylation of Src Protein to Modulate Motoneuronal Depolarization*

    PubMed Central

    Bigford, Gregory E.; Chaudhry, Nauman S.; Keane, Robert W.; Holohean, Alice M.

    2012-01-01

    N-Methyl-d-aspartate (NMDA)-gated ion channels are known to play a critical role in motoneuron depolarization, but the molecular mechanisms modulating NMDA activation in the spinal cord are not well understood. This study demonstrates that activated 5HT2C receptors enhance NMDA depolarizations recorded electrophysiologically from motoneurons. Pharmacological studies indicate involvement of Src tyrosine kinase mediates 5HT2C facilitation of NMDA. RT-PCR analysis revealed edited forms of 5HT2C were present in mammalian spinal cord, indicating the availability of G-protein-independent isoforms. Spinal cord neurons treated with the 5HT2C agonist MK 212 showed increased SrcTyr-416 phosphorylation in a dose-dependent manner thus verifying that Src is activated after treatment. In addition, 5HT2C antagonists and tyrosine kinase inhibitors blocked 5HT2C-mediated SrcTyr-416 phosphorylation and also enhanced NMDA-induced motoneuron depolarization. Co-immunoprecipitation of synaptosomal fractions showed that GluN2A, 5HT2C receptors, and Src tyrosine kinase form protein associations in synaptosomes. Moreover, immunohistochemical analysis demonstrated GluN2A and 5HT2C receptors co-localize on the processes of spinal neurons. These findings reveal that a distinct multiprotein complex links 5-hydroxytryptamine-activated intracellular signaling events with NMDA-mediated functional activity. PMID:22291020

  2. Spectroscopic (FT-IR, 1H, 13C NMR, UV), DOS and orbital overlap population analysis of copper complex of (E)-4-(2-(4-nitrophenyl) diazenyl)-N, N bis ((pyridin-2-yl) methyl) benzamine by density functional theory

    NASA Astrophysics Data System (ADS)

    Diwaker

    2015-02-01

    The geometric parameters, chemical shifts, FTIR, NMR and orbital overlap population along with DOS (density of states) to know different kinds of interactions for binding of copper atom with (E)-4-(2-(4-nitrophenyl) diazenyl)-N, N bis ((pyridin-2-yl) methyl) benzamine to form its copper complex has been reported by DFT methods. The theoretically predicted values for structural parameters are in agreement with the experimentally reported values. NMR chemical shifts calculated using B3LYP/DFT/GIAO level of theory gives information about binding of copper atom with three nitrogen atoms namely N (3, 8 and 11). Orbital overlap population analysis using DFT/B3LYP/SDD level of theory is used to study the kind of interactions involved in binding of copper with the three nitrogen atoms. DOS studies are done to know about the contribution of alpha, beta electrons to the valence and conduction band. IR spectroscopy investigations gave the absorption bands for the formation of title compound. Electronic spectrum along with HOMO-LUMO energies of the title compound has been investigated using Time-dependent (TD-DFT) approach.

  3. [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

  4. 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.

  5. DNA methylation and cancer.

    PubMed

    Kulis, Marta; Esteller, Manel

    2010-01-01

    DNA methylation is one of the most intensely studied epigenetic modifications in mammals. In normal cells, it assures the proper regulation of gene expression and stable gene silencing. DNA methylation is associated with histone modifications and the interplay of these epigenetic modifications is crucial to regulate the functioning of the genome by changing chromatin architecture. The covalent addition of a methyl group occurs generally in cytosine within CpG dinucleotides which are concentrated in large clusters called CpG islands. DNA methyltransferases are responsible for establishing and maintenance of methylation pattern. It is commonly known that inactivation of certain tumor-suppressor genes occurs as a consequence of hypermethylation within the promoter regions and a numerous studies have demonstrated a broad range of genes silenced by DNA methylation in different cancer types. On the other hand, global hypomethylation, inducing genomic instability, also contributes to cell transformation. Apart from DNA methylation alterations in promoter regions and repetitive DNA sequences, this phenomenon is associated also with regulation of expression of noncoding RNAs such as microRNAs that may play role in tumor suppression. DNA methylation seems to be promising in putative translational use in patients and hypermethylated promoters may serve as biomarkers. Moreover, unlike genetic alterations, DNA methylation is reversible what makes it extremely interesting for therapy approaches. The importance of DNA methylation alterations in tumorigenesis encourages us to decode the human epigenome. Different DNA methylome mapping techniques are indispensable to realize this project in the future. PMID:20920744

  6. Histone Arginine Methylation

    PubMed Central

    Lorenzo, Alessandra Di; Bedford, Mark T.

    2012-01-01

    Arginine methylation is a common posttranslational modification (PTM). This type of PTM occurs on both nuclear and cytoplasmic proteins, and is particularly abundant on shuttling proteins. In this review, we will focus on one aspect of this PTM: the diverse roles that arginine methylation of the core histone tails play in regulating chromatin function. A family of nine protein arginine methyltransferases (PRMTs) catalyze methylation reactions, and a subset target histones. Importantly, arginine methylation of histone tails can promote or prevent the docking of key transcriptional effector molecules, thus playing a central role in the orchestration of the histone code. PMID:21074527

  7. 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

  8. Pharmacokinetics and pharmacodynamics of methyl parathion.

    PubMed

    Kramer, Robert E; Ho, Ing K

    2002-05-01

    Methyl parathion and other organophosphorus insecticides are widely used in agriculture. Poisonings to this class of compounds are common and exerted primarily through inhibition of acetylcholinesterase. Methyl parathion became a major health concern when it was illegally sprayed in private homes. Since there are limited data with which to predict the long-term effects resulting from a pattern of exposure to methyl parathion that may have occurred in domestic settings, studies were performed to compare its pharmacokinetics and pharmacodynamics after intravenous, oral or dermal exposure. Methyl parathion was given to adult female rats as a single dose intravenously (2.5 mg/kg) through a femoral catheter, orally (2.5 mg/kg) by gavage, or dermally (< or = 50 mg/kg) by application to shaved skin at the nape of the neck. Blood (200 microl) was collected at increasing times from a separate catheter or from the retro-orbital sinus. Cholinesterase activity was measured in blood and normalized to hemoglobin content, whereas activities in brain and peripheral tissues were normalized to protein. Blood methyl parathion was quantitated by gas chromatography-electron capture. The pharmacokinetics of methyl parathion after intravenous exposure best fit a model in which it was distributed between two compartments and rapidly eliminated. Maximal concentrations of methyl parathion ranged from 200 to 350 ng/ml. The half-life of methyl parathion was 51 minutes, its volume of distribution was 10.1 L/kg, and clearance was 108 ml/min/kg. The kinetics of methyl parathion after single oral exposure contrasted with those after intravenous exposure. Despite a high absorption coefficient, oral bioavailability of methyl parathion was less than 5%, and concentrations in blood were 2% or less of those after intravenous exposure. After single dermal exposure (25 or 50 mg/kg), blood methyl parathion levels increased during the first 6 h and then remained constant for the next 42 h at about 150 ng/ml. Despite differences in its pharmacokinetics, methyl parathion caused similar time-dependent changes in blood and brain cholinesterase activities after intravenous or oral administration. Maximal inhibition of blood cholinesterase occurred within 15-60 min, and activities recovered within 30 - 48 h. In contrast, inhibition of blood cholinesterase caused by single dermal exposure (> or = 25 mg/kg) to methyl parathion developed gradually over 24 h, but was sustained. Cholinesterase inhibited by a lower dose (< or = 12 mg/kg) of methyl parathion required up to 21 days to recover fully. The pharmacokinetics and pharmacodynamics of methyl parathion are complex, and the complexity varies with the route of exposure. A significant 'first pass' effect for methyl parathion is seen with oral administration. Dermal exposure to methyl parathion, as likely occurred with the illegal spraying of private homes and businesses, may exacerbate toxicity and increase the potential for long-term adverse health effects. PMID:12166762

  9. Employment of methyl 2-pyridyl ketone oxime in 3d/4f-metal chemistry: dinuclear nickel(II)/lanthanide(III) species and complexes containing the metals in separate ions.

    PubMed

    Polyzou, Christina D; Nikolaou, Helen; Papatriantafyllopoulou, Constantina; Psycharis, Vassilis; Terzis, Aris; Raptopoulou, Catherine P; Escuer, Albert; Perlepes, Spyros P

    2012-11-28

    The use of methyl 2-pyridyl ketone oxime (mpkoH) for the synthesis of Ni(II)/Ln(III) (Ln = lanthanide) complexes, using "one-pot" reactions in the absence of an external base, is described. Depending on the reaction and crystallization conditions employed, two families of complexes have been obtained. The first family consists of true heterometallic species and involves complexes [NiLn(mpko)(3)(mpkoH)(3)](ClO(4))(2), where Ln = Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho and Er. The second family contains the pseudo heterometallic complexes [Ni(mpkoH)(3)](2)[Ln(NO(3))(6)](ClO(4)), where Ln = La, Ce, Pr, Nd and Sm. The crystal structures of [NiCe(mpko)(3)(mpkoH)(3)](ClO(4))(2) (1), [NiDy(mpko)(3)(mpkoH)(3)](ClO(4))(2) (8) and [Ni(mpkoH)(3)](2)[La(NO(3))(6)](ClO(4)) (11) have been determined by single-crystal, X-ray crystallography. Complexes 11.2MeOH0.6H(2)O and 81.2MeOH0.6H(2)O crystallise in the monoclinic space group P2(1)/a and are isomorphous; there are two crystallographically independent cations in the unit cell, but their interatomic distances and angles differ little. The Ni(II) and Ln(III) ions are bridged by three oximate groups belonging to the ?(1):?(1):?(1):? mpko(-) ligands. The Ni(II) centre is octahedrally coordinated by the six nitrogen atoms of the mpko(-) ligands in a facial arrangement. The Ln(III) centre is bound to an (O(oximate))(3)N(6) set of donor atoms, the nitrogen atoms belonging to the three N,N'-bidentate chelating mpkoH ligands. The stereochemistry of the Ln(III) atoms has been evaluated by means of continuous shape measures (CShM). The two crystallographically independent Ce(III) atoms in 1 have tricapped trigonal prismatic and capped square antiprismatic coordination geometries, while the polyhedra of the Dy(III) atoms in 8 are both close to a tricapped trigonal prism. The octahedral Ni(II) atoms in 11 are both facially bound to a N(6) set of donor atoms from three N,N'-bidentate chelating mpkoH ligands, while the 12-coordinate La(III) centre in [La(NO(3))(6)](3-) is coordinated by six bidentate chelating nitrato groups. Variable-temperature, solid state dc magnetic susceptibility studies were carried out on complexes 2, 6, 7 and 8. The dc susceptibility data for 6 in the 2.0-300 K range have been fit to a model with one J value, revealing an antiferromagnetic Ni(II)Gd(III) exchange interaction [J = -1.1 cm(-1) based on H = -J (?(Ni)?(Gd))]. Antiferromagnetic Ni(II)Pr(III), Ni(II)Tb(III) and Ni(II)Dy(III) exchange interactions have also been suggested for 2, 7 and 8, respectively. The combined work demonstrates the usefulness of mpko(-) in the preparation of interesting Ni(II)/Ln(III) compounds, without requiring the presence of external base and ancillary organic ligands. PMID:23069731

  10. DNA Methylation: Bisulphite Modification and Analysis

    PubMed Central

    Qu, Wenjia; Clark, Susan

    2011-01-01

    Epigenetics describes the heritable changes in gene function that occur independently to the DNA sequence. The molecular basis of epigenetic gene regulation is complex, but essentially involves modifications to the DNA itself or the proteins with which DNA associates. The predominant epigenetic modification of DNA in mammalian genomes is methylation of cytosine nucleotides (5-MeC). DNA methylation provides instruction to gene expression machinery as to where and when the gene should be expressed. The primary target sequence for DNA methylation in mammals is 5'-CpG-3' dinucleotides (Figure 1). CpG dinucleotides are not uniformly distributed throughout the genome, but are concentrated in regions of repetitive genomic sequences and CpG "islands" commonly associated with gene promoters (Figure 1). DNA methylation patterns are established early in development, modulated during tissue specific differentiation and disrupted in many disease states including cancer. To understand the biological role of DNA methylation and its role in human disease, precise, efficient and reproducible methods are required to detect and quantify individual 5-MeCs. This protocol for bisulphite conversion is the "gold standard" for DNA methylation analysis and facilitates identification and quantification of DNA methylation at single nucleotide resolution. The chemistry of cytosine deamination by sodium bisulphite involves three steps (Figure 2). (1) Sulphonation: The addition of bisulphite to the 5-6 double bond of cytosine (2) Hydrolic Deamination: hydrolytic deamination of the resulting cytosine-bisulphite derivative to give a uracil-bisulphite derivative (3) Alkali Desulphonation: Removal of the sulphonate group by an alkali treatment, to give uracil. Bisulphite preferentially deaminates cytosine to uracil in single stranded DNA, whereas 5-MeC, is refractory to bisulphite-mediated deamination. Upon PCR amplification, uracil is amplified as thymine while 5-MeC residues remain as cytosines, allowing methylated CpGs to be distinguished from unmethylated CpGs by presence of a cytosine "C" versus thymine "T" residue during sequencing. DNA modification by bisulphite conversion is a well-established protocol that can be exploited for many methods of DNA methylation analysis. Since the detection of 5-MeC by bisulphite conversion was first demonstrated by Frommer et al.1 and Clark et al.2, methods based around bisulphite conversion of genomic DNA account for the majority of new data on DNA methylation. Different methods of post PCR analysis may be utilized, depending on the degree of specificity and resolution of methylation required. Cloning and sequencing is still the most readily available method that can give single nucleotide resolution for methylation across the DNA molecule. PMID:22042230

  11. DNA methylation: bisulphite modification and analysis.

    PubMed

    Patterson, Kate; Molloy, Laura; Qu, Wenjia; Clark, Susan

    2011-01-01

    Epigenetics describes the heritable changes in gene function that occur independently to the DNA sequence. The molecular basis of epigenetic gene regulation is complex, but essentially involves modifications to the DNA itself or the proteins with which DNA associates. The predominant epigenetic modification of DNA in mammalian genomes is methylation of cytosine nucleotides (5-MeC). DNA methylation provides instruction to gene expression machinery as to where and when the gene should be expressed. The primary target sequence for DNA methylation in mammals is 5'-CpG-3' dinucleotides (Figure 1). CpG dinucleotides are not uniformly distributed throughout the genome, but are concentrated in regions of repetitive genomic sequences and CpG "islands" commonly associated with gene promoters (Figure 1). DNA methylation patterns are established early in development, modulated during tissue specific differentiation and disrupted in many disease states including cancer. To understand the biological role of DNA methylation and its role in human disease, precise, efficient and reproducible methods are required to detect and quantify individual 5-MeCs. This protocol for bisulphite conversion is the "gold standard" for DNA methylation analysis and facilitates identification and quantification of DNA methylation at single nucleotide resolution. The chemistry of cytosine deamination by sodium bisulphite involves three steps (Figure 2). (1) Sulphonation: The addition of bisulphite to the 5-6 double bond of cytosine (2) Hydrolic Deamination: hydrolytic deamination of the resulting cytosine-bisulphite derivative to give a uracil-bisulphite derivative (3) Alkali Desulphonation: Removal of the sulphonate group by an alkali treatment, to give uracil. Bisulphite preferentially deaminates cytosine to uracil in single stranded DNA, whereas 5-MeC, is refractory to bisulphite-mediated deamination. Upon PCR amplification, uracil is amplified as thymine while 5-MeC residues remain as cytosines, allowing methylated CpGs to be distinguished from unmethylated CpGs by presence of a cytosine "C" versus thymine "T" residue during sequencing. DNA modification by bisulphite conversion is a well-established protocol that can be exploited for many methods of DNA methylation analysis. Since the detection of 5-MeC by bisulphite conversion was first demonstrated by Frommer et al. and Clark et al., methods based around bisulphite conversion of genomic DNA account for the majority of new data on DNA methylation. Different methods of post PCR analysis may be utilized, depending on the degree of specificity and resolution of methylation required. Cloning and sequencing is still the most readily available method that can give single nucleotide resolution for methylation across the DNA molecule. PMID:22042230

  12. 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

  13. Positioned nucleosomes inhibit Dam methylation in vivo.

    PubMed Central

    Kladde, M P; Simpson, R T

    1994-01-01

    Escherichia coli Dam DNA methyltransferase can methylate genomic GATC sites when expressed in Saccharomyces cerevisiae. Others have observed changes in the level of methylation at specific sites and suggested that these changes are related to transcriptional state or chromosomal context. To test directly the influence of nucleosome location on the ability of Dam methyltransferase to modify GATC sites in chromatin, we analyzed minichromosomes containing precisely positioned nucleosomes in dam-expressing yeast strains. Levels of methylation at individual GATC sites were rigorously quantified by an oligonucleotide-probing procedure. Within the linker and adjacent 21 bp of nucleosome-associated DNA, GATC sites were highly methylated, whereas methylation was severely inhibited by histone-DNA contacts nearer to the nucleosomal pseudodyad. Other DNA-protein complexes also interfere with Dam methylation. These data are consistent with a model in which nucleosomes exert a repressive influence on the biological functions of DNA by restricting access of trans-acting factors to DNA. Images PMID:8108416

  14. 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

  15. Methylations: a radical mechanism.

    PubMed

    Fontecave, Marc

    2011-05-27

    On the basis of labeling experiments, Grove etal. (2011) have shown how an electrophilic carbon (from anRNA adenosine) can be methylated by S-adenosylmethionine-dependent methyltransferases though an original radical mechanism. PMID:21609836

  16. 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...

  17. DNA methylation and differentiation

    SciTech Connect

    Michalowky, L.A.; Jones, P.A. )

    1989-03-01

    The methylation of specific cytosine residues in DNA has been implicated in regulating gene expression and facilitating functional specialization of cellular phenotypes. Generally, the demethylation of certain CpG sites correlates with transcriptional activation of genes. 5-Azacytidine is an inhibitor of DNA methylation and has been widely used as a potent activator of suppressed genetic information. Treatment of cells with 5-azacytidine results in profound phenotypic alterations. The drug-induced hypomethylation of DNA apparently perturbs DNA-protein interactions that may consequently alter transcriptional activity and cell determination. The inhibitory effect of cytosine methylation may be exerted via altered DNA-protein interactions specifically or may be transduced by a change in the conformation of chromatin. Recent studies have demonstrated that cytosine methylation also plays a central role in parental imprinting, which in turn determines the differential expression of maternal and paternal genomes during embryogenesis. In other words, methylation is the mechanism whereby the embryo retains memory of the gametic origin of each component of genetic information. A memory of this type would probably persist during DNA replication and cell division as methylation patterns are stable and heritable.

  18. Employment of methyl 2-pyridyl ketone oxime in manganese non-carboxylate chemistry: Mn(II)(2)Mn(IV) and Mn(II)(2)Mn(III)(6) complexes.

    PubMed

    Stoumpos, Constantinos C; Stamatatos, Theocharis C; Sartzi, Harikleia; Roubeau, Olivier; Tasiopoulos, Anastasios J; Nastopoulos, Vassilios; Teat, Simon J; Christou, George; Perlepes, Spyros P

    2009-02-14

    The employment of the anion of methyl 2-pyridyl ketone oxime (mpko(-)) as a tridentate chelating/bridging ligand in manganese chemistry is described. The inorganic anion (Br(-), ClO(4)(-)) used in the reaction affects the identity of the product. The reaction of MnBr(2) and one equivalent of mpkoH in the presence of a base affords [Mn(3)(OMe)(2)(mpko)(4)Br(2)] (3), which is mixed-valence (2Mn(II), Mn(IV)). The central Mn(IV) atom in each of the two, crystallographically independent, centrosymmetric molecules is coordinated by four oximate oxygen atoms belonging to the eta(1):eta(1):eta(1):mu mpko(-) ligands, and two eta(1):mu MeO(-) groups, while six coordination at each terminal Mn(II) atom is completed by four nitrogen atoms belonging to the 'chelating' part of two mpko(-) ligands, and one Br(-) ion. The Mn(II) atoms have trigonal prismatic coordination geometry. The reaction of Mn(ClO(4))(2).6H(2)O, mpkoH and OH(-) (1:2:1) in MeOH gives [Mn(8)O(4)(OMe)(mpko)(9)(mpkoH)](ClO(4))(4) (4), which is also mixed-valence (2Mn(II), 6Mn(III)) and possesses the novel [Mn(8)(mu(3)-O)(4)(mu-OMe)(mu-OR'')(2)](11+) core. The latter possesses a U-shaped sequence of four fused {Mn(II)Mn(III)(2)(mu(3)-O)}(6+) triangular units, with a Mn(III)-Mn(III) edge being shared between the central triangles. Variable-temperature, solid-state dc and ac magnetic susceptibility studies were carried out on complexes 3 and 4 . The dc susceptibility data for 3 in the 5.0-300 K range have been fit to a model with two J values, revealing weak ferromagnetic Mn(II)Mn(IV) (J = +3.4 cm(-1)) and Mn(II)Mn(II) (J' = +0.3 cm(-1)) exchange interactions. Fitting of the magnetization vs. H/T data by matrix diagonalization and including only axial anisotropy (ZFS, D) gave ground state spin (S) and D values of S = 13/2, D = +0.17 cm(-1) for and S = 3, D = -0.09 cm(-1) for 4 . The combined work demonstrates the usefulness of mpko(-) in the preparation of interesting Mn clusters, without requiring the co-presence of carboxylate ligands. PMID:19173083

  19. Smyd2 controls cytoplasmic lysine methylation of Hsp90 and myofilament organization

    PubMed Central

    Donlin, Laura T.; Andresen, Christian; Just, Steffen; Rudensky, Eugene; Pappas, Christopher T.; Kruger, Martina; Jacobs, Erica Y.; Unger, Andreas; Zieseniss, Anke; Dobenecker, Marc-Werner; Voelkel, Tobias; Chait, Brian T.; Gregorio, Carol C.; Rottbauer, Wolfgang; Tarakhovsky, Alexander; Linke, Wolfgang A.

    2012-01-01

    Protein lysine methylation is one of the most widespread post-translational modifications in the nuclei of eukaryotic cells. Methylated lysines on histones and nonhistone proteins promote the formation of protein complexes that control gene expression and DNA replication and repair. In the cytoplasm, however, the role of lysine methylation in protein complex formation is not well established. Here we report that the cytoplasmic protein chaperone Hsp90 is methylated by the lysine methyltransferase Smyd2 in various cell types. In muscle, Hsp90 methylation contributes to the formation of a protein complex containing Smyd2, Hsp90, and the sarcomeric protein titin. Deficiency in Smyd2 results in the loss of Hsp90 methylation, impaired titin stability, and altered muscle function. Collectively, our data reveal a cytoplasmic protein network that employs lysine methylation for the maintenance and function of skeletal muscle. PMID:22241783

  20. Reconfiguration of DNA methylation in aging.

    PubMed

    Zampieri, Michele; Ciccarone, Fabio; Calabrese, Roberta; Franceschi, Claudio; Brkle, Alexander; Caiafa, Paola

    2015-11-01

    A complex interplay between multiple biological effects shapes the aging process. The advent of genome-wide quantitative approaches in the epigenetic field has highlighted the effective impact of epigenetic deregulation, particularly of DNA methylation, on aging. Age-associated alterations in DNA methylation are commonly grouped in the phenomenon known as "epigenetic drift" which is characterized by gradual extensive demethylation of genome and hypermethylation of a number of promoter-associated CpG islands. Surprisingly, specific DNA regions show directional epigenetic changes in aged individuals suggesting the importance of these events for the aging process. However, the epigenetic information obtained until now in aging needs a re-consideration due to the recent discovery of 5-hydroxymethylcytosine, a new DNA epigenetic mark present on genome. A recapitulation of the factors involved in the regulation of DNA methylation and the changes occurring in aging will be described in this review also considering the data available on 5 hmC. PMID:25708826

  1. 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, Franois M; Tost, Jrg; Cartron, Pierre-Franois

    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

  2. Global DNA Methylation of Ischemic Stroke Subtypes

    PubMed Central

    Soriano-Trraga, Carolina; Jimnez-Conde, Jordi; Giralt-Steinhauer, Eva; Mola, Marina; Ois, ngel; Rodrguez-Campello, Ana; Cuadrado-Godia, Elisa; Fernndez-Cadenas, Israel; Carrera, Caty; Montaner, Joan; Elosua, Roberto; Roquer, Jaume

    2014-01-01

    Ischemic stroke (IS), a heterogeneous multifactorial disorder, is among the leading causes of mortality and long-term disability in the western world. Epidemiological data provides evidence for a genetic component to the disease, but its epigenetic involvement is still largely unknown. Epigenetic mechanisms, such as DNA methylation, change over time and may be associated with aging processes and with modulation of the risk of various pathologies, such as cardiovascular disease and stroke. We analyzed 2 independent cohorts of IS patients. Global DNA methylation was measured by luminometric methylation assay (LUMA) of DNA blood samples. Univariate and multivariate regression analyses were used to assess the methylation differences between the 3 most common IS subtypes, large-artery atherosclerosis (LAA), small-artery disease (SAD), and cardio-aortic embolism (CE). A total of 485 IS patients from 2 independent hospital cohorts (n?=?281 and n?=?204) were included, distributed across 3 IS subtypes: LAA (78/281, 59/204), SAD (97/281, 53/204), and CE (106/281, 89/204). In univariate analyses, no statistical differences in LUMA levels were observed between the 3 etiologies in either cohort. Multivariate analysis, adjusted by age, sex, hyperlipidemia, and smoking habit, confirmed the lack of differences in methylation levels between the analyzed IS subtypes in both cohorts. Despite differences in pathogenesis, our results showed no global methylation differences between LAA, SAD, and CE subtypes of IS. Further work is required to establish whether the epigenetic mechanism of methylation might play a role in this complex disease. PMID:24788121

  3. Cation-? Interactions of Methylated Ammonium Ions: A Quantum Mechanical Study

    PubMed Central

    Rapp, Chaya; Goldberger, Elizabeth; Tishbi, Nasim; Kirshenbaum, Rachel

    2014-01-01

    Cation-? interactions of methylated ammonium ions play a key role in a broad range of biochemical systems. These include methyl-lysine binding proteins which bind to methylated sites on histone proteins, lysine demethylase enzymes which demethylate these sites, and neurotransmitter receptor complexes which bind choline derived ligands. Recognition in these systems is achieved through an aromatic cage motif in the binding site. Here we use high level quantum mechanical calculations to address how cation-? interactions of methylated ammonium ions are modulated by a change in methylation state and interaction geometry. We survey methyl-lysine and choline derived complexes in the Protein Databank to validate our results against available structural data. A quantitative description of cation-? interactions of methylated ammonium systems is critical to structure-based efforts to target methyl-lysine binding proteins and demethylase enzymes in the treatment of unregulated transcriptional control, and neurotransmitter receptors in the treatment of neurological disease. It is our hope that our work will serve as a benchmark for the development of physical chemistry based force fields that can accurately model the contribution of cation-? interactions to binding and specificity in these systems. PMID:24464782

  4. Cation-? interactions of methylated ammonium ions: a quantum mechanical study.

    PubMed

    Rapp, Chaya; Goldberger, Elizabeth; Tishbi, Nasim; Kirshenbaum, Rachel

    2014-07-01

    Cation-? interactions of methylated ammonium ions play a key role in a broad range of biochemical systems. These include methyl-lysine binding proteins which bind to methylated sites on histone proteins, lysine demethylase enzymes which demethylate these sites, and neurotransmitter receptor complexes which bind choline-derived ligands. Recognition in these systems is achieved through an 'aromatic cage' motif in the binding site. Here we use high-level quantum mechanical calculations to address how cation-? interactions of methylated ammonium ions are modulated by a change in methylation state and interaction geometry. We survey methyl-lysine and choline-derived complexes in the Protein Databank to validate our results against available structural data. A quantitative description of cation-? interactions of methylated ammonium systems is critical to structure-based efforts to target methyl-lysine binding proteins and demethylase enzymes in the treatment of unregulated transcriptional control, and neurotransmitter receptors in the treatment of neurological disease. It is our hope that our work will serve as a benchmark for the development of physical chemistry based force fields that can accurately model the contribution of cation-? interactions to binding and specificity in these systems. PMID:24464782

  5. Array-based DNA methylation profiling in follicular lymphoma

    PubMed Central

    ORiain, Ciarn; OShea, 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

  6. 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 μg/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

  7. Characterization and properties of monoammine nitroimidazole complexes of platinum (PtCl sub 2 (NH sub 3 )(NO sub 2 Im)). Crystal and molecular structure of cis-Amminedichloro(1-((((2-hydroxyethyl)amino)carbonyl)methyl)-2-nitroimidazole)platinum(II)

    SciTech Connect

    Rochon, F.D.; Pichang Kong; Melanson, R. ); Skov, K.A. ); Farrell, N. )

    1991-11-27

    The characterization of monoammine(nitroimidazole)platinum(II) complexes of structure (PtCl{sub 2}(NH{sub 3})(NO{sub 2}Im)) (NO{sub 2}Im = 1-((((2-hydroxyethyl)amino)carbonyl)methyl)-2-nitroimidazole, Etanidazole (I), 1-(2-nitro-1-imidazolyl)-3-methoxy2-propanol, Misonidazole (II), and 1-(2-hydroxyethyl)-2-methyl-5-nitroimidazole, Metronidazole (III)) is reported. Both is cis and trans isomers may be isolated for II and III. The crystal structure of cis-amminedichloro(1-((((2-hydroxyethyl)amino)carbonyl)methyl)-2-nitroimidazole)platinum(II) has been determined by X-ray diffraction. The crystals are orthorhombic, space group Pnab with cell dimensions a = 14.867 (7) {angstrom}, b = 9.915 (5) {angstrom}, c = 19.015 (9) {angstrom}, and Z = 8. The structure was refined to R = 0.062 and R{sub w} = 0.052. Platinum has the expected square-planar coordination. The Pt-Cl bond trans to the nitroimidazole ligand is shorter (2.269 (3) {angstrom}) than normal. The dihedral angle between the platinum plane and the imidazole ring is 111{degree}, while the nitro group makes an angle of 31{degree} with the imidazole ring plane. Electrochemistry and {sup 195}Pt NMR data are also reported. The relevance of the chemical properties to their biological properties as radiosensitizers and hypoxic cytotoxins is discussed.

  8. Metabolic production of methylated selenium species requires adequate methylation status

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Obesity negatively impacts methylation status and markers of methylation status vary according to selenium status in supplemented subjects. We have proposed that disruptions in methylation capacity induced by obesity compromise demonstrable anti-cancer effects of Se supplementation. In order to addr...

  9. DNA Methylation and Cancer Diagnosis

    PubMed Central

    Delpu, Yannick; Cordelier, Pierre; Cho, William C.; Torrisani, Jrme

    2013-01-01

    DNA methylation is a major epigenetic modification that is strongly involved in the physiological control of genome expression. DNA methylation patterns are largely modified in cancer cells and can therefore be used to distinguish cancer cells from normal tissues. This review describes the main technologies available for the detection and the discovery of aberrantly methylated DNA patterns. It also presents the different sources of biological samples suitable for DNA methylation studies. We discuss the interest and perspectives on the use of DNA methylation measurements for cancer diagnosis through examples of methylated genes commonly documented in the literature. The discussion leads to our consideration for why DNA methylation is not commonly used in clinical practice through an examination of the main requirements that constitute a reliable biomarker. Finally, we describe the main DNA methylation inhibitors currently used in clinical trials and those that exhibit promising results. PMID:23873296

  10. Simultaneous hyper- and hypomethylation at imprinted loci in a subset of patients with GNAS epimutations underlies a complex and different mechanism of multilocus methylation defect in pseudohypoparathyroidism type 1b.

    PubMed

    Maupetit-Méhouas, Stéphanie; Azzi, Salah; Steunou, Virginie; Sakakini, Nathalie; Silve, Caroline; Reynes, Christelle; Perez de Nanclares, Guiomar; Keren, Boris; Chantot, Sandra; Barlier, Anne; Linglart, Agnès; Netchine, Irène

    2013-08-01

    Most patients with pseudohypoparathyroidism type 1b (PHP-1b) display a loss of imprinting (LOI) encompassing the GNAS locus resulting in PTH resistance. In other imprinting disorders, such as Russell-Silver or Beckwith-Wiedemann syndrome, we and others have shown that the LOI is not restricted to one imprinted locus but may affect other imprinted loci for some patients. Therefore, we hypothesized that patients with PHP-1b might present multilocus imprinting defects. We investigated, in 63 patients with PHP-1b, the methylation pattern of eight imprinted loci: GNAS, ZAC1, PEG1/MEST, ICR1, and ICR2 on chromosome 11p15, SNRPN, DLK1/GTL2 IG-DMR, and L3MBTL1. We found multilocus imprinting defects in four PHP-1b patients carrying broad LOI at the GNAS locus (1) simultaneous hypermethylation at L3MBTL1 differentially methylated region 3 (DMR3), and hypomethylation at PEG1/MEST DMR (n = 1), (2) hypermethylation at the L3MBTL1 (DMR3) (n = 1) and at the DLK1/GTL2 IG-DMR (n = 1), and (3) hypomethylation at the L3MBTL1 DMR3 (n = 1). We suggest that mechanisms underlying multilocus imprinting defects in PHP-1b differ from those of other imprinting disorders having only multilocus loss of methylation. Furthermore, our results favor the hypothesis of "epidominance", that is, the phenotype is controlled by the most severely affected imprinted locus. PMID:23649963

  11. 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

  12. 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

  13. 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

  14. 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

  15. Methyl ethyl ketone (MEK)

    Integrated Risk Information System (IRIS)

    Methyl ethyl ketone ( MEK ) ( CASRN 78 - 93 - 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 Nonc

  16. 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

  17. Methyl isobutyl ketone (MIBK)

    Integrated Risk Information System (IRIS)

    EPA / 635 / R - 03 / 002 TOXICOLOGICAL REVIEW OF METHYL ISOBUTYL KETONE ( CAS No . 108 - 10 - 1 ) In Support of Summary Information on the Integrated Risk Information System ( IRIS ) March 2003 U.S . Environmental Protection Agency Washington DC DISCLAIMER This document has been reviewed in accordan

  18. 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

  19. 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...

  20. 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...

  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. Human body epigenome maps reveal noncanonical DNA methylation variation.

    PubMed

    Schultz, Matthew D; He, Yupeng; Whitaker, John W; Hariharan, Manoj; Mukamel, Eran A; Leung, Danny; Rajagopal, Nisha; Nery, Joseph R; Urich, Mark A; Chen, Huaming; Lin, Shin; Lin, Yiing; Jung, Inkyung; Schmitt, Anthony D; Selvaraj, Siddarth; Ren, Bing; Sejnowski, Terrence J; Wang, Wei; Ecker, Joseph R

    2015-07-01

    Understanding the diversity of human tissues is fundamental to disease and requires linking genetic information, which is identical in most of an individual's cells, with epigenetic mechanisms that could have tissue-specific roles. Surveys of DNA methylation in human tissues have established a complex landscape including both tissue-specific and invariant methylation patterns. Here we report high coverage methylomes that catalogue cytosine methylation in all contexts for the major human organ systems, integrated with matched transcriptomes and genomic sequence. By combining these diverse data types with each individuals' phased genome, we identified widespread tissue-specific differential CG methylation (mCG), partially methylated domains, allele-specific methylation and transcription, and the unexpected presence of non-CG methylation (mCH) in almost all human tissues. mCH correlated with tissue-specific functions, and using this mark, we made novel predictions of genes that escape X-chromosome inactivation in specific tissues. Overall, DNA methylation in several genomic contexts varies substantially among human tissues. PMID:26030523

  3. Human Body Epigenome Maps Reveal Noncanonical DNA Methylation Variation

    PubMed Central

    Schultz, Matthew D.; He, Yupeng; Whitaker, John W.; Hariharan, Manoj; Mukamel, Eran A.; Leung, Danny; Rajagopal, Nisha; Nery, Joseph R.; Urich, Mark A.; Chen, Huaming; Lin, Shin; Lin, Yiing; Jung, Inkyung; Schmitt, Anthony D.; Selvaraj, Siddarth; Ren, Bing; Sejnowski, Terrence J.; Wang, Wei; Ecker, Joseph R.

    2015-01-01

    Summary Understanding the diversity of human tissues is fundamental to disease and requires linking genetic information, which is identical in most of an individual’s cells, with epigenetic mechanisms that could play tissue-specific roles. Surveys of DNA methylation in human tissues have established a complex landscape including both tissue-specific and invariant methylation patterns1,2. Here we report high coverage methylomes that catalogue cytosine methylation in all contexts for the major human organ systems, integrated with matched transcriptomes and genomic sequence. By combining these diverse data types with each individuals’ phased genome3, we identified widespread tissue-specific differential CG methylation (mCG), partially methylated domains, allele-specific methylation and transcription, and the unexpected presence of non-CG methylation (mCH) in almost all human tissues. mCH correlated with tissue-specific functions, and using this mark, we made novel predictions of genes that escape X-chromosome inactivation in specific tissues. Overall, DNA methylation in multiple genomic contexts varies substantially among human tissues. PMID:26030523

  4. 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. PMID:26740923

  5. 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

  6. 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.

    PubMed

    Adly, Omima M I; Emara, Adel A A

    2014-11-11

    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. PMID:24858350

  7. 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.

  8. What difference does a methyl group make: pentamethylbenzene?

    PubMed

    Mudge, Matthew; Ng, Boon K; Onie, Catherine Jessica; Bhadbhade, Mohan; Mole, Richard A; Rule, Kirrily C; Stampfl, Anton P J; Stride, John A

    2014-12-01

    The crystal structure of pentamethylbenzene has been obtained for the first time with the use of synchrotron radiation, whilst the low-energy spectrum of lattice dynamics, dominated by the methyl group torsions, was obtained using inelastic neutron scattering. The effect of symmetry lowering by the removal of a single methyl group relative to hexamethylbenzene has been investigated, including the role that this plays in the charge-transfer characteristics of complexes formed with tetracyanoethylene. PMID:25212729

  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. Crystal structure of hexa­kis­(dmpu)-di-μ2-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-μ2-hydroxido-bis­{tris­[1,3-di­methyl­tetra­hydro­pyrimidin-2(1H)-one-κO]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

  11. Mechanism of human methyl-directed DNA methyltransferase and the fidelity of cytosine methylation.

    PubMed Central

    Smith, S S; Kaplan, B E; Sowers, L C; Newman, E M

    1992-01-01

    The properties of the methyl-directed DNA (cytosine-5-)-methyltransferase (EC 2.1.1.37) suggest that it is the enzyme that maintains patterns of methylation in the human genome. Proposals for the enzyme's mechanism of action suggest that 5-methyldeoxycytidine is produced from deoxycytidine via a dihydrocytosine intermediate. We have used an oligodeoxynucleotide containing 5-fluorodeoxycytidine as a suicide substrate to capture the enzyme and the dihydrocytosine intermediate. Gel retardation experiments demonstrate the formation of the expected covalent complex between duplex DNA containing 5-fluorodeoxycytidine and the human enzyme. Formation of the complex was dependent upon the presence of the methyl donor S-adenosylmethionine, suggesting that it comprises an enzyme-linked 5-substituted dihydrocytosine moiety in DNA. Dihydrocytosine derivatives are extremely labile toward hydrolytic deamination in aqueous solution. Because C-to-T transition mutations are especially prevalent at CG sites in human DNA, we have used high-performance liquid chromatography to search for thymidine that might be generated by hydrolysis during the methyl transfer reaction. Despite the potential for deamination inherent in the formation of the intermediate, the methyltransferase did not produce detectable amounts of thymidine. The data suggest that the ability of the human methyltransferase to preserve genetic information when copying a methylation pattern (i.e., its fidelity) is comparable to the ability of a mammalian DNA polymerase to preserve genetic information when copying a DNA sequence. Thus the high frequency of C-to-T transitions at CG sites in human DNA does not appear to be due to the normal enzymatic maintenance of methylation patterns. Images PMID:1584813

  12. 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 (ATRXDnmt3Dnmt3L [ADD], CysXXCys [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

  13. Spectroscopic studies of the 1:1 complexes of 4-nitrophenyl[bis(ethylsulfonyl)]methane and phenyl[bis(ethylsulfonyl)]methane with 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene and 1,5,7-triazabicyclo[4.4.0]dec-5-ene

    NASA Astrophysics Data System (ADS)

    Huczyński, A.; Binkowska, I.; Jarczewski, A.; Brzezinski, B.

    2007-09-01

    The 1:1 complexes of 4-nitrophenyl[bis(diethylsulfonyl)]methane (CH1) and phenyl[bis(diethylsulfonyl)]methane (CH2) with 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) and 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene (MTBD) have been synthesized and their structures have been studied using the FT-IR, 1H NMR and PM5 semiempirical methods. In all complexes a proton has been transferred from C-H acid to TBD or MTBD molecules to yield ionic pairs. On the basis of the FT-IR and 1H NMR studies of the MTBD complexes, in acetonitrile, the ions have been shown to be fully dissociated. In the case of TBD formation of non-cyclic hydrogen bonded structures have been proposed for the complex being partially dissociated. The calculated structure of the CH2-TBD complex has shown very high similarity to the structure in the solid state.

  14. 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.

  15. HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher's exact test.

    PubMed

    Sun, Shuying; Yu, Xiaoqing

    2016-03-01

    DNA methylation is an epigenetic event that plays an important role in regulating gene expression. It is important to study DNA methylation, especially differential methylation patterns between two groups of samples (e.g. patients vs. normal individuals). With next generation sequencing technologies, it is now possible to identify differential methylation patterns by considering methylation at the single CG site level in an entire genome. However, it is challenging to analyze large and complex NGS data. In order to address this difficult question, we have developed a new statistical method using a hidden Markov model and Fisher's exact test (HMM-Fisher) to identify differentially methylated cytosines and regions. We first use a hidden Markov chain to model the methylation signals to infer the methylation state as Not methylated (N), Partly methylated (P), and Fully methylated (F) for each individual sample. We then use Fisher's exact test to identify differentially methylated CG sites. We show the HMM-Fisher method and compare it with commonly cited methods using both simulated data and real sequencing data. The results show that HMM-Fisher outperforms the current available methods to which we have compared. HMM-Fisher is efficient and robust in identifying heterogeneous DM regions. PMID:26854292

  16. 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)⋯π(ring) and nitrate(π)⋯π(ring) inter-actions.

    PubMed

    Granifo, Juan; Suarez, Sebastián; Baggio, Ricardo

    2015-08-01

    The centrosymmetric dinuclear complex bis-(μ-3-carb-oxy-6-methyl-pyridine-2-carboxyl-ato)-κ(3) N,O (2):O (2);κ(3) O (2):N,O (2)-bis-[(2,2'-bi-pyridine-κ(2) N,N')(nitrato-κO)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 μ-κ(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 μ-κ(3) coordination mode found in the title compound. PMID:26396748

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

    PubMed Central

    Granifo, Juan; Suarez, Sebastián; Baggio, Ricardo

    2015-01-01

    The centrosymmetric dinuclear complex bis­(μ-3-carb­oxy-6-methyl­pyridine-2-carboxyl­ato)-κ3 N,O 2:O 2;κ3 O 2:N,O 2-bis­[(2,2′-bi­pyridine-κ2 N,N′)(nitrato-κO)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 μ-κ3 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 μ-κ3 coordination mode found in the title compound. PMID:26396748

  18. 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

    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

  19. 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

  20. MethylSig: a whole genome DNA methylation analysis pipeline

    PubMed Central

    Park, Yongseok; Figueroa, Maria E.; Rozek, Laura S.; Sartor, Maureen A.

    2014-01-01

    Motivation: DNA methylation plays critical roles in gene regulation and cellular specification without altering DNA sequences. The wide application of reduced representation bisulfite sequencing (RRBS) and whole genome bisulfite sequencing (bis-seq) opens the door to study DNA methylation at single CpG site resolution. One challenging question is how best to test for significant methylation differences between groups of biological samples in order to minimize false positive findings. Results: We present a statistical analysis package, methylSig, to analyse genome-wide methylation differences between samples from different treatments or disease groups. MethylSig takes into account both read coverage and biological variation by utilizing a beta-binomial approach across biological samples for a CpG site or region, and identifies relevant differences in CpG methylation. It can also incorporate local information to improve group methylation level and/or variance estimation for experiments with small sample size. A permutation study based on data from enhanced RRBS samples shows that methylSig maintains a well-calibrated type-I error when the number of samples is three or more per group. Our simulations show that methylSig has higher sensitivity compared with several alternative methods. The use of methylSig is illustrated with a comparison of different subtypes of acute leukemia and normal bone marrow samples. Availability: methylSig is available as an R package at http://sartorlab.ccmb.med.umich.edu/software. Contact: sartorma@umich.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24836530

  1. Cytosine methylation regulates oviposition in the pathogenic blood fluke Schistosoma mansoni

    PubMed Central

    Geyer, Kathrin K.; Rodrguez Lpez, Carlos M.; Chalmers, Iain W.; Munshi, Sabrina E.; Truscott, Martha; Heald, James; Wilkinson, Mike J.; Hoffmann, Karl F.

    2011-01-01

    Similar to other metazoan pathogens, Schistosoma mansoni undergoes transcriptional and developmental regulation during its complex lifecycle and host interactions. DNA methylation as a mechanism to control these processes has, to date, been discounted in this parasite. Here we show the first evidence for cytosine methylation in the S. mansoni genome. Transcriptional coregulation of novel DNA methyltransferase (SmDnmt2) and methyl-CpG-binding domain proteins mirrors the detection of cytosine methylation abundance and implicates the presence of a functional DNA methylation machinery. Genome losses in cytosine methylation upon SmDnmt2 silencing and the identification of a hypermethylated, repetitive intron within a predicted forkhead gene confirm this assertion. Importantly, disruption of egg production and egg maturation by 5-azacytidine establishes an essential role for 5-methylcytosine in this parasite. These findings provide the first functional confirmation for this epigenetic modification in any worm species and link the cytosine methylation machinery to platyhelminth oviposition processes. PMID:21829186

  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. Role of DNA methylation in colorectal carcinogenesis.

    PubMed

    Patai, Arpd V; Molnr, Bla; Kalmr, Alexandra; Schller, Andrea; Tth, 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

  5. DNA Methylation and Colorectal Cancer

    PubMed Central

    Ashktorab, Hassan; Brim, Hassan

    2014-01-01

    Colorectal cancer (CRC) is one of the major cancers in the world and second death-causing cancer in the US. CRC development involves genetic and epigenetic alterations. Changes in DNA methylation status are believed to be involved at different stages of CRC. Promoter silencing via DNA methylation and hypomethylation of oncogenes alter genes expression, and can be used as a tool for the early detection of colonic lesions. DNA methylation use as diagnostic and prognostic marker has been described for many cancers including CRC. CpG Islands Methylator Phenotype (CIMP) is one of the underlying CRC mechanisms. This review aims to define methylation signatures in CRC. The analysis of DNA methylation profile in combination with the pathological diagnosis would be useful in predicting CRC tumors evolution and their prognostic behavior. PMID:25580099

  6. Unprecedented syndioselectivity and syndiotactic polyolefin melting temperature: polypropylene and poly(4-methyl-1-pentene) from a highly active, sterically expanded eta1-fluorenyl-eta1-amido zirconium complex.

    PubMed

    Irwin, Levi J; Miller, Stephen A

    2005-07-20

    The structurally unique, sterically expanded eta1-fluorenyl-eta1-amido single-site precatalyst, Me2Si(eta1-N-tBu)(eta1-C29H36)ZrCl2.OEt2 (3), upon activation with methylaluminoxane (MAO), is remarkably active and constitutes the most syndioselective alpha-olefin polymerization catalyst system yet reported. 3/MAO affords as-prepared syndiotactic polypropylene with [rrrr] > 99% and unprecedented melting temperatures for the unannealed (165 degrees C) and annealed (174 degrees C) polymers. The activity of this system is 4 times that of the prototypical syndioselective catalyst Me2C(eta5-C5H4)(eta5-C13H8)ZrCl2/MAO. The high activity and syndioselectivity of 3/MAO can be extended to the production of syndiotactic poly(4-methyl-1-pentene) with a record melting temperature of 215 degrees C and [rrrr] = 97%. PMID:16011340

  7. Differential methylation of the TRPA1 promoter in pain sensitivity.

    PubMed

    Bell, J T; Loomis, A K; Butcher, L M; Gao, F; Zhang, B; Hyde, C L; Sun, J; Wu, H; Ward, K; Harris, J; Scollen, S; Davies, M N; Schalkwyk, L C; Mill, J; Williams, F M K; Li, N; Deloukas, P; Beck, S; McMahon, S B; Wang, J; John, S L; Spector, T D

    2014-01-01

    Chronic pain is a global public health problem, but the underlying molecular mechanisms are not fully understood. Here we examine genome-wide DNA methylation, first in 50 identical twins discordant for heat pain sensitivity and then in 50 further unrelated individuals. Whole-blood DNA methylation was characterized at 5.2 million loci by MeDIP sequencing and assessed longitudinally to identify differentially methylated regions associated with high or low pain sensitivity (pain DMRs). Nine meta-analysis pain DMRs show robust evidence for association (false discovery rate 5%) with the strongest signal in the pain gene TRPA1 (P=1.2 10(-13)). Several pain DMRs show longitudinal stability consistent with susceptibility effects, have similar methylation levels in the brain and altered expression in the skin. Our approach identifies epigenetic changes in both novel and established candidate genes that provide molecular insights into pain and may generalize to other complex traits. PMID:24496475

  8. Hydridomethyl iridium complex

    DOEpatents

    Bergman, Robert G.; Buchanan, J. Michael; Stryker, Jeffrey M.; Wax, Michael J.

    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.

  9. Methylation-Specific PCR Unraveled

    PubMed Central

    Derks, Sarah; Lentjes, Marjolein H. F. M.; Hellebrekers, Debby M. E. I.; de Brune, Adriaan P.; Herman, James G.; van Engeland, Manon

    2004-01-01

    Methylation?specific PCR (MSP) is a simple, quick and cost?effective method to analyze the DNA methylation status of virtually any group of CpG sites within a CpG island. The technique comprises two parts: (1) sodium bisulfite conversion of unmethylated cytosine's to uracil under conditions whereby methylated cytosines remains unchanged and (2) detection of the bisulfite induced sequence differences by PCR using specific primer sets for both unmethylated and methylated DNA. This review discusses the critical parameters of MSP and presents an overview of the available MSP variants and the (clinical) applications. PMID:15623939

  10. Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns

    PubMed Central

    2010-01-01

    Introduction Five different molecular subtypes of breast cancer have been identified through gene expression profiling. Each subtype has a characteristic expression pattern suggested to partly depend on cellular origin. We aimed to investigate whether the molecular subtypes also display distinct methylation profiles. Methods We analysed methylation status of 807 cancer-related genes in 189 fresh frozen primary breast tumours and four normal breast tissue samples using an array-based methylation assay. Results Unsupervised analysis revealed three groups of breast cancer with characteristic methylation patterns. The three groups were associated with the luminal A, luminal B and basal-like molecular subtypes of breast cancer, respectively, whereas cancers of the HER2-enriched and normal-like subtypes were distributed among the three groups. The methylation frequencies were significantly different between subtypes, with luminal B and basal-like tumours being most and least frequently methylated, respectively. Moreover, targets of the polycomb repressor complex in breast cancer and embryonic stem cells were more methylated in luminal B tumours than in other tumours. BRCA2-mutated tumours had a particularly high degree of methylation. Finally, by utilizing gene expression data, we observed that a large fraction of genes reported as having subtype-specific expression patterns might be regulated through methylation. Conclusions We have found that breast cancers of the basal-like, luminal A and luminal B molecular subtypes harbour specific methylation profiles. Our results suggest that methylation may play an important role in the development of breast cancers. PMID:20565864

  11. 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 μg/ml for ligand, Cu(II) and Ni(II) complexes, respectively. In vitro antioxidant activity of the newly synthesized compounds has also been evaluated.

  12. Managing Nematodes without Methyl Bromide

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Methyl bromide is an effective pre-plant soil fumigant used to control nematodes in many high-input, high-value production systems including vegetables, nurseries, ornamentals, tree fruits, strawberries, and grapes. Because methyl bromide has provided a reliable return on investment for nematode c...

  13. 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

  14. 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.

  15. Neural Tube Defects, Folic Acid and Methylation

    PubMed Central

    Imbard, Apolline; Benoist, Jean-Franois; 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

  16. Reversing aberrant methylation patterns in cancer.

    PubMed

    Poke, F S; Qadi, A; Holloway, A F

    2010-01-01

    Changes to the epigenetic information within a cell play a significant role in cancer development and progression. These epigenetic changes are important in establishing the aberrant gene expression patterns that are a feature of cancer cell biology. We are currently experiencing a rapid advance in our understanding of how epigenetic information is written and interpreted in the cell, and the enzymes involved in these processes have been recognised as prime targets for therapeutic intervention. Reagents that target these enzymes have the potential to inhibit or reverse epigenetic changes in cancer cells. Evidence suggests that the aberrant regulation of two gene silencing pathways; involving DNA methylation and histone methylation, play an important role in cancer development. Considerable effort is being exerted in the development of inhibitors of these pathways. However, complex functional interactions exist between the DNA and histone methylation pathways, and these interactions will need to be considered in the design of inhibitory molecules. This review details current research into agents developed as inhibitors of these epigenetic pathways, focusing on the types of epigenetic modifications being targeted, interactions between these modifications and the use of these inhibitory agents in cancer treatment. PMID:20166939

  17. Synthesis and structural characterization of molybdenum(VI) and iron(II) coordination compounds with S-alkyl-N-methyl-S-(2-pyridyl)sulfoximines and catalytic epoxidation activity of the molybdenum complexes.

    PubMed

    Brussaard, Yvonne; Olbrich, Falk; Schaumann, Ernst

    2013-11-18

    Coordination compounds oxido(diperoxido)(S-butyl-N-methyl-S-(2-pyridyl)sulfoximine)molybdenum(VI), [MoO(O2)2{SO(NMe)(n)Bu(NC5H4)}] (5c), and bis{(dichlorido)(N,S-dimethyl-2-pyridylsulfoximine)iron(II)}, tetrahydrofuran solvate (1:1) (6), [FeCl2{SO(NMe)Me(NC5H4)}]2THF are prepared from the free ligand 4 and molybdenum(VI) oxidediperoxide(dihydrate) and iron dichloride, respectively. The crystal structures reveal a trigonal bipyramid with the pyridine ring and the single oxygen on molybdenum in a trans arrangement for 5c and a planar ?(2)-Cl2Fe2 ring with trans-oriented exocyclic Cl atoms for 6 whereas the structures of the N,N-dicoordinated ligands are only little effected by the metals. Coordination compounds (5) efficiently catalyze the epoxidation of cyclooctene or of monosubstituted alkenes by tert-butyl hydroperoxide. PMID:24180337

  18. 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 E7Dnmt1 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

  19. 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.

  20. Radical SAM-Mediated Methylation of Ribosomal RNA.

    PubMed

    Stojković, Vanja; Fujimori, Danica Galonić

    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

  1. New [LNiII2]+ complexes incorporating 2-formyl or 2,6-diformyl-4-methyl phenol as inhibitors of the hydrolysis of the ligand L3-: Ni...Ni ferromagnetic coupling and S=2 ground states.

    PubMed

    Paital, Alok Ranjan; Wong, Wing Tak; Arom, Guillem; Ray, Debashis

    2007-07-01

    Reaction of the dinucleating ligand H3L (2-(2'-hydroxyphenyl)-1,3-bis[4-(2-hydroxyphenyl)-3-azabut-3-enyl]-1,3-imidazolidine) with Ni(NO3)(2).6H2O produces the dimer of monomers [Ni(HL1)]2(NO3)(2).4H2O (1.4H2O) following the hydrolysis of H3L. If the reaction occurs in the presence of 2-formylphenol (Hfp) or 2,6-diformyl-4-methylphenol (Hdfp), this hydrolysis is prevented by incorporation of these co-ligands into the structure and stabilization of the new complexes [Ni2L(fp)(H2O)].3H2O (2.3H2O) and [Ni2L(dfp)].4.5H2O (3.4.5H2O), respectively. Complexes 2 and 3 may be considered to be structural models of the active site of urease, where coordination of the carbonyl ligand mimics binding of urea. In complex 2, coordination of terminal water reproduces the binding of this substrate of the enzyme to the active site. In both dinuclear complexes, the NiII ions are coupled ferromagnetically to yield S=2 ground states, whereas complex 1 exhibits weak intradimer antiferromagnetic exchange through hydrogen bonds. The magnetic data can be modeled by using the Van Vleck equation, incorporating intermolecular interactions, or by diagonalization of a spin Hamiltonian that includes single-ion anisotropy. PMID:17569529

  2. 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.

  3. 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

  4. 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-HCl, 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

  5. Differentially Methylated Regions of Imprinted Genes in Prenatal, Perinatal and Postnatal Human Tissues

    PubMed Central

    Murphy, Susan K.; Huang, Zhiqing; Hoyo, Cathrine

    2012-01-01

    Epigenetic plasticity in relation to in utero exposures may mechanistically explain observed differences in the likelihood of developing common complex diseases including hypertension, diabetes and cardiovascular disease through the cumulative effects of subtle alterations in gene expression. Imprinted genes are essential mediators of growth and development and are characterized by differentially methylated regulatory regions (DMRs) that carry parental allele-specific methylation profiles. This theoretical 50% level of methylation provides a baseline from which endogenously- or exogenously-induced deviations in methylation can be detected. We quantified DNA methylation at imprinted gene DMRs in a large panel of human conceptal tissues, in matched buccal cell specimens collected at birth and at one year of age, and in the major cell fractions of umbilical cord blood to assess the stability of methylation at these regions. DNA methylation was measured using validated pyrosequencing assays at seven DMRs regulating the IGF2/H19, DLK1/MEG3, MEST, NNAT and SGCE/PEG10 imprinted domains. DMR methylation did not significantly differ for the H19, MEST and SGCE/PEG10 DMRs across all conceptal tissues analyzed (ANOVA p>0.10). Methylation differences at several DMRs were observed in tissues from brain (IGF2 and MEG3-IG DMRs), liver (IGF2 and MEG3 DMRs) and placenta (both DLK1/MEG3 DMRs and NNAT DMR). In most infants, methylation profiles in buccal cells at birth and at one year of age were comparable, as was methylation in the major cell fractions of umbilical cord blood. Several infants showed temporal deviations in methylation at multiple DMRs. Similarity of inter-individual and intra-individual methylation at some, but not all of the DMRs analyzed supports the possibility that methylation of these regions can serve as useful biosensors of exposure. PMID:22808284

  6. Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease

    PubMed Central

    Cloos, Paul A.C.; Christensen, Jesper; Agger, Karl; Helin, Kristian

    2008-01-01

    The enzymes catalyzing lysine and arginine methylation of histones are essential for maintaining transcriptional programs and determining cell fate and identity. Until recently, histone methylation was regarded irreversible. However, within the last few years, several families of histone demethylases erasing methyl marks associated with gene repression or activation have been identified, underscoring the plasticity and dynamic nature of histone methylation. Recent discoveries have revealed that histone demethylases take part in large multiprotein complexes synergizing with histone deacetylases, histone methyltransferases, and nuclear receptors to control developmental and transcriptional programs. Here we review the emerging biochemical and biological functions of the histone demethylases and discuss their potential involvement in human diseases, including cancer. PMID:18451103

  7. 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

  8. COMPARATIVE IN VITRO METHYLATION OF TRIVALENT AND PENTAVALENT ARSENIC SPECIES

    EPA Science Inventory

    The time course and extent of methylation of 1 uM arsenite (iAsIII), arsenate (iAsV), methylarsenite (MeAsV), methylarsenate (MeAsV) and MeAsIII - diglutathione complex (MAsIII(GS)2) were examined in an in vitro assay system that contained rat liver cytosol. recursor arsenicals a...

  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

    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.

  10. 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

  11. Novel pattern of DNA methylation in Neurospora crassa transgenic for the foreign gene hph.

    PubMed Central

    Codn, A C; Lee, Y S; Russo, V E

    1997-01-01

    It has previously been reported that multiple copies of the hph gene integrated into the genome of Neurospora crassa are methylated at Hpa II sites (CCGG) during the vegetative life cycle of the fungus, while hph genes integrated as single copies are not methylated. Furthermore, methylation is correlated with silencing of the gene. We report here the methylation state of cytosine residues of the major part of the promoter region of the hph gene integrated into the genome of the multiple copy strain HTA5.7 during the vegetative stage of the life cycle. Cytosine methylation is sequence dependent, but the sequence specificity is complex and is different from the sequence specificity known for mammals and plants (CpG and CpNpG). The pattern of DNA methylation reported here is very different from that measured after meiosis in Neurospora or in Ascobulus . After the sexual cycle in those two fungi all the cytosines of multiple stretches of DNA are heavily methylated. This indicates that the still unknown methyltransferase in Neurospora has a different specificity in the sexual and the vegetative stages of the life cycle or that there are different methyltransferases. The pattern of methylation reported here is also different from the pattern of cytosine methylation of transgenes of Petunia , the only pattern published until now in plants that has DNA methylation at cytosines which are not in the canonical sequences CpG and CpNpG. PMID:9171093

  12. Methylation of the phosphoryl group by methyl iodide

    SciTech Connect

    Koidan, G.N.; Marchenko, A.P.; Pinchuk, A.M.

    1986-01-10

    The authors have established that hexaalkyltriamidophosphazo groups are unusually strong electron-donor substituents at P /SUP III/ , causing the extremely high basicity of such compounds. This paper performs methylation of tris (tris (N,N-dimethylamido) phosphazo) phosphate and tris (tris (N,N-dimethylamido) phosphazo) methoxyphosphonium iodide (I) using methyl oxide. The NMR spectra were recorded on a Bruker WP-20 spectrometer, and hexamethyldisiloxane and 85% H/sub 3/PO/sub 4/ were used as the standard.

  13. DNA methylation analyses of urothelial carcinoma reveal distinct epigenetic subtypes and an association between gene copy number and methylation status.

    PubMed

    Lauss, Martin; Aine, Mattias; Sjdahl, Gottfrid; Veerla, Srinivas; Patschan, Oliver; Gudjonsson, Sigurdur; Chebil, Gunilla; Lvgren, Kristina; Fern, Mrten; Mnsson, Wiking; Liedberg, Fredrik; Ringnr, Markus; Lindgren, David; Hglund, Mattias

    2012-08-01

    We assessed DNA methylation and copy number status of 27,000 CpGs in 149 urothelial carcinomas and integrated the findings with gene expression and mutation data. Methylation was associated with gene expression for 1,332 CpGs, of which 26% showed positive correlation with expression, i.e., high methylation and high gene expression levels. These positively correlated CpGs were part of specific transcription factor binding sites, such as sites for MYC and CREBP1, or located in gene bodies. Furthermore, we found genes with copy number gains, low expression and high methylation levels, revealing an association between methylation and copy number levels. This phenomenon was typically observed for developmental genes, such as HOX genes, and tumor suppressor genes. In contrast, we also identified genes with copy number gains, high expression and low methylation levels. This was for instance observed for some keratin genes. Tumor cases could be grouped into four subgroups, termed epitypes, by their DNA methylation profiles. One epitype was influenced by the presence of infiltrating immune cells, two epitypes were mainly composed of non-muscle invasive tumors, and the remaining epitype of muscle invasive tumors. The polycomb complex protein EZH2 that blocks differentiation in embryonic stem cells showed increased expression both at the mRNA and protein levels in the muscle invasive epitype, together with methylation of polycomb target genes and HOX genes. Our data highlights HOX gene silencing and EZH2 expression as mechanisms to promote a more undifferentiated and aggressive state in UC. PMID:22705924

  14. 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.

  15. Regulation of histone methylation by noncoding RNAs.

    PubMed

    Joh, Richard I; Palmieri, Christina M; Hill, Ian T; Motamedi, Mo

    2014-12-01

    Cells can adapt to their environment and develop distinct identities by rewiring their transcriptional networks to regulate the output of key biological pathways without concomitant mutations to the underlying genes. These alterations, called epigenetic changes, persist stably through mitotic or, in some instances, meiotic cell divisions. In eukaryotes, heritable changes to chromatin structure are a prominent, but not exclusive, mechanism by which epigenetic changes are mediated. These changes are initiated by sequence-specific events, which trigger a cascade of molecular interactions resulting in feedback mechanisms, alterations in chromatin structure, histone posttranslational modifications (PTMs), and ultimately establishment of distinct transcriptional states. In recent years, advances in next generation sequencing have led to the discovery of several novel classes of noncoding RNAs (ncRNAs). In addition to their well-established cytoplasmic roles in posttranscriptional regulation of gene expression, ncRNAs have emerged as key regulators of epigenetic changes via chromatin-dependent mechanisms in organisms ranging from yeast to man. They function by affecting chromatin structure, histone PTMs, and the recruitment of transcriptional activating or repressing complexes. Among histone PTMs, lysine methylation serves as the binding substrate for the recruitment of key protein complexes involved in the regulation of genome architecture, stability, and gene expression. In this review, we will outline the known mechanisms by which ncRNAs of different origins regulate histone methylation, and in doing so contribute to a variety of genome regulatory functions in eukaryotes. PMID:24954181

  16. Regulation of histone methylation by noncoding RNAs

    PubMed Central

    Joh, Richard I.; Palmieri, Christina M.; Hill, Ian T; Motamedi, Mo

    2014-01-01

    Cells can adapt to their environment and develop distinct identities by rewiring their transcriptional networks to regulate the output of key biological pathways without concomitant mutations to the underlying genes. These alterations, called epigenetic changes, persist stably through mitotic or, in some instances, meiotic cell divisions. In eukaryotes, heritable changes to chromatin structure are a prominent, but not exclusive, mechanism by which epigenetic changes are mediated. These changes are initiated by sequence-specific events, which trigger a cascade of molecular interactions resulting in feedback mechanisms, alterations in chromatin structure, histone posttranslational modifications (PTMs), and ultimately establishment of distinct transcriptional states. In recent years, advances in next generation sequencing have led to the discovery of several novel classes of noncoding RNAs (ncRNAs). In addition to their well-established cytoplasmic roles in posttranscriptional regulation of gene expression, ncRNAs have emerged as key regulators of epigenetic changes via chromatin-dependent mechanisms in organisms ranging from yeast to man. They function by affecting chromatin structure, histone PTMs, and the recruitment of transcriptional activating or repressing complexes. Among histone PTMs, lysine methylation serves as the binding substrate for the recruitment of key protein complexes involved in regulation of genome architecture, stability, and gene expression. In this review, we will outline the known mechanisms by which ncRNAs of different origins regulate histone methylation, and in doing so contribute to a variety of genome regulatory functions in eukaryotes. PMID:24954181

  17. 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, α = 90°, β = 108.213(2)°, γ = 90° and Z = 4 for 1, a = 9.5019(3)Å, b = 11.3 801(3)Å, c = 25.3168(14)Å, α = 90°, β = 100.583(4)°, γ = 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.

  18. Methyl tunnelling in solid diacetyl

    NASA Astrophysics Data System (ADS)

    Alsanoosi, A. M.; Horsewill, A. J.

    1992-02-01

    The techniques of dipole-dipole driven low-field NMR spectroscopy have been employed to measure the tunnelling frequency, ν t, of methyl groups in solid diacetyl (2,3-butanedione) at 4 K. The value of ν t is 74±1 kHz from which the height of the barrier to reorientation (assumed to have three-fold symmetry) is deduced to be 1845 K (15.3 kJ mol -1). The intermolecular contribution to the barrier has been calculated by evaluating the lattice sum of pairwise interatomic potentials as a function of methyl group orientation. This analysis reveals that the predominant contribution to the barrier arises from the methyl group of a neighbouring molecule. Temperature dependence measurements of the spin-lattice relaxation time have also been employed to study the dynamics of methyl reorientation in diacetyl and in the related molecule acetonylacetone (2,5-hexanedione).

  19. Whole-Genome DNA Methylation Profile of the Jewel Wasp (Nasonia vitripennis)

    PubMed Central

    Beeler, Suzannah M.; Wong, Garrett T.; Zheng, Jennifer M.; Bush, Eliot C.; Remnant, Emily J.; Oldroyd, Benjamin P.; Drewell, Robert A.

    2014-01-01

    The epigenetic mark of DNA methylation, the addition of a methyl (CH3) group to a cytosine residue, has been extensively studied in many mammalian genomes and, although it is commonly found at the promoter regions of genes, it is also involved in a number of different biological functions. In other complex animals, such as social insects, DNA methylation has been determined to be involved in caste differentiation and to occur primarily in gene bodies. The role of methylation in nonsocial insects, however, has not yet been explored thoroughly. Here, we present the whole-genome DNA methylation profile of the nonsocial hymenopteran, the jewel wasp (Nasonia vitripennis). From high-throughput sequencing of bisulfite-converted gDNA extracted from male Nasonia thoraces, we were able to determine which cytosine residues are methylated in the entire genome. We found that an overwhelming majority of methylated sites (99.7%) occur at cytosines followed by a guanine in the 3? direction (CpG sites). Additionally, we found that a majority of methylation in Nasonia occurs within exonic regions of the genome (more than 62%). Overall, methylation is sparse in Nasonia, occurring only at 0.18% of all sites and at 0.63% of CpGs. Our analysis of the Nasonia methylome revealed that in contrast to the methylation profile typically seen in mammals, methylation is sparse and is constrained primarily to exons. This methylation profile is more similar to that of the social hymenopteran species, the honey bee (Apis mellifera). In presenting the Nasonia methylome, we hope to promote future investigation of the regulatory function of DNA methylation in both social and nonsocial hymenoptera. PMID:24381191

  20. DNA methylation analysis in human cancer

    PubMed Central

    O'Sullivan, Eileen; Goggins, Michael

    2014-01-01

    Chapter summary The functional impact of aberrant DNA methylation and the widespread alterations in DNA methylation in cancer development has led to the development of a variety of methods to characterize the DNA methylation patterns. This chapter will critique and describe the major approaches to analyzing DNA methylation. PMID:23359152

  1. Towards understanding the breast cancer epigenome: a comparison of genome-wide DNA methylation and gene expression data.

    PubMed

    Singhal, Sandeep K; Usmani, Nawaid; Michiels, Stefan; Metzger-Filho, Otto; Saini, Kamal S; Kovalchuk, Olga; Parliament, Matthew

    2016-01-19

    Until recently, an elevated disease risk has been ascribed to a genetic predisposition, however, exciting progress over the past years has discovered alternate elements of inheritance that involve epigenetic regulation. Epigenetic changes are heritably stable alterations that include DNA methylation, histone modifications and RNA-mediated silencing. Aberrant DNA methylation is a common molecular basis for a number of important human diseases, including breast cancer. Changes in DNA methylation profoundly affect global gene expression patterns. What is emerging is a more dynamic and complex association between DNA methylation and gene expression than previously believed. Although many tools have already been developed for analyzing genome-wide gene expression data, tools for analyzing genome-wide DNA methylation have not yet reached the same level of refinement. Here we provide an in-depth analysis of DNA methylation in parallel with gene expression data characteristics and describe the particularities of low-level and high-level analyses of DNA methylation data. Low-level analysis refers to pre-processing of methylation data (i.e. normalization, transformation and filtering), whereas high-level analysis is focused on illustrating the application of the widely used class comparison, class prediction and class discovery methods to DNA methylation data. Furthermore, we investigate the influence of DNA methylation on gene expression by measuring the correlation between the degree of CpG methylation and the level of expression and to explore the pattern of methylation as a function of the promoter region. PMID:26657508

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

    PubMed

    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

  3. 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

  4. [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

  5. The controversial denouement of vertebrate DNA methylation research.

    PubMed

    Ehrlich, M

    2005-05-01

    The study of the biological role of DNA methylation in vertebrates has involved considerable controversy. Research in this area has proceeded well despite the complexity of the subject and the difficulties in establishing biological roles, some of which are summarized in this review. Now there is justifiably much more interest in DNA methylation than previously, and many more laboratories are engaged in this research. The results of numerous studies indicate that some tissue-specific differences in vertebrate DNA methylation help maintain patterns of gene expression or are involved in fine-tuning or establishing expression patterns. Therefore, vertebrate DNA methylation cannot just be assigned a role in silencing transposable elements and foreign DNA sequences, as has been suggested. DNA methylation is clearly implicated in modulating X chromosome inactivation and in establishing genetic imprinting. Also, hypermethylation of CpG-rich promoters of tumor suppressor genes in cancer has a critical role in downregulating expression of these genes and thus participating in carcinogenesis. The complex nature of DNA methylation patterns extends to carcinogenesis because global DNA hypomethylation is found in the same cancers displaying hypermethylation elsewhere in the genome. A wide variety of cancers display both DNA hypomethylation and hypermethylation, and either of these types of changes can be significantly associated with tumor progression. These findings and the independence of cancer-linked DNA hypomethylation from cancer-linked hypermethylation strongly implicate DNA hypomethylation, as well as hypermethylation, in promoting carcinogenesis. Furthermore, various DNA demethylation methodologies have been shown to increase the formation of certain types of cancers in animals, and paradoxically, DNA hypermethylation can cause carcinogenesis in other model systems. Therefore, there is a need for caution in the current use of demethylating agents as anti-cancer drugs. Nonetheless, DNA demethylation therapy clearly may be very useful in cases where better alternatives do not exist. PMID:15948710

  6. Comparative epigenomics: a powerful tool to understand the evolution of DNA methylation.

    PubMed

    Zhong, Xuehua

    2016-04-01

    76 I. 76 II. 77 III. 78 IV. 78 V. 79 80 References 80 SUMMARY: Understanding how developmental and functional complexity of organisms evolves is a longstanding challenge in biology. Genetic mutation has long been thought to be the cause of biological complexity. However, increasing evidence indicates that epigenetic variation provides a parallel path for the evolution of biological complexity. Cytosine DNA methylation, the addition of a chemical mark on DNA, is a conserved and essential gene regulatory mechanism. Recent studies have greatly advanced our understanding of the DNA methylation landscapes and key regulatory components across many species. In this review, I summarize recent advances in understanding DNA methylation from an evolutionary perspective. Using comparative approaches, I highlight the conservation and divergence of DNA methylation patterns and regulatory machinery in plants and other eukaryotic organisms. PMID:26137858

  7. Anticancer Activity of Methyl-Substituted Oxaliplatin Analogs†

    PubMed Central

    Jungwirth, Ute; Xanthos, Dimitris N.; Gojo, Johannes; Bytzek, Anna K.; Körner, Wilfried; Heffeter, Petra; Abramkin, Sergey A.; Jakupec, Michael A.; Hartinger, Christian G.; Windberger, Ursula; Galanski, Markus; Keppler, Bernhard K.; Berger, Walter

    2012-01-01

    Oxaliplatin is successfully used in systemic cancer therapy. However, resistance development and severe adverse effects are limiting factors for curative cancer treatment with oxaliplatin. The purpose of this study was to comparatively investigate in vitro and in vivo anticancer properties as well as the adverse effects of two methyl-substituted enantiomerically pure oxaliplatin analogs [[(1R,2R,4R)-4-methyl-1,2-cyclohexanediamine] oxalatoplatinum(II) (KP1537), and [(1R,2R,4S)-4-methyl-1,2-cyclohexanediamine]oxalatoplatinum(II) (KP1691)] and to evaluate the impact of stereoisomerism. Although the novel oxaliplatin analogs demonstrated in multiple aspects activities comparable with those of the parental compound, several key differences were discovered. The analogs were characterized by reduced vulnerability to resistance mechanisms such as p53 mutations, reduced dependence on immunogenic cell death induction, and distinctly attenuated adverse effects including weight loss and cold hyperalgesia. Stereoisomerism of the substituted methyl group had a complex and in some aspects even contradictory impact on drug accumulation and anticancer activity both in vitro and in vivo. To summarize, methyl-substituted oxaliplatin analogs harbor improved therapeutic characteristics including significantly reduced adverse effects. Hence, they might be promising metal-based anticancer drug candidates for further (pre)clinical evaluation. PMID:22331606

  8. 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

  9. INFLUENCE OF BIOLOGICAL METHYLATION ON THE BIOSYNTHESIS OF MITOMYCIN A

    PubMed Central

    Kirsch, E. J.; Korshalla, J. D.

    1964-01-01

    Kirsch, E. J. (Lederle Laboratories, Pearl River, N.Y.), and J. D. Korshalla. Influence of biological methylation on the biosynthesis of mitomycin A. J. Bacteriol. 87:247–255. 1964.—Methionine-methyl-C14 was shown to contribute radioactive carbon to the mitomycin antibiotic complex synthesized by Streptomyces verticillatus in a simple synthetic medium containing glucose and inorganic salts. The position of radioactivity in mitomycin A was determined by selective hydrolysis of the 7 and 9a methoxyl functions. Essentially all of the radioactivity incorporated was distributed evenly between these two substituent groups. Mitomycin A, synthesized by washed resting cells of S. verticillatus at the expense of internal metabolites, also incorporated methyl label. When the methionine antagonist, d,l-ethionine, was added to resting cells at a concentration causing 65% inhibition of antibiotic synthesis, incorporation of radioactive methyl groups was reduced to the same extent. Synthetic medium supplemented with d,l-ethionine supported about 90% maximal growth of the culture, but antibiotic biosynthesis was markedly inhibited. The addition of the inhibitor during the period of rapid antibiotic synthesis resulted in cessation of further increases in antibiotic titer. l-Methionine was shown to be capable of reversing ethionine inhibition; the extent of reversal was dependent on the concentration, as well as on the time of addition of amino acid. The data suggest the critical nature of a methyl transfer system in the biogenesis of biologically active mitomycins. PMID:14151041

  10. Tissue-specific dysregulation of DNA methylation in aging

    PubMed Central

    Thompson, Reid F.; Atzmon, Gil; Gheorghe, Ciprian; Liang, Hong Qian; Lowes, Christina; Greally, John M.; Barzilai, Nir

    2010-01-01

    SUMMARY The normal aging process is a complex phenomenon associated with physiological alterations in the function of cells and organs over time. Although an attractive candidate for mediating transcriptional dysregulation, the contribution of epigenetic dysregulation to these progressive changes in cellular physiology remains unclear. In this study, we employed the genome-wide HELP assay to define patterns of cytosine methylation throughout the rat genome, and the LUMA assay to measure global levels of DNA methylation in the same samples. We studied both liver and visceral adipose tissue, and demonstrated significant differences in DNA methylation with age at >5% of sites analyzed. Furthermore, we showed that epigenetic dysregulation with age is a highly tissue-dependent phenomenon. The most distinctive loci were located at intergenic sequences and conserved non-coding elements, and not at promoters nor at CG-dinucleotide dense loci. Despite this, we found that there was a subset of genes at which cytosine methylation and gene expression changes were concordant. Finally, we demonstrated that changes in methylation occur consistently near genes that are involved in metabolism and metabolic regulation, implicating their potential role in the pathogenesis of age-related diseases. We conclude that different patterns of epigenetic dysregulation occur in each tissue over time and may cause some of the physiological changes associated with normal aging. PMID:20497131

  11. PGC−1α 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 α (PGC−1α) 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−1α 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−1α 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−1α promoter methylation in different cell types from the CNS. Indeed, in mouse primary cortical neurons, microglia and astrocytes, palmitate causes PGC−1α gene promoter non-canonical cytosine methylation, reduced expression of the gene and reduced mitochondrial content. Moreover, intracerebroventricular (ICV) injection of palmitate to transgenic human α−synuclein mutant mice resulted in increased PGC−1α promoter methylation, decreased PGC−1α expression and reduced mitochondrial content in substantia nigra. Finally we provide evidence that dysregulation of ER stress and inflammatory signaling is associated with PGC−1α promoter methylation. Together, these data strengthen the connection between saturated fatty acids, neuroflammation, ER stress, epigenetic alteration and bioenergetic compromise in PD. PMID:26317511

  12. Nanopore-based assay for detection of methylation in double-stranded DNA fragments.

    PubMed

    Shim, Jiwook; Kim, Younghoon; Humphreys, Gwendolyn I; Nardulli, Ann M; Kosari, Farhad; Vasmatzis, George; Taylor, William R; Ahlquist, David A; Myong, Sua; Bashir, Rashid

    2015-01-27

    DNA methylation is an epigenetic modification of DNA in which methyl groups are added at the 5-carbon position of cytosine. Aberrant DNA methylation, which has been associated with carcinogenesis, can be assessed in various biological fluids and potentially can be used as markers for detection of cancer. Analytically sensitive and specific assays for methylation targeting low-abundance and fragmented DNA are needed for optimal clinical diagnosis and prognosis. We present a nanopore-based direct methylation detection assay that circumvents bisulfite conversion and polymerase chain reaction amplification. Building on our prior work, we used methyl-binding proteins (MBPs), which selectively label the methylated DNA. The nanopore-based assay selectively detects methylated DNA/MBP complexes through a 19 nm nanopore with significantly deeper and prolonged nanopore ionic current blocking, while unmethylated DNA molecules were not detectable due to their smaller diameter. Discrimination of hypermethylated and unmethylated DNA on 90, 60, and 30 bp DNA fragments was demonstrated using sub-10 nm nanopores. Hypermethylated DNA fragments fully bound with MBPs are differentiated from unmethylated DNA at 2.1- to 6.5-fold current blockades and 4.5- to 23.3-fold transport durations. Furthermore, these nanopore assays can detect the CpG dyad in DNA fragments and could someday profile the position of methylated CpG sites on DNA fragments. PMID:25569824

  13. 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, Sbastien 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

  14. CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize

    PubMed Central

    Gent, Jonathan I.; Ellis, Nathanael A.; Guo, Lin; Harkess, Alex E.; Yao, Yingyin; Zhang, Xiaoyu; Dawe, R. Kelly

    2013-01-01

    Small RNA-mediated regulation of chromatin structure is an important means of suppressing unwanted genetic activity in diverse plants, fungi, and animals. In plants specifically, 24-nt siRNAs direct de novo methylation to repetitive DNA, both foreign and endogenous, in a process known as RNA-directed DNA methylation (RdDM). Many components of the de novo methylation machinery have been identified recently, including multiple RNA polymerases, but specific genetic features that trigger methylation remain poorly understood. By applying whole-genome bisulfite sequencing to maize, we found that transposons close to cellular genes (particularly within 1 kb of either a gene start or end) are strongly associated with de novo methylation, as evidenced both by 24-nt siRNAs and by methylation specifically in the CHH sequence context. In addition, we found that the major classes of transposons exhibited a gradient of CHH methylation determined by proximity to genes. Our results further indicate that intergenic chromatin in maize exists in two major forms that are distinguished based on proximity to genesone form marked by dense CG and CHG methylation and lack of transcription, and one marked by CHH methylation and activity of multiple forms of RNA polymerase. The existence of the latter, which we call CHH islands, may have implications for how cellular gene expression could be coordinated with immediately adjacent transposon repression in a large genome with a complex organization of genes interspersed in a landscape of transposons. PMID:23269663

  15. 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, Sbastien 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

  16. 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 280nm to standardize the concentrations. Using model compounds, we demonstrate that the dimethylation of lysyl ?-amines does not affect the proteins' molar extinction coefficients at 280nm. 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

  17. Genome-Wide Methylated DNA Immunoprecipitation Analysis of Patients with Polycystic Ovary Syndrome

    PubMed Central

    Shen, Hao-ran; Qiu, Li-hua; Zhang, Zhi-qing; Qin, Yuan-yuan; Cao, Cong; Di, Wen

    2013-01-01

    Polycystic ovary syndrome (PCOS) is a complex, heterogeneous disorder of uncertain etiology. Recent studies suggested that insulin resistance (IR) plays an important role in the development of PCOS. In the current study, we aimed to investigate the molecular mechanism of IR in PCOS. We employed genome-wide methylated DNA immunoprecipitation (MeDIP) analysis to characterize genes that are differentially methylated in PCOS patients vs. healthy controls. Besides, we also identified the differentially methylated genes between patients with PCOS-non-insulin resistance (PCOS-NIR) and PCOS-insulin resistance (PCOS-IR). A total of 79 genes were differentially methylated between PCOS-NIR vs. PCOS-IR patients, and 40 genes were differentially methylated in PCOS patients vs. healthy controls. We analyzed these differentially methylated genes by constructing regulatory networks and protein-protein interaction (PPI) networks. Further, Gene Ontology (GO) and pathway enrichment analysis were also performed to investigate the biological functions of networks. We identified multiple categories of genes that were differentially methylated between PCOS-NIR and PCOS-IR patients, or between PCOS patients and healthy controls. Significantly, GO categories of immune response were differentially methylated in PCOS-IR vs. PCOS-NIR. Further, genes in cancer pathways were also differentially methylated in PCOS-NIR vs. PCOS-IR patients or in PCOS patients vs. healthy controls. The results of this current study will help to further understand the mechanism of PCOS. PMID:23705014

  18. Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated

    PubMed Central

    2010-01-01

    Background DNA methylation can regulate gene expression by modulating the interaction between DNA and proteins or protein complexes. Conserved consensus motifs exist across the human genome ("predicted transcription factor binding sites": "predicted TFBS") but the large majority of these are proven by chromatin immunoprecipitation and high throughput sequencing (ChIP-seq) not to be biological transcription factor binding sites ("empirical TFBS"). We hypothesize that DNA methylation at conserved consensus motifs prevents promiscuous or disorderly transcription factor binding. Results Using genome-wide methylation maps of the human heart and sperm, we found that all conserved consensus motifs as well as the subset of those that reside outside CpG islands have an aggregate profile of hyper-methylation. In contrast, empirical TFBS with conserved consensus motifs have a profile of hypo-methylation. 40% of empirical TFBS with conserved consensus motifs resided in CpG islands whereas only 7% of all conserved consensus motifs were in CpG islands. Finally we further identified a minority subset of TF whose profiles are either hypo-methylated or neutral at their respective conserved consensus motifs implicating that these TF may be responsible for establishing or maintaining an un-methylated DNA state, or whose binding is not regulated by DNA methylation. Conclusions Our analysis supports the hypothesis that at least for a subset of TF, empirical binding to conserved consensus motifs genome-wide may be controlled by DNA methylation. PMID:20875111

  19. 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

  20. Alcohol, DNA Methylation, and Cancer

    PubMed Central

    Varela-Rey, Marta; Woodhoo, Ashwin; Martinez-Chantar, Maria-Luz; Mato, Jos M.; Lu, Shelly C.

    2013-01-01

    Cancer is one of the most significant diseases associated with chronic alcohol consumption, and chronic drinking is a strong risk factor for cancer, particularly of the upper aerodigestive tract, liver, colorectum, and breast. Several factors contribute to alcohol-induced cancer development (i.e., carcinogenesis), including the actions of acetaldehyde, the first and primary metabolite of ethanol, and oxidative stress. However, increasing evidence suggests that aberrant patterns of DNA methylation, an important epigenetic mechanism of transcriptional control, also could be part of the pathogenetic mechanisms that lead to alcohol-induced cancer development. The effects of alcohol on global and local DNA methylation patterns likely are mediated by its ability to interfere with the availability of the principal biological methyl donor, S-adenosylmethionine (SAMe), as well as pathways related to it. Several mechanisms may mediate the effects of alcohol on DNA methylation, including reduced folate levels and inhibition of key enzymes in one-carbon metabolism that ultimately lead to lower SAMe levels, as well as inhibition of activity and expression of enzymes involved in DNA methylation (i.e., DNA methyltransferases). Finally, variations (i.e., polymorphisms) of several genes involved in one-carbon metabolism also modulate the risk of alcohol-associated carcinogenesis. PMID:24313162

  1. 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.

  2. N-methylation of calmodulin

    SciTech Connect

    Rowe, P.M.

    1985-01-01

    S-adenosylmethionine: calmodulin (lysine) N-methyltransferase (CLNMT, E.C. 2.1.1.60) catalyzes the post translational conversion of lysine/sub 115/ of calmodulin to trimethyllysine in most species. Two radiometric assays for CLNMT were developed; both measured incorporation of (/sup 3/H)methyl groups from S-adenosyl-(methyl-/sup 3/H)-methionine (SAM) into non-N-methylated calmodulin isolated from Dictyostelium discoideum. One assay measured incorporation of radioactivity into acid-precipitable protein; in the other assay, (/sup 3/H)methyl calmodulin was reisolated from reaction mixtures by calcium-dependent chromatography on phenyl-Sepharose. CLNMT is cytosolic. Its levels were determined in seven tissues; in five tissues, the rank order of CLNMT content was the same as the rank order of calmodulin content. From high levels to low; testis, brain, liver, heart, and skeletal muscle. In spleen and kidney, CLMNT levels were high, similar to the levels in brain and testis, while calmodulin levels were moderate, similar to those in liver. The variation in calmodulin levels from the highest to the lowest tissue was about 11-fold, while the variation in CLNMT levels was 90-fold; tissues with the lowest calmodulin and CLNMT levels also had the lowest ratios of CLNMT to calmodulin. No additional substrates for CLNMT, other than calmodulin, were detected. Calmodulins from skeletal muscle, heart and liver were found to be incompletely methylated.

  3. Negative regulation of DNA methylation in plants.

    PubMed

    Saze, Hidetoshi; Sasaki, Taku; Kakutani, Tetsuji

    2008-01-01

    Cytosine methylation of repeats and genes is important for coordination of genome stability and proper gene function. In plants, DNA methylation is regulated by DNA methyltransferases, chromatin remodeling factors and RNAi machinery. Ectopic DNA hypermethylation at genes causes transcriptional repression and silencing, and the methylation patterns often become heritable over generations. DNA methylation is antagonized by the DNA demethylation enzymes. Recently, we identified a novel jmjC-domain containing gene IBM1 (increase in bonsai methylation1) that also negatively regulates DNA methylation in Arabidopsis. The ibm1 plants show a variety of developmental phenotypes. IBM1 prevents ectopic accumulation of DNA methylation at the BNS genic region, likely through removal of heterochromatic H3K9 methylation mark. DNA and histone demethylation pathways are important for genome-wide patterning of DNA methylation and for epigenetic regulation of plant development. PMID:18567943

  4. Neurospora Importin α 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 α). 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, Franois 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. Neuropsychiatric manifestations of methyl iodide

    PubMed Central

    Parkar, Shubhangi R.; Mayanil, Tushita S.

    2012-01-01

    Methyl iodide is a monohalomethane and with a chemical formula CH3I. Acute exposures to methyl iodide have frequently occurred in the workplace. Predominantly, neuropsychiatric symptoms of acute exposure to monohalomethanes consist of headache, nausea, vomiting, drowsiness, dizziness, giddiness, diarrhea, confusion, ataxia, slurred speech, paralysis, convulsions, delirium, coma, and death. We report two cases who presented to our emergency services after accidental exposure to methyl iodide for a short duration. These case reports highlighted concurrence of frankly psychotic features and acute confusional state in workers vulnerable to industrial exposure to toxic chemicals. Understanding the mechanism of neuro-toxicity will perhaps throw some light on co-existence of both psychiatric and neurological symptoms. Awareness of these toxic effects at vulnerable work places will lead to timely and appropriate interventions. Importance of safety precautions and education of both workers and supervisors cannot be overemphasized here PMID:23112506

  7. The energetic and wave function properties of atomic, molecular, and solid state systems: Hydrogen ion and the lithium, neon, and phosphorus atoms; Boron trifluoride-ammonia molecular complex and methyl derivatives; Vanadium, chromium, and manganese ions and neutral manganese transition metal impurities in silicon

    NASA Astrophysics Data System (ADS)

    Pink, Roger H.

    The variational Hartree-Fock-Roothaan (HF) method with correlation corrections introduced through Many Body Perturbation Theory (MBPT) and the variational Density Functional Theory (DFT) have been investigated for atomic systems to provide insights into the strengths and weaknesses of each variational approach to solving the multicenter many-electron Hamiltonian. The HF+MBPT method, having been found to be more reliable and physically relevant from the atomic investigations, is used to investigate the electronic structures and associated properties of the BF3?NH3 molecular complex, and through cluster methods, the most likely locations of the transitional metal impurities V2+, Cr+, Mn2+ and Mn 0 in Silicon. Atomic systems are ideal for studying the effectiveness of different modern variational techniques such as HF+MBPT and DFT because of the depth of earlier investigations by rigorous techniques such as the Linked Cluster Many Body Perturbation Theory (LCMBPT). An in-depth comparison of the calculated energetic and magnetic hyperfine properties of carefully selected atomic systems with earlier calculated LCMBPT results and experiment will be presented. It will be shown that through varying the types of gaussians included in the basis sets used for these variational calculations one can illustrate the inherent assumptions and difficulties of the respective theories. These results coupled with a fundamental understanding of the respective theories leads to the conclusion that for a detailed quantitative investigation the HF+MBPT method is more physically intuitive and accurate, though not without its own deficiencies that should be addressed in the future. The BF3?NH3 molecular complex, along with its methyl derivatives BF3?NHx(CH3) 3-x (x=0,1,2) is investigated and relative covalency and instantaneous van der Waals contributions to the complexation bond are presented. The accuracy of the calculated results are tested by comparison of the calculated 19F* nuclear quadrupole interaction (NQI) coupling constants and asymmetry parameters with experiment. The complexation bonds are shown to have increasing van der Waals contributions with the addition of methyl groups to the ammonia. Finally investigations into the possible locations of the transition metal impurities V2+, Cr+, Mn2+, and Mn0 in a silicon lattice will be presented. Binding energies, geometry of the potential energy surface, and magnetic hyperfine calculations, as well as probability of formation will all be considered while differentiating between the possible Hexagonal Interstitial (Hi), Tetrahedral Interstitial (Ti), and Substitutional (S) locations in the silicon lattice. The Ti site will be shown to be the most likely location in the silicon lattice for all of the transition metal impurities investigated. The Substitutional site will be shown to be a stable location if a pre-existing vacancy exists in the silicon lattice.

  8. 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.

  9. Methyl-beta-cyclodextrins: the role of number and types of substituents in solubilizing power.

    PubMed

    Fenyvesi, va; Szemn, Julianna; Csabai, Katalin; Malanga, Milo; Szente, Lajos

    2014-05-01

    Methylated cyclodextrins (CDs) are effective solubilizers of poorly soluble organic compounds. In this work, we compared various methylated ?-CDs concerning their structure characterized by nuclear magnetic resonance spectroscopy, composition analyzed by HPLC and solubilizing capability by using model compounds such as cholesterol, fatty acids, furosemide, tamoxifen, and amiodarone. All the commercially available methylated ?-CDs are mixtures of various isomers and homologues except trimethyl ?-CD. The effects of the degree of methylation, the composition, as well as the influence of further derivatization with ionic groups were studied. The number of methyl groups in a CD ring should be around 14 to get the highest solubility for the included guest molecules. Although the distribution of isomers and related compounds has hardly any effect at constant degree of substitution, the introduction of amino and succinyl moieties on the CD ring adds ionic interactions to the hydrophobic interactions of the inclusion complex formation, which might result in synergic effect in solubilization. PMID:24590624

  10. 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

  11. The p120 catenin partner Kaiso is a DNA methylation-dependent transcriptional repressor

    PubMed Central

    Prokhortchouk, Anna; Hendrich, Brian; Jrgensen, Helle; Ruzov, Alexei; Wilm, Matthias; Georgiev, Georgii; Bird, Adrian; Prokhortchouk, Egor

    2001-01-01

    We describe a novel mammalian DNA binding activity that requires at least two symmetrically methylated CpG dinucleotides in its recognition sequence, preferably within the sequence 5?CGCG. A key component of the activity is Kaiso, a protein with POZ and zinc-finger domains that is known to associate with p120 catenin. We find that Kaiso behaves as a methylation-dependent transcriptional repressor in transient transfection assays. Kaiso is a constituent of one of two methylCpG binding complexes originally designated as MeCP1. The data suggest that zinc-finger motifs are responsible for DNA binding, and may therefore target repression to specific methylated regions of the genome. As Kaiso associates with p120 catenin, Kaiso may link events at the cell surface with DNA methylation-dependent gene silencing. PMID:11445535

  12. 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…

  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. 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...

  15. DNA Methylation of Cancer Genome

    PubMed Central

    Cheung, Hoi-Hung; Lee, Tin-Lap; Rennert, Owen M.; Chan, Wai-Yee

    2010-01-01

    DNA methylation plays an important role in regulating normal development and carcinogenesis. Current understanding of the biological roles of DNA methylation is limited to its role in the regulation of gene transcription, genomic imprinting, genomic stability, and X chromosome inactivation. In the past 2 decades, a large number of changes have been identified in cancer epigenomes when compared with normals. These alterations fall into two main categories, namely, hypermethylation of tumor suppressor genes and hypomethylation of oncogenes or heterochromatin, respectively. Aberrant methylation of genes controlling the cell cycle, proliferation, apoptosis, metastasis, drug resistance, and intracellular signaling has been identified in multiple cancer types. Recent advancements in whole-genome analysis of methylome have yielded numerous differentially methylated regions, the functions of which are largely unknown. With the development of high resolution tiling microarrays and high throughput DNA sequencing, more cancer methylomes will be profiled, facilitating the identification of new candidate genes or ncRNAs that are related to oncogenesis, new prognostic markers, and the discovery of new target genes for cancer therapy. PMID:19960550

  16. 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

  17. 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

  18. 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

  19. 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....

  20. 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.

  1. 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

  2. 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...

  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. 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,...

  5. Genome-wide DNA methylation profiling of non-small cell lung carcinomas

    PubMed Central

    2012-01-01

    Background Non-small cell lung carcinoma (NSCLC) is a complex malignancy that owing to its heterogeneity and poor prognosis poses many challenges to diagnosis, prognosis and patient treatment. DNA methylation is an important mechanism of epigenetic regulation involved in normal development and cancer. It is a very stable and specific modification and therefore in principle a very suitable marker for epigenetic phenotyping of tumors. Here we present a genome-wide DNA methylation analysis of NSCLC samples and paired lung tissues, where we combine MethylCap and next generation sequencing (MethylCap-seq) to provide comprehensive DNA methylation maps of the tumor and paired lung samples. The MethylCap-seq data were validated by bisulfite sequencing and methyl-specific polymerase chain reaction of selected regions. Results Analysis of the MethylCap-seq data revealed a strong positive correlation between replicate experiments and between paired tumor/lung samples. We identified 57 differentially methylated regions (DMRs) present in all NSCLC tumors analyzed by MethylCap-seq. While hypomethylated DMRs did not correlate to any particular functional category of genes, the hypermethylated DMRs were strongly associated with genes encoding transcriptional regulators. Furthermore, subtelomeric regions and satellite repeats were hypomethylated in the NSCLC samples. We also identified DMRs that were specific to two of the major subtypes of NSCLC, adenocarcinomas and squamous cell carcinomas. Conclusions Collectively, we provide a resource containing genome-wide DNA methylation maps of NSCLC and their paired lung tissues, and comprehensive lists of known and novel DMRs and associated genes in NSCLC. PMID:22726460

  6. 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.; Rltgen, 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

  7. 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.

  8. Pillar[6]arene Containing Multilayer Films: Reversible Uptake and Release of Guest Molecules with Methyl Viologen Moieties.

    PubMed

    Yuan, Bin; Xu, Jiang-Fei; Sun, Cai-Li; Nicolas, Henning; Schönhoff, Monika; Yang, Qing-Zheng; Zhang, Xi

    2016-02-17

    Pillar[6]arene-containing multilayer films have been fabricated by alternating deposition of a stoichiometric complex consisting of both pillar[6]arene and methyl viologen with a photoreactive polyelectrolyte, diazoresin (DAR). After photoinduced cross-linking of the multilayer films, the guest molecule, methyl viologen, can be removed. Then, multilayer films with artificial binding sites are fabricated. The films show good properties for molecular uptake and release as well as selectivity for molecules with methyl viologen moieties. It is anticipated that this kind of multilayer films have future applications in the fields of enrichment of molecular dyes and purification of methyl viologen-polluted water. PMID:26465379

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. Crystal structure of tris(dimethylamido-?N)bis(dimethylamine-?N)zirconium(IV) iodide

    PubMed Central

    Clark, Wesley D.; Akurathi, Gopalakrishna; Valle, Henry U.; Hollis, T. Keith

    2016-01-01

    Zirconium amides have become increasingly popular and useful due to their widespread use as precursors to other zirconium complexes and their use in the production of solid oxide fuel cells (SOFCs). Herein we report the molecular structure of tris(dimethylamido)bis(dimethylamine)zirconium(IV) iodide, [Zr(C2H6N)3(C2H7N)2]I. The bond lengths and bond angles are consistent with a slightly distorted trigonalbipyramidal coordination geometry around the metal atom. N?I contacts of 3.6153?(15) and 3.5922?(14)? are consistent with the presence of NH?I interactions. These NH?I interactions link the complex cations and iodide anions into extended chains that propagate parallel to the a axis. PMID:26870590

  15. 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

  16. Selenium reduces the retention of methyl mercury in the brown shrimp Crangon crangon.

    PubMed

    Bjerregaard, Poul; Christensen, Alan

    2012-06-01

    Methyl mercury accumulated at the top of aquatic food chains constitutes a toxicological risk to humans and other top predators. Because the methyl mercury enters the aquatic food chains at the lower trophic levels, uptake and elimination processes at these levels affect the methyl mercury content at the higher levels. Selenium modulates the biokinetics of mercury in aquatic organisms in fairly complex ways, increasing mercury retention in some aquatic mammals, but decreasing methyl mercury retention in fish. However, it is not known if selenium modulates methyl mercury accumulation at lower trophic levels in aquatic food chains. Here, we show that selenium administered via the food augments the elimination of methyl mercury from marine shrimp and that the effect is dose-dependent, demonstrable down to natural selenium concentrations in aquatic food items. Selenite, seleno-cystine, and seleno-methionine exert this effect but selenate does not. Our results suggest that the selenium naturally present at the lower trophic levels in marine food chains may play an essential role as a modifier of methyl mercury accumulation at these levels, thereby potentially also affecting biomagnification of methyl mercury toward the higher trophic levels in the aquatic food chains. PMID:22550937

  17. 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.

  18. 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...

  19. Coordination Chemistry of N-Alkylbenzamide-2,3-dithiolates as an Approach to Poly(dithiolate) Ligands: 1,4-Bis[(2,3-dimercaptobenzamido)methyl]benzene and Its Chelate Complex with the (C(5)H(5))Ti Fragment.

    PubMed

    Seidel, Wolfram W.; Hahn, F. Ekkehardt; Lgger, Thomas

    1998-12-28

    The bidentate dithiolate ligands N,N-diethyl-2,3-dimercaptobenzamide (H(2)-1), bis(N,N-diethyl-2,3-dimercaptoterephthalamide (H(2)-2), and 1,4-bis(hydroxymethyl)-2,3-dimercaptobenzene (H(4)-3) were synthesized from 2,3-dimercaptobenzoic acid or 2,3-dimercaptoterephthalic acid. The air-sensitive ligands form metallocene complexes of the type [(eta(5)-C(5)H(5))(2)Ti(1)] (13), [(eta(5)-C(5)H(5))(2)Mo(1)] (15), [(eta(5)-C(5)H(5))(2)Ti(3)] (16), and [(eta(5)-C(5)H(5))(2)Ti(2)] (17). Complexes 15 and 16 were characterized by X-ray diffraction. Selected crystallographic details for 15 are as follows: formula C(21)H(23)MoNOS(2); M = 465.49; Pbca; a = 12.536(3), b = 14.313(3), c = 22.463(3) ; V = 4031(2) (3); Z = 8; R = 3.56 and R(w) = 4.49 for 2111 structure factors (F(o)(2) >/= 3sigma(F(o)(2))) and 254 refined parameters. The molybdenum complex 15 shows an almost planar Mo(&mgr;-S)(2)C(2) chelate ring. Selected crystallographic details for 16 are as follows: formula C(18)H(18)O(2)S(2)Ti; M = 378.35; P&onemacr;; a = 10.1778(11), b = 11.5806(14), c = 22.967(3) ; alpha = 96.42(1), beta = 101.74(1), gamma = 108.82(1) degrees; V = 2462.3(5) (3); Z = 6; R = 4.79 and R(w) = 13.27 for 5426 structure factors (I >/= 2sigma(I)) and 766 refined parameters. All titanocene derivatives assume the envelope conformation. The free activation energy for the flip around the S-S axis was determined for 13 to be 69 kJ/mol. The bis(dithiolate) ligand 1,4-bis[(2,3-dimercaptobenzamido)methyl]benzene (H(4)-4) was prepared from 2,3-dimercaptobenzoic acid and converted into the dinuclear air-stable titanocene complex [{(eta(5)-C(5)H(5))(2)Ti}(2)(4)] (19). Complex 19 reacts with HCl/CHCl(3) with liberation of free H(4)-4 while reaction with NMe(4)Cl results in an intramolecular dithiolate shift under formal liberation of [(C(5)H(5))(3)TiCl] and formation of the square-pyramidal chelate complex (NMe(4))[(eta(5)-C(5)H(5))Ti(4)], (NMe(4))[20]. Crystallographic details for (NMe(4))[20].CH(2)Cl(2) are as follows: formula C(32)H(35)Cl(2)N(3)O(2)S(4)Ti; M = 740.67; P&onemacr;; a = 11.579(4), b = 12.210(4), c = 14.016(4) ; alpha = 112.28(2), beta = 94.46(3), gamma = 104.22(3) degrees; V = 1744.9(10) (3); Z = 2; R = 5.35 and R(w) = 12.84 for 2870 structure factors (I >/= 2sigma(I)) and 397 refined parameters. The chelate rings in [20](-) assume an endo/exo conformation. PMID:11670790

  20. 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, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 24 2011-07-01 2011-07-01 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...

  1. 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...

  2. 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.

  3. Folate deficiency affects histone methylation.

    PubMed

    Garcia, Benjamin A; Luka, Zigmund; Loukachevitch, Lioudmila V; Bhanu, Natarajan V; Wagner, Conrad

    2016-03-01

    Formaldehyde is extremely toxic reacting with proteins to crosslinks peptide chains. Formaldehyde is a metabolic product in many enzymatic reactions and the question of how these enzymes are protected from the formaldehyde that is generated has largely remained unanswered. Early experiments from our laboratory showed that two liver mitochondrial enzymes, dimethylglycine dehydrogenase (DMGDH) and sarcosine dehydrogenase (SDH) catalyze oxidative demethylation reactions (sarcosine is a common name for monomethylglycine). The enzymatic products of these enzymes were the demethylated substrates and formaldehyde, produced from the removed methyl group. Both DMGDH and SDH contain FAD and both have tightly bound tetrahydrofolate (THF), a folate coenzyme. THF binds reversibly with formaldehyde to form 5,10-methylene-THF. At that time we showed that purified DMGDH, with tightly bound THF, reacted with formaldehyde generated during the reaction to form 5,10-methylene-THF. This effectively scavenged the formaldehyde to protect the enzyme. Recently, post-translational modifications on histone tails have been shown to be responsible for epigenetic regulation of gene expression. One of these modifications is methylation of lysine residues. The first enzyme discovered to accomplish demethylation of these modified histones was histone lysine demethylase (LSD1). LSD1 specifically removes methyl groups from di- and mono-methylated lysines at position 4 of histone 3. This enzyme contained tightly bound FAD and the products of the reaction were the demethylated lysine residue and formaldehyde. The mechanism of LSD1 demethylation is analogous to the mechanism previously postulated for DMGDH, i.e. oxidation of the N-methyl bond to the methylene imine followed by hydrolysis to generate formaldehyde. This suggested that THF might also be involved in the LSD1 reaction to scavenge the formaldehyde produced. Our hypotheses are that THF is bound to native LSD1 by analogy to DMGDH and SDH and that the bound THF serves to protect the FAD class of histone demethylases from the destructive effects of formaldehyde generation by formation of 5,10-methylene-THF. We present pilot data showing that decreased folate in livers as a result of dietary folate deficiency is associated with increased levels of methylated lysine 4 of histone 3. This can be a result of decreased LSD1 activity resulting from the decreased folate available to scavenge the formaldehyde produced at the active site caused by the folate deficiency. Because LSD1 can regulate gene expression this suggests that folate may play a more important role than simply serving as a carrier of one-carbon units and be a factor in other diseases associated with low folate. PMID:26880641

  4. Recognition of Methylated Peptides by Drosophila melanogaster Polycomb Chromodomain

    PubMed Central

    Stein, Richard S. L.; Li, Nan; He, Wei; Komives, Elizabeth

    2014-01-01

    Lysine methylation is one of the important post-translational modifications (PTMs) that regulate protein functions. Up to now, proteomic identification of this PTM remains a challenge due to the lack of effective enrichment methods in mass spectrometry experiments. To address this challenge, we present here a systematic approach to predicting peptides in which lysine residues may be methylated to mediate proteinprotein interactions. We used the chromodomain of the polycomb protein in Drosophila melanogaster as a model system to illustrate the success of this approach. We started with molecular dynamics simulations and free energy analyses on the histone peptides complexed with the polycomb chromodomain to understand how the binding specificity is achieved. We next conducted virtual mutagenesis to quantify each domain and peptide residue's contribution to the domain-peptide recognition, based on which scoring scheme was developed to evaluate the possibility of any lysine-containing peptides to be methylated and recognized by the chromodomain. A peptide microarray experiment on a panel of conserved histone peptides showed a satisfactory prediction accuracy of the scoring scheme. Next, we implemented a bioinformatics pipeline that integrates multiple lines of evidence including conservation, subcellular localization, and mass spectrometry data to scan the fly proteome for a systematic identification of possible methyllysine-containing peptides. These putative chromodomain-binding peptides suggest unknown functions of the important regulator protein polycomb and provide a list of candidate methylation events for follow-up investigations. PMID:23320494

  5. Altered DNA methylation in PAH deficient phenylketonuria.

    PubMed

    Dobrowolski, Steven F; Lyons-Weiler, James; Spridik, Kayla; Biery, Amy; Breck, Jane; Vockley, Jerry; Yatsenko, Svetlana; Sultana, Tamanna

    2015-01-01

    While phenylalanine (PHE) is the toxic insult in phenylketonuria (PKU), mechanisms underlying PHE toxicity remain ill-defined. Altered DNA methylation in response to toxic exposures is well-recognized. DNA methylation patterns were assessed in blood and brain from PKU patients to determine if PHE toxicity impacts methylation. Methylome assessment, utilizing methylated DNA immunoprecipitation and paired-end sequencing, was performed in DNA obtained from brain tissue of classical PKU patients, leukocytes from poorly controlled PKU patients, leukocytes from well controlled PKU patients, and appropriate control tissues. In PKU brain tissue, expression analysis determined the impact of methylation on gene function. Differential methylation was observed in brain tissue of PKU patients and expression studies identified downstream impact on gene expression. Altered patterns of methylation were observed in leukocytes of well controlled and poorly controlled patients with more extensive methylation in patients with high PHE exposure. Differential methylation of noncoding RNA genes was extensive in patients with high PHE exposure but minimal in well controlled patients. Methylome repatterning leading to altered gene expression was present in brain tissue of PKU patients, suggesting a role in neuropathology. Aberrant methylation is observed in leukocytes of PKU patients and is influenced by PHE exposure. DNA methylation may provide a biomarker relating to historic PHE exposure. PMID:25990862

  6. PCR Techniques in Characterizing DNA Methylation.

    PubMed

    Wani, Khalida; Aldape, Kenneth D

    2016-01-01

    DNA methylation was the first epigenetic mark to be discovered, involving the addition of a methyl group to the 5' position of cytosine by DNA methyltransferases, and can be inherited through cell division. DNA methylation plays an important role in normal human development and is associated with the regulation of gene expression, tumorigenesis, and other genetic and epigenetic diseases. Differential methylation is now known to play a central role in the development and outcome of most if not all human malignancies.Bisulfite conversion is a commonly used approach for gene-specific DNA methylation analysis. Treatment of DNA with bisulfite converts cytosine to uracil while leaving 5-methylcytosine intact, allowing for single-nucleotide resolution information about the methylated areas of DNA. PCR-based methods are routinely used to study DNA methylation on a gene-specific basis, after bisulfite treatment. Variations of this method include bisulfite sequencing, methylation-specific PCR, real-time PCR-based MethyLight, and methylation-sensitive high-resolution melting PCR. Several whole-epigenome profiling technologies such as MethylC-seq reduced representation bisulfite sequencing (RRBS) and the Infinium Human methylation 450 K bead chip are now available allowing for the identification of epigenetic drivers of disease processes as well as biomarkers that could potentially be integrated into clinical practice. PMID:26843056

  7. DNA methylation profiling of hematopoietic stem cells.

    PubMed

    Begtrup, Amber Hogart

    2014-01-01

    DNA methylation is a key epigenetic mark that is essential for properly functioning hematopoietic stem cells. Determining where functionally relevant DNA methylation marks exist in the genome is crucial to understanding the role that methylation plays in hematopoiesis. This chapter describes a method to profile DNA methylation by selectively enriching methylated DNA sequences that are bound in vitro by methyl-binding domain (MBD) proteins. The MBD-pulldown approach selects for DNA sequences that have the potential to be "read" by the endogenous machinery involved in epigenetic regulation. Furthermore, this approach is feasible with very small quantities of DNA, and is compatible with the use of any downstream high-throughput sequencing approach. This technique offers a reliable, simple, and powerful tool for exploration of the role of DNA methylation in hematopoietic stem cells. PMID:25062626

  8. 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

  9. Conventional and nanotechniques for DNA methylation profiling.

    PubMed

    Shanmuganathan, Rajasree; Basheer, Nazeema B; Amirthalingam, Laxmi; Muthukumar, Harshiny; Kaliaperumal, Rajendran; Shanmugam, Kumaran

    2013-01-01

    DNA methylation is critical for gene silencing and is associated with the incidence of many diseases, including cancer. Underlying molecular mechanisms of human diseases and tissue-specific gene expression have been elucidated based on DNA methylation studies. This review highlights the advantages and drawbacks of various methylation screening techniques: blotting, genomic sequencing, bisulfite sequencing, methylation-specific PCR, methylated DNA immunoprecipitation, microarray analysis, matrix-assisted laser desorption ionization time-of-flight mass spectroscopy, nanowire transistor detection procedure, quantum dot-based nanoassay, single-molecule real-time detection, fluorimetric assay, electrochemical detection, and atomic force spectroscopy. The review provides insight for selecting a method or a combination of methods for DNA methylation analysis. Convergence of conventional and contemporary nanotechniques to enumerate methylation at specific CpG sites of oncogene would fill the gap in diagnosis of cancer. PMID:23127612

  10. Methods in DNA methylation profiling

    PubMed Central

    Zuo, Tao; Tycko, Benjamin; Liu, Ta-Ming; Lin, Huey-Jen L; Huang, Tim H-M

    2010-01-01

    Metastable and somatically heritable patterns of DNA methylation provide an important level of genomic regulation. In this article, we review methods for analyzing these genome-wide epigenetic patterns and offer a perspective on the ever-expanding literature, which we hope will be useful for investigators who are new to this area. The historical aspects that we cover will be helpful in interpreting this literature and we hope that our discussion of the newest analytical methods will stimulate future progress. We emphasize that no single approach can provide a complete view of the overall methylome, and that combinations of several modalities applied to the same sample set will give the clearest picture. Given the unexpected epigenomic patterns and new biological principles, as well as new disease markers, that have been uncovered in recent studies, it is likely that important discoveries will continue to be made using genome-wide DNA methylation profiling. PMID:20526417

  11. 78 FR 32157 - Methyl 5-(dimethylamino)-2-methyl-5-oxopentanoate; Exemption from the Requirement of a Tolerance

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-29

    ... assessment of exposures and risks associated with methyl 5-(dimethylamino)-2-methyl-5-oxopentanoate follows... received and the nature of the adverse effects caused by methyl 5-(dimethylamino)-2-methyl-5- oxopentanoate... treatment with methyl 5-(dimethylamino)-2-methyl-5-oxopentanoate. A Mammalian Erythrocyte Micronucleus...

  12. Cytosine methylation and DNA repair.

    PubMed

    Walsh, C P; Xu, G L

    2006-01-01

    Cytosine methylation is a common form of post-replicative DNA modification seen in both bacteria and eukaryotes. Modified cytosines have long been known to act as hotspots for mutations due to the high rate of spontaneous deamination of this base to thymine, resulting in a G/T mismatch. This will be fixed as a C-->T transition after replication if not repaired by the base excision repair (BER) pathway or specific repair enzymes dedicated to this purpose. This hypermutability has led to depletion of the target dinucleotide CpG outside of special CpG islands in mammals, which are normally unmethylated. We review the importance of C-->T transitions at non-island CpGs in human disease: When these occur in the germline, they are a common cause of inherited diseases such as epidermolysis bullosa and mucopolysaccharidosis, while in the soma they are frequently found in the genes for tumor suppressors such as p53 and the retinoblastoma protein, causing cancer. We also examine the specific repair enzymes involved, namely the endonuclease Vsr in Escherichia coli and two members of the uracil DNA glycosylase (UDG) superfamily in mammals, TDG and MBD4. Repair brings its own problems, since it will require remethylation of the replacement cytosine, presumably coupling repair to methylation by either the maintenance methylase Dnmt1 or a de novo enzyme such as Dnmt3a. Uncoupling of methylation from repair may be one way to remove methylation from DNA. We also look at the possible role of specific cytosine deaminases such as Aid and Apobec in accelerating deamination of methylcytosine and consequent DNA demethylation. PMID:16570853

  13. 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

  14. 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.

  15. Protein Arginine Methyltransferase 1 Methylates Smurf2

    PubMed Central

    Cha, Boksik; Park, Yaerin; Hwang, Byul Nim; Kim, So-young; Jho, Eek-hoon

    2015-01-01

    Smurf2, a member of the HECT domain E3 ligase family, is well known for its role as a negative regulator of TGF-β signaling by targeting Smads and TGF-β receptor. However, the regulatory mechanism of Smurf2 has not been elucidated. Arginine methylation is a type of post-translational modification that produces monomethylated or dimethylated arginine residues. In this report, we demonstrated methylation of Smurf2 by PRMT1. In vitro methylation assay showed that Smurf2, not Smurf1, was methylated by PRMT1. Among the type I PRMT family, only PRMT1 showed activity for Smurf2. Transiently expressed Smurf2 was methylated by PRMT1, indicating Smurf2 is a novel substrate of PRMT1. Using deletion constructs, methylation sites were shown to be located within amino acid region 224–298 of Smurf2. In vitro methylation assay following point mutation of putative methylation sites confirmed the presence of Arg232, Arg234, Arg237, and Arg239. Knockdown of PRMT1 resulted in increased Smurf2 expression as well as inhibition of TGF-β-mediated reporter activity. Although it is unclear whether or not increased Smurf2 expression can be directly attributed to lack of methylation of arginine residues, our results suggest that methylation by PRMT1 may regulate Smurf2 stability and control TGF-β signaling. PMID:26126536

  16. 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.

  17. The i.r. spectra of 3-methyl-2-butenenitrile and 3-methyl-3-butenenitrile

    NASA Astrophysics Data System (ADS)

    Compton, D. A. C.; Murphy, W. F.; Mantsch, H. H.

    A commercial sample of supposedly 3-methyl-3-butenenitrile was separated by gas chromatography into two components. Analysis of the i.r. and NMR spectra of these two components showed that the original mixture contained 25% 3-methyl-3-butenenitrile and 75% 3-methyl-2-butenenitrile, and that an i.r. spectrum recently reported in this journal [1] for 3-methyl-3-butenenitrile was actually that of 3-methyl-2-butenenitrile. Thus, the spectral data reported for 3-methyl-3-butenenitrile [1] and the resulting conclusions regarding the nature of the conformational equilibrium in this molecule should be disregarded.

  18. DNA methylation in gastric cancer, related to Helicobacter pylori and Epstein-Barr virus

    PubMed Central

    Matsusaka, Keisuke; Funata, Sayaka; Fukayama, Masashi; Kaneda, Atsushi

    2014-01-01

    Gastric cancer is a leading cause of cancer death worldwide, and significant effort has been focused on clarifying the pathology of gastric cancer. In particular, the development of genome-wide analysis tools has enabled the detection of genetic and epigenetic alterations in gastric cancer; for example, aberrant DNA methylation in gene promoter regions is thought to play a crucial role in gastric carcinogenesis. The etiological viewpoint is also essential for the study of gastric cancers, and two distinct pathogens, Helicobacter pylori (H. pylori) and Epstein-Barr virus (EBV), are known to participate in gastric carcinogenesis. Chronic inflammation of the gastric epithelium due to H. pylori infection induces aberrant polyclonal methylation that may lead to an increased risk of gastric cancer. In addition, EBV infection is known to cause extensive methylation, and EBV-positive gastric cancers display a high methylation epigenotype, in which aberrant methylation extends to not only Polycomb repressive complex (PRC)-target genes in embryonic stem cells but also non-PRC-target genes. Here, we review aberrant DNA methylation in gastric cancer and the association between methylation and infection with H. pylori and EBV. PMID:24744581

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

    PubMed Central

    Knzel, 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

  20. 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

  1. A sensitive microfluidic platform for a high throughput DNA methylation assay.

    PubMed

    Ronen, Maria; Avrahami, Dorit; Gerber, Doron

    2014-07-01

    DNA methylation is an epigenetic modification essential for normal development and maintenance of somatic biological functions. DNA methylation provides heritable, long-term chromatin regulation and the aberrant methylation pattern is associated with complex diseases including cancer. Discovering novel therapeutic targets demands development of high-throughput, sensitive and inexpensive screening platforms for libraries of chemical or biological matter involved in DNA methylation establishment and maintenance. Here, we present a universal, high-throughput, microfluidic-based fluorometric assay for studying DNA methylation in vitro. The enzymatic activity of bacterial HPAII DNA methyltransferase and its kinetic properties are measured using the assay (K(m)(DNA) = 5.8 nM, K(m)(SAM) = 9.8 nM and Kcat = 0.04 s(-1)). Using the same platform, we then demonstrate a two-step approach for high-throughput in vitro identification and characterization of small molecule inhibitors of methylation. The approach is examined using known non-nucleoside inhibitors, SGI-1027 and RG108, for which we measured IC50 of 4.5 ?M and 87.5 nM, respectively. The dual role of the microfluidic-based methylation assay both for the quantitative characterization of enzymatic activity and high-throughput screening of non-nucleoside inhibitors coupled with quantitative characterization of the inhibition potential highlights the advantages of our system for epigenetic studies. PMID:24841578

  2. 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

  3. N6-Adenosine Methylation in MiRNAs

    PubMed Central

    Berulava, Tea; Rahmann, Sven; Rademacher, Katrin; Klein-Hitpass, Ludgar; Horsthemke, Bernhard

    2015-01-01

    Methylation of N6-adenosine (m6A) has been observed in many different classes of RNA, but its prevalence in microRNAs (miRNAs) has not yet been studied. Here we show that a knockdown of the m6A demethylase FTO affects the steady-state levels of several miRNAs. Moreover, RNA immunoprecipitation with an anti-m6A-antibody followed by RNA-seq revealed that a significant fraction of miRNAs contains m6A. By motif searches we have discovered consensus sequences discriminating between methylated and unmethylated miRNAs. The epigenetic modification of an epigenetic modifier as described here adds a new layer to the complexity of the posttranscriptional regulation of gene expression. PMID:25723394

  4. 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

  5. The Dynamics of DNA Methylation in Schizophrenia and Related Psychiatric Disorders

    PubMed Central

    Grayson, Dennis R; Guidotti, Alessandro

    2013-01-01

    Major psychiatric disorders such as schizophrenia (SZ) and bipolar disorder (BP) with psychosis (BP+) express a complex symptomatology characterized by positive symptoms, negative symptoms, and cognitive impairment. Postmortem studies of human SZ and BP+ brains show considerable alterations in the transcriptome of a variety of cortical structures, including multiple mRNAs that are downregulated in both inhibitory GABAergic and excitatory pyramidal neurons compared with non-psychiatric subjects (NPS). Several reports show increased expression of DNA methyltransferases in telencephalic GABAergic neurons. Accumulating evidence suggests a critical role for altered DNA methylation processes in the pathogenesis of SZ and related psychiatric disorders. The establishment and maintenance of CpG site methylation is essential during central nervous system differentiation and this methylation has been implicated in synaptic plasticity, learning, and memory. Atypical hypermethylation of candidate gene promoters expressed in GABAergic neurons is associated with transcriptional downregulation of the corresponding mRNAs, including glutamic acid decarboxylase 67 (GAD67) and reelin (RELN). Recent reports indicate that the methylation status of promoter proximal CpG dinucleotides is in a dynamic balance between DNA methylation and DNA hydroxymethylation. Hydroxymethylation and subsequent DNA demethylation is more complex and involves additional proteins downstream of 5-hydroxymethylcytosine, including members of the base excision repair (BER) pathway. Recent advances in our understanding of altered CpG methylation, hydroxymethylation, and active DNA demethylation provide a framework for the identification of new targets, which may be exploited for the pharmacological intervention of the psychosis associated with SZ and possibly BP+. PMID:22948975

  6. 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

  7. [Bifunctional role of domain zinc fingers of methyl-DNA-binding protein Kaiso].

    PubMed

    Zhigalova, N A; Zhenilo, S V; Aĭtkhozhina, D S; Prokhorchuk, E B

    2010-01-01

    DNA methylation in mammals is one of the major epigenetic mark that associates with inactive chromatin state. Methyl-DNA-binding proteins bind methylated DNA and silence gene transcription by recruiting repression complexes. Kaiso is one of the methyl-DNA-binding proteins. It has a domain structure: N-terminal BTB/POZ domain involved in protein-protein interaction and C-terminal zinc-fingers of C2H2 type that bind methylated DNA (mCGmCG) or nonmethylated - TCCTGCNA. Here we show that Kaiso interacts with p120 catenin through zinc finger 2 and 3. This interaction has dual consequences. Firstly, binding to p120 inhibits nuclear import of Kaiso that results in most of Kaiso-p120 complexes becoming cytoplasmic. And secondly, bound p120 makes impossible interaction of the zinc fingers with methylated DNA. These modes of Kaiso modulation by p120 can open attractive perspectives in linking events on cell membrane and changes in nuclear gene expression. PMID:20586187

  8. An integrated workflow for DNA methylation analysis.

    PubMed

    Li, Pingchuan; Demirci, Feray; Mahalingam, Gayathri; Demirci, Caghan; Nakano, Mayumi; Meyers, Blake C

    2013-05-20

    The analysis of cytosine methylation provides a new way to assess and describe epigenetic regulation at a whole-genome level in many eukaryotes. DNA methylation has a demonstrated role in the genome stability and protection, regulation of gene expression and many other aspects of genome function and maintenance. BS-seq is a relatively unbiased method for profiling the DNA methylation, with a resolution capable of measuring methylation at individual cytosines. Here we describe, as an example, a workflow to handle DNA methylation analysis, from BS-seq library preparation to the data visualization. We describe some applications for the analysis and interpretation of these data. Our laboratory provides public access to plant DNA methylation data via visualization tools available at our "Next-Gen Sequence" websites (http://mpss.udel.edu), along with small RNA, RNA-seq and other data types. PMID:23706300

  9. 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.

  10. The functional diversity of protein lysine methylation.

    PubMed

    Lanouette, Sylvain; Mongeon, Vanessa; Figeys, Daniel; Couture, Jean-Franois

    2014-01-01

    Large-scale characterization of post-translational modifications (PTMs), such as phosphorylation, acetylation and ubiquitination, has highlighted their importance in the regulation of a myriad of signaling events. While high-throughput technologies have tremendously helped cataloguing the proteins modified by these PTMs, the identification of lysine-methylated proteins, a PTM involving the transfer of one, two or three methyl groups to the ?-amine of a lysine side chain, has lagged behind. While the initial findings were focused on the methylation of histone proteins, several studies have recently identified novel non-histone lysine-methylated proteins. This review provides a compilation of all lysine methylation sites reported to date. We also present key examples showing the impact of lysine methylation and discuss the circuitries wired by this important PTM. PMID:24714364

  11. Crystal structure of tris(N-methylsalicylaldiminato-?2 N,O)chromium(III)

    PubMed Central

    Hilbert, Jessica; Kabus, Sven; Nther, Christian; Bensch, Wolfgang

    2015-01-01

    The crystal structure of the title compound, [Cr(C8H8NO)3], is isotypic with the vanadium(III) analogue. The asymmetric unit consists of one Cr3+ cation and three N-methylsalicylaldiminate anions. The metal cation is octahedrally coordinated by three N,O-chelating N-methylsalicylaldiminate ligands, leading to discrete and neutral complexes. In the crystal, neighbouring complexes are linked via CH?O hydrogen-bonding interactions into chains propagating parallel to the c axis. PMID:26870448

  12. Crystal structure of di-aqua-bis-(2,6-di-methyl-pyrazine-?N)bis-(thio-cyanato-?N)cobalt(II) 2,5-di-methyl-pyrazine tris-olvate.

    PubMed

    Suckert, Stefan; Whlert, Susanne; Jess, Inke; Nther, Christian

    2015-12-01

    In the crystal structure of the title compound, [Co(NCS)2(C6H8N2)2(H2O)2]3C6H8N2, the Co(II) cation is coordinated by two terminally N-bound thio-cyanate anions, two water mol-ecules and two 2,6-di-methyl-pyrazine ligands, forming a discrete complex with a slightly distorted octa-hedral N4O2 coordination environment. The asymmetric unit contains one Co(II) cation and three halves of 2,5-di-methyl-pyrazine solvate mol-ecules, all entities being completed by inversion symmetry, as well as one thio-cyanate anion, an aqua ligand and a 2,6-di-methyl-pyrazine ligand, all in general positions. In the crystal, discrete complexes are arranged in a way that cavities are formed where the noncoordinating 2,5-di-methyl-pyrazine mol-ecules are located. The coordination of the latter to the metal is prevented due to the bulky methyl groups in vicinal positions to the N atoms, leading to a preferential coordination through the 2,6-di-methyl-pyrazine ligands. The complex mol-ecules are linked by O-H?N hydrogen bonds between the water H atoms and the N atoms of 2,5-di-methyl-pyrazine solvent mol-ecules, leading to a layered structure extending parallel to (100). PMID:26870459

  13. Crystal structure of tri-aqua-(2,6-di-methyl-pyrazine-?N (4))bis-(thio-cyanato-?N)manganese(II) 2,5-di-methyl-pyrazine disolvate.

    PubMed

    Suckert, Stefan; Whlert, Susanne; Jess, Inke; Nther, Christian

    2015-12-01

    In the crystal structure of the title complex, [Mn(NCS)2(C6H8N2)(H2O)3]2C6H8N2, the Mn(II) cation is coordinated by two terminally N-bonded thio-cyanate anions, three water mol-ecules and one 2,6-di-methyl-pyrazine ligand within a slightly distorted N3O3 octa-hedral geometry; the entire complex mol-ecule is generated by the application of a twofold rotation axis. The asymmetric unit also contains an uncoordinating 2,5-di-methyl-pyrazine ligand in a general position. Obviously, the coordination to the 2,6-di-methyl-pyrazine ligand is preferred because coordination to the 2,5-di-methyl-pyrazine is hindered due to the bulky methyl group proximate to the N atom. The discrete complexes are linked by water-O-H?N(2,6-di-methyl-pyzazine/2,5-di-methyl-pyza-zine) hydrogen bonding, forming a three-dimensional network. In the crystal, mol-ecules are arranged in a way that cavities are formed in which unspecified, disordered solvent molecules reside. These were modelled employing the SQUEEZE routine in PLATON [Spek (2015 ?). Acta Cryst. C71, 9-18]. The composition of the unit cell does not take into account the presence of the unspecified solvent. PMID:26870435

  14. Crystal structure of triaqua(2,6-dimethylpyrazine-?N 4)bis(thiocyanato-?N)manganese(II) 2,5-dimethylpyrazine disolvate

    PubMed Central

    Suckert, Stefan; Whlert, Susanne; Jess, Inke; Nther, Christian

    2015-01-01

    In the crystal structure of the title complex, [Mn(NCS)2(C6H8N2)(H2O)3]2C6H8N2, the MnII cation is coordinated by two terminally N-bonded thiocyanate anions, three water molecules and one 2,6-dimethylpyrazine ligand within a slightly distorted N3O3 octahedral geometry; the entire complex molecule is generated by the application of a twofold rotation axis. The asymmetric unit also contains an uncoordinating 2,5-dimethylpyrazine ligand in a general position. Obviously, the coordination to the 2,6-dimethylpyrazine ligand is preferred because coordination to the 2,5-dimethylpyrazine is hindered due to the bulky methyl group proximate to the N atom. The discrete complexes are linked by water-OH?N(2,6-dimethylpyzazine/2,5-dimethylpyzazine) hydrogen bonding, forming a three-dimensional network. In the crystal, molecules are arranged in a way that cavities are formed in which unspecified, disordered solvent molecules reside. These were modelled employing the SQUEEZE routine in PLATON [Spek (2015 ?). Acta Cryst. C71, 918]. The composition of the unit cell does not take into account the presence of the unspecified solvent. PMID:26870435

  15. DNA Methylation of BDNF Gene in Schizophrenia.

    PubMed

    po?lu, mit Sertan; Igci, Mehri; Bozgeyik, Esra; Kokaya, M Hanifi; ??ci, Yusuf Ziya; Dokuyucu, Recep; Ari, Mustafa; Sava?, Haluk A

    2016-01-01

    BACKGROUND Although genetic factors are risk factors for schizophrenia, some environmental factors are thought to be required for the manifestation of disease. Epigenetic mechanisms regulate gene functions without causing a change in the nucleotide sequence of DNA. Brain-derived neurotrophic factor (BDNF) is a neurotrophin that regulates synaptic transmission and plasticity. It has been suggested that BDNF may play a role in the pathophysiology of schizophrenia. It is established that methylation status of the BDNF gene is associated with fear learning, memory, and stressful social interactions. In this study, we aimed to investigate the DNA methylation status of BDNF gene in patients with schizophrenia. MATERIAL AND METHODS The study included 49 patients (33 male and 16 female) with schizophrenia and 65 unrelated healthy controls (46 male and 19 female). Determination of methylation pattern of CpG islands was based on the principle that bisulfite treatment of DNA results in conversion of unmethylated cytosine residues into uracil, whereas methylated cytosine residues remain unmodified. Methylation-specific PCR was performed with primers specific for either methylated or unmethylated DNA. RESULTS There was no significant difference in methylated or un-methylated status for BDNF promoters between schizophrenia patients and controls. The mean duration of illness was significantly lower in the hemi-methylated group compared to the non-methylated group for BDNF gene CpG island-1 in schizophrenia patients. CONCLUSIONS Although there were no differences in BDNF gene methylation status between schizophrenia patients and healthy controls, there was an association between duration of illness and DNA methylation. PMID:26851233

  16. DNA Methylation of BDNF Gene in Schizophrenia

    PubMed Central

    Çöpoğlu, Ümit Sertan; İğci, Mehri; Bozgeyik, Esra; Kokaçya, M. Hanifi; İğci, Yusuf Ziya; Dokuyucu, Recep; Arı, Mustafa; Savaş, Haluk A.

    2016-01-01

    Background Although genetic factors are risk factors for schizophrenia, some environmental factors are thought to be required for the manifestation of disease. Epigenetic mechanisms regulate gene functions without causing a change in the nucleotide sequence of DNA. Brain-derived neurotrophic factor (BDNF) is a neurotrophin that regulates synaptic transmission and plasticity. It has been suggested that BDNF may play a role in the pathophysiology of schizophrenia. It is established that methylation status of the BDNF gene is associated with fear learning, memory, and stressful social interactions. In this study, we aimed to investigate the DNA methylation status of BDNF gene in patients with schizophrenia. Material/Methods The study included 49 patients (33 male and 16 female) with schizophrenia and 65 unrelated healthy controls (46 male and 19 female). Determination of methylation pattern of CpG islands was based on the principle that bisulfite treatment of DNA results in conversion of unmethylated cytosine residues into uracil, whereas methylated cytosine residues remain unmodified. Methylation-specific PCR was performed with primers specific for either methylated or unmethylated DNA. Results There was no significant difference in methylated or un-methylated status for BDNF promoters between schizophrenia patients and controls. The mean duration of illness was significantly lower in the hemi-methylated group compared to the non-methylated group for BDNF gene CpG island-1 in schizophrenia patients. Conclusions Although there were no differences in BDNF gene methylation status between schizophrenia patients and healthy controls, there was an association between duration of illness and DNA methylation. PMID:26851233

  17. 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

  18. Hypoxic radiosensitization by the antimicrobial methyl paraben

    SciTech Connect

    Jacobs, G.P.; Sade, N.

    1984-08-01

    The antimicrobial preservative, methyl paraben (methyl-4-hydroxybenzoate) sensitizes anoxic buffered suspensions of Staphylococcus aureus to gamma-radiation. The maximal response at an 0.5 mM concentration represents a 150 percent increase in response over that for deoxygenated suspensions without additive, and 80 percent of the response for aerated suspensions alone. Methyl paraben is not toxic to the test organism under the present test conditions.

  19. 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

  20. Influence of the protonation state on the binding mode of methyl orange with cucurbiturils

    NASA Astrophysics Data System (ADS)

    He, Suhang; Sun, Xuzhuo; Zhang, Haibo

    2016-03-01

    Binding modes of methyl orange (MO) with cucurbiturils (CBs) have been investigated by Single Crystal X-ray Diffraction and NMR Spectroscopy. Detailed study of intermolecular interactions was supported by the Hirshfeld surface analysis. Protonation state of the anionic part of methyl orange has greatly influenced the binding mode of the complex. Stabilized by hydrogen bonding at the portal, hydrophobic and dispersion interactions in the cavity, the protonated methyl orange was deeply inserted into the cavity. On the contrary, the anionic methyl orange has been pushed towards the outside of the cavity by the electrostatic repulsion between the azo group and the portal oxygen. A "water bridge" was found in MO@CB8 linking both host and guest via hydrogen bonds.

  1. A novel methyl-binding domain protein enrichment method for identifying genome-wide tissue-specific DNA methylation from nanogram DNA samples

    PubMed Central

    2013-01-01

    Background Growing evidence suggests that DNA methylation plays a role in tissue-specific differentiation. Current approaches to methylome analysis using enrichment with the methyl-binding domain protein (MBD) are restricted to large (≥1 μg) DNA samples, limiting the analysis of small tissue samples. Here we present a technique that enables characterization of genome-wide tissue-specific methylation patterns from nanogram quantities of DNA. Results We have developed a methodology utilizing MBD2b/MBD3L1 enrichment for methylated DNA, kinase pre-treated ligation-mediated PCR amplification (MeKL) and hybridization to the comprehensive high-throughput array for relative methylation (CHARM) customized tiling arrays, which we termed MeKL-chip. Kinase modification in combination with the addition of PEG has increased ligation-mediated PCR amplification over 20-fold, enabling >400-fold amplification of starting DNA. We have shown that MeKL-chip can be applied to as little as 20 ng of DNA, enabling comprehensive analysis of small DNA samples. Applying MeKL-chip to the mouse retina (a limited tissue source) and brain, 2,498 tissue-specific differentially methylated regions (T-DMRs) were characterized. The top five T-DMRs (Rgs20, Hes2, Nfic, Cckbr and Six3os1) were validated by pyrosequencing. Conclusions MeKL-chip enables genome-wide methylation analysis of nanogram quantities of DNA with a wide range of observed-to-expected CpG ratios due to the binding properties of the MBD2b/MBD3L1 protein complex. This methodology enabled the first analysis of genome-wide methylation in the mouse retina, characterizing novel T-DMRs. PMID:23759032

  2. Methylation-Specific MLPA (MS-MLPA): simultaneous detection of CpG methylation and copy number changes of up to 40 sequences

    PubMed Central

    Nygren, Anders O. H.; Ameziane, Najim; Duarte, Helena M. B.; Vijzelaar, Raymon N. C. P.; Waisfisz, Quinten; Hess, Corine J.; Schouten, Jan P.; Errami, Abdellatif

    2005-01-01

    Copy number changes and CpG methylation of various genes are hallmarks of tumor development but are not yet widely used in diagnostic settings. The recently developed multiplex ligation-dependent probe amplification (MLPA) method has increased the possibilities for multiplex detection of gene copy number aberrations in a routine laboratory. Here we describe a novel robust method: the methylation-specific MLPA (MS-MLPA) that can detect changes in both CpG methylation as well as copy number of up to 40 chromosomal sequences in a simple reaction. In MS-MLPA, the ligation of MLPA probe oligonucleotides is combined with digestion of the genomic DNAprobe hybrid complexes with methylation-sensitive endonucleases. Digestion of the genomic DNAprobe complex, rather than double-stranded genomic DNA, allowed the use of DNA derived from the formalin treated paraffin-embedded tissue samples, enabling retrospective studies. To validate this novel method, we used MS-MLPA to detect aberrant methylation in DNA samples of patients with PraderWilly syndrome, Angelman syndrome or acute myeloid leukemia. PMID:16106041

  3. 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.

  4. 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

  5. Seasonality modifies methylation profiles in healthy people.

    PubMed

    Ricceri, Fulvio; Trevisan, Morena; Fiano, Valentina; Grasso, Chiara; Fasanelli, Francesca; Scoccianti, Chiara; De Marco, Laura; Tos, Anna Gillio; Vineis, Paolo; Sacerdote, Carlotta

    2014-01-01

    DNA methylation is a well-characterized epigenetic modification that plays an important role in the regulation of gene expression. There is growing evidence on the involvement of epigenetic mechanisms in disease onset, including cancer. Environmental factors seem to induce changes in DNA methylation affecting human health. However, little is known about basal methylation levels in healthy people and about the correlation between environmental factors and different methylation profiles. We investigated the effect of seasonality on basal methylation by testing methylation levels in the long interspersed nucleotide element-1 (LINE-1) and in two cancer-related genes (RASSF1A and MGMT) of 88 healthy male heavy smokers involved in an Italian randomized study; at enrolment the subjects donated a blood sample collected in different months. Methylation analyses were performed by pyrosequencing. Mean methylation percentage was higher in spring and summer for the LINE1, RASSF1A and MGMT genes (68.26%, 2.35%, and 9.52% respectively) compared with autumn and winter (67.43%, 2.17%, and 8.60% respectively). In particular, LINE-1 was significantly hypomethylated (p = 0.04 or 0.05 depending on the CpG island involved) in autumn and winter compared with spring and summer. Seasonality seems to be a modifier of methylation levels and this observation should be taken into account in future analyses. PMID:25210735

  6. Analysing and interpreting DNA methylation data.

    PubMed

    Bock, Christoph

    2012-10-01

    DNA methylation is an epigenetic mark that has suspected regulatory roles in a broad range of biological processes and diseases. The technology is now available for studying DNA methylation genome-wide, at a high resolution and in a large number of samples. This Review discusses relevant concepts, computational methods and software tools for analysing and interpreting DNA methylation data. It focuses not only on the bioinformatic challenges of large epigenome-mapping projects and epigenome-wide association studies but also highlights software tools that make genome-wide DNA methylation mapping more accessible for laboratories with limited bioinformatics experience. PMID:22986265

  7. Microbial methylation of mercury in estuarine sediments

    SciTech Connect

    Compeau, G.C.

    1985-01-01

    Mercury is a common and potentially hazardous pollutant. Although all forms of the element are toxic, alkylated mercurials are particularly toxic and accumulate in living tissues. Factors affecting the availability of mercury and the microorganisms responsible for methylation are described. The methylation of mercuric ions (Hg/sup + +/) was investigated in pure culture, in estuarine sediments, and as a function of the anionic constituents of seawater. Studies on abiotic methylation of Hg/sup + +/ by methylcobalamin in the presence of sea salts showed that only the sulfide (formed in sulfate reduction) and bicarbonate components interfere with Hg/sup + +/ methylation. Other sea salt anions have no significant influence on the methylation of Hg/sup + +/. Methylation, demethylation, and volatilization of Hg/sup + +/ were studied in estuarine sediments maintained at present values of pH, redox, and salinity. Volatilization of Hg/sup 0/ and CH/sub 3/HgCH/sub 3/ were found to be minimal. Methylation was favored at low redox potential (-220 mW) and low salinity (0.4%) conditions. High salinity (2.5%) decreased methylation at -220 mV, but not at (+110 mV). Demethylation of CH/sub 3/HgCl was favored at +110 mV regardless of the salinity level. Low redox potential under low salinity conditions inhibited demethylation, but high salinity reversed this inhibition. The sulfate-reducing bacteria were identified as the principal Hg/sup + +/ methylating population in anaerobic estuarine sediments.

  8. Seasonality Modifies Methylation Profiles in Healthy People

    PubMed Central

    Ricceri, Fulvio; Trevisan, Morena; Fiano, Valentina; Grasso, Chiara; Fasanelli, Francesca; Scoccianti, Chiara; De Marco, Laura; Tos, Anna Gillio; Vineis, Paolo; Sacerdote, Carlotta

    2014-01-01

    DNA methylation is a well-characterized epigenetic modification that plays an important role in the regulation of gene expression. There is growing evidence on the involvement of epigenetic mechanisms in disease onset, including cancer. Environmental factors seem to induce changes in DNA methylation affecting human health. However, little is known about basal methylation levels in healthy people and about the correlation between environmental factors and different methylation profiles. We investigated the effect of seasonality on basal methylation by testing methylation levels in the long interspersed nucleotide element-1 (LINE-1) and in two cancer-related genes (RASSF1A and MGMT) of 88 healthy male heavy smokers involved in an Italian randomized study; at enrolment the subjects donated a blood sample collected in different months. Methylation analyses were performed by pyrosequencing. Mean methylation percentage was higher in spring and summer for the LINE1, RASSF1A and MGMT genes (68.26%, 2.35%, and 9.52% respectively) compared with autumn and winter (67.43%, 2.17%, and 8.60% respectively). In particular, LINE-1 was significantly hypomethylated (p = 0.04 or 0.05 depending on the CpG island involved) in autumn and winter compared with spring and summer. Seasonality seems to be a modifier of methylation levels and this observation should be taken into account in future analyses. PMID:25210735

  9. DNA Methylation Landscapes of Human Fetal Development

    PubMed Central

    van Iperen, Liesbeth; Suchiman, H. Eka D.; Tobi, Elmar W.; Carlotti, Franoise; 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. Proposed roles for DNA methylation in Alu transcriptional repression and mutational inactivation.

    PubMed Central

    Liu, W M; Schmid, C W

    1993-01-01

    Methylation at CpG dinucleotides to produce 5 methyl cytosine (5me-C) has been proposed to regulate the transcriptional expression of human Alu repeats. Similarly, methylation has been proposed to indirectly favor the transpositional activity of young Alu repeats by transcriptionally inactivating older Alu's through the very rapid transition of 5me-C to T. Both hypotheses are examined here by RNA polymerase III (Pol III) in vitro transcription of Alu templates using HeLa cell extracts. A limiting factor represses the template activity of methylated Alu repeats. Competition by methylated prokaryotic vector DNA's relieves repression, showing that the factor is not sequence specific. This competitor has no effect on the activity of unmethylated templates showing that the repressor is highly specific toward methylated DNA. While methylation of a single pair of CpG dinucleotides in the A box of the Poll III promoter is sufficient to cause repression, methylation elsewhere within the template also causes repression. The repressor causing these effects on the Pol III directed transcription of Alu repeats is thought to be a previously reported, repressor for Pol II directed templates. Young Alu repeats are transcriptionally more active templates than a representative older Alu subfamily member. Also, younger Alu's form stable transcriptional complexes faster, potentially giving them an additional advantage. The mutation of three CpG's to CpA's within and near the A box drastically decreases both the template activity and rate of stable complex formation by a young Alu member. The sensitivity of Alu template activity to CpG transitions within the A box partially explains the selective transpositional advantage enjoyed by young Alu members. Images PMID:8464725

  11. Hierarchical Clustering of Breast Cancer Methylomes Revealed Differentially Methylated and Expressed Breast Cancer Genes

    PubMed Central

    Lin, I-Hsuan; Chen, Dow-Tien; Chang, Yi-Feng; Lee, Yu-Ling; Su, Chia-Hsin; Cheng, Ching; Tsai, Yi-Chien; Ng, Swee-Chuan; Chen, Hsiao-Tan; Lee, Mei-Chen; Chen, Hong-Wei; Suen, Shih-Hui; Chen, Yu-Cheng; Liu, Tze-Tze; Chang, Chuan-Hsiung; Hsu, Ming-Ta

    2015-01-01

    Oncogenic transformation of normal cells often involves epigenetic alterations, including histone modification and DNA methylation. We conducted whole-genome bisulfite sequencing to determine the DNA methylomes of normal breast, fibroadenoma, invasive ductal carcinomas and MCF7. The emergence, disappearance, expansion and contraction of kilobase-sized hypomethylated regions (HMRs) and the hypomethylation of the megabase-sized partially methylated domains (PMDs) are the major forms of methylation changes observed in breast tumor samples. Hierarchical clustering of HMR revealed tumor-specific hypermethylated clusters and differential methylated enhancers specific to normal or breast cancer cell lines. Joint analysis of gene expression and DNA methylation data of normal breast and breast cancer cells identified differentially methylated and expressed genes associated with breast and/or ovarian cancers in cancer-specific HMR clusters. Furthermore, aberrant patterns of X-chromosome inactivation (XCI) was found in breast cancer cell lines as well as breast tumor samples in the TCGA BRCA (breast invasive carcinoma) dataset. They were characterized with differentially hypermethylated XIST promoter, reduced expression of XIST, and over-expression of hypomethylated X-linked genes. High expressions of these genes were significantly associated with lower survival rates in breast cancer patients. Comprehensive analysis of the normal and breast tumor methylomes suggests selective targeting of DNA methylation changes during breast cancer progression. The weak causal relationship between DNA methylation and gene expression observed in this study is evident of more complex role of DNA methylation in the regulation of gene expression in human epigenetics that deserves further investigation. PMID:25706888

  12. Identification of a new ribose methylation in the 18S rRNA of S. cerevisiae

    PubMed Central

    Yang, Jun; Sharma, Sunny; Ktter, Peter; Entian, Karl-Dieter

    2015-01-01

    Methylation of ribose sugars at the 2?-OH group is one of the major chemical modifications in rRNA, and is catalyzed by snoRNA directed C/D box snoRNPs. Previous biochemical and computational analyses of the C/D box snoRNAs have identified and mapped a large number of 2?-OH ribose methylations in rRNAs. In the present study, we systematically analyzed ribose methylations of 18S rRNA in Saccharomyces cerevisiae, using mung bean nuclease protection assay and RP-HPLC. Unexpectedly, we identified a hitherto unknown ribose methylation at position G562 in the helix 18 of 5? central domain of yeast 18S rRNA. Furthermore, we identified snR40 as being responsible to guide snoRNP complex to catalyze G562 ribose methylation, which makes it only second snoRNA known so far to target three ribose methylation sites: Gm562, Gm1271 in 18S rRNA, and Um898 in 25S rRNA. Our sequence and mutational analysis of snR40 revealed that snR40 uses the same D? box and methylation guide sequence for both Gm562 and Gm1271 methylation. With the identification of Gm562 and its corresponding snoRNA, complete set of ribose methylations of 18S rRNA and their corresponding snoRNAs have finally been established opening great prospects to understand the physiological function of these modifications. PMID:25653162

  13. Global LINE-1 DNA methylation is associated with blood glycaemic and lipid profiles

    PubMed Central

    Pearce, Mark S; McConnell, James C; Potter, Catherine; Barrett, Laura M; Parker, Louise; Mathers, John C; Relton, Caroline L

    2012-01-01

    Background Patterns of DNA methylation change with age and these changes are believed to be associated with the development of common complex diseases. The hypothesis that Long Interspersed Nucleotide Element 1 (LINE-1) DNA methylation (an index of global DNA methylation) is associated with biomarkers of metabolic health was investigated in this study. Methods Global LINE-1 DNA methylation was quantified by pyrosequencing in blood-derived DNA samples from 228 individuals, aged 4951 years, from the Newcastle Thousand Families Study (NTFS). Associations between log-transformed LINE-1 DNA methylation levels and anthropometric and blood biochemical measurements, including triglycerides, total cholesterol, low-density lipoprotein (LDL) and high-density lipoprotein (HDL) cholesterol, fasting glucose and insulin secretion and resistance were examined. Results Linear regression, after adjustment for sex, demonstrated positive associations between log-transformed LINE-1 DNA methylation and fasting glucose {coefficient 2.80 [95% confidence interval (CI) 0.395.22]}, total cholesterol [4.76 (95% CI 1.438.10)], triglycerides [3.83 (95% CI 1.306.37)] and LDL-cholesterol [5.38 (95% CI 2.128.64)] concentrations. A negative association was observed between log-transformed LINE-1 methylation and both HDL cholesterol concentration [?1.43 (95% CI ?2.38 to ?0.48)] and HDL:LDL ratio [?1.06 (95% CI ?1.76 to ?0.36)]. These coefficients reflect the millimoles per litre change in biochemical measurements per unit increase in log-transformed LINE-1 methylation. Conclusions These novel associations between global LINE-1 DNA methylation and blood glycaemic and lipid profiles highlight a potential role for epigenetic biomarkers as predictors of metabolic disease and may be relevant to future diagnosis, prevention and treatment of this group of disorders. Further work is required to establish the role of confounding and reverse causation in the observed associations. PMID:22422454

  14. A Genome-wide screen identifies frequently methylated genes in haematological and epithelial cancers

    PubMed Central

    2010-01-01

    Background Genetic as well as epigenetic alterations are a hallmark of both epithelial and haematological malignancies. High throughput screens are required to identify epigenetic markers that can be useful for diagnostic and prognostic purposes across malignancies. Results Here we report for the first time the use of the MIRA assay (methylated CpG island recovery assay) in combination with genome-wide CpG island arrays to identify epigenetic molecular markers in childhood acute lymphoblastic leukemia (ALL) on a genome-wide scale. We identified 30 genes demonstrating methylation frequencies of ≥25% in childhood ALL, nine genes showed significantly different methylation frequencies in B vs T-ALL. For majority of the genes expression could be restored in methylated leukemia lines after treatment with 5-azaDC. Forty-four percent of the genes represent targets of the polycomb complex. In chronic myeloid leukemia (CML) two of the genes, (TFAP2A and EBF2), demonstrated increased methylation in blast crisis compared to chronic phase (P < 0.05). Furthermore hypermethylation of an autophagy related gene ATG16L2 was associated with poorer prognosis in terms of molecular response to Imatinib treatment. Lastly we demonstrated that ten of these genes were also frequently methylated in common epithelial cancers. Conclusion In summary we have identified a large number of genes showing frequent methylation in childhood ALL, methylation status of two of these genes is associated with advanced disease in CML and methylation status of another gene is associated with prognosis. In addition a subset of these genes may act as epigenetic markers across hematological malignancies as well as common epithelial cancers. PMID:20184741

  15. Investigating DNA methylation dynamics and safety of human embryonic stem cell differentiation toward striatal neurons.

    PubMed

    Baronchelli, Simona; La Spada, Alberto; Conforti, Paola; Redaelli, Serena; Dalpr, Leda; De Blasio, Pasquale; Cattaneo, Elena; Biunno, Ida

    2015-10-15

    The potential use of human embryonic stem cells (hESCs) in cell-based therapies points out the critical importance of epigenomic evaluation for cell-based therapies. Specifically, DNA methylation appears to be a crucial player in establishing cell fate commitment and lineage choices. In this study, we report the global changes observed on the CpG islands distributed in promoters, gene bodies, and intergenic regions and the major biochemical pathways and genes involved in methylation changes as H9-hESCs turn into a neuronal culture containing medium-sized spiny striatal neurons (MSNs). Using an ontogeny-recapitulating protocol of striatal neuron differentiation, we analyzed DNA methylation profiles during the conversion from pluripotency to neuropotency up to the acquisition of a mature neuronal phenotype. H9-hESCs changed the methylation pattern both through de novo methylation and hypomethylation of specific gene promoters. Bioinformatic analysis allowed us to identify a panel of striatal-associated genes, which were regulated by DNA methylation and differentially expressed during striatal commitment. Importantly, DNA methylation analysis revealed that H9-hESCs did not acquire methylation-based oncogenic properties after differentiation. Indeed, hypermethylation of cancer-associated genes that characterize transformed cells, such as Polycomb repressive complex-associated genes, was not detected in the neuronal cultures. However, the oncosuppressor gene, BCL2L11, became hypermethylated in H9-hESC-derived mature neurons. Whole-genome DNA methylation profiling could become a technological platform to predict the differentiative potential of hESC-derived cultures and establish further biosafety assessment quality control tools of the cell-based products. PMID:26132372

  16. Identification of a new ribose methylation in the 18S rRNA of S. cerevisiae.

    PubMed

    Yang, Jun; Sharma, Sunny; Kötter, Peter; Entian, Karl-Dieter

    2015-02-27

    Methylation of ribose sugars at the 2'-OH group is one of the major chemical modifications in rRNA, and is catalyzed by snoRNA directed C/D box snoRNPs. Previous biochemical and computational analyses of the C/D box snoRNAs have identified and mapped a large number of 2'-OH ribose methylations in rRNAs. In the present study, we systematically analyzed ribose methylations of 18S rRNA in Saccharomyces cerevisiae, using mung bean nuclease protection assay and RP-HPLC. Unexpectedly, we identified a hitherto unknown ribose methylation at position G562 in the helix 18 of 5' central domain of yeast 18S rRNA. Furthermore, we identified snR40 as being responsible to guide snoRNP complex to catalyze G562 ribose methylation, which makes it only second snoRNA known so far to target three ribose methylation sites: Gm562, Gm1271 in 18S rRNA, and Um898 in 25S rRNA. Our sequence and mutational analysis of snR40 revealed that snR40 uses the same D' box and methylation guide sequence for both Gm562 and Gm1271 methylation. With the identification of Gm562 and its corresponding snoRNA, complete set of ribose methylations of 18S rRNA and their corresponding snoRNAs have finally been established opening great prospects to understand the physiological function of these modifications. PMID:25653162

  17. 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

  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. 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...

  20. 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...

  1. 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

  2. Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity.

    PubMed

    Schmidl, Christian; Klug, Maja; Boeld, Tina J; Andreesen, Reinhard; Hoffmann, Petra; Edinger, Matthias; Rehli, Michael

    2009-07-01

    DNA methylation participates in establishing and maintaining chromatin structures and regulates gene transcription during mammalian development and cellular differentiation. With few exceptions, research thus far has focused on gene promoters, and little is known about the extent, functional relevance, and regulation of cell type-specific DNA methylation at promoter-distal sites. Here, we present a comprehensive analysis of differential DNA methylation in human conventional CD4(+) T cells (Tconv) and CD4(+)CD25(+) regulatory T cells (Treg), cell types whose differentiation and function are known to be controlled by epigenetic mechanisms. Using a novel approach that is based on the separation of a genome into methylated and unmethylated fractions, we examined the extent of lineage-specific DNA methylation across whole gene loci. More than 100 differentially methylated regions (DMRs) were identified that are present mainly in cell type-specific genes (e.g., FOXP3, IL2RA, CTLA4, CD40LG, and IFNG) and show differential patterns of histone H3 lysine 4 methylation. Interestingly, the majority of DMRs were located at promoter-distal sites, and many of these areas harbor DNA methylation-dependent enhancer activity in reporter gene assays. Thus, our study provides a comprehensive, locus-wide analysis of lineage-specific methylation patterns in Treg and Tconv cells, links cell type-specific DNA methylation with histone methylation and regulatory function, and identifies a number of cell type-specific, CpG methylation-sensitive enhancers in immunologically relevant genes. PMID:19494038

  3. 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...

  4. Pathodiagnostic parameters and evaluation of O⁶- methyl guanine methyl transferase gene promoter methylation in meningiomas.

    PubMed

    Jabini, Raheleh; Moradi, Afshin; Afsharnezhad, Sima; Ayatollahi, Hossein; Behravan, Javad; Raziee, Hamid Reza; Mosaffa, Fatemeh

    2014-04-01

    Histopathological evaluation and grading of meningioma give important prognostic information. We evaluated retrospectively monotonous sheeting, necrosis, hypercellularity, nuclear pleomorphism, small cell changes, brain invasion, mitosis, mast cells, psammoma bodies, MIB-1 labeling index (MIB-1 LI) and histological grade of 230 primary meningioma tumors according to the latest World Health Organization (WHO) classification. To reveal any possible association between clinical features and promoter hypermethylation of O(6)-methylguanine-DNA methyltransferase (MGMT) as an important epigenetic modification in many human cancers, we also evaluated the methylation status of MGMT in meningiomas by a SYBR-green-based real-time PCR method. There was a female predominance (2.38 to 1) in the meningiomas. The mean age of the patients was 49.9 ± 12.6 years (range 16 to 78 years). Transitional meningiomas were the most common subtype of the meningiomas (35.21%, n=81). Most of the meningiomas were located in the falx and parasagital area. There was a significant correlation between histopathological features of malignancy. These features were observed more frequently and with statistical relation to grade II rather than grade I. Mast cells, psammoma bodies and nuclear pleomorphism had poor associations (P>0.05). When we re-evaluated the tumor grading, 31 patients with grade I meningiomas were upgraded to grade II. None of the meningiomas tested by MSQP were methylated in MGMT promoter sequence. High MIB-1 LI could be indicative for higher grade of meningioma. Continuous revision of the classification system is needed to improve the accuracy of prognostic judgments in meningioma. The data confirm that there is no rationale to test meningiomas for MGMT methylation status. PMID:24398011

  5. 9-Methyl-beta-carboline has restorative effects in an animal model of Parkinson's disease.

    PubMed

    Wernicke, Catrin; Hellmann, Julian; Zieba, Barbara; Kuter, Katarzyna; Ossowska, Krystyna; Frenzel, Monika; Dencher, Norbert A; Rommelspacher, Hans

    2010-01-01

    In a previous study, a primary culture of midbrain cells was exposed to 9-methyl-beta-carboline for 48 h, which caused an increase in the number of tyrosine hydroxylase-positive cells. Quantitative RT-PCR revealed increased transcription of genes participating in the maturation of dopaminergic neurons. These in vitro findings prompted us to investigate the restorative actions of 9-methyl-beta-carboline in vivo. The compound was delivered for 14 days into the left cerebral ventricle of rats pretreated with the neurotoxin 1-methyl-4-phenyl-pyridinium ion (MPP+) for 28 days applying a dose which lowered dopamine by approximately 50%. Interestingly, 9-methyl-beta-carboline reversed the dopamine-lowering effect of the neurotoxin in the left striatum. Stereological counts of tyrosine hydroxylase-immunoreactive cells in the substantia nigra revealed that the neurotoxin caused a decrease in the number of those cells. However, when treated subsequently with 9-methyl-beta-carboline, the number reached normal values. In search of an explanation for the restorative activity, we analyzed the complexes that compose the respiratory chain in striatal mitochondria by 2-dimension gel electrophoresis followed by MALDI-TOF peptide mass fingerprinting.We found no changes in the overall composition of the complexes. However, the activity of complex I was increased by approximately 80% in mitochondria from rats treated with MPP+ and 9-methyl-beta-carboline compared to MPP+ and saline and to sham-operated rats, as determined by measurements of nicotinamide adenine dinucleotide dehydrogenase activity. Microarray technology and single RT-PCR revealed the induction of neurotrophins: brain-derived neurotrophic factor, conserved dopamine neurotrophic factor, cerebellin 1 precursor protein, and ciliary neurotrophic factor. Selected western blots yielded consistent results. The findings demonstrate restorative effects of 9-methyl-beta-carboline in an animal model of Parkinson's disease that improve the effectiveness of the respiratory chain and promote the transcription and expression of neurotrophin-related genes. PMID:20360614

  6. Shrubland fluxes of methyl bromide and methyl chloride

    NASA Astrophysics Data System (ADS)

    Rhew, Robert C.; Miller, Benjamin R.; Vollmer, Martin K.; Weiss, Ray F.

    2001-09-01

    Flux measurements in coastal sage scrub, chamise chaparral, and creosote bush scrub environments show that methyl bromide (CH3Br) and methyl chloride (CH3Cl), compounds that are involved in stratospheric ozone depletion, are both produced and consumed by southern California shrubland ecosystems. CH3Br and CH3Cl are produced in association with a variety of plants and are consumed by the soils, although there is a large variability in the fluxes, depending on predominant vegetation and environmental conditions. At sites with a net uptake of both compounds the fluxes of CH3Cl and CH3Br show a strong correlation, with a molar ratio of roughly 40:1, pointing to a similar mechanism of consumption. In contrast, the net production rates of these compounds show no apparent correlation with each other. The average observed net CH3Br uptake rates are an order of magnitude smaller than the previously reported average soil consumption rates assigned to shrublands. Extrapolations from our field measurements suggest that shrublands globally have a maximum net consumption of <1 Gg yr-1 for CH3Br and <20 Gg yr-1 for CH3Cl and may, in fact, be net sources for these compounds. Consequently, the measured net fluxes from shrubland ecosystems can account for part of the present imbalance in the CH3Br budget by adding a new source term and potentially reducing the soil sink term. These results also suggest that while shrubland soil consumption of CH3Cl may be small, soils in general may be a globally significant sink for CH3Cl.

  7. 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

  8. Interaction between N-vinylpyrrolidone and methyl methacrylate

    NASA Astrophysics Data System (ADS)

    Zaitseva, V. V.; Shtonda, A. V.; Tyurina, T. G.; Bagdasarova, A. R.; Zaitsev, S. Yu.

    2014-04-01

    It is established that the interaction of the isomers of N-vinylpyrrolidone (NVP) and methyl methacrylate (MMA) leads to the formation of molecular ?-H- and H-complexes with energies within the limits of 10.2-13.6 (AM1) or 18.2-24.0 (B3LYP/6-311++G( d)) kJ/mol. The structures of complex-bound molecules are examined with respect to changes in the charges on terminal -C1=C2- groups, the distance between them and atoms in an H-bond, and the presence of combined overlapping molecular orbitals (MOs). The presence of an averaged complex that includes presumably all possible structures and allows us to perform the copolymerization of specified monomers in the absence of an initiator is confirmed by means of UV and NMR spectroscopy.

  9. 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

  10. 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,...

  11. 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)

  12. Effects of DNA methylation on nucleosome stability.

    PubMed

    Collings, Clayton K; Waddell, Peter J; Anderson, John N

    2013-03-01

    Methylation of DNA at CpG dinucleotides represents one of the most important epigenetic mechanisms involved in the control of gene expression in vertebrate cells. In this report, we conducted nucleosome reconstitution experiments in conjunction with high-throughput sequencing on 572 KB of human DNA and 668 KB of mouse DNA that was unmethylated or methylated in order to investigate the effects of this epigenetic modification on the positioning and stability of nucleosomes. The results demonstrated that a subset of nucleosomes positioned by nucleotide sequence was sensitive to methylation where the modification increased the affinity of these sequences for the histone octamer. The features that distinguished these nucleosomes from the bulk of the methylation-insensitive nucleosomes were an increase in the frequency of CpG dinucleotides and a unique rotational orientation of CpGs such that their minor grooves tended to face toward the histones in the nucleosome rather than away. These methylation-sensitive nucleosomes were preferentially associated with exons as compared to introns while unmethylated CpG islands near transcription start sites became enriched in nucleosomes upon methylation. The results of this study suggest that the effects of DNA methylation on nucleosome stability in vitro can recapitulate what has been observed in the cell and provide a direct link between DNA methylation and the structure and function of chromatin. PMID:23355616

  13. 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 ...

  14. 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 ...

  15. Epigenetic DNA Methylation Linked to Social Dominance

    PubMed Central

    Lenkov, Kapa; Lee, Mi H.; Lenkov, Olga D.; Swafford, Andrew; Fernald, Russell D.

    2015-01-01

    Social status hierarchies are ubiquitous in vertebrate social systems, including humans. It is well known that social rank can influence quality of life dramatically among members of social groups. For example, high-ranking individuals have greater access to resources, including food and mating prerogatives that, in turn, have a positive impact on their reproductive success and health. In contrast low ranking individuals typically have limited reproductive success and may experience lasting social and physiological costs. Ultimately, social rank and behavior are regulated by changes in gene expression. However, little is known about mechanisms that transduce social cues into transcriptional changes. Since social behavior is a dynamic process, we hypothesized that a molecular mechanism such as DNA methylation might play a role these changes. To test this hypothesis, we used an African cichlid fish, Astatotilapia burtoni, in which social rank dictates reproductive access. We show that manipulating global DNA methylation state strongly biases the outcomes of social encounters. Injecting DNA methylating and de-methylating agents in low status animals competing for status, we found that animals with chemically increased methylation states were statistically highly likely to ascend in rank. In contrast, those with inhibited methylation processes and thus lower methylation levels were statistically highly unlikely to ascend in rank. This suggests that among its many roles, DNA methylation may be linked to social status and more generally to social behavior. PMID:26717574

  16. Measuring methyl bromide emissions from fields

    SciTech Connect

    Yates, S.R.; Gan, J.; Ernst, F.F.; Yates, M.V.

    1995-12-31

    Methyl bromide is used extensively for pest control. Recent evidence suggests that methyl bromide may react with stratospheric ozone and, due to the Clean Air Act, is scheduled for phase-out within the next 5 to 10 years. As indicated in a recent report from The National Agricultural Pesticide Impact Assessment Program, there will be substantial economic impact on the agricultural community if the use of methyl bromide is restricted. There are several areas of uncertainty concerning the agricultural use of methyl bromide. Foremost is the quantification of mass emitted to the atmosphere from agricultural fields. To address this, two field experiments were conducted to directly measure methyl bromide emissions. In the first experiment, methyl bromide was injected at approximately 25 cm depth and the soil was covered with 1 mil high-density polyethylene plastic. The second experiment was similar except that methyl bromide was injected at approximately 68 cm depth and the soil was not covered. From these experiments, the emission rate into the atmosphere and the subsurface transport of methyl bromide was determined. Both experiments include a field-scale mass balance to verify the accuracy of the flux-measurement methods as well as to check data consistency. The volatilization rate and mass lost was determined from estimates of the degradation and from several atmospheric and chamber flux methods.

  17. 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 21.116 Methyl alcohol. Specific gravity at 15.56...

  18. 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.

  19. 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

  20. Arginine methylation initiates BMP-induced Smad signaling

    PubMed Central

    Xu, Jian; Wang, A. Hongjun; Oses-Prieto, Juan; Makhijani, Kalpana; Katsuno, Yoko; Pei, Ming; Yan, Leilei; Zheng, Y. George; Burlingame, Alma; Brckner, Katja; Derynck, Rik

    2014-01-01

    Summary Kinase activation and substrate phosphorylation commonly form the backbone of signaling cascades. Bone morphogenetic proteins (BMPs), a subclass of TGF-? family ligands, induce activation of their signaling effectors, the Smads, through C-terminal phosphorylation by transmembrane receptor kinases. However, the slow kinetics of Smad activation in response to BMP suggests a preceding step in the initiation of BMP signaling. We now show that arginine methylation, which is known to regulate gene expression, yet also modifies some signaling mediators, initiates BMP-induced Smad signaling. BMP-induced receptor complex formation promotes interaction of the methyltransferase PRMT1 with the inhibitory Smad6, resulting in Smad6 methylation and relocalization at the receptor, leading to activation of effector Smads through phosphorylation. PRMT1 is required for BMP-induced biological responses across species, as evidenced by the role of its ortholog Dart1 in BMP signaling during Drosophila wing development. Activation of signaling by arginine methylation may also apply to other signaling pathways. PMID:23747011

  1. Cardiovascular epigenetics: from DNA methylation to microRNAs.

    PubMed

    Udali, Silvia; Guarini, Patrizia; Moruzzi, Sara; Choi, Sang-Woon; Friso, Simonetta

    2013-01-01

    Epigenetic phenomena are defined as heritable mechanisms that establish and maintain mitotically stable patterns of gene expression without modifying the base sequence of DNA. The major epigenetic features of mammalian cells include DNA methylation, post-translational histone modifications and RNA-based mechanisms including those controlled by small non-coding RNAs (miRNAs). The impact of epigenetic mechanisms in cardiovascular pathophysiology is now emerging as a major player in the interface between genotype to phenotype variability. This topic of research has strict implications on disease development and progression, and opens up possible novel preventive strategies in cardiovascular disease. An important aspect of epigenetic mechanisms is that they are potentially reversible and may be influenced by nutritional-environmental factors and through gene-environment interactions, all of which have an important role in complex, multifactorial diseases such as those affecting the cardiovascular system. Gene expression regulation through the interplay of DNA methylation and histone modifications is well-established, although the knowledge about the function of epigenetic signatures in cardiovascular disease is still largely unexplored. The study of epigenetic markers is, therefore, a very promising frontier of science which may aid in a deeper understanding of molecular mechanisms underlying the modulation of gene expression in the biomolecule pathways linked to cardiovascular diseases. This review focuses on up-to-date knowledge pertaining to the role of epigenetics, from DNA methylation to miRNAs, in major cardiovascular diseases such as ischemic heart disease, hypertension, heart failure and stroke. PMID:22981780

  2. Crystal structure of di-aqua-bis-(2,6-di-methyl-pyrazine-?N (4))bis-(thio-cyanato-?N)cobalt(II) 2,5-di-methyl-pyrazine monosolvate.

    PubMed

    Suckert, Stefan; Whlert, Susanne; Jess, Inke; Nther, Christian

    2015-12-01

    In the crystal structure of the title compound, [Co(NCS)2(C6H8N2)2(H2O)2]C6H8N2, the Co(II) cation is coordinated by the N atoms of two terminal thio-cyanate anions, the O atoms of two water mol-ecules and two N atoms of two 2,6-di-methyl-pyrazine ligands. The coordination sphere of the resulting discrete complex is that of a slightly distorted octa-hedron. The asymmetric unit comprises a Co(II) cation and half of a 2,5-di-methyl-pyrazine ligand, both of which are located on centres of inversion, and a water ligand, a 2,6-di--methyl-pyrazine ligand and one thio-cyanate anion in general positions. In the crystal, the discrete complexes are arranged in such a way that cavities are formed in which the 2,5-di-methyl-pyrazine solvent mol-ecules are located. The coordination of the 2,5-di-methyl-pyrazine mol-ecules to the metal is apparently hindered due to the bulky methyl groups in vicinal positions to the N atoms, leading to a preferential coordination of the 2,6-di-methyl-pyrazine ligands. The discrete complexes are linked by O-H?N hydrogen bonds between one water H atom and the non-coordinating N atom of the 2,6-di-methyl-pyrazine ligands. The remaining water H atom is hydrogen bonded to one N atom of the 2,5-di-methyl-pyrazine solvent mol-ecule. This arrangement leads to the formation of a two-dimensional network extending parallel to (010). PMID:26870445

  3. Crystal structure of diaquabis(2,6-dimethylpyrazine-?N 4)bis(thiocyanato-?N)cobalt(II) 2,5-dimethylpyrazine monosolvate

    PubMed Central

    Suckert, Stefan; Whlert, Susanne; Jess, Inke; Nther, Christian

    2015-01-01

    In the crystal structure of the title compound, [Co(NCS)2(C6H8N2)2(H2O)2]C6H8N2, the CoII cation is coordinated by the N atoms of two terminal thiocyanate anions, the O atoms of two water molecules and two N atoms of two 2,6-dimethylpyrazine ligands. The coordination sphere of the resulting discrete complex is that of a slightly distorted octahedron. The asymmetric unit comprises a CoII cation and half of a 2,5-dimethylpyrazine ligand, both of which are located on centres of inversion, and a water ligand, a 2,6-dimethylpyrazine ligand and one thiocyanate anion in general positions. In the crystal, the discrete complexes are arranged in such a way that cavities are formed in which the 2,5-dimethylpyrazine solvent molecules are located. The coordination of the 2,5-dimethylpyrazine molecules to the metal is apparently hindered due to the bulky methyl groups in vicinal positions to the N atoms, leading to a preferential coordination of the 2,6-dimethylpyrazine ligands. The discrete complexes are linked by OH?N hydrogen bonds between one water H atom and the non-coordinating N atom of the 2,6-dimethylpyrazine ligands. The remaining water H atom is hydrogen bonded to one N atom of the 2,5-dimethylpyrazine solvent molecule. This arrangement leads to the formation of a two-dimensional network extending parallel to (010). PMID:26870445

  4. Mercury methylation by fish intestinal contents.

    PubMed Central

    Rudd, J W; Furutani, A; Turner, M A

    1980-01-01

    A new radiochemical method has been applied to the examination of mercury methylation in fish intestinal contents. Intestinal contents of six freshwater fish species were found capable of converting 203Hg2+ to CH3203Hg+. This activity was observed in fish from five of six lakes tested whether or not there was mercury pollution. Bacterial activity in the intestinal contents is most likely responsible for this methylation. Methylating activity of piscivors increased with decreasing quantity of intestinal contents. Generally, pike and walleye intestinal contents methylated a larger fraction of 203Hg2+ than those of whitefish and suckers. These data contradict the previous general conclusion that there is no mercury methylation in fish. PMID:7425625

  5. 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.

  6. 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

  7. Targets of RNA-directed DNA methylation.

    PubMed

    Matzke, Marjori; Kanno, Tatsuo; Huettel, Bruno; Daxinger, Lucia; Matzke, Antonius J M

    2007-10-01

    RNA-directed DNA methylation contributes substantially to epigenetic regulation of the plant genome. Methylation is guided to homologous DNA target sequences by 24 nt 'heterochromatic' small RNAs produced by nucleolar-localized components of the RNAi machinery and a plant-specific RNA polymerase, Pol IV. Plants contain unusually large and diverse populations of small RNAs, many of which originate from transposons and repeats. These sequences are frequent targets of methylation, and they are able to bring plant genes in their vicinity under small RNA-mediated control. RNA-directed DNA methylation can be removed by enzymatic demethylation, providing plants with a versatile system that facilitates epigenetic plasticity. In addition to subduing transposons, RNA-directed DNA methylation has roles in plant development and, perhaps, stress responses. PMID:17702644

  8. 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

  9. DNA methylation and hydroxymethylation in stem cells.

    PubMed

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

    2015-06-01

    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

  10. DMEAS: DNA methylation entropy analysis software

    PubMed Central

    He, Jianlin; Sun, Xinxi; Shao, Xiaojian; Liang, Liji; Xie, Hehuang

    2013-01-01

    Summary: DMEAS is the first user-friendly tool dedicated to analyze the distribution of DNA methylation patterns for the quantification of epigenetic heterogeneity. It supports the analysis of both locus-specific and genome-wide bisulfite sequencing data. DMEAS progressively scans the mapping results of bisulfite sequencing reads to extract DNA methylation patterns for contiguous CpG dinucleotides. It determines the DNA methylation level and calculates methylation entropy for genomic segments to enable the quantitative assessment of DNA methylation variations observed in cell populations. Availability and implementation: DMEAS program, user guide and all the testing data are freely available from http://sourceforge.net/projects/dmeas/files/ Contact: davidxie@vt.edu Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:23749987

  11. 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

  12. DNA Methylation Profiling Identifies Global Methylation Differences and Markers of Adrenocortical Tumors

    PubMed Central

    Rechache, Nesrin S.; Wang, Yonghong; Stevenson, Holly S.; Killian, J. Keith; Edelman, Daniel C.; Merino, Maria; Zhang, Lisa; Nilubol, Naris; Stratakis, Constantine A.; Meltzer, Paul S.

    2012-01-01

    Context: It is not known whether there are any DNA methylation alterations in adrenocortical tumors. Objective: The objective of the study was to determine the methylation profile of normal adrenal cortex and benign and malignant adrenocortical tumors. Methods: Genome-wide methylation status of CpG regions were determined in normal (n = 19), benign (n = 48), primary malignant (n = 8), and metastatic malignant (n = 12) adrenocortical tissue samples. An integrated analysis of genome-wide methylation and mRNA expression in benign vs. malignant adrenocortical tissue samples was also performed. Results: Methylation profiling revealed the following: 1) that methylation patterns were distinctly different and could distinguish normal, benign, primary malignant, and metastatic tissue samples; 2) that malignant samples have global hypomethylation; and 3) that the methylation of CpG regions are different in benign adrenocortical tumors by functional status. Normal compared with benign samples had the least amount of methylation differences, whereas normal compared with primary and metastatic adrenocortical carcinoma samples had the greatest variability in methylation (adjusted P ? 0.01). Of 215 down-regulated genes (?2-fold, adjusted P ? 0.05) in malignant primary adrenocortical tumor samples, 52 of these genes were also hypermethylated. Conclusions: Malignant adrenocortical tumors are globally hypomethylated as compared with normal and benign tumors. Methylation profile differences may accurately distinguish between primary benign and malignant adrenocortical tumors. Several differentially methylated sites are associated with genes known to be dysregulated in malignant adrenocortical tumors. PMID:22472567

  13. The origin and fate of 4-methyl steroid hydrocarbons. I. Diagenesis of 4-methyl sterenes

    NASA Astrophysics Data System (ADS)

    Wolff, George A.; Lamb, Neil A.; Maxwell, James R.

    1986-03-01

    Treatment of 4-methylcholest-4-ene under mild acid conditions at low temperatures gives chemical evidence for certain features seen in the distributions of sedimentary 4-methyl steroid hydrocarbons, and further indicates that many low temperature diagenetic reactions of steroids are explicable in terms of acid catalysed rearrangements. Specifically, the results provide: (i) Indirect evidence that the 4-ene skeleton is a key intermediate in the dehydration of 4-methyl stanols in sediments. (ii) An explanation for the distribution of 4-methyl sterenes and A-nor sterenes in the lacustrine Messel shale (Eocene). (iii) An explanation for the presence of 4?-methyl steranes in relatively immature sedimentary rocks, despite the precursor stanols having the 4?-methyl configuration. With increasing maturity in the Paris Basin shales (Lower Toarcian), the less stable 4?-methyl steranes decrease gradually in abundance relative to their 4?-methyl counterparts, at a rate fairly similar to the change in pristane stereochemistry.

  14. 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

  15. cis-Dichloridobis(ethyl methyl sulfide-?S)oxidovanadium(IV)

    PubMed Central

    Matsuura, Masatoshi; Fujihara, Takashi; Nagasawa, Akira

    2013-01-01

    The mononuclear title complex, [VCl2O(C3H8S)2], features a VIV=O double bond [1.5845?(15)?] in an overall trigonalbipyramidal coordination environment defined by two Cl? and the S atoms of two (CH3CH2)(CH3)S ligands. In the crystal, pairs of molecules form centrosymmetric dimers via CH?O hydrogen bonds between the methyl CH group and the oxidovanadium O atom of a neighbouring molecule. PMID:23634004

  16. 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

  17. Is the Fungus Magnaporthe Losing DNA Methylation?

    PubMed Central

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

    2013-01-01

    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

  18. 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

    ... substances benzenamine, 4-chloro-2-methyl- (CAS Number 95-69-2); benzenamine, 4-chloro-2-methyl-, hydrochloride (CAS Number 3165-93-3); and benzenamine, 2-chloro-6-methyl- (CAS Number 87-63-8) are subject...

  19. 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. PMID:25690533

  20. 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

  1. Hormone stimulation of androgen receptor mediates dynamic changes in DNA methylation patterns at regulatory elements

    PubMed Central

    Dhiman, Vineet K.; Attwood, Kristopher; Campbell, Moray J.; Smiraglia, Dominic J.

    2015-01-01

    DNA methylation is an epigenetic modification that contributes to stable gene silencing by interfering with the ability of transcriptional regulators to bind to DNA. Recent findings have revealed that hormone stimulation of certain nuclear receptors induces rapid, dynamic changes in DNA methylation patterns alongside transcriptional responses at a subset of target loci, over time. However, the ability of androgen receptor (AR) to dynamically regulate gene transcription is relatively under-studied and its role in the regulation of DNA methylation patterns remains to be elucidated. Here we demonstrate in normal prostate cells that hormone stimulated AR activity results in dynamic changes in the transcription rate and DNA methylation patterns at the AR target genes, TIPARP and SGK1. Time-resolved chromatin immunoprecipitation experiments on the SGK1 locus reveals dynamic recruitment of AR and RNA Polymerase II, as well as the recruitment of proteins involved in the DNA demethylation process, TET1 and TDG. Furthermore, the presence of DNA methylation at dynamic regions inhibits protein binding and transcriptional activity of SGK1. These findings establish AR activity as a contributing factor to the dynamic regulation of DNA methylation patterns at target genes in prostate biology and infer further complexity involved in nuclear receptor mediation of transcriptional regulation. PMID:26646795

  2. An Alternative Mechanism for the Methylation of Phosphoethanolamine Catalyzed by Plasmodium falciparum Phosphoethanolamine Methyltransferase*?

    PubMed Central

    Saen-oon, Suwipa; Lee, Soon Goo; Jez, Joseph M.; Guallar, Victor

    2014-01-01

    The phosphobase methylation pathway catalyzed by the phosphoethanolamine methyltransferase in Plasmodium falciparum (PfPMT), the malaria parasite, offers an attractive target for anti-parasitic drug development. PfPMT methylates phosphoethanolamine (pEA) to phosphocholine for use in membrane biogenesis. Quantum mechanics and molecular mechanics (QM/MM) calculations tested the proposed reaction mechanism for methylation of pEA involving the previously identified Tyr-19His-132 dyad, which indicated an energetically unfavorable mechanism. Instead, the QM/MM calculations suggested an alternative mechanism involving Asp-128. The reaction coordinate involves the stepwise transfer of a proton to Asp-128 via a bridging water molecule followed by a typical Sn2-type methyl transfer from S-adenosylmethionine to pEA. Functional analysis of the D128A, D128E, D128Q, and D128N PfPMT mutants shows a loss of activity with pEA but not with the final substrate of the methylation pathway. X-ray crystal structures of the PfPMT-D128A mutant in complex with S-adenosylhomocysteine and either pEA or phosphocholine reveal how mutation of Asp-128 disrupts a hydrogen bond network in the active site. The combined QM/MM, biochemical, and structural studies identify a key role for Asp-128 in the initial step of the phosphobase methylation pathway in Plasmodium and provide molecular insight on the evolution of multiple activities in the active site of the PMT. PMID:25288796

  3. 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

  4. 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 genotypemethylation correlations within a 1.01.5 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

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

    PubMed Central

    Nicolas, Pierre; Kim, Kyoung-Mee; Shibata, Darryl; Tavar, 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 cellniche 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

  6. Examining the Causes and Consequences of Context-Specific Differential DNA Methylation in Maize.

    PubMed

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

    2015-08-01

    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

  7. Hormone stimulation of androgen receptor mediates dynamic changes in DNA methylation patterns at regulatory elements.

    PubMed

    Dhiman, Vineet K; Attwood, Kristopher; Campbell, Moray J; Smiraglia, Dominic J

    2015-12-15

    DNA methylation is an epigenetic modification that contributes to stable gene silencing by interfering with the ability of transcriptional regulators to bind to DNA. Recent findings have revealed that hormone stimulation of certain nuclear receptors induces rapid, dynamic changes in DNA methylation patterns alongside transcriptional responses at a subset of target loci, over time. However, the ability of androgen receptor (AR) to dynamically regulate gene transcription is relatively under-studied and its role in the regulation of DNA methylation patterns remains to be elucidated. Here we demonstrate in normal prostate cells that hormone stimulated AR activity results in dynamic changes in the transcription rate and DNA methylation patterns at the AR target genes, TIPARP and SGK1. Time-resolved chromatin immunoprecipitation experiments on the SGK1 locus reveals dynamic recruitment of AR and RNA Polymerase II, as well as the recruitment of proteins involved in the DNA demethylation process, TET1 and TDG. Furthermore, the presence of DNA methylation at dynamic regions inhibits protein binding and transcriptional activity of SGK1. These findings establish AR activity as a contributing factor to the dynamic regulation of DNA methylation patterns at target genes in prostate biology and infer further complexity involved in nuclear receptor mediation of transcriptional regulation. PMID:26646795

  8. Polycomb Binding Precedes Early-Life Stress Responsive DNA Methylation at the Avp Enhancer

    PubMed Central

    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

  9. 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

  10. 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 (± 1σ) 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.

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. Structural insights into the methyl donor recognition model of a novel membrane-binding protein UbiG

    PubMed Central

    Zhu, Yuwei; Jiang, Xuguang; Wang, Chongyuan; Liu, Yang; Fan, Xiaojiao; Zhang, Linjuan; Niu, Liwen; Teng, Maikun; Li, Xu

    2016-01-01

    UbiG is a SAM-dependent O-methyltransferase, catalyzing two O-methyl transfer steps for ubiquinone biosynthesis in Escherichia coli. UbiG possesses a unique sequence insertion between β4 and α10, which is used for membrane lipid interaction. Interestingly, this sequence insertion also covers the methyl donor binding pocket. Thus, the relationship between membrane binding and entrance of the methyl donor of UbiG during the O-methyl transfer process is a question that deserves further exploration. In this study, we reveal that the membrane-binding region of UbiG gates the entrance of methyl donor. When bound with liposome, UbiG displays an enhanced binding ability toward the methyl donor product S-adenosylhomocysteine. We further employ protein engineering strategies to design UbiG mutants by truncating the membrane interacting region or making it more flexible. The ITC results show that the binding affinity of these mutants to SAH increases significantly compared with that of the wild-type UbiG. Moreover, we determine the structure of UbiG∆165–187 in complex with SAH. Collectively, our results provide a new angle to cognize the relationship between membrane binding and entrance of the methyl donor of UbiG, which is of benefit for better understanding the O-methyl transfer process for ubiquinone biosynthesis. PMID:26975567

  16. 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

  17. Structural insights into the methyl donor recognition model of a novel membrane-binding protein UbiG.

    PubMed

    Zhu, Yuwei; Jiang, Xuguang; Wang, Chongyuan; Liu, Yang; Fan, Xiaojiao; Zhang, Linjuan; Niu, Liwen; Teng, Maikun; Li, Xu

    2016-01-01

    UbiG is a SAM-dependent O-methyltransferase, catalyzing two O-methyl transfer steps for ubiquinone biosynthesis in Escherichia coli. UbiG possesses a unique sequence insertion between β4 and α10, which is used for membrane lipid interaction. Interestingly, this sequence insertion also covers the methyl donor binding pocket. Thus, the relationship between membrane binding and entrance of the methyl donor of UbiG during the O-methyl transfer process is a question that deserves further exploration. In this study, we reveal that the membrane-binding region of UbiG gates the entrance of methyl donor. When bound with liposome, UbiG displays an enhanced binding ability toward the methyl donor product S-adenosylhomocysteine. We further employ protein engineering strategies to design UbiG mutants by truncating the membrane interacting region or making it more flexible. The ITC results show that the binding affinity of these mutants to SAH increases significantly compared with that of the wild-type UbiG. Moreover, we determine the structure of UbiG∆(165-187) in complex with SAH. Collectively, our results provide a new angle to cognize the relationship between membrane binding and entrance of the methyl donor of UbiG, which is of benefit for better understanding the O-methyl transfer process for ubiquinone biosynthesis. PMID:26975567

  18. HDA6, a putative histone deacetylase needed to enhance DNA methylation induced by double-stranded RNA

    PubMed Central

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

    2002-01-01

    To analyze relationships between RNA signals, DNA methylation and chromatin modifications, we performed a genetic screen to recover Arabidopsis mutants defective in RNA-directed transcriptional silencing and methylation of a nopaline synthase promoterneomycinphosphotransferase II (NOSpro NPTII) target gene. Mutants were identified by screening for recovery of kanamycin resistance in the presence of an unlinked silencing complex encoding NOSpro double-stranded RNA. One mutant, rts1 (RNA-mediated transcriptional silencing), displayed moderate recovery of NPTII gene expression and partial loss of methylation in the target NOSpro, predominantly at symmetrical C(N)Gs. The RTS1 gene was isolated by positional cloning and found to encode a putative histone deacetylase, HDA6. The more substantial decrease in methylation of symmetrical compared with asymmetrical cytosines in rts1 mutants suggests that HDA6 is dispensable for RNA-directed de novo methylation, which results in intermediate methylation of cytosines in all sequence contexts, but is necessary for reinforcing primarily C(N)G methylation induced by RNA. Because CG methylation in centromeric and rDNA repeats was not reduced in rts1 mutants, HDA6 might be specialized for the RNA- directed pathway of genome modification. PMID:12486004

  19. Regulation of the transcriptional program by DNA methylation during human αβ T-cell development

    PubMed Central

    Rodriguez, Ramon M.; Suarez-Alvarez, Beatriz; Mosén-Ansorena, David; García-Peydró, Marina; Fuentes, Patricia; García-León, María J.; Gonzalez-Lahera, Aintzane; Macias-Camara, Nuria; Toribio, María L.; Aransay, Ana M.; Lopez-Larrea, Carlos

    2015-01-01

    Thymocyte differentiation is a complex process involving well-defined sequential developmental stages that ultimately result in the generation of mature T-cells. In this study, we analyzed DNA methylation and gene expression profiles at successive human thymus developmental stages. Gain and loss of methylation occurred during thymocyte differentiation, but DNA demethylation was much more frequent than de novo methylation and more strongly correlated with gene expression. These changes took place in CpG-poor regions and were closely associated with T-cell differentiation and TCR function. Up to 88 genes that encode transcriptional regulators, some of whose functions in T-cell development are as yet unknown, were differentially methylated during differentiation. Interestingly, no reversion of accumulated DNA methylation changes was observed as differentiation progressed, except in a very small subset of key genes (RAG1, RAG2, CD8A, PTCRA, etc.), indicating that methylation changes are mostly unique and irreversible events. Our study explores the contribution of DNA methylation to T-cell lymphopoiesis and provides a fine-scale map of differentially methylated regions associated with gene expression changes. These can lay the molecular foundations for a better interpretation of the regulatory networks driving human thymopoiesis. PMID:25539926

  20. A Short and Efficient Synthetic Route to Methyl ?-Trioxacarcinoside B and Anomerically Activated Derivatives

    PubMed Central

    Magauer, Thomas; Myers, Andrew G.

    2011-01-01

    A 9-step synthetic route to the complex carbohydrate me