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Sample records for methylated caffeine-silveri complex

  1. Methyl Complexes of the Transition Metals.

    PubMed

    Campos, Jesús; López-Serrano, Joaquín; Peloso, Riccardo; Carmona, Ernesto

    2016-05-01

    Organometallic chemistry can be considered as a wide area of knowledge that combines concepts of classic organic chemistry, that is, based essentially on carbon, with molecular inorganic chemistry, especially with coordination compounds. Transition-metal methyl complexes probably represent the simplest and most fundamental way to view how these two major areas of chemistry combine and merge into novel species with intriguing features in terms of reactivity, structure, and bonding. Citing more than 500 bibliographic references, this review aims to offer a concise view of recent advances in the field of transition-metal complexes containing M-CH3 fragments. Taking into account the impressive amount of data that are continuously provided by organometallic chemists in this area, this review is mainly focused on results of the last five years. After a panoramic overview on M-CH3 compounds of Groups 3 to 11, which includes the most recent landmark findings in this area, two further sections are dedicated to methyl-bridged complexes and reactivity.

  2. Environmental effects of inclusion complexation between methylated beta-cyclodextrin and diclofop-methyl.

    PubMed

    Cai, Xiyun; Liu, Weiping; Chen, Shengwen

    2005-08-24

    Diclofop-methyl (DM) is a broad-spectrum herbicide but often shows a reduced biological activity against the target grasses due to its poor water solubility and slow translocation within plant tissues. Randomly methylated beta-cyclodextrin (MCD) is an effective inclusion complexation agent and, as a potential formulation additive, may thus improve the behavior of DM. We evaluated the complexing role of MCD by measuring the solubility and soil sorption of DM as a function of MCD concentration, as well as the dissolution rates of DM-MCD complexes. The complex was also extensively characterized by UV, fluorescence, Fourier transform infrared, nuclear magnetic resonance, and differential scanning calorimetry techniques. The apparent solubility of DM linearly increased with MCD concentration, indicating the formation of a 1:1 complex. In contrast, diclofop was not complexed by MCD. The DM-MCD complex appeared to have formed within the hydrophobic cavity of MCD. With the measured stability constant of 4740 L mol(-)(1), the complex was apparently stable, which resulted in DM resistant to hydrolysis, and hence the ratio of DM to the sum of DM and diclofop increased toward unity with increasing MCD concentration. The DM-MCD complex also quickly dissolved to a maximum within 5 min, due presumably to the hydrophilicity of MCD. The sorption of DM by soil was significantly reduced in the presence of MCD. All the results suggest that MCD may effectively improve the availability of DM to pests and for bioremediation.

  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. An osmium-DNA interstrand complex: application to facile DNA methylation analysis.

    PubMed

    Tanaka, Kazuo; Tainaka, Kazuki; Umemoto, Tadashi; Nomura, Akiko; Okamoto, Akimitsu

    2007-11-21

    Nucleic acids often acquire new functions by forming a variety of complexes with metal ions. Osmium, in an oxidized state, also reacts with C5-methylated pyrimidines. However, control of the sequence specificity of osmium complexation with DNA is still immature, and the value of the resulting complexes is unknown. We have designed a bipyridine-attached adenine derivative for sequence-specific osmium complexation. Sequence-specific osmium complexation was achieved by hybridization of a short DNA molecule containing this functional nucleotide to a target DNA sequence and resulted in the formation of a cross-linked structure. The interstrand cross-link clearly distinguished methylated cytosines from unmethylated cytosines and was used to quantify the degree of methylation at a specific cytosine in the genome.

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

    PubMed

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

    2015-01-01

    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.

  6. 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

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

    SciTech Connect

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

    2012-10-23

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

  8. G9a/GLP Complex Maintains Imprinted DNA Methylation in Embryonic Stem Cells

    PubMed Central

    Zhang, Tuo; Termanis, Ausma; Özkan, Burak; Bao, Xun X.; Culley, Jayne; de Lima Alves, Flavia; Rappsilber, Juri; Ramsahoye, Bernard; Stancheva, Irina

    2016-01-01

    Summary DNA methylation at imprinting control regions (ICRs) is established in gametes in a sex-specific manner and has to be stably maintained during development and in somatic cells to ensure the correct monoallelic expression of imprinted genes. In addition to DNA methylation, the ICRs are marked by allele-specific histone modifications. Whether these marks are essential for maintenance of genomic imprinting is largely unclear. Here, we show that the histone H3 lysine 9 methylases G9a and GLP are required for stable maintenance of imprinted DNA methylation in embryonic stem cells; however, their catalytic activity and the G9a/GLP-dependent H3K9me2 mark are completely dispensable for imprinting maintenance despite the genome-wide loss of non-imprinted DNA methylation in H3K9me2-depleted cells. We provide additional evidence that the G9a/GLP complex protects imprinted DNA methylation by recruitment of de novo DNA methyltransferases, which antagonize TET dioxygenass-dependent erosion of DNA methylation at ICRs. PMID:27052169

  9. Methylation of secondary amines with dialkyl carbonates and hydrosilanes catalysed by iron complexes.

    PubMed

    Zheng, Jianxia; Darcel, Christophe; Sortais, Jean-Baptiste

    2014-11-25

    Methylation of secondary amines was achieved using dimethyl carbonate or diethyl carbonate as the C1 source under the catalysis of well-defined half-sandwich iron complexes bearing an N-heterocyclic carbene ligand. The reaction proceeded under mild conditions in the presence of hydrosilanes as the reductants, and the amines were obtained with good to excellent isolated yields. PMID:25285339

  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. Using epigenome-wide association scans of DNA methylation in age-related complex human traits.

    PubMed

    Tsai, Pei-Chien; Spector, Tim D; Bell, Jordana T

    2012-10-01

    With rapid technological advancements emerging epigenetic studies of complex traits have shifted from candidate gene analyses towards epigenome-wide association studies (EWAS). EWAS aim to systematically identify epigenetic variants across the genome that associate with complex phenotypes. Recent EWAS using case-control and disease-discordant identical twin designs have identified phenotype-associated differentially methylated regions for several traits. However, EWAS still face many challenges related to methodology, design and interpretation, owing to the dynamic nature of epigenetic variants over time. This article reviews analytical considerations in conducting EWAS and recent applications of this approach to human aging and age-related complex traits. PMID:23130833

  12. 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.

  13. Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation

    PubMed Central

    Zhang, Yi; Ng, Huck-Hui; Erdjument-Bromage, Hediye; Tempst, Paul; Bird, Adrian; Reinberg, Danny

    1999-01-01

    ATP-dependent nucleosome remodeling and core histone acetylation and deacetylation represent mechanisms to alter nucleosome structure. NuRD is a multisubunit complex containing nucleosome remodeling and histone deacetylase activities. The histone deacetylases HDAC1 and HDAC2 and the histone binding proteins RbAp48 and RbAp46 form a core complex shared between NuRD and Sin3-histone deacetylase complexes. The histone deacetylase activity of the core complex is severely compromised. A novel polypeptide highly related to the metastasis-associated protein 1, MTA2, and the methyl-CpG-binding domain-containing protein, MBD3, were found to be subunits of the NuRD complex. MTA2 modulates the enzymatic activity of the histone deacetylase core complex. MBD3 mediates the association of MTA2 with the core histone deacetylase complex. MBD3 does not directly bind methylated DNA but is highly related to MBD2, a polypeptide that binds to methylated DNA and has been reported to possess demethylase activity. MBD2 interacts with the NuRD complex and directs the complex to methylated DNA. NuRD may provide a means of gene silencing by DNA methylation. PMID:10444591

  14. Allele-Specific Methylation Occurs at Genetic Variants Associated with Complex Disease

    PubMed Central

    Hutchinson, John N.; Raj, Towfique; Fagerness, Jes; Stahl, Eli; Viloria, Fernando T.; Gimelbrant, Alexander; Seddon, Johanna; Daly, Mark; Chess, Andrew; Plenge, Robert

    2014-01-01

    We hypothesize that the phenomenon of allele-specific methylation (ASM) may underlie the phenotypic effects of multiple variants identified by Genome-Wide Association studies (GWAS). We evaluate ASM in a human population and document its genome-wide patterns in an initial screen at up to 380,678 sites within the genome, or up to 5% of the total genomic CpGs. We show that while substantial inter-individual variation exists, 5% of assessed sites show evidence of ASM in at least six samples; the majority of these events (81%) are under genetic influence. Many of these cis-regulated ASM variants are also eQTLs in peripheral blood mononuclear cells and monocytes and/or in high linkage-disequilibrium with variants linked to complex disease. Finally, focusing on autoimmune phenotypes, we extend this initial screen to confirm the association of cis-regulated ASM with multiple complex disease-associated variants in an independent population using next-generation bisulfite sequencing. These four variants are implicated in complex phenotypes such as ulcerative colitis and AIDS progression disease (rs10491434), Celiac disease (rs2762051), Crohn's disease, IgA nephropathy and early-onset inflammatory bowel disease (rs713875) and height (rs6569648). Our results suggest cis-regulated ASM may provide a mechanistic link between the non-coding genetic changes and phenotypic variation observed in these diseases and further suggests a route to integrating DNA methylation status with GWAS results. PMID:24911414

  15. 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.

  16. Allele-specific methylation occurs at genetic variants associated with complex disease.

    PubMed

    Hutchinson, John N; Raj, Towfique; Fagerness, Jes; Stahl, Eli; Viloria, Fernando T; Gimelbrant, Alexander; Seddon, Johanna; Daly, Mark; Chess, Andrew; Plenge, Robert

    2014-01-01

    We hypothesize that the phenomenon of allele-specific methylation (ASM) may underlie the phenotypic effects of multiple variants identified by Genome-Wide Association studies (GWAS). We evaluate ASM in a human population and document its genome-wide patterns in an initial screen at up to 380,678 sites within the genome, or up to 5% of the total genomic CpGs. We show that while substantial inter-individual variation exists, 5% of assessed sites show evidence of ASM in at least six samples; the majority of these events (81%) are under genetic influence. Many of these cis-regulated ASM variants are also eQTLs in peripheral blood mononuclear cells and monocytes and/or in high linkage-disequilibrium with variants linked to complex disease. Finally, focusing on autoimmune phenotypes, we extend this initial screen to confirm the association of cis-regulated ASM with multiple complex disease-associated variants in an independent population using next-generation bisulfite sequencing. These four variants are implicated in complex phenotypes such as ulcerative colitis and AIDS progression disease (rs10491434), Celiac disease (rs2762051), Crohn's disease, IgA nephropathy and early-onset inflammatory bowel disease (rs713875) and height (rs6569648). Our results suggest cis-regulated ASM may provide a mechanistic link between the non-coding genetic changes and phenotypic variation observed in these diseases and further suggests a route to integrating DNA methylation status with GWAS results.

  17. 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

  18. Structure and electronic spectra of purine-methyl viologen charge transfer complexes.

    PubMed

    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 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 (1)H 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 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 (DAD'DAD' type) and 7-deazaguanosine (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.

  19. IDN2 and Its Paralogs Form a Complex Required for RNA–Directed DNA Methylation

    PubMed Central

    Zhang, Cui-Jun; Ning, Yong-Qiang; Zhang, Su-Wei; Chen, Qing; Shao, Chang-Rong; Guo, Yan-Wu; Zhou, Jin-Xing; Li, Lin; Chen, She; He, Xin-Jian

    2012-01-01

    IDN2/RDM12 has been previously identified as a component of the RNA–directed DNA methylation (RdDM) machinery in Arabidopsis thaliana, but how it functions in RdDM remains unknown. By affinity purification of IDN2, we co-purified two IDN2 paralogs IDP1 and IDP2 (IDN2 PARALOG 1 and 2). The coiled-coil domain between the XS and XH domains of IDN2 is essential for IDN2 homodimerization, whereas the IDN2 C-terminal XH domain but not the coiled-coil domain is required for IDN2 interaction with IDP1 and IDP2. By introducing the wild-type IDN2 sequence and its mutated derivatives into the idn2 mutant for complementation testing, we demonstrated that the previously uncharacterized IDN2 XH domain is required for the IDN2-IDP1/IDP2 complex formation as well as for IDN2 function. IDP1 is required for de novo DNA methylation, siRNA accumulation, and transcriptional gene silencing, whereas IDP2 has partially overlapping roles with IDP1. Unlike IDN2, IDP1 and IDP2 are incapable of binding double-stranded RNA, suggesting that the roles of IDP1 and IDP2 are different from those of IDN2 in the IDN2-IDP1/IDP2 complex and that IDP1 and IDP2 are essential for the functioning of the complex in RdDM. PMID:22570638

  20. Temperature dependent luminescence of a europium complex incorporated in poly(methyl methacrylate).

    PubMed

    Liang, Hao; Xie, Fang; Ren, Xiaojun; Chen, Yifa; Chen, Biao; Guo, Fuquan

    2013-12-01

    An europium β-diketonate complex with a dipyrazolyltriazine derivative ligand, Eu(TTA)3DPBT, has been incorporated into poly(methyl methacryate) (PMMA). The influence of temperature on its luminescence properties has been investigated. The fluorescence emission spectra and luminescence lifetimes showed temperature sensitivity. The analysis of the relative intensity ratio (R) of (5)D0 → (7)F2 to (5)D0 → (7)F1 transition and Judd-Ofelt experimental intensity parameters Ω2 indicated that the local structure and asymmetry in the vicinity of europium ions show no obvious change when the temperature is increased.

  1. Influence of Ionic Complexes on Phase Behavior of Polystyrene-b-poly(methyl methacrylate) Copolymers

    SciTech Connect

    Wang,J.; Chen, W.; Roy, C.; Sievert, J.; Russell, T.

    2008-01-01

    The influence of ionic complexes on phase behavior of PS-b-PMMA copolymers over a wide range of molecular weights and PS volume fractions was investigated by small-angle X-ray scattering (SAXS), grazing incidence small-angle X-ray scattering (GISAXS), transmission electron microscopy (TEM), and neutron reflectivity (NR). The disorder-to-order transition (DOT) in both symmetric and asymmetric copolymers indicates that the overall Flory-Huggins segmental interaction parameter, eff, between polystyrene (PS) and poly(methyl methacrylate) (PMMA) blocks with lithium-PMMA complexes is increased compared to that of the neat copolymers. This enhanced eff further results in an order-to-order transition (OOT), from spheres to cylinders, and an increase in the ordering and spacing of microdomains. Moreover, transitional metal ionic complexes, such as copper-PMMA complexes, are found to have the similar influence on phase behavior of PS-b-PMMA copolymers. The formation of ionic complexes in the copolymers not only offers a parameter to tune the degree of microphase separation of PS-b-PMMA copolymers but also provides a way to fabricate multifunctional materials.

  2. 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 β-cyclodextrin (β-CD) and HP-β-cyclodextrin (HP-β-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 β-CD inclusion complexes is much longer than that of HP-β-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.

  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. 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.

  5. 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).

  6. Properties of amylose-oleic acid inclusion complexes from corn starch grafted with poly(methyl acrylate)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Corn starch granules have been previously investigated as fillers in polymers. In this study, much smaller particles in the form of spherulites produced by steam jet-cooking high-amylose corn starch and oleic acid to form amylose inclusion complexes were graft polymerized with methyl acrylate, both ...

  7. 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...

  8. Synthesis and characterization of Pd(II)-methyl complexes with N-heterocyclic carbene-amine ligands.

    PubMed

    Warsink, Stefan; de Boer, Sandra Y; Jongens, Lianne M; Fu, Ching-Feng; Liu, Shiuh-Tzung; Chen, Jwu-Ting; Lutz, Martin; Spek, Anthony L; Elsevier, Cornelis J

    2009-09-21

    A number of palladium(ii) complexes with a heteroditopic NHC-amine ligand and their precursor silver(i) carbene complexes have been efficiently prepared and their structural features have been investigated. The heteroditopic coordination of this ligand class was unequivocally shown by NMR-spectroscopy and X-ray crystallographic analysis. The neutral and cationic cis-methyl-palladium(NHC) complexes are not prone to reductive elimination, which is normally a major degenerative pathway for this type of complex. In contrast, under carbon monoxide atmosphere rapid reductive elimination of the acyl-imidazolium salt was observed.

  9. Structural basis of N(6)-adenosine methylation by the METTL3-METTL14 complex.

    PubMed

    Wang, Xiang; Feng, Jing; Xue, Yuan; Guan, Zeyuan; Zhang, Delin; Liu, Zhu; Gong, Zhou; Wang, Qiang; Huang, Jinbo; Tang, Chun; Zou, Tingting; Yin, Ping

    2016-06-23

    Chemical modifications of RNA have essential roles in a vast range of cellular processes. N(6)-methyladenosine (m(6)A) is an abundant internal modification in messenger RNA and long non-coding RNA that can be dynamically added and removed by RNA methyltransferases (MTases) and demethylases, respectively. An MTase complex comprising methyltransferase-like 3 (METTL3) and methyltransferase-like 14 (METTL14) efficiently catalyses methyl group transfer. In contrast to the well-studied DNA MTase, the exact roles of these two RNA MTases in the complex remain to be elucidated. Here we report the crystal structures of the METTL3-METTL14 heterodimer with MTase domains in the ligand-free, S-adenosyl methionine (AdoMet)-bound and S-adenosyl homocysteine (AdoHcy)-bound states, with resolutions of 1.9, 1.71 and 1.61 Å, respectively. Both METTL3 and METTL14 adopt a class I MTase fold and they interact with each other via an extensive hydrogen bonding network, generating a positively charged groove. Notably, AdoMet was observed in only the METTL3 pocket and not in METTL14. Combined with biochemical analysis, these results suggest that in the m(6)A MTase complex, METTL3 primarily functions as the catalytic core, while METTL14 serves as an RNA-binding platform, reminiscent of the target recognition domain of DNA N(6)-adenine MTase. This structural information provides an important framework for the functional investigation of m(6)A. PMID:27281194

  10. π Interactions Studied with Electronic Structure Methods: The Ethyne Methyl Isocyanide Complex and Thioanisole.

    PubMed

    Bretherick, Natalie H; van Mourik, Tanja

    2010-09-14

    Two molecular systems for which previous studies had found qualitative differences in the results from calculations with the B3LYP and MP2 methods are investigated with a range of different electronic structure methods, including meta and double hybrid density functionals and DFT-D (DFT augmented with an empirical dispersion term). The performance of the different methods is assessed by comparison to estimated CCSD(T)/CBS (complete basis set) results. The first molecular system studied is the ethyne methyl isocyanide complex (CH3NC-C2H2), which exhibits π hydrogen bonds involving the C≡C and N≡C triple bonds. Earlier work on this system had shown that B3LYP predicts significantly longer hydrogen-bond distances than MP2. Here, we show that this is likely due to missing dispersion in the B3LYP calculations. On the basis of the CCSD(T) results, the ethyne methyl isocyanide interaction energy is estimated to be 12 ± 1 kJ/mol. B3LYP significantly underestimates the stability of the complex, whereas MP2 slightly overestimates. M05-2X, B3LYP-D, and (CP-corrected) mPW2-PLYP-D give results in close proximity to the CCSD(T) reference values. The second molecule investigated is thioanisole (C6H6SCH3), which can adopt two different conformations (thiomethyl group either planar or perpendicular with respect to the benzene ring). Potential energy curves for rotation around the C(sp(2))-S bond are computed and compared to the estimated CCSD(T)/CBS curve. CCSD(T) predicts the planar conformation to be the global minimum, with a plateau region near the perpendicular conformation (∼4 kJ/mol higher in energy than the planar conformation). The shape of the curve, and location of minima and barriers, is very dependent on the method and basis set employed. MP2, B3LYP, M05-2X, mPW2-PLYP, and mPW2-PLYP-D (employing basis sets of double- or triple-ζ quality) give results in reasonable agreement with the CCSD(T) results, whereas B3LYP-D and M06-L give vastly overestimated barriers

  11. Cationic methyl complexes of the rare-earth metals: an experimental and computational study on synthesis, structure, and reactivity.

    PubMed

    Kramer, Mathias U; Robert, Dominique; Arndt, Stefan; Zeimentz, Peter M; Spaniol, Thomas P; Yahia, Ahmed; Maron, Laurent; Eisenstein, Odile; Okuda, Jun

    2008-10-20

    Synthesis, structure, and reactivity of two families of rare-earth metal complexes containing discrete methyl cations [LnMe(2-x)(thf)n]((1+x)+) (x = 0, 1; thf = tetrahydrofuran) have been studied. As a synthetic equivalent for the elusive trimethyl complex [LnMe3], lithium methylates of the approximate composition [Li3LnMe6(thf)n] were prepared by treating rare-earth metal trichlorides [LnCl3(thf)n] with 6 equiv of methyllithium in diethyl ether. Heteronuclear complexes of the formula [Li3Ln2Me9L(n)] (Ln = Sc, Y, Tb; L = Et2O, thf) were isolated by crystallization from diethyl ether. Single crystal X-ray diffraction studies revealed a heterometallic aggregate of composition [Li3Ln2Me9(thf)n(Et2O)m] with a [LiLn2Me9](2-) core (Ln = Sc, Y, Tb). When tris(tetramethylaluminate) [Ln(AlMe4)3] (Ln = Y, Lu) was reacted with less than 1 equiv of [NR3H][BPh4], the dimethyl cations [LnMe2(thf)n][BPh4] were obtained. The coordination number as well as cis/trans isomer preference was studied by crystallographic and computational methods. Dicationic methyl complexes of the rare-earth metals of the formula [LnMe(thf)n][BAr4]2 (Ln = Sc, Y, La-Nd, Sm, Gd-Lu; Ar = Ph, C6H4F-4) were synthesized, by protonolysis of either the ate complex [Li3LnMe6(thf)n] (Ln = Sc, Y, Gd-Lu) or the tris(tetramethylaluminate) [Ln(AlMe4)3] (Ln = La-Nd, Sm, Dy, Gd) with ammonium borates [NR3H][BAr4] in thf. The number of coordinated thf ligands varied from n = 5 (Ln = Sc, Tm) to n = 6 (Ln = La, Y, Sm, Dy, Ho). The configuration of representative examples was determined by X-ray diffraction studies and confirmed by density-functional theory calculations. The highly polarized bonding between the methyl group and the rare-earth metal center results in the reactivity pattern dominated by the carbanionic character and the pronounced Lewis acidity: The dicationic methyl complex [YMe(thf)6](2+) inserted benzophenone as an electrophile to give the alkoxy complex [Y(OCMePh2)(thf)5](2+). Nucleophilic addition of

  12. 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

  13. α-[11C]-Methyl-l-tryptophan–PET 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 α-[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 κ 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

  14. 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.

  15. 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.

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

    PubMed Central

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

    2015-01-01

    Summary 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 for the 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

  17. 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; Bäckdahl, 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

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

    PubMed

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

    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 for the 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.

  19. Yttrium Siloxide Complexes Bearing Terminal Methyl Ligands: Molecular Models for Ln-CH3 Terminated Silica Surfaces.

    PubMed

    Dettenrieder, Nicole; Dietrich, H Martin; Maichle-Mössmer, Cäcilia; Anwander, Reiner

    2016-09-01

    Surface organometallic chemistry (SOMC) on silica materials is a prominent approach for the generation of highly active heterogenized polymerization catalysts. Despite advanced methods of characterization, the elucidation of the catalytically active surface species remains a challenging task. Alkylated rare-earth metal siloxide complexes can be regarded as molecular models of respective covalently bonded alkylated surface species, primarily used for 1,3-diene polymerization. Here, we performed both salt metathesis reactions of [Y(MMe4 )3 ] (M = Al, Ga) with [K{OSi(OtBu)3 }] and alkylation reactions of [Y{OSi(OtBu)3 }3 ]2 with AlMe3 . The obtained complexes [Y(CH3 )[(AlMe2 ){OSi(OtBu)3 }2 ](AlMe4 )]2 , [Y(CH3 )[(AlMe2 ){OSi(OtBu)3 }2 ]-{OSi(OtBu)3 }], [Y{OSi(OtBu)3 }3 (μ-Me)Y(μ-Me)2 Y{OSi(OtBu)3 }2 (AlMe4 )], and [Y(CH3 )(GaMe4 ){OSi(OtBu)3 }]2 represent rare examples of organoyttrium species with terminal methyl groups. The formation and purity of the mixed methyl/siloxy yttrium complexes could be enhanced by treating [Y(MMe4 )3 ] with [K(MMe2 ){OSi(OtBu)3 }2 ]n (M=Al: n=2; M=Ga: n=∞). Complexes [K(MMe2 ){OSi(OtBu)3 }2 ]n were obtained by addition of [K{OSi(OtBu)3 }] to [Me2 M{OSi(OtBu)3 }]2 . Deeper insight into the fluxional behavior of the mixed methyl/siloxy yttrium complexes in solution was gained by (1) H and (13) C NMR spectroscopic studies at variable temperature and (1) H-(89) Y HSQC NMR spectroscopy. PMID:27492852

  20. Yttrium Siloxide Complexes Bearing Terminal Methyl Ligands: Molecular Models for Ln-CH3 Terminated Silica Surfaces.

    PubMed

    Dettenrieder, Nicole; Dietrich, H Martin; Maichle-Mössmer, Cäcilia; Anwander, Reiner

    2016-09-01

    Surface organometallic chemistry (SOMC) on silica materials is a prominent approach for the generation of highly active heterogenized polymerization catalysts. Despite advanced methods of characterization, the elucidation of the catalytically active surface species remains a challenging task. Alkylated rare-earth metal siloxide complexes can be regarded as molecular models of respective covalently bonded alkylated surface species, primarily used for 1,3-diene polymerization. Here, we performed both salt metathesis reactions of [Y(MMe4 )3 ] (M = Al, Ga) with [K{OSi(OtBu)3 }] and alkylation reactions of [Y{OSi(OtBu)3 }3 ]2 with AlMe3 . The obtained complexes [Y(CH3 )[(AlMe2 ){OSi(OtBu)3 }2 ](AlMe4 )]2 , [Y(CH3 )[(AlMe2 ){OSi(OtBu)3 }2 ]-{OSi(OtBu)3 }], [Y{OSi(OtBu)3 }3 (μ-Me)Y(μ-Me)2 Y{OSi(OtBu)3 }2 (AlMe4 )], and [Y(CH3 )(GaMe4 ){OSi(OtBu)3 }]2 represent rare examples of organoyttrium species with terminal methyl groups. The formation and purity of the mixed methyl/siloxy yttrium complexes could be enhanced by treating [Y(MMe4 )3 ] with [K(MMe2 ){OSi(OtBu)3 }2 ]n (M=Al: n=2; M=Ga: n=∞). Complexes [K(MMe2 ){OSi(OtBu)3 }2 ]n were obtained by addition of [K{OSi(OtBu)3 }] to [Me2 M{OSi(OtBu)3 }]2 . Deeper insight into the fluxional behavior of the mixed methyl/siloxy yttrium complexes in solution was gained by (1) H and (13) C NMR spectroscopic studies at variable temperature and (1) H-(89) Y HSQC NMR spectroscopy.

  1. Glycolic Acid Silences Inflammasome Complex Genes, NLRC4 and ASC, by Inducing DNA Methylation in HaCaT Cells.

    PubMed

    Tang, Sheau-Chung; Yeh, Jih-I; Hung, Sung-Jen; Hsiao, Yu-Ping; Liu, Fu-Tong; Yang, Jen-Hung

    2016-03-01

    AHAs (α-hydroxy acids), including glycolic acid (GA), have been widely used in cosmetic products and superficial chemical peels. Inflammasome complex has been shown to play critical roles in inflammatory pathways in human keratinocytes. However, the anti-inflammatory mechanism of GA is still unknown. The aim of this study is to investigate the relationship between the expression of the inflammasome complex and epigenetic modification to elucidate the molecular mechanism of the anti-inflammatory effect of GA in HaCaT cells. We evaluated NLRP3, NLRC4, AIM2, and ASC inflammasome complex gene expression on real-time polymerase chain reaction (PCR). Methylation changes were detected in these genes following treatment with DNA methyltransferase (DNMT) inhibitor 5-aza-2'-deoxycytidine (5-Aza) with or without the addition of GA using methylation-specific PCR (MSP). GA inhibited the expressions of these inflammasome complex genes, and the decreases in the expressions of mRNA were reversed by 5-Aza treatment. Methylation was detected in NLRC4 and ASC on MSP, but not in NLRP3 or AIM2. GA decreased NLRC4 and ASC gene expression by increasing not only DNA methyltransferase 3B (DNMT-3B) protein level, but also total DNMT activity. Furthermore, silencing of DNMT-3B (shDNMT-3B) increased the expressions of NLRC4 and ASC. Our data demonstrated that GA treatment induces hypermethylation of promoters of NLRC4 and ASC genes, which may subsequently lead to the hindering of the assembly of the inflammasome complex in HaCaT cells. These results highlight the anti-inflammatory potential of GA-containing cosmetic agents in human skin cells and demonstrate for the first time the role of aberrant hypermethylation in this process.

  2. 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.

  3. 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.

  4. Domain–domain interactions in full-length p53 and a specific DNA complex probed by methyl NMR spectroscopy

    PubMed Central

    Bista, Michal; Freund, Stefan M.; Fersht, Alan R.

    2012-01-01

    The tumor suppressor p53 is a homotetramer of 4 × 393 residues. Its core domain and tetramerization domain are linked and flanked by intrinsically disordered sequences, which hinder its full structural characterization. There is an outstanding problem of the state of the tetramerization domain. Structural studies on the isolated tetramerization domain show it is in a folded tetrameric conformation, but there are conflicting models from electron microscopy of the full-length protein, one of which proposes that the domain is not tetramerically folded and the tetrameric protein is stabilized by interactions between the N and C termini. Here, we present methyl-transverse relaxation optimized NMR spectroscopy (methyl-TROSY) investigations on the full-length and separate domains of the protein with its methionine residues enriched with 13C to probe its quaternary structure. We obtained high-quality spectra of both the full-length tetrameric p53 and its DNA complex, observing the environment at 11 specific methyl sites. The tetramerization domain was as tetramerically folded in the full-length constructs as in the isolated domain. The N and C termini were intrinsically disordered in both the full-length protein and its complex with a 20-residue specific DNA sequence. Additionally, we detected in the interface of the core (DNA-binding) and N-terminal parts of the protein a slow conformational exchange process that was modulated by specific recognition of DNA, indicating allosteric processes. PMID:22972749

  5. 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

  6. 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. PMID:26997691

  7. Thermal history effects and methyl tunneling dynamics in a supramolecular complex of calixarene and para-xylene

    NASA Astrophysics Data System (ADS)

    Panesar, K. S.; Horsewill, A. J.; Cuda, F.; Carravetta, M.; Mamone, S.; Danquigny, A.; Grossel, M. C.; Levitt, M. H.

    2008-04-01

    The low-temperature structure and dynamics of guest molecules of p-xylene incorporated in the isopropyl-calix[4] arene(2:1) p-xylene complex have been investigated by solid state nuclear magnetic resonance (NMR). Using one-dimensional H1-decoupled C13 cross-polarization magic-angle-spinning (MAS) NMR and two-dimensional H1-C13 correlation spectroscopy, a full assignment of the C13 and H1 chemical shifts has been made. Using H1 NMR relaxometry, the effects of thermal history on the structure of the system have been investigated. Rapidly cooled samples have H1 spin-lattice relaxation times T1, which at low temperature (T<60K) are typically two orders of magnitude faster than those observed in annealed samples which have been cooled slowly over many hours. In both forms, the low-temperature relaxation is driven by the dynamics of the weakly hindered methyl rotors of the p-xylene guest. The substantial difference in T1 is attributed in the rapidly cooled sample to disorder in the structure of the complex leading to a wide distribution of correlation times and methyl barrier heights. A comparison of the linewidths and splittings in the high resolution C13 MAS spectra of the two forms provides structural insight into the nature of the disorder. Using H1 field-cycling NMR relaxometry, the methyl dynamics of the p-xylene guest in the annealed sample have been fully characterized. The B-field dependence of the H1 T1 maps out the spectral density from which the correlation times are directly measured. The methyl barrier heights are determined from an analysis of the temperature dependence.

  8. Model studies of methyl CoM reductase: methane formation via CH3-S bond cleavage of Ni(I) tetraazacyclic complexes having intramolecular methyl sulfide pendants.

    PubMed

    Nishigaki, Jun-ichi; Matsumoto, Tsuyoshi; Tatsumi, Kazuyuki

    2012-05-01

    The Ni(I) tetraazacycles [Ni(dmmtc)](+) and [Ni(mtc)](+), which have methylthioethyl pendants, were synthesized as models of the reduced state of the active site of methyl coenzyme M reductase (MCR), and their structures and redox properties were elucidated (dmmtc, 1,8-dimethyl-4,11-bis{(2-methylthio)ethyl}-1,4,8,11-tetraaza-1,4,8,11-cyclotetradecane; mtc, 1,8-{bis(2-methylthio)ethyl}-1,4,8,11-tetraaza-1,4,8,11-cyclotetradecane). The intramolecular CH(3)-S bond of the thioether pendant of [Ni(I)(dmmtc)](OTf) was cleaved in THF at 75 °C in the presence of the bulky thiol DmpSH, which acts as a proton source, and methane was formed in 31% yield and a Ni(II) thiolate complex was concomitantly obtained (Dmp = 2,6-dimesityphenyl). The CH(3)-S bond cleavage of [Ni(I)(mtc)](+) also proceeded similarly, but under milder conditions probably due to the lower potential of the [Ni(I)(mtc)](+) complex. These results indicate that the robust CH(3)-S bond can be homolytically cleaved by the Ni(I) center when they are properly arranged, which highlights the significance of the F430 Ni environment in the active site of the MCR protein. PMID:22439643

  9. 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...

  10. Spectroscopic studies of inclusion complexes of methyl- p-dimethylaminobenzoate and its ortho derivative with α- and β-cyclodextrins

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

    The effects of α- and β-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 α- and β-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 α-CD and β-CD, both 1:1 and 1:2 inclusion complexes are formed, whereas only 1:1 inclusion complex is formed between II and β-CD.

  11. Metal(II) complexes synthesized based on quinoline-2,3-dicarboxylate as electrocatalysts for the degradation of methyl orange.

    PubMed

    Gong, Yun; Zhang, Miao Miao; Qin, Jian Bo; Li, Jian; Meng, Jiang Ping; Lin, Jian Hua

    2014-06-14

    Based on quinoline-2,3-dicarboxylic acid (H2L), two metal(II) complexes formulated as MnL(phen)(H2O)·H2O (phen = 1,10-phenanthroline) (1) and Co(HL)2(PPA)·4H2O (PPA = N(1),N(4)-di(pyridin-4-yl)terephthalamide) (2) were synthesized and structurally characterized by single-crystal X-ray diffraction. Both complexes 1 and 2 exhibit one-dimensional (1D) chain-like structures, in which stable five-membered rings are observed. Different chains are linked by strong π-π stacking interactions into a three-dimensional (3D) supramolecular architecture. Both complexes can increase the degradation rate of methyl orange (MO), which is expected to be associated with their electrocatalytic activities for the H2 evolution reaction from water. PMID:24741675

  12. A jumonji (Jarid2) protein complex represses cyclin D1 expression by methylation of histone H3-K9.

    PubMed

    Shirato, Haruki; Ogawa, Satoko; Nakajima, Kuniko; Inagawa, Masayo; Kojima, Mizuyo; Tachibana, Makoto; Shinkai, Yoichi; Takeuchi, Takashi

    2009-01-01

    Covalent modifications of histone tails have critical roles in regulating gene expression. Previously, we identified the jumonji (jmj, Jarid2) gene, the jmjC domain, and a Jmj family. Recently, many Jmj family proteins have been shown to be histone demethylases, and jmjC is the catalytic domain. However, Jmj does not have histone demethylase activity because the jmjC domain lacks conserved residues for binding to cofactors. Independently of these studies, we previously showed that Jmj binds to the cyclin D1 promoter and represses the transcription of cyclin D1. Here, we show the mechanisms by which Jmj represses the transcription of cyclin D1. We found that a protein complex of Jmj had histone methyltransferase activity toward histone H3 lysine 9 (H3-K9). We also found that Jmj bound to the H3-K9 methyltransferases G9a and GLP. Expression of Jmj recruited G9a and GLP to the cyclin D1 promoter and increased H3-K9 methylation. Inactivation of both G9a and GLP, but not of only G9a, inhibited the methylation of H3-K9 in the cyclin D1 promoter and repression of cyclin D1 expression by Jmj. These results suggest that Jmj methylates H3-K9 and represses cyclin D1 expression through G9a and GLP, and that Jmj family proteins can regulate gene expression by not only histone demethylation but also other histone modification.

  13. A simple, low-cost, and rapid device for a DNA methylation-specific amplification/detection system using a flexible plastic and silicon complex.

    PubMed

    Lee, Tae Yoon; Shin, Yong; Park, Mi Kyoung

    2014-11-01

    Abnormal DNA methylation has been associated with the development and progression of several human cancers and is a potential target for treatment. Thus, myriad technologies for the analysis of DNA methylation have been developed over the past few decades. However, most of these technologies are still far from ideal because they are time-consuming, labor-intensive, and complex, and there is the risk of contamination of samples. Here, we present an innovative DNA methylation-specific amplification/detection device for analysis of DNA methylation in cancer-related DNA biomarkers. The assay is based on a microfluidic system that is coupled to a flexible plastic-based on-chip endonuclease digestion device with optimized magnetic field effect and a methylation-specific isothermal solid-phase amplification/detection technique to allow a low-cost, simple, and rapid analysis of DNA methylation status in a label-free and real-time manner. This flexible plastic/silicon-based microfluidic device is relatively simple to fabricate with a flexible thin film and a magnet array by using a laser machine that can overcome the limitations of a PDMS-based microfluidic device. We demonstrated the ability of the methylation analysis based on the proposed flexible device to detect the methylated RARβ gene, which is a common DNA methylation biomarker in several human cancers. The simple platform detected the methylated gene in genomic DNA from human cancer cell lines within 65 min, whereas other methods required at least several hours. Therefore, this simple, low-cost, and rapid methylation analysis platform will be useful for the detection of DNA methylation in point-of-care applications.

  14. 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

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

    PubMed Central

    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.

    2015-01-01

    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

  16. 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.

  17. 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.

  18. Hydrogen-bonding interactions in cinchonidine-2-methyl-2-hexenoic acid complexes: a combined spectroscopic and theoretical study.

    PubMed

    Meier, Daniel M; Urakawa, Atsushi; Turrà, Natascia; Rüegger, Heinz; Baiker, Alfons

    2008-07-10

    Molecular interactions between cinchonidine (CD) and 2-methyl-2-hexenoic acid (MHA) have been studied by means of NMR, ATR-IR MES, DFT, and ab initio molecular dynamics. These interactions are of particular interest due to their pivotal role in the chiral induction occurring in the heterogeneous catalytic asymmetric hydrogenation of alpha,beta-unsaturated acids. The population density of the Open(3) conformer of CD, the most populated one at room temperature in apolar solvents, considerably increased to a maximum by addition of MHA to CD in toluene. The CD-MHA complex showed prominent symmetric and asymmetric carboxylate stretching vibrations in the regions of 1350-1410 and 1520-1580 cm(-1), respectively. DFT calculations revealed that these vibrational frequencies are expected to significantly shift depending on the chemical surrounding of MHA, that is, the hydrogen bond network. Earlier postulated 1:1 binding between CD and MHA was considered unlikely; instead, a dynamic equilibrium involving the MHA monomer and dimer, the 1:3 and possibly 1:2 CD-MHA complexes, were rationalized. Stable CD-MHA structures suggested by DFT calculations are the "1:3, halfN, cyclic" and the "1:3, halfN, cyclic tilted" complexes, where three MHA molecules are connected in wire by hydrogen bonding, two having direct interaction with CD. The confinement of CD's torsional motions in the complexes, leading to a slightly distorted Open(3) conformer via specific hydrogen-bonding interactions, was clearly reproduced by ab initio molecular dynamics, and the stable and flexible nature of the interaction was verified. Theoretical IR spectra of the complexes reproduced the characteristic vibrational frequencies of the complexes observed experimentally, supporting the stability of the 1:3 and implying the possibility of even higher molecular weight CD-MHA complexes.

  19. Coupling of histone methylation and RNA processing by the nuclear mRNA cap-binding complex.

    PubMed

    Li, Zicong; Jiang, Danhua; Fu, Xing; Luo, Xiao; Liu, Renyi; He, Yuehui

    2016-01-01

    In eukaryotes, genes are transcribed into pre-mRNAs that are subsequently processed into mature mRNAs by adding a 5'-cap and a 3'-polyA tail and splicing introns. Pre-mRNA processing involves their binding proteins and processing factors, whereas gene transcription often involves chromatin modifiers. It has been unclear how the factors involved in chromatin modifications and RNA processing function in concert to control mRNA production. Here, we show that in Arabidopsis thaliana, the evolutionarily conserved nuclear mRNA cap-binding complex (CBC) forms multi-protein complexes with a conserved histone 3 lysine 4 (H3K4) methyltransferase complex called COMPASS-like and a histone 3 lysine 36 (H3K36) methyltransferase to integrate active histone methylations with co-transcriptional mRNA processing and cap preservation, leading to a high level of mature mRNA production. We further show that CBC is required for H3K4 and H3K36 trimethylation, and the histone methyltransferases are required for CBC-mediated mRNA cap preservation and efficient pre-mRNA splicing at their target loci, suggesting that these factors are functionally interdependent. Our study reveals novel roles for histone methyltransferases in RNA-processing-related events and provides mechanistic insights into how the 'downstream' RNA CBC controls eukaryotic gene transcription. PMID:27249350

  20. Biochemical reconstitution and phylogenetic comparison of human SET1 family core complexes involved in histone methylation.

    PubMed

    Shinsky, Stephen A; Monteith, Kelsey E; Viggiano, Susan; Cosgrove, Michael S

    2015-03-01

    Mixed lineage leukemia protein-1 (MLL1) is a member of the SET1 family of histone H3 lysine 4 (H3K4) methyltransferases that are required for metazoan development. MLL1 is the best characterized human SET1 family member, which includes MLL1-4 and SETd1A/B. MLL1 assembles with WDR5, RBBP5, ASH2L, DPY-30 (WRAD) to form the MLL1 core complex, which is required for H3K4 dimethylation and transcriptional activation. Because all SET1 family proteins interact with WRAD in vivo, it is hypothesized they are regulated by similar mechanisms. However, recent evidence suggests differences among family members that may reflect unique regulatory inputs in the cell. Missing is an understanding of the intrinsic enzymatic activities of different SET1 family complexes under standard conditions. In this investigation, we reconstituted each human SET1 family core complex and compared subunit assembly and enzymatic activities. We found that in the absence of WRAD, all but one SET domain catalyzes at least weak H3K4 monomethylation. In the presence of WRAD, all SET1 family members showed stimulated monomethyltransferase activity but differed in their di- and trimethylation activities. We found that these differences are correlated with evolutionary lineage, suggesting these enzyme complexes have evolved to accomplish unique tasks within metazoan genomes. To understand the structural basis for these differences, we employed a "phylogenetic scanning mutagenesis" assay and identified a cluster of amino acid substitutions that confer a WRAD-dependent gain-of-function dimethylation activity on complexes assembled with the MLL3 or Drosophila trithorax proteins. These results form the basis for understanding how WRAD differentially regulates SET1 family complexes in vivo.

  1. Biochemical Reconstitution and Phylogenetic Comparison of Human SET1 Family Core Complexes Involved in Histone Methylation*

    PubMed Central

    Shinsky, Stephen A.; Monteith, Kelsey E.; Viggiano, Susan; Cosgrove, Michael S.

    2015-01-01

    Mixed lineage leukemia protein-1 (MLL1) is a member of the SET1 family of histone H3 lysine 4 (H3K4) methyltransferases that are required for metazoan development. MLL1 is the best characterized human SET1 family member, which includes MLL1–4 and SETd1A/B. MLL1 assembles with WDR5, RBBP5, ASH2L, DPY-30 (WRAD) to form the MLL1 core complex, which is required for H3K4 dimethylation and transcriptional activation. Because all SET1 family proteins interact with WRAD in vivo, it is hypothesized they are regulated by similar mechanisms. However, recent evidence suggests differences among family members that may reflect unique regulatory inputs in the cell. Missing is an understanding of the intrinsic enzymatic activities of different SET1 family complexes under standard conditions. In this investigation, we reconstituted each human SET1 family core complex and compared subunit assembly and enzymatic activities. We found that in the absence of WRAD, all but one SET domain catalyzes at least weak H3K4 monomethylation. In the presence of WRAD, all SET1 family members showed stimulated monomethyltransferase activity but differed in their di- and trimethylation activities. We found that these differences are correlated with evolutionary lineage, suggesting these enzyme complexes have evolved to accomplish unique tasks within metazoan genomes. To understand the structural basis for these differences, we employed a “phylogenetic scanning mutagenesis” assay and identified a cluster of amino acid substitutions that confer a WRAD-dependent gain-of-function dimethylation activity on complexes assembled with the MLL3 or Drosophila trithorax proteins. These results form the basis for understanding how WRAD differentially regulates SET1 family complexes in vivo. PMID:25561738

  2. Biochemical reconstitution and phylogenetic comparison of human SET1 family core complexes involved in histone methylation.

    PubMed

    Shinsky, Stephen A; Monteith, Kelsey E; Viggiano, Susan; Cosgrove, Michael S

    2015-03-01

    Mixed lineage leukemia protein-1 (MLL1) is a member of the SET1 family of histone H3 lysine 4 (H3K4) methyltransferases that are required for metazoan development. MLL1 is the best characterized human SET1 family member, which includes MLL1-4 and SETd1A/B. MLL1 assembles with WDR5, RBBP5, ASH2L, DPY-30 (WRAD) to form the MLL1 core complex, which is required for H3K4 dimethylation and transcriptional activation. Because all SET1 family proteins interact with WRAD in vivo, it is hypothesized they are regulated by similar mechanisms. However, recent evidence suggests differences among family members that may reflect unique regulatory inputs in the cell. Missing is an understanding of the intrinsic enzymatic activities of different SET1 family complexes under standard conditions. In this investigation, we reconstituted each human SET1 family core complex and compared subunit assembly and enzymatic activities. We found that in the absence of WRAD, all but one SET domain catalyzes at least weak H3K4 monomethylation. In the presence of WRAD, all SET1 family members showed stimulated monomethyltransferase activity but differed in their di- and trimethylation activities. We found that these differences are correlated with evolutionary lineage, suggesting these enzyme complexes have evolved to accomplish unique tasks within metazoan genomes. To understand the structural basis for these differences, we employed a "phylogenetic scanning mutagenesis" assay and identified a cluster of amino acid substitutions that confer a WRAD-dependent gain-of-function dimethylation activity on complexes assembled with the MLL3 or Drosophila trithorax proteins. These results form the basis for understanding how WRAD differentially regulates SET1 family complexes in vivo. PMID:25561738

  3. 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

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

    PubMed

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

    2015-09-30

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

  5. C-H bond activation of the methyl group of the supporting ligand in an osmium(III) complex upon reaction with H2O2: formation of an organometallic osmium(IV) complex.

    PubMed

    Sugimoto, Hideki; Ashikari, Kenji; Itoh, Shinobu

    2013-01-18

    Oxidation of the hydroxoosmium(III) complex resulted in C-H bond activation of the methyl group of the supporting ligand (N,N'-dimethyl-2,11-diaza[3.3](2,6)pyridinophane). The product was an osmium(IV) complex exhibiting a seven-coordinate structure with an additional Os-CH(2) bond.

  6. Novel Bivalent 99mTc-Complex with N-Methyl-Substituted Hydroxamamide as Probe for Imaging of Cerebral Amyloid Angiopathy

    PubMed Central

    Iikuni, Shimpei; Ono, Masahiro; Watanabe, Hiroyuki; Yoshimura, Masashi; Ishibashi-Ueda, Hatsue; Ihara, Masafumi; Saji, Hideo

    2016-01-01

    Cerebral amyloid angiopathy (CAA) is characterized by the deposition of amyloid aggregates in the walls of the cerebral vasculature. Recently, the development of molecular imaging probes targeting CAA has been attracting much attention. We previously reported the 99mTc-hydroxamamide (99mTc-Ham) complex with a bivalent benzothiazole scaffold as a binding moiety for amyloid aggregates ([99mTc]BT2) and its utility for CAA-specific imaging. However, the simultaneous generation of two radiolabeled complexes derived from the geometric isomers was observed in the 99mTc-labeling reaction. It was recently reported that the complexation reaction of 99Tc with N-methyl-substituted Ham provided a single 99Tc-Ham complex consisting of two N-methylated Ham ligands with marked stability. In this article, we designed and synthesized a novel N-methylated bivalent 99mTc-Ham complex ([99mTc]MBT2) and evaluated its utility for CAA-specific imaging. N-Methyl substitution of [99mTc]BT2 prevented the generation of its isomer in the 99mTc-labeling reaction. Enhanced in vitro stability of [99mTc]MBT2 as compared with [99mTc]BT2 was observed. [99mTc]MBT2 showed very low brain uptake, which is favorable for CAA-specific imaging. An in vitro inhibition assay using β-amyloid aggregates and in vitro autoradiographic examination of brain sections from a Tg2576 mouse and a CAA patient showed a decline in the binding affinity for amyloid aggregates due to N-methylation of the 99mTc-Ham complex. These results suggest that the scaffold of the 99mTc-Ham complex may play important roles in the in vitro stability and the binding affinity for amyloid aggregates. PMID:27689870

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

    PubMed

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

    2015-12-01

    Type 2 brittle cornea syndrome (BCS2) is an inherited connective tissue disease with a devastating ocular phenotype caused by mutations in the transcription factor PR domain containing 5 (PRDM5) hypothesized to exert epigenetic effects through histone and DNA methylation. Here we investigate clinical samples, including skin fibroblasts and retinal tissue from BCS2 patients, to elucidate the epigenetic role of PRDM5 and mechanisms of its dysregulation in disease. First we report abnormal retinal vascular morphology in the eyes of two cousins with BCS2 (PRDM5 Δ exons 9-14) using immunohistochemistry, and mine data from skin fibroblast expression microarrays from patients with PRDM5 mutations p.Arg590* and Δ 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 Δ exons 9-14) by western blotting. These findings suggest that defective interaction of PRDM5 with repressive complexes, and dysregulation of H3K9me2, play a role in PRDM5-associated disease. PMID:26395458

  8. Protein-arginine methyltransferase 1 (PRMT1) methylates Ash2L, a shared component of mammalian histone H3K4 methyltransferase complexes.

    PubMed

    Butler, Jill S; Zurita-Lopez, Cecilia I; Clarke, Steven G; Bedford, Mark T; Dent, Sharon Y R

    2011-04-01

    Multiple enzymes and enzymatic complexes coordinately regulate the addition and removal of post-translational modifications on histone proteins. The oncoprotein Ash2L is a component of the mixed lineage leukemia (MLL) family members 1-4, Setd1A, and Setd1B mammalian histone H3K4 methyltransferase complexes and is essential to maintain global trimethylation of histone H3K4. However, regulation of these complexes at the level of expression and activity remains poorly understood. In this report, we demonstrate that Ash2L is methylated on arginine residues both in vitro and in cells. We found that both protein-arginine methyltransferases 1 and 5 methylate Arg-296 within Ash2L. These findings are the first to demonstrate that post-translational modifications occur on the Ash2L protein and provide a novel example of cross-talk between chromatin-modifying enzyme complexes. PMID:21285357

  9. 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.

  10. 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.

  11. 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.

  12. Pyridyl group assisted deprotonation of a methyl group on silicon: complex induced proximity effect and novel hydroxymethylation.

    PubMed

    Itami, K; Kamei, T; Mitsudo, K; Nokami, T; Yoshida, J I

    2001-06-01

    A novel methodology for the deprotonation of a methyl group on silicon has been developed. This newly developed alpha-lithiation protocol is based on the intramolecular pyridyl group coordination to stabilize the alpha-silyl carbanion together with the inherent silicon alpha effect. It was found that the deprotonation (t-BuLi/Et(2)O/-78 degrees C) occurs with 2-pyridyltrimethylsilane but not with other related silanes such as phenyltrimethylsilane, 3-pyridyltrimethylsilane, and 4-pyridyltrimethylsilane. It seems that this deprotonation proceeded through the agency of the complex-induced proximity effect (CIPE) of a 2-pyridyl group on silicon. (1)H NMR analysis of (2-pyridyldimethylsilyl)methyllithium revealed the intramolecular coordination of a pyridyl group to lithium. (2-Pyridyldimethylsilyl)methyllithium was found to react with chlorosilanes, hydrosilanes, chlorostannanes, bromine, iodine, organic bromides, aldehydes, and ketones in good to excellent yields. The resultant adducts were further oxidized with H(2)O(2)/KF to give the corresponding alcohols in excellent yields. Thus, this two-step transformation provides an efficient method for the nucleophilic hydroxymethylation.

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

    NASA Astrophysics Data System (ADS)

    Demir, Selçuk; Eren, Bilge; Hołyńska, Małgorzata

    2015-02-01

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

  14. Palladium(II) Complexes Containing Mixed Nitrogen-Sulphur Donor Ligands: Interaction of [Pd(Methionine Methyl Ester)(H2O)2]2+ with Biorelevant Ligands

    PubMed Central

    Shoukry, Mohamed M.; Ezzat, Sameya M. T.

    2014-01-01

    Pd(MME)Cl2 complex (MME = methionine methyl ester) was synthesised and characterized by physicochemical measurements. The reaction of [Pd(MME)(H2O)2]2+ with amino acids, peptides, or dicarboxylic acids was investigated at 25°C and 0.1 M ionic strength. Amino acids and dicarboxylic acids form 1 : 1 complexes. Peptides form both 1 : 1 complexes and the corresponding deprotonated amide species. The stability of the complexes formed was determined and the binding centres of the ligands were assigned. Effect of solvent on the stability constant of Pd(MME)-CBDCA complex, taken as a representative example, shows that the complex is more favoured in a medium of low dielectric constant. The concentration distribution diagrams of the complexes were evaluated. PMID:25214826

  15. Mechanistic Photochemistry of Methyl-4-hydroxycinnamate Chromophore and Its One-Water Complexes: Insights from MS-CASPT2 Study.

    PubMed

    Xie, Xiao-Ying; Li, Chun-Xiang; Fang, Qiu; Cui, Ganglong

    2016-08-01

    Herein we computationally studied the excited-state properties and decay dynamics of methyl-4-hydroxycinnamate (OMpCA) in the lowest three electronic states, that is, (1)ππ*, (1)nπ*, and S0 using combined MS-CASPT2 and CASSCF electronic structure methods. We found that one-water hydration can significantly stabilize and destabilize the vertical excitation energies of the spectroscopically bright (1)ππ* and dark (1)nπ* excited singlet states, respectively; in contrast, it has a much smaller effect on the (1)ππ* and (1)nπ* adiabatic excitation energies. Mechanistically, we located two (1)ππ* excited-state relaxation channels. One is the internal conversion to the dark (1)nπ* state, and the other is the (1)ππ* photoisomerization that eventually leads the system to a (1)ππ*/S0 conical intersection region, near which the radiationless internal conversion to the S0 state occurs. These two (1)ππ* relaxation pathways play distinct roles in OMpCA and its two one-water complexes (OMpCA-W1 and OMpCA-W2). In OMpCA, the predominant (1)ππ* decay route is the state-switching to the dark (1)nπ* state, while in one-water complexes, the importance of the (1)ππ* photoisomerization is significantly enhanced because the internal conversion to the (1)nπ* state is heavily suppressed due to the one-water hydration. PMID:27398611

  16. Mechanistic Photochemistry of Methyl-4-hydroxycinnamate Chromophore and Its One-Water Complexes: Insights from MS-CASPT2 Study.

    PubMed

    Xie, Xiao-Ying; Li, Chun-Xiang; Fang, Qiu; Cui, Ganglong

    2016-08-01

    Herein we computationally studied the excited-state properties and decay dynamics of methyl-4-hydroxycinnamate (OMpCA) in the lowest three electronic states, that is, (1)ππ*, (1)nπ*, and S0 using combined MS-CASPT2 and CASSCF electronic structure methods. We found that one-water hydration can significantly stabilize and destabilize the vertical excitation energies of the spectroscopically bright (1)ππ* and dark (1)nπ* excited singlet states, respectively; in contrast, it has a much smaller effect on the (1)ππ* and (1)nπ* adiabatic excitation energies. Mechanistically, we located two (1)ππ* excited-state relaxation channels. One is the internal conversion to the dark (1)nπ* state, and the other is the (1)ππ* photoisomerization that eventually leads the system to a (1)ππ*/S0 conical intersection region, near which the radiationless internal conversion to the S0 state occurs. These two (1)ππ* relaxation pathways play distinct roles in OMpCA and its two one-water complexes (OMpCA-W1 and OMpCA-W2). In OMpCA, the predominant (1)ππ* decay route is the state-switching to the dark (1)nπ* state, while in one-water complexes, the importance of the (1)ππ* photoisomerization is significantly enhanced because the internal conversion to the (1)nπ* state is heavily suppressed due to the one-water hydration.

  17. A high molar extinction coefficient bisterpyridyl homoleptic ru(II) complex with trans-2-methyl-2-butenoic acid functionality: potential dye for dye-sensitized solar cells.

    PubMed

    Adeloye, Adewale O; Olomola, Temitope O; Adebayo, Akinbulu I; Ajibade, Peter A

    2012-01-01

    In our continued efforts in the synthesis of ruthenium(II) polypyridine complexes as potential dyes for use in varied applications, such as the dye-sensitized solar cells (DSSCs), this work particularly describes the synthesis, absorption spectrum, redox behavior and luminescence properties of a new homoleptic ruthenium(II) complex bearing a simple trans-2-methyl-2-butenoic acid functionality as the anchoring ligand on terpyridine moiety. The functionalized terpyridine ligand: 4'-(trans-2-methyl-2-butenoic acid)-terpyridyl (L1) was synthesized by aryl bromide substitution on terpyridine in a basic reaction condition under palladium carbide catalysis. In particular, the photophysical and redox properties of the complex formulated as: bis-4'-(trans-2-methyl-2-butenoic acid)-terpyridyl ruthenium(II) bis-hexafluorophosphate [Ru(L1)(2)(PF(6))(2)] are significantly better compared to those of [Ru(tpy)(2)](2+) and compare well with those of the best emitters of Ru(II) polypyridine family containing tridentate ligands. Reasons for the improved photophysical and redox properties of the complex may be attributed partly to the presence of a substituted α,β-unsaturated carboxylic acid moiety leading to increase in the length of π-conjugation bond thereby enhancing the MLCT-MC (Metal-to-ligand-charge transfer-metal centred) energy gap, and to the reduced difference between the minima of the excited and ground states potential energy surfaces.

  18. A High Molar Extinction Coefficient Bisterpyridyl Homoleptic Ru(II) Complex with trans-2-Methyl-2-butenoic Acid Functionality: Potential Dye for Dye-Sensitized Solar Cells

    PubMed Central

    Adeloye, Adewale O.; Olomola, Temitope O.; Adebayo, Akinbulu I.; Ajibade, Peter A.

    2012-01-01

    In our continued efforts in the synthesis of ruthenium(II) polypyridine complexes as potential dyes for use in varied applications, such as the dye-sensitized solar cells (DSSCs), this work particularly describes the synthesis, absorption spectrum, redox behavior and luminescence properties of a new homoleptic ruthenium(II) complex bearing a simple trans-2-methyl-2-butenoic acid functionality as the anchoring ligand on terpyridine moiety. The functionalized terpyridine ligand: 4′-(trans-2-methyl-2-butenoic acid)-terpyridyl (L1) was synthesized by aryl bromide substitution on terpyridine in a basic reaction condition under palladium carbide catalysis. In particular, the photophysical and redox properties of the complex formulated as: bis-4′-(trans-2-methyl-2-butenoic acid)-terpyridyl ruthenium(II) bis-hexafluorophosphate [Ru(L1)2(PF6)2] are significantly better compared to those of [Ru(tpy)2]2+ and compare well with those of the best emitters of Ru(II) polypyridine family containing tridentate ligands. Reasons for the improved photophysical and redox properties of the complex may be attributed partly to the presence of a substituted α,β-unsaturated carboxylic acid moiety leading to increase in the length of π-conjugation bond thereby enhancing the MLCT-MC (Metal-to-ligand-charge transfer-metal centred) energy gap, and to the reduced difference between the minima of the excited and ground states potential energy surfaces. PMID:22489165

  19. Charge-based interaction conserved within histone H3 lysine 4 (H3K4) methyltransferase complexes is needed for protein stability, histone methylation, and gene expression.

    PubMed

    Mersman, Douglas P; Du, Hai-Ning; Fingerman, Ian M; South, Paul F; Briggs, Scott D

    2012-01-20

    Histone H3 lysine 4 (H3K4) methyltransferases are conserved from yeast to humans, assemble in multisubunit complexes, and are needed to regulate gene expression. The yeast H3K4 methyltransferase complex, Set1 complex or complex of proteins associated with Set1 (COMPASS), consists of Set1 and conserved Set1-associated proteins: Swd1, Swd2, Swd3, Spp1, Bre2, Sdc1, and Shg1. The removal of the WD40 domain-containing subunits Swd1 and Swd3 leads to a loss of Set1 protein and consequently a complete loss of H3K4 methylation. However, until now, how these WD40 domain-containing proteins interact with Set1 and contribute to the stability of Set1 and H3K4 methylation has not been determined. In this study, we identified small basic and acidic patches that mediate protein interactions between the C terminus of Swd1 and the nSET domain of Set1. Absence of either the basic or acidic patches of Set1 and Swd1, respectively, disrupts the interaction between Set1 and Swd1, diminishes Set1 protein levels, and abolishes H3K4 methylation. Moreover, these basic and acidic patches are also important for cell growth, telomere silencing, and gene expression. We also show that the basic and acidic patches of Set1 and Swd1 are conserved in their human counterparts SET1A/B and RBBP5, respectively, and are needed for the protein interaction between SET1A and RBBP5. Therefore, this charge-based interaction is likely important for maintaining the protein stability of the human SET1A/B methyltransferase complexes so that proper H3K4 methylation, cell growth, and gene expression can also occur in mammals. PMID:22147691

  20. A bis(acetylacetonato)uranium(IV) complex of the Schiff base N,N'-bis(3-hydroxysalicylidene)-2-methyl-1,2-propanediamine.

    PubMed

    Salmon, Lionel; Thuéry, Pierre; Ephritikhine, Michel

    2003-06-01

    The title complex, bis(acetylacetonato-kappa(2)O,O')[N,N'-bis(3-hydroxy-2-oxidobenzaldimino)-2-methyl-1,2-propanediamine-kappa(4)N,O,O',N']uranium(IV) tetrahydrofuran solvate, [U(C(18)H(18)N(2)O(4))(C(5)H(7)O(2))(2)].C(4)H(8)O, is a rare example of a uranium(IV) complex with a compartmental Schiff base. The U atom is located in the N(2)O(2) inner site of the hexadentate N,N'-bis(3-hydroxy-2-oxidobenzaldimino)-2-methyl-1,2-propanediamine group and is bound also to the two O atoms of both acetylacetonate moieties, which results in a dodecahedral coordination environment. Centrosymmetric dimers are formed through intermolecular hydrogen bonds that link the terminal uncoordinated hydroxy groups to one another and to the O atoms of the acetylacetonate ligands. PMID:12794336

  1. Methyl ether derivatives of p-tert-Butyl[3.1.3.1]homooxacalixarene. Formation, structure, and complexes with quaternary ammonium ions.

    PubMed

    Masci, Bernardo; Mortera, Stefano Levi; Persiani, Daniela; Thuéry, Pierre

    2006-01-20

    [structure: see text] The whole set (five compounds) of partially O-methylated products of p-tert-butyl[3.1.3.1]homooxacalixarene, currently named p-tert-butyltetrahomodioxacalix[4]arene, have been prepared. Their structure has been investigated in solution through NMR techniques and in the solid state by single-crystal X-ray diffraction. A systematic investigation, extended to the parent tetraphenol and to the tetramethyl ether derivative, has been carried out on the complexation of tetramethylammonium, acetylcholine, N-methylpyridinium, and tetraethylammonium picrate in CDCl3. The observed trends in the binding and in the selectivity of the strictly related hosts could be analyzed on the basis of the varying importance of intramolecular hydrogen bonding and its effects on the conformation of the free and of the complexed ligands. On increasing the number of methyl ether functions, the cone conformation appears to be relatively less stable but deeper, so small organic cations can be more effectively encircled.

  2. Synthesis, photophysical and electrochemical properties of a mixed bipyridyl-phenanthrolyl ligand Ru(II) heteroleptic complex having trans-2-methyl-2-butenoic acid functionalities.

    PubMed

    Adeloye, Adewale O

    2011-01-01

    In this work, two ligands: 4-(trans-2-Methyl-2-butenoic acid)-2,2'-bipyridine) (L(1)) and 5-(trans-2-methyl-2-butenoic acid)-1,10-phenanthroline (L(2)), with the corresponding mixed-ligand heteroleptic Ru(II) complex were synthesized and characterized by FT-IR, 1H-, 13C-NMR spectroscopy and elemental analysis. The influence of the mixed functionalized polypyridyl ruthenium(II) complex on the photophysical and electrochemical properties were investigated and compared to individual single-ligand homoleptic complexes. Interestingly, the mixed-ligand complex formulated as [RuL(1)L(2)(NCS)(2)] exhibits broad and intense metal-to-ligand charge transfer (MLCT) absorption with a high molar extinction coefficient (λ(max) = 514 nm, ε = 69,700 M(-1) cm(-1)), better than those of individual single-ligand complexes, [Ru(L(1))(2)(NCS)(2)] and [Ru(L(2))(2)(NCS)(2)], and a strong photoluminescence intensity ratio in the red region at λ(em) = 686 nm. The electrochemical properties of the complex indicated that the redox processes are ligand-based.

  3. Solid-state flurbiprofen and methyl-β-cyclodextrin inclusion complexes prepared using a single-step, organic solvent-free supercritical fluid process.

    PubMed

    Rudrangi, Shashi Ravi Suman; Kaialy, Waseem; Ghori, Muhammad U; Trivedi, Vivek; Snowden, Martin J; Alexander, Bruce David

    2016-07-01

    The aim of this study was to enhance the apparent solubility and dissolution properties of flurbiprofen through inclusion complexation with cyclodextrins. Especially, the efficacy of supercritical fluid technology as a preparative technique for the preparation of flurbiprofen-methyl-β-cyclodextrin inclusion complexes was evaluated. The complexes were prepared by supercritical carbon dioxide processing and were evaluated by solubility, differential scanning calorimetry, X-ray powder diffraction, scanning electron microscopy, practical yield, drug content estimation and in vitro dissolution studies. Computational molecular docking studies were conducted to study the possibility of molecular arrangement of inclusion complexes between flurbiprofen and methyl-β-cyclodextrin. The studies support the formation of stable molecular inclusion complexes between the drug and cyclodextrin in a 1:1 stoichiometry. In vitro dissolution studies showed that the dissolution properties of flurbiprofen were significantly enhanced by the binary mixtures prepared by supercritical carbon dioxide processing. The amount of flurbiprofen dissolved into solution alone was very low with 1.11±0.09% dissolving at the end of 60min, while the binary mixtures processed by supercritical carbon dioxide at 45°C and 200bar released 99.39±2.34% of the drug at the end of 30min. All the binary mixtures processed by supercritical carbon dioxide at 45°C exhibited a drug release of more than 80% within the first 10min irrespective of the pressure employed. The study demonstrated the single step, organic solvent-free supercritical carbon dioxide process as a promising approach for the preparation of inclusion complexes between flurbiprofen and methyl-β-cyclodextrin in solid-state.

  4. Preparation of olanzapine and methyl-β-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-β-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-β-cyclodextrin. All the binary mixtures of olanzapine with methyl-β-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-β-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-β-cyclodextrin. The preliminary data also suggests that the complexes of olanzapine with methyl-β-cyclodextrin will lead to better therapeutic efficacy due to better solubility and dissolution properties.

  5. Preparation of olanzapine and methyl-β-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-β-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-β-cyclodextrin. All the binary mixtures of olanzapine with methyl-β-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-β-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-β-cyclodextrin. The preliminary data also suggests that the complexes of olanzapine with methyl-β-cyclodextrin will lead to better therapeutic efficacy due to better solubility and dissolution properties. PMID:26315120

  6. 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.

  7. [Study on S-benzyl-N-(ferrocenyl-1-methyl-metylidene)-dithiocarbazate nickel (II)/cobalt (II) complexes by in-situ FTIR spectroelectrochemistry].

    PubMed

    Wang, Xia-yan; Jin, Bao-kang; Tian, Yu-peng; Lin, Xiang-qin

    2003-02-01

    Comparative studies were carried out by using electrochemistry and in-situ FTIR spectroelectrochemistry for nonlinear optical complexes, S-benzyl-N-(ferrocenyl-1-methyl-metylidene)-dithiocarbazate nickel (II)/cobalt (II) complexes (Ni(LSB)2/Co (LSB)2). The results indicated that Ni(LSB)2 involves two consecutive reversible one-electron oxidation steps, while Co(LSB)2 involves only one two-electron oxidation step. Ni(LSB)2 complex that has a square planar configuration exhibits a moderately strong electronic communication between the two-ferrocene moieties, taking place through the skeleton chain of the ligand due to the extensive electron delocalization in the whole molecule and leads to the appearance of a strong nu c-c vibration band at 1,453 cm-1 during the oxidation process, while Co(LSB)2 complex that has a tetrahedral configuration shows low electron delocalization and has two almost identical ferrocene moieties.

  8. Complexes of Fe2+ with diethyldithiocarbamate or N-methyl-D-glucamine dithiocarbamate as traps of nitric oxide in animal tissues: comparative investigations.

    PubMed

    Mikoyan, V D; Kubrina, L N; Serezhenkov, V A; Stukan, R A; Vanin, A F

    1997-08-29

    In EPR experiments on mice it was demonstrated that a hydrophobic complex Fe2+ with diethyldithiocarbamate (DETC) is a more efficient selective NO trap than a hydrophilic complex Fe2+ with N-methyl-D-glutamine dithiocarbamate (MGD). This difference can be due to the higher stability of paramagnetic nitrosyl iron complex with DETC (MNIC-DETC) formed by NO binding to Fe2+-DETC in animal tissues in vivo. The complex analogue MNIC-MGD is reversibly oxidized in animal blood to transform into the diamagnetic EPR-silent form. The latter is detectable also in urine of animals, especially of those treated with bacterial lipopolysaccharide which initiates the enhanced NO production in the organism. We suggest that NO2 or peroxynitrite formed from endogenous NO can serve as an agent reversibly oxidizing MNIC-MGD in these animals. PMID:9305794

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. Biological activities of Zn(II)-S-methyl-cysteine complex as antiradical, inhibitor of acid phosphatase enzyme and in vivo antidepressant effects.

    PubMed

    Escudero, Graciela E; Martini, Nancy; Jori, Khalil; Jori, Nadir; Maresca, Nahuel R; Laino, Carlos H; Naso, Luciana G; Williams, Patricia A M; Ferrer, Evelina G

    2016-12-01

    The antidepressant effect of simple Zn(II) salts has been proved in several animal models of depression. In this study, a coordination metal complex of Zn(II) having a sulfur containing ligand is tested as antidepressant for the first time. Forced swimming test method on male Wistar rats shows a decrease in the immobility and an increase in the swimming behavior after treatment with [Zn(S-Met)2] (S-Met=S-methyl-l-cysteine) being more effective and remarkable than ZnCl2. The thiobarbituric acid and the pyranine consumption (hydroxyl and peroxyl radicals, respectively) methods were applied to evaluate the antioxidant activity of S-Met and [Zn(S-Met)2] showing evidence of attenuation of hydroxyl but not peroxyl radicals activities. UV-vis studies on the inhibition of acid phosphatase enzyme (AcP) demonstrated that S-methyl-l-cysteine did not produce any effect but, in contrast, [Zn(S-Met)2] complex behaved as a moderate inhibitor. Finally, bioavailability studies were performed by fluorescence spectroscopy denoting the ability of the albumin to transport the complex.

  17. 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.

  18. 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.

  19. 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.

  20. Synthesis, characterization, crystal structure and theoretical approach of Cu(II) complex with 4-{(Z)-[(2-hydroxybenzoyl)hydrazono]methyl}benzoic acid

    NASA Astrophysics Data System (ADS)

    Chen, Shi-Liang; Liu, Zheng; Liu, Jie; Han, Guo-Cheng; Li, Yan-Hong

    2012-04-01

    The metal complex of [CuL2]·2DMF (L = 4-{(Z)-[(2-hydroxybenzoyl)hydrazono]methyl}benzoic acid, DMF = N,N-dimethylformamide) (1) had been synthesized and characterized by spectral method(IR), UV-Vis electronic absorption spectra, fluorescence spectra, elemental analysis, electrochemistry, thermal analysis (TG, DTG) and single crystal X-ray diffraction techniques. In the complex, the ligands act as univalent anion bidentate and coordination takes place in the enol tautomeric form with the enolic oxygen and azomethine nitrogen atoms. Molecular geometry from X-ray experiment of the title compound in the ground-state has been compared using the density functional method (B3LYP) and LANL2DZ basis set. DFT calculations at B3LYP/LANL2DZ level of theory prove that the electronic spectra of CuL2·2DMF is attributed to intra-complex electronic transitions as well as π-π* electronic transitions. Also, Mulliken charge analysis, natural bond orbitals (NBO), Wiberg bond index and frontier molecular orbitals (FMO) were performed at B3LYP/LANL2DZ level of theory. In addition, complex 1 exhibits strong photoluminescent emission at room temperature. The electrochemical studies reveal that redox of Cu2+/Cu+ in the complex are quasi-reversible processes. The result of TG analysis shows that the title complex was stable under 100.0 °C.

  1. 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.

  2. Thermal stability of the anionic sigma complexes of 2,4,6-trinitroanisole with the methylates of the alkaline-earth metals

    SciTech Connect

    Glaz, A.I.; Soldatova, T.A.; Golopolosova, T.V.; Gitis, S.S.

    1987-09-10

    The study of the stability of the 1,1-dimethoxy-2,4,6-trinitrocyclohexadienates of the alkali metals when they are heated in air showed that their temperature of decomposition and the heat effect of the process are dependent on the nature of the cation. Our study centered on the thermal decomposition of the products resulting from the addition of the methylates of calcium, strontium, and barium to 2,4,6-trinitroanisole. For a quantitative assessment of the process we used the combined methods of differential-thermal analysis and differential thermogravimetry. The anionic sigma-complexes of 2,4,6-trinitroanisole with the methylates of the alkaline-earth metals decompose on heating into the corresponding picrates; at the same time, when one passes from the calcium slat to the strontium and barium salts the decomposition temperature and the heat effect of the process show a drop which is linked to the structure both of the complexes and of the picrates forming therefrom.

  3. Heritable DNA Methylation in CD4+ Cells among Complex Families Displays Genetic and Non-Genetic Effects

    PubMed Central

    Alonso, Arnald; Irvin, Marguerite R.; Zhi, Degui; Thibeault, Krista S.; Aslibekyan, Stella; Hidalgo, Bertha; Borecki, Ingrid B.; Ordovas, Jose M.; Arnett, Donna K.; Tiwari, Hemant K.; Absher, Devin M.

    2016-01-01

    DNA methylation at CpG sites is both heritable and influenced by environment, but the relative contributions of each to DNA methylation levels are unclear. We conducted a heritability analysis of CpG methylation in human CD4+ cells across 975 individuals from 163 families in the Genetics of Lipid-lowering Drugs and Diet Network (GOLDN). Based on a broad-sense heritability (H2) value threshold of 0.4, we identified 20,575 highly heritable CpGs among the 174,445 most variable autosomal CpGs (SD > 0.02). Tests for associations of heritable CpGs with genotype at 2,145,360 SNPs using 717 of 975 individuals showed that ~74% were cis-meQTLs (< 1 Mb away from the CpG), 6% of CpGs exhibited trans-meQTL associations (>1 Mb away from the CpG or located on a different chromosome), and 20% of CpGs showed no strong significant associations with genotype (based on a p-value threshold of 1e-7). Genes proximal to the genotype independent heritable CpGs were enriched for functional terms related to regulation of T cell activation. These CpGs were also among those that distinguished T cells from other blood cell lineages. Compared to genes proximal to meQTL-associated heritable CpGs, genotype independent heritable CpGs were moderately enriched in the same genomic regions that escape erasure during primordial germ cell development and could carry potential for generational transmission. PMID:27792787

  4. Synthesis, spectroscopic properties, crystal structure and density functional studies of Cu(II) complex with 2-((dehydroabietylamine)methyl)-6-methoxyphenol

    NASA Astrophysics Data System (ADS)

    Liu, Bao-Yu; Liu, Zheng; Han, Guo-Cheng; Li, Yan-Hong

    2010-06-01

    The metal complex of CuL 2 (L = 2-((dehydroabietylamine)methyl)-6-methoxyphenol) has been synthesized and characterized by spectral method (IR), elemental analysis, thermal analysis (TG, DTG) and single crystal X-ray diffraction techniques. Molecular geometry from X-ray experiment of the title compound in the ground-state has been compared using the density functional method (B3LYP) with LANL2DZ basis set. UV-vis spectra has been measured and DFT calculations at B3LYP/LANL2DZ level of theory proved that the electronic spectra of CuL 2 was attributed to intra-complex electronic transitions as well as d- d electronic transitions. Besides, Mulliken charge analysis, natural bond orbitals (NBO), frontier molecular orbitals (FMO) were performed at B3LYP/LANL2DZ level of theory.

  5. Synthesis and spectroscopic studies of 4-phenylacetyl-3-methyl-1-phenylpyrazolone-5 and its thorium(VI), lanthanum(III) and lead(II) complexes

    NASA Astrophysics Data System (ADS)

    Uzoukwu, Bieluonwu Augustus; Adiukwu, Patricia Ugboaku

    1995-12-01

    The synthesis of 4-phenylacetyl-3-methyl-1-phenylpyrazolone-5 is reported. Analysis of its IR and NMR spectral data has revealed that the ligand is bidentate and has spectral properties that resemble neither those of the 4-benzoyl, 4-acetyl derivatives nor those of the trihaloacetyl derivatives which have p Ka values < 4.0. Instead the spectral properties are similar to those of the 4-alkanoyl derivatives which have p Ka values . 4.0. The thorium(VI), lanthanum(III) and lead(II) complexes were isolated and characterized by UV, IR and 1H, 13C NMR spectral studies. The complexes were anhydrous and conform to a general molecular formula ML n where M( n) is Th(VI), La(III), Pb(II).

  6. Inorganic and organic structures as interleavers among [bis(1-methyl-3-(p-carboxylatephenyl)triazenide 1-oxide)Ni(II)] complexes to form supramolecular arrangements

    NASA Astrophysics Data System (ADS)

    Santos, Aline Joana Rolina Wohlmuth Alves; dos Santos Hackbart, Helen Cristina; Giacomini, Gabriela Xavier; Bersch, Patrícia; Paraginski, Gustavo Luiz; Hörner, Manfredo

    2016-12-01

    Alternative compounds to capture metal ions are triazenes 1-oxide since they are basic compounds O(N) with negative charge in the deprotonated form. The proximity of both coordination sites (O and N) enables these compounds to have good chelating ability and a tendency to stabilize in the formation of rings with soft and hard transition metal ions. The structure analysis by single crystal X-ray diffraction of compounds (1) and (2) demonstrate the formation of 3D supramolecular arrangements through ion-ion, ion-dipolo and dipolo-dipolo interactions. In one of them, there are [(H2O)2(CH3CH3SO)K2]2+ as linkers of polymerization and, in another complex, there are [(H2O)(CH3CH3SO)Ni(H2O)6]2+ as a linker of polymerization. These linkers act in the polymerization of the novel mononuclear complex [bis(1-methyl (p-carboxylatephenyl) triazenide 1-oxide) NiII] (3). The crystallography analysis of (1) and (2) showed distorted quadratic geometry for Ni (II), thus, there are two axial positions available in Ni (II) to be used in catalysis studies and as sensor or biosensor. In addition, this study shows the support of this novel mononuclear complex of Ni (II) (3) on protonated chitosan chains (4). The compounds (3) and (4) were characterized by spectroscopic analysis, infrared (IR) and energy dispersive X-ray detector (EDS), and by differential scanning calorimetry analysis (DSC). The specificity of ligand 1-methyl (p-carboxyphenyl) triazene 1-oxide to capture potassium and nickel ions will be tested at different pH values, as well as the capacity of the triazenide 1-oxide of Ni (II) complex, supported on chitosan polymer, or not, to act as a catalyst for organic reactions and biomimetic organic reactions.

  7. 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

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

    NASA Astrophysics Data System (ADS)

    Serbest, Kerim; Karaoğlu, Kaan; Erman, Murat; Er, Mustafa; Değirmencioğlu, İsmail

    2010-10-01

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

  9. 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.

  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. 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

  12. 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

  13. 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.

  14. 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.

  15. Methylation matters

    PubMed Central

    Costello, J.; Plass, C.

    2001-01-01

    DNA methylation is not just for basic scientists any more. There is a growing awareness in the medical field that having the correct pattern of genomic methylation is essential for healthy cells and organs. If methylation patterns are not properly established or maintained, disorders as diverse as mental retardation, immune deficiency, and sporadic or inherited cancers may follow. Through inappropriate silencing of growth regulating genes and simultaneous destabilisation of whole chromosomes, methylation defects help create a chaotic state from which cancer cells evolve. Methylation defects are present in cells before the onset of obvious malignancy and therefore cannot be explained simply as a consequence of a deregulated cancer cell. Researchers are now able to detect with exquisite sensitivity the cells harbouring methylation defects, sometimes months or years before the time when cancer is clinically detectable. Furthermore, aberrant methylation of specific genes has been directly linked with the tumour response to chemotherapy and patient survival. Advances in our ability to observe the methylation status of the entire cancer cell genome have led us to the unmistakable conclusion that methylation abnormalities are far more prevalent than expected. This methylomics approach permits the integration of an ever growing repertoire of methylation defects with the genetic alterations catalogued from tumours over the past two decades. Here we discuss the current knowledge of DNA methylation in normal cells and disease states, and how this relates directly to our current understanding of the mechanisms by which tumours arise.


Keywords: methylation; cancer PMID:11333864

  16. Inclusion complexation of isoprenaline and methyl dopa with α- and β-cyclodextrin nanocavities: Spectral and theoretical study

    NASA Astrophysics Data System (ADS)

    Rajendiran, N.; Thulasidhasan, J.; Saravanan, J.

    2014-03-01

    Inclusion complex formation of isoprenaline (ISOP) and methyldopa (MDOP) with α-CD and β-CD were investigated. Solid inclusion complex nanomaterials were characterized by SEM, TEM, FTIR, DSC, 1H NMR and XRD methods. Spectral results showed that single emission (monomer) noticed in aqueous solution where as dual emission (excimer) in CD. Both drugs formed 1:2 (CD-drug2) inclusion complexes with CDs. Time-resolved fluorescence studies show that single exponential decay observed in water whereas biexponential decay observed in CD. Nano-sized particles were found in ISOP/CD while vesicles were obtained in MDOP/CD complexes. DSC results revealed that the thermal stability of drugs was improved when it was included in the CD nanocavity. Based on PM3 calculations, the inclusion structure of ISOP/CD and MDOP/CD complexes were proposed. Thermodynamic parameters and binding affinity of complexation of CD were determined by PM3 method.

  17. Inclusion complexation of isoprenaline and methyl dopa with α- and β-cyclodextrin nanocavities: spectral and theoretical study.

    PubMed

    Rajendiran, N; Thulasidhasan, J; Saravanan, J

    2014-03-25

    Inclusion complex formation of isoprenaline (ISOP) and methyldopa (MDOP) with α-CD and β-CD were investigated. Solid inclusion complex nanomaterials were characterized by SEM, TEM, FTIR, DSC, (1)H NMR and XRD methods. Spectral results showed that single emission (monomer) noticed in aqueous solution where as dual emission (excimer) in CD. Both drugs formed 1:2 (CD-drug2) inclusion complexes with CDs. Time-resolved fluorescence studies show that single exponential decay observed in water whereas biexponential decay observed in CD. Nano-sized particles were found in ISOP/CD while vesicles were obtained in MDOP/CD complexes. DSC results revealed that the thermal stability of drugs was improved when it was included in the CD nanocavity. Based on PM3 calculations, the inclusion structure of ISOP/CD and MDOP/CD complexes were proposed. Thermodynamic parameters and binding affinity of complexation of CD were determined by PM3 method.

  18. Excited state complex formation between methyl glyoxal and some aromatic bio-molecules: a fluorescence quenching study

    NASA Astrophysics Data System (ADS)

    Banerjee, D.; Mandal, A.; Mukherjee, S.

    2003-01-01

    Fluorescence quenching of some important aromatic bio-molecules (ABM) such as 3-aminophthalhydrazide (luminol), tryptophan (Try), phenylalanine and tyrosine (Tyr) by methyl glyoxal (MG) has been studied employing different spectroscopic techniques. The interaction of MG with ABM in the excited state has been analysed using Stern-Volmer (S-V) mechanism. In the case of MG-luminol system time correlated single photon counting (TCSPC) technique has also been applied to explain the S-V mechanism. The bimolecular rate constants obtained are found to be higher than the rate constant for diffusion controlled process. A plausible explanation of the quenching mechanism has been discussed on the basis of hydrogen bonding, charge transfer and energy transfer interaction between the colliding species.

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

    PubMed

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

    2015-09-01

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

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

    PubMed

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

    2015-09-01

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

  1. A new μ3-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(μ3-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 (ΔE = 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.

  2. 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.

  3. Analysis of three crystal structure determinations of a 5-methyl-6-N-methylanilino pyridopyrimidine antifolate complex with human dihydrofolate reductase.

    PubMed

    Cody, Vivian; Luft, Joseph R; Pangborn, Walter; Gangjee, Aleem

    2003-09-01

    Structural data are reported for the first example of the potent antifolate inhibitor 2,4-diamino-5-methyl-6-[(3',4',5'-trimethoxy-N-methylanilino)methyl]pyrido[2,3-d]pyrimidine (1) in complex with human dihydrofolate reductase (hDHFR) and NADPH. Small differences in crystallization conditions resulted in the growth of two different forms of a binary complex. The structure determination of an additional crystal of a ternary complex of hDHFR with NADPH and (1) grown under similar conditions is also reported. Diffraction data were collected to 2.1 A resolution for an R3 lattice from a hDHFR ternary complex with NADPH and (1) and to 2.2 A resolution from a binary complex. Data were also collected to 2.1 A resolution from a binary complex with hDHFR and (1) in the first example of a tetragonal P4(3)2(1)2 lattice. Comparison of the intermolecular contacts among these structures reveals differences in the backbone conformation (1.9-3.2 A) for flexible loop regions (residues 40-46, 77-83 and 103-107) that reflect differences in the packing environment between the rhombohedral and tetragonal space groups. Analysis of the packing environments shows that the tetragonal lattice is more tightly packed, as reflected in its smaller V(M) value and lower solvent content. The conformation of the inhibitor (1) is similar in all structures and is also similar to that observed for TMQ, the parent quinazoline compound. The activity profile for this series of 5-deaza N-substituted non-classical trimethoxybenzyl antifolates shows that the N10-CH(3) substituted (1) has the greatest potency and selectivity for Toxoplasma gondii DHFR (tgDHFR) compared with its N-H or N-CHO analogs. Models of the tgDHFR active site indicate preferential contacts with (1) that are not present in either the human or Pneumocystis carinii DHFR structures. Differences in the acidic residue (Glu30 versus Asp for tgDHFR) affect the precise positioning of the diaminopyridopyrimidine ring, while changes in other

  4. 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 β-CD was obtained.) The inclusion complex obtained between AMP and β-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.

  5. DNA-binding and molecular mechanics modelling studies of the bulky chiral platinum(II) complex [PtCl(2)(mepyrr)] (mepyrr=N-methyl-2-aminomethylpyrrolidine).

    PubMed

    Diakos, Connie I; Fenton, Ronald R; Hambley, Trevor W

    2006-12-01

    Detailed studies were carried out on the binding of the enantiomers of [PtCl(2)(mepyrr)] (mepyrr=N-methyl-2-aminomethylpyrrolidine) to dG, d(GpG) and a 52-mer oligonucleotide. The pyrrolidine ligand structure was found to be neither sufficiently rigid nor bulky to enforce a single chirality at the exocyclic amine site in this complex, resulting in the presence of diastereomers that complicated the binding studies. Reaction of the (GpG) dinucleotide with R- and S-[PtCl(2)(mepyrr)] resulted in formation of four [Pt{d(GpG)}(mepyrr)] isomers for each enantiomer as a consequence of the existence of two orientational isomers and two diastereomers. These isomers formed in different amounts most likely as a consequence of the unequal formation of the diastereomers together with stereoselectivity induced by interactions between the dinucleotide and the mepyrr ligand. The [PtCl(2)(mepyrr)] complexes displayed stereoselectivity and enantioselectivity in their reactions with a 52-mer duplex designed to allow formation of only GpG intrastrand adducts. All four bifunctional adducts formed for each enantiomer, providing further evidence of the lack of directing ability of the ligand in formation of the 1,2-intrastrand adduct. Significant amounts of monofunctional species remained in these assays suggesting that the introduction of the methyl substituent to the exocyclic amine inhibited ring-closure to the bifunctional adduct. This was not sufficient to achieve enantiospecificity, but in the case of the R-enantiomer, one of the bifunctional adducts formed in only small amounts. PMID:17083976

  6. Solvent extraction of N-Cyclohexyl-N-Nitrosohydroxylamine (cnha) into some organic solvents and of the Cu(II)-cnha complex into methyl isobutyl ketone.

    PubMed

    Rauret, G; Pineda, L; Ventura, M; Compaño, R

    1986-02-01

    The distribution equilibria of N-cyclohexyl-N-nitrosohydroxylamine (cnha) in the water-chloroform, water-hexane, water-methyl isobutyl ketone (MIBK) and water-isopentyl alcohol systems, and of the Cu(II)-cnha complex in the water-MIBK system have been studied. From the distribution data the dissociation and distribution constants of the reagent have been calculated; their values are pK(a) = 5.55 +/- 0.10; log K(DR) = 2.46 +/- 0.05 (chloroform), 1.76 +/- 0.11 (MIBK), 1.06 +/- 0.07 (hexane) and 1.48 +/- 0.06 (isopentyl alcohol). In the same way the values of the distribution and stability constants of the Cu(II) complex have been obtained; log K(DC) = 3.51; log beta(1) = 7.23 +/- 0.10 and log beta(2) = 12.00 +/- 0.08. For the determination of cnha in the aqueous phase saturated with MIBK, a spectrophotometric method based on the coloured complex formed by the reagent with Fe(III) has been established. Finally, an analytical method for Cu(II) by atomic-absorption spectrometry after its extraction with cnha into MIBK, is proposed. Its detection limit is 4.6 mug l ., its precision +/- 2.1% and its accuracy 97.5%. This method has been applied to the determination of the copper content in the surface water of the Congest River of Catalonia (Spain). PMID:18964050

  7. 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

  8. Enzyme inhibitor studies reveal complex control of methyl-D-erythritol 4-phosphate (MEP) pathway enzyme expression in Catharanthus roseus.

    PubMed

    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.

  9. 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).

  10. DNA methylation in plants.

    PubMed

    Vanyushin, B F

    2006-01-01

    DNA in plants is highly methylated, containing 5-methylcytosine (m5C) and N6-methyladenine (m6A); m5C is located mainly in symmetrical CG and CNG sequences but it may occur also in other non-symmetrical contexts. m6A but not m5C was found in plant mitochondrial DNA. DNA methylation in plants is species-, tissue-, organelle- and age-specific. It is controlled by phytohormones and changes on seed germination, flowering and under the influence of various pathogens (viral, bacterial, fungal). DNA methylation controls plant growth and development, with particular involvement in regulation of gene expression and DNA replication. DNA replication is accompanied by the appearance of under-methylated, newly formed DNA strands including Okazaki fragments; asymmetry of strand DNA methylation disappears until the end of the cell cycle. A model for regulation of DNA replication by methylation is suggested. Cytosine DNA methylation in plants is more rich and diverse compared with animals. It is carried out by the families of specific enzymes that belong to at least three classes of DNA methyltransferases. Open reading frames (ORF) for adenine DNA methyltransferases are found in plant and animal genomes, and a first eukaryotic (plant) adenine DNA methyltransferase (wadmtase) is described; the enzyme seems to be involved in regulation of the mitochondria replication. Like in animals, DNA methylation in plants is closely associated with histone modifications and it affects binding of specific proteins to DNA and formation of respective transcription complexes in chromatin. The same gene (DRM2) in Arabidopsis thaliana is methylated both at cytosine and adenine residues; thus, at least two different, and probably interdependent, systems of DNA modification are present in plants. Plants seem to have a restriction-modification (R-M) system. RNA-directed DNA methylation has been observed in plants; it involves de novo methylation of almost all cytosine residues in a region of si

  11. N-methyl-D-Aspartate Receptors Contribute to Complex Spike Signaling in Cerebellar Purkinje Cells: An In vivo Study in Mice.

    PubMed

    Liu, Heng; Lan, Yan; Bing, Yan-Hua; Chu, Chun-Ping; Qiu, De-Lai

    2016-01-01

    N-methyl-D-aspartate receptors (NMDARs) are post-synaptically expressed at climbing fiber-Purkinje cell (CF-PC) synapses in cerebellar cortex in adult mice and contributed to CF-PC synaptic transmission under in vitro conditions. In this study, we investigated the role of NMDARs at CF-PC synapses during the spontaneous complex spike (CS) activity in cerebellar cortex in urethane-anesthetized mice, by in vivo whole-cell recording technique and pharmacological methods. Under current-clamp conditions, cerebellar surface application of NMDA (50 μM) induced an increase in the CS-evoked pause of simple spike (SS) firing accompanied with a decrease in the SS firing rate. Under voltage-clamp conditions, application of NMDA enhanced the waveform of CS-evoked inward currents, which expressed increases in the area under curve (AUC) and spikelet number of spontaneous CS. NMDA increased the AUC of spontaneous CS in a concentration-dependent manner. The EC50 of NMDA for increasing AUC of spontaneous CS was 33.4 μM. Moreover, NMDA significantly increased the amplitude, half-width and decay time of CS-evoked after-hyperpolarization (AHP) currents. Blockade of NMDARs with D-(-)-2-amino-5-phosphonopentanoic acid (D-APV, 250 μM) decreased the AUC, spikelet number, and amplitude of AHP currents. In addition, the NMDA-induced enhancement of CS activity could not be observed after α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors were blocked. The results indicated that NMDARs of CF-PC synapses contributed to the spontaneous CS activity by enhancing CS-evoked inward currents and AHP currents. PMID:27445699

  12. N-methyl-D-Aspartate Receptors Contribute to Complex Spike Signaling in Cerebellar Purkinje Cells: An In vivo Study in Mice

    PubMed Central

    Liu, Heng; Lan, Yan; Bing, Yan-Hua; Chu, Chun-Ping; Qiu, De-Lai

    2016-01-01

    N-methyl-D-aspartate receptors (NMDARs) are post-synaptically expressed at climbing fiber-Purkinje cell (CF-PC) synapses in cerebellar cortex in adult mice and contributed to CF-PC synaptic transmission under in vitro conditions. In this study, we investigated the role of NMDARs at CF-PC synapses during the spontaneous complex spike (CS) activity in cerebellar cortex in urethane-anesthetized mice, by in vivo whole-cell recording technique and pharmacological methods. Under current-clamp conditions, cerebellar surface application of NMDA (50 μM) induced an increase in the CS-evoked pause of simple spike (SS) firing accompanied with a decrease in the SS firing rate. Under voltage-clamp conditions, application of NMDA enhanced the waveform of CS-evoked inward currents, which expressed increases in the area under curve (AUC) and spikelet number of spontaneous CS. NMDA increased the AUC of spontaneous CS in a concentration-dependent manner. The EC50 of NMDA for increasing AUC of spontaneous CS was 33.4 μM. Moreover, NMDA significantly increased the amplitude, half-width and decay time of CS-evoked after-hyperpolarization (AHP) currents. Blockade of NMDARs with D-(-)-2-amino-5-phosphonopentanoic acid (D-APV, 250 μM) decreased the AUC, spikelet number, and amplitude of AHP currents. In addition, the NMDA-induced enhancement of CS activity could not be observed after α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors were blocked. The results indicated that NMDARs of CF-PC synapses contributed to the spontaneous CS activity by enhancing CS-evoked inward currents and AHP currents. PMID:27445699

  13. Experimental and theoretical studies on the inclusion complexation of syringic acid with alpha-, beta-, gamma- and heptakis(2,6-di-O-methyl)-beta-cyclodextrin.

    PubMed

    Song, Le Xin; Wang, Hai Ming; Xu, Peng; Yang, Yan; Zhang, Zi Qiang

    2008-04-01

    Intermolecular interactions of alpha-, beta-, gamma- and heptakis(2,6-di-O-methyl)-beta-cyclodextrin (CD) with syringic acid (Syr) in aqueous solution are investigated by fluorescence spectroscopy. The fluorescence intensity of Syr gradually increases with the addition of the CDs. The formation constants (K) of the host-guest inclusion complexes are determined using a nonlinear analysis. The association abilities of Syr with the CDs decrease in the order gamma->beta->alpha- approximately DMbeta-CD. Both the intrinsic binding abilities of the CDs and the structural effect of Syr are taken into consideration when comparing the K values. Based on the results of NMR experimental and theoretical PM3 calculations both in vacuo and in water, it is found that Syr stays near the wider rim of alpha-CD cavity. Both the number of substituted groups (NSG) in a guest and the molar volume ratio of the guest to host cavity (MVR) play an important role in forming the CD supramolecular complexes of a homologous series of phenol derivatives, such as 2-methoxylphenol (2-Mop), eugenol (Eug) and Syr, i.e., an appropriate NSG or MVR in an inclusion system, such as in 2-Mop-alpha-CD, Eug-beta-CD and Syr-gamma-CD systems, can maximize the intermolecular interaction between host and guest.

  14. 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)

    Barczyński, 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 O·H·O hydrogen bond of 2.450(2) Å. 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.

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

    PubMed Central

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

    2014-01-01

    Albendazole is a benzimidazole carbamate extensively used in oral chemotherapy against intestinal parasites, due to its broad spectrum activity, good tolerance and low cost. However, the drug has the disadvantage of poor bioavailability due to its very low solubility in water; as a consequence, a very active area of research focuses on the development of new pharmaceutical formulations to increase its solubility, dissolution rate, and bioavailability. The primary objective of this study was to prepare randomly methylated β-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

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

    Two manganese complexes containing 4,4'-bipyridine and methyl benzoate as ligands have been prepared and crystallized by solvent evaporation method in DMF. The single crystal X-ray crystallographic analyses reveal that the complexes crystallize in monoclinic system. Crystal of 1 [Mn2(4,4'-bipy)2 (o-MBA)4]n has space group of P21/c with unit cell parameters of a = 17.508 (Å), b = 11.6229 (Å), c = 27.983 (Å), β = 128.123°, V = 4.4797 nm3, empirical formula: C52H44Mn2N4O8, Mr = 962.79, Z = 4, Dc = 1.428 g/cm3, μ = 0.625 mm-1, and F(000) = 1992. The crystal of 2 [Mn (4,4'-bipy)(m-MBA)2]n belongs to space group C2/c with a = 16.079 (Å), b = 11.652 (Å), c = 24.887 (Å), β = 92.02°, V = 4.660 nm3, empirical formula: C26H22MnN2O4, Mr = 481.40, Z = 8, Dc = 1.372 g/cm3, μ = 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, π-π stacking and Csbnd H⋯π 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.

  19. 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

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

    PubMed

    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

  1. Co(II), Ni(II) and Cu(II) complexes of methyl-5-(Phenylthio) benzimidazole-2-carbamate: Molecular structures, spectral and DFT calculations

    NASA Astrophysics Data System (ADS)

    Mansour, Ahmed M.; El Bakry, Eslam M.; Abdel-Ghani, Nour T.

    2016-05-01

    [Co(FBZ)2(H2O)]·2NO3·0.5H2O (1), [Ni(FBZ)2X2]·zH2O (X = Cl​-, z = 0.5 (2) and X = CH3COO-, z = 1 (3)) and [Cu(FBZ)2(H2O) (NO3)]·NO3·1.5H2O (4) (FBZ = methyl-5-(Phenylthio) benzimidazole-2-carbamate; Fenbendazole) complexes were synthesized and characterized by elemental analysis, thermal, IR, EPR, UV-Vis, magnetic and conductance measurements. Geometry optimization, molecular electrostatic potential maps and natural bond orbital analysis were carried out at DFT/B3LYP/6-31G∗ level of theory. FBZ behaves as a neutral bidentate ligand via the pyridine-type nitrogen of the benzimidazole moiety and the carbamate group. Three-step ionization with pKa values of 3.38, 4.06 and 10.07 were reported for FBZ. The coordination of FBZ to the metal ions led to an increase in the antibacterial activity against the tested Staphylococcus aureus and Escherichia coli bacteria.

  2. Atomic layer deposition of indium oxide thin film from a liquid indium complex containing 1-dimethylamino-2-methyl-2-propoxy ligands

    NASA Astrophysics Data System (ADS)

    Han, Jeong Hwan; Jung, Eun Ae; Kim, Hyo Yeon; Kim, Da Hye; Park, Bo Keun; Park, Jin-Seong; Son, Seung Uk; Chung, Taek-Mo

    2016-10-01

    In2O3 thin films were grown from a newly developed, liquid, homoleptic, In-based complex, tris(1-dimethylamino-2-methyl-2-propoxy)indium [In(dmamp)3], and O3 by atomic layer deposition (ALD) at growth temperatures of 150-200 °C. In(dmamp)3 exhibited single-step evaporation with negligible residue and excellent thermal stability between 30 and 250 °C. The self-limiting surface reaction of In2O3 during ALD was demonstrated by varying the In(dmamp)3 and O3 pulse lengths, with a growth rate of 0.027 nm/cycle achieved at 200 °C. The In2O3 films grown at temperatures over 175 °C exhibited negligible concentrations of impurities, whereas that grown below 175 °C had concentrations of residual C of 6-8 at.%. Glancing angle X-ray diffraction revealed that the In2O3 films were polycrystalline in nature when the deposition temperature was greater than 200 °C. The In2O3 films grown at 150-200 °C exhibited carrier concentrations of 1.5 × 1018-6.6 × 1019 cm-3, resistivities of 15.1-2 × 10-3 Ω cm, and Hall mobilities of 0.8-42 cm2/(V s).

  3. Selective electrocatalytic oxidation of a re-methyl complex to methanol by a surface-bound Ru(II) polypyridyl catalyst.

    PubMed

    Coggins, Michael K; Méndez, Manuel A; Concepcion, Javier J; Periana, Roy A; Meyer, Thomas J

    2014-11-12

    The complex [Ru(Mebimpy)(4,4'-((HO)2OPCH2)2bpy)(OH2)](2+) surface bound to tin-doped indium oxide mesoporous nanoparticle film electrodes (nanoITO-Ru(II)(OH2)(2+)) is an electrocatalyst for the selective oxidation of methylrhenium trioxide (MTO) to methanol in acidic aqueous solution. Oxidative activation of the catalyst to nanoITO-Ru(IV)(OH)(3+) induces oxidation of MTO. The reaction is first order in MTO with rate saturation observed at [MTO] > 12 mM with a limiting rate constant of k = 25 s(-1). Methanol is formed selectively in 87% Faradaic yield in controlled potential electrolyses at 1.3 V vs NHE. At higher potentials, oxidation of MTO by nanoITO-Ru(V)(O)(3+) leads to multiple electrolysis products. The results of an electrochemical kinetics study point to a mechanism in which surface oxidation to nanoITO-Ru(IV)(OH)(3+) is followed by direct insertion into the rhenium-methyl bond of MTO with a detectable intermediate. PMID:25325162

  4. 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.

  5. Novel Cobalt(II) complexes containing N,N-di(2-picolyl)amine based ligands; Synthesis, characterization and application towards methyl methacrylate polymerisation

    NASA Astrophysics Data System (ADS)

    Ahn, Seoung Hyun; Choi, Sang-Il; Jung, Maeng Joon; Nayab, Saira; Lee, Hyosun

    2016-06-01

    The reaction of [CoCl2·6H2O] with N‧-substituted N,N-di(2-picolyl)amine ligands such as 1-cyclohexyl-N,N-bis(pyridin-2-ylmethyl)methanamine (LA), 2-methoxy-N,N-bis(pyridin-2-ylmethyl)ethan-1-amine (LB), and 3-methoxy-N,N-bis(pyridin-2-ylmethyl)propan-1-amine (LC), yielded [LnCoCl2] (Ln = LA, LB and LC), respectively. The Co(II) centre in [LnCoCl2] (Ln = LA, and LC) adopted distorted bipyramidal geometries through coordination of nitrogen atoms of di(2-picolyl)amine moiety to the Co(II) centre along with two chloro ligands. The 6-coordinated [LBCoCl2] showed a distorted octahedral geometry, achieved through coordination of the two pyridyl units, two chloro units, and bidentate coordination of nitrogen and oxygen in the N‧-methoxyethylamine to the Co(II) centre. [LCCoCl2] (6.70 × 104 gPMMA/molCo h) exhibited higher catalytic activity for the polymerisation of methyl methacrylate (MMA) in the presence of modified methylaluminoxane (MMAO) compared to rest of Co(II) complexes. The catalytic activity was considered as a function of steric properties of ligand architecture and increased steric bulk around the metal centre resulted in the decrease catalytic activity. All Co(II) initiators yielded syndiotactic poly(methylmethacrylate) (PMMA).

  6. 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

    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

    2013-07-01

    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.

  7. 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

  8. 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

  9. Synthesis, characterization, crystal structure determination and computational study of a new Cu(II) complex of bis [2-{(E)-[2-chloroethyl)imino]methyl}phenolato)] copper(II) Schiff base complex

    NASA Astrophysics Data System (ADS)

    Grivani, Gholamhossein; Vakili, Mohammad; Khalaji, Aliakbar Dehno; Bruno, Giuseppe; Rudbari, Hadi Amiri; Taghavi, Maedeh

    2016-07-01

    The copper (II) Schiff base complex of [CuL2] (1), HL = 2-{(E)-[2-chloroethyl) imino]methyl}phenol, has been synthesized and characterized by elemental (CHN) analysis, UV-Vis and FT-IR spectroscopy. The molecular structure of 1 was determined by single crystal X-ray diffraction technique. The conformational analysis and molecular structures of CuL2 were investigated by means of density functional theory (DFT) calculations at B3LYP/6-311G* level. An excellent agreement was observed between theoretical and experimental results. The Schiff base ligand of HL acts as a chelating ligand and coordinates via one nitrogen atom and one oxygen atom to the metal center. The copper (II) center is coordinated by two nitrogen atoms and two oxygen atoms from two Schiff base ligands in an approximately square planar trans-[MN2O2] coordination geometry. Thermogravimetric analysis of CuL2 showed that it was decomposed in five stages. In addition, the CuL2 complex thermally decomposed in air at 660 °C and the XRD pattern of the obtained solid showed the formation of CuO nanoparticles with an average size of 34 nm.

  10. DNA Methylation

    PubMed Central

    Marinus, M.G.; Løbner-Olesen, A.

    2014-01-01

    The DNA of E. coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcm methyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during repair of replication errors, controlling the frequency of initiation of chromosome replication at oriC, and regulation of transcription initiation at promoters containing GATC sequences. In contrast, there is no known function for Dcm methylation although Dcm recognition sites constitute sequence motifs for Very Short Patch repair of T/G base mismatches. In certain bacteria (e.g., Vibrio cholerae, Caulobacter crescentus) adenine methylation is essential and in C. crescentus, it is important for temporal gene expression which, in turn, is required for coordinating chromosome initiation, replication and division. In practical terms, Dam and Dcm methylation can inhibit restriction enzyme cleavage; decrease transformation frequency in certain bacteria; decrease the stability of short direct repeats; are necessary for site-directed mutagenesis; and to probe eukaryotic structure and function. PMID:26442938

  11. 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.

  12. 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

  13. Metal Complexes of New Bioactive Pyrazolone Phenylhydrazones; Crystal Structure of 4-Acetyl-3-methyl-1-phenyl-2-pyrazoline-5-one phenylhydrazone Ampp-Ph

    PubMed Central

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

    2016-01-01

    The condensation reaction of phenylhydrazine and dinitrophenylhydrazine with 4-acetyl and 4-benzoyl pyrazolone precipitated air-stable acetyldinitrophenylhydrazone Ampp-Dh, benzoylphenylhydrazone Bmpp-Ph and benzoyldinitrophenylhydrazone Bmpp-Dh in their keto imine form; a study inspired by the burning interest for the development of new bioactive materials with novel properties that may become alternative therapeutic agents. Elemental analysis, FTIR, 1H, and 13C NMR, and mass spectroscopy have been used to justify their proposed chemical structures, which were in agreement with the single crystal structure of Bmpp-Dh earlier reported according to X-ray crystallography. The single crystal structure of 4-acetyl-3-methyl-1-phenyl--pyrazoline-5-one phenylhydrazone Ampp-Ph, which crystallizes in a triclinic crystal system with a P-1 (No. 2) space group is presented. Octahedral Mn(II), Ni(II), Co(II), and Cu(II) complexes of these respective ligands with two molecules each of the bidentate Schiff base, coordinating to the metal ion through the azomethine nitrogen C=N and the keto oxygen C=O, which were afforded by the reaction of aqueous solutions of the corresponding metal salts with the ligands are also reported. Their identity and proposed structures were according to elemental analysis, FTIR spectroscopy, UV-VIS spectrophotometry (electronic spectra) and Bohr magnetic moments, as well as thermogravimetric analysis (TGA) results. A look at the antibacterial and antioxidant activities of synthesized compounds using the methods of the disc diffusion against some selected bacterial isolates and 1,1-diphenyl-2-picryl-hydrazil (DPPH) respectively, showed biological activities in relation to employed standard medicinal drugs. PMID:27213342

  14. Crystal structures of artocarpin, a Moraceae lectin with mannose specificity, and its complex with methyl-alpha-D-mannose: implications to the generation of carbohydrate specificity.

    PubMed

    Pratap, J V; Jeyaprakash, A Arockia; Rani, P Geetha; Sekar, K; Surolia, A; Vijayan, M

    2002-03-22

    The seeds of jack fruit (Artocarpus integrifolia) contain two tetrameric lectins, jacalin and artocarpin. Jacalin was the first lectin found to exhibit the beta-prism I fold, which is characteristic of the Moraceae plant lectin family. Jacalin contains two polypeptide chains produced by a post-translational proteolysis which has been shown to be crucial for generating its specificity for galactose. Artocarpin is a single chain protein with considerable sequence similarity with jacalin. It, however, exhibits many properties different from those of jacalin. In particular, it is specific to mannose. The structures of two crystal forms, form I and form II, of the native lectin have been determined at 2.4 and 2.5 A resolution, respectively. The structure of the lectin complexed with methyl-alpha-mannose, has also been determined at 2.9 A resolution. The structure is similar to jacalin, although differences exist in details. The crystal structures and detailed modelling studies indicate that the following differences between the carbohydrate binding sites of artocarpin and jacalin are responsible for the difference in the specificities of the two lectins. Firstly, artocarpin does not contain, unlike jacalin, an N terminus generated by post-translational proteolysis. Secondly, there is no aromatic residue in the binding site of artocarpin whereas there are four in that of jacalin. A comparison with similar lectins of known structures or sequences, suggests that, in general, stacking interactions with aromatic residues are important for the binding of galactose while such interactions are usually absent in the carbohydrate binding sites of mannose-specific lectins with the beta-prism I fold.

  15. Two orthorhombic crystal structures of a galactose-specific lectin from Artocarpus hirsuta in complex with methyl-alpha-D-galactose.

    PubMed

    Rao, K N; Suresh, C G; Katre, U V; Gaikwad, S M; Khan, M I

    2004-08-01

    Based on their carbohydrate specificity, the jacalin family of lectins can be divided into two groups: galactose-specific and mannose-specific. The former are cytoplasmic proteins, whereas the latter are localized in the storage vacuoles of cells. It has been proposed that the post-translational modification in some of the lectins that splits their polypeptide chains into two may be crucial for galactose specificity. The mannose-specific members of the family are single-chain proteins that lack the above modification. Although the galactose-specific and the mannose-specific jacalin-type lectins differ in their sequences, they share a common fold: the beta-prism I fold, which is characteristic of Moraceae plant lectins. Here, two crystal structures of a jacalin-related lectin from Artocarpus hirsuta, which is specific for galactose, in complex with methyl-alpha-D-galactose are reported. The lectin crystallized in two orthorhombic forms and one hexagonal form under similar conditions. The crystals had an unusually high solvent content. The structure was solved using the molecular-replacement method using the jacalin structure as a search model. The two orthorhombic forms were refined using data to 2.5 and 3.0 A resolution, respectively. The structures of the A. hirsuta lectin and jacalin are identical. In orthorhombic form I the crystal packing provides three different micro-environments for sugar binding in the same crystal. The observed difference in the specificity for oligosaccharides between the A. hirsuta lectin and jacalin could only be explained based on differences in the molecular associations in the packing and variation of the C-terminal length of the beta-chain. The observed insecticidal activity of A. hirsuta lectin may arise from its similar fold to domain II of the unrelated delta-endotoxin from Bacillus thuringiensis.

  16. Metal Complexes of New Bioactive Pyrazolone Phenylhydrazones; Crystal Structure of 4-Acetyl-3-methyl-1-phenyl-2-pyrazoline-5-one phenylhydrazone Ampp-Ph.

    PubMed

    Idemudia, Omoruyi G; Sadimenko, Alexander P; Hosten, Eric C

    2016-01-01

    The condensation reaction of phenylhydrazine and dinitrophenylhydrazine with 4-acetyl and 4-benzoyl pyrazolone precipitated air-stable acetyldinitrophenylhydrazone Ampp-Dh, benzoylphenylhydrazone Bmpp-Ph and benzoyldinitrophenylhydrazone Bmpp-Dh in their keto imine form; a study inspired by the burning interest for the development of new bioactive materials with novel properties that may become alternative therapeutic agents. Elemental analysis, FTIR, ¹H, and (13)C NMR, and mass spectroscopy have been used to justify their proposed chemical structures, which were in agreement with the single crystal structure of Bmpp-Dh earlier reported according to X-ray crystallography. The single crystal structure of 4-acetyl-3-methyl-1-phenyl--pyrazoline-5-one phenylhydrazone Ampp-Ph, which crystallizes in a triclinic crystal system with a P-1 (No. 2) space group is presented. Octahedral Mn(II), Ni(II), Co(II), and Cu(II) complexes of these respective ligands with two molecules each of the bidentate Schiff base, coordinating to the metal ion through the azomethine nitrogen C=N and the keto oxygen C=O, which were afforded by the reaction of aqueous solutions of the corresponding metal salts with the ligands are also reported. Their identity and proposed structures were according to elemental analysis, FTIR spectroscopy, UV-VIS spectrophotometry (electronic spectra) and Bohr magnetic moments, as well as thermogravimetric analysis (TGA) results. A look at the antibacterial and antioxidant activities of synthesized compounds using the methods of the disc diffusion against some selected bacterial isolates and 1,1-diphenyl-2-picryl-hydrazil (DPPH) respectively, showed biological activities in relation to employed standard medicinal drugs. PMID:27213342

  17. 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

  18. 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

  19. Asymmetric Synthesis of Chiral α-Methyl-α,β-diamino Acid Derivatives via Group-Assisted Purification Chemistry Using N-Phosphonyl Imines and a Ni(II)-Complexed Alanine Schiff Base.

    PubMed

    Zhang, Haowei; Yang, Bing; Yang, Zhen; Lu, Hongjian; Li, Guigen

    2016-09-01

    The Mannich reaction between chiral N-phosphonyl imines and a Ni(II)-complexed alanine Schiff base (Ala-Ni) is reported. With a chiral phosphonyl auxiliary, a single isomer of α-methyl-α,β-diamino acid derivative containing vicinal chiral centers, including a chiral quaternary carbon center, can be obtained simply by washing the crude mixture with cosolvents. The absolute stereochemistry of the enantiomerically pure product has been unambiguously determined by X-ray crystallographic analysis. PMID:27459278

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. Convergent evolution of chromatin modification by structurally distinct enzymes: comparative enzymology of histone H3 Lys²⁷ methylation by human polycomb repressive complex 2 and vSET.

    PubMed

    Swalm, Brooke M; Hallenbeck, Kenneth K; Majer, Christina R; Jin, Lei; Scott, Margaret Porter; Moyer, Mikel P; Copeland, Robert A; Wigle, Tim J

    2013-07-15

    H3K27 (histone H3 Lys27) methylation is an important epigenetic modification that regulates gene transcription. In humans, EZH (enhancer of zeste homologue) 1 and EZH2 are the only enzymes capable of catalysing methylation of H3K27. There is great interest in understanding structure-function relationships for EZH2, as genetic alterations in this enzyme are thought to play a causal role in a number of human cancers. EZH2 is challenging to study because it is only active in the context of the multi-subunit PRC2 (polycomb repressive complex 2). vSET is a viral lysine methyltransferase that represents the smallest protein unit capable of catalysing H3K27 methylation. The crystal structure of this minimal catalytic protein has been solved and researchers have suggested that vSET might prove useful as an EZH2 surrogate for the development of active site-directed inhibitors. To test this proposition, we conducted comparative enzymatic analysis of human EZH2 and vSET and report that, although both enzymes share similar preferences for methylation of H3K27, they diverge in terms of their permissiveness for catalysing methylation of alternative histone lysine sites, their relative preferences for utilization of multimeric macromolecular substrates, their active site primary sequences and, most importantly, their sensitivity to inhibition by drug-like small molecules. The cumulative data led us to suggest that EZH2 and vSET have very distinct active site structures, despite the commonality of the reaction catalysed by the two enzymes. Hence, the EZH2 and vSET pair of enzymes represent an example of convergent evolution in which distinct structural solutions have developed to solve a common catalytic need.

  8. 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).

  9. 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.

  10. 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, 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)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.

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

    PubMed Central

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

    2014-01-01

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

  12. 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.

  13. Crystal structure and catecholase-like activity of a mononuclear complex [Cu(EDTB)]2+ (EDTB=N,N,N',N'-tetrakis(2'-benzimidazolyl methyl)-1,2-ethanediamine).

    PubMed

    Chen, Zhan-Fen; Liao, Zhan-Ru; Li, Dong-Feng; Li, Wu-Ke; Meng, Xiang-Gao

    2004-08-01

    The crystal structure and catecholase-like activity of a mononuclear complex, Cu(EDTB)(NO3)2.C2H5OH (here EDTB stands N,N,N',N'-tetrakis(2'-benzimidazolyl methyl)-1,2-ethanediamine) has been studied in comparison with a binuclear complex Cu2(EDTB)(NO3)4.3H2O. The results show that the reactive rate constants increase with increases of reaction temperature and pH value of intermediate. Electrospray ionization mass spectrum (ESI-MS) shows that tautomerism isomers of catechol with the title complex exist in reaction solution, and catechol is oxidized to quinone, then it is further oxidized resulting in muconic acid and its derivatives via an intradiol mechanism, just like that catalyzed by a mononuclear non-heme iron-containing dioxygenase. PMID:15271507

  14. DNA methylation in endometrial cancer

    PubMed Central

    Freudenheim, Jo L

    2010-01-01

    Endometrial cancer is the most commonly diagnosed gynecological cancer, and it has been shown to be a complex disease driven by abnormal genetic and epigenetic alterations, as well as environmental factors. Epigenetic changes resulting in aberrant gene expression are dynamic and modifiable features of many cancer types. A significant epigenetic change is aberrant DNA methylation. In this review, we review evidence on the role of aberrant DNA methylation, examining changes in relation to endometrial carcinogenesis, and report on recent advances in the understanding of the contribution of aberrant DNA methylation to endometrial cancer with the emphasis on the role of dietary/lifestyle and environmental factors, as well as opportunities and challenges of DNA methylation in endometrial cancer management and prevention. PMID:20543579

  15. 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]2·nH2O·zMeOH, 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.

  16. 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]2·nH2O·zMeOH, 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.

  17. 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.

  18. 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 255.2 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. PMID:26745510

  19. Crystal structure of silkworm Bombyx mori JHBP in complex with 2-methyl-2,4-pentanediol: plasticity of JH-binding pocket and ligand-induced conformational change of the second cavity in JHBP.

    PubMed

    Fujimoto, Zui; Suzuki, Rintaro; Shiotsuki, Takahiro; Tsuchiya, Wataru; Tase, Akira; Momma, Mitsuru; Yamazaki, Toshimasa

    2013-01-01

    Juvenile hormones (JHs) control a diversity of crucial life events in insects. In Lepidoptera which major agricultural pests belong to, JH signaling is critically controlled by a species-specific high-affinity, low molecular weight JH-binding protein (JHBP) in hemolymph, which transports JH from the site of its synthesis to target tissues. Hence, JHBP is expected to be an excellent target for the development of novel specific insect growth regulators (IGRs) and insecticides. A better understanding of the structural biology of JHBP should pave the way for the structure-based drug design of such compounds. Here, we report the crystal structure of the silkworm Bombyx mori JHBP in complex with two molecules of 2-methyl-2,4-pentanediol (MPD), one molecule (MPD1) bound in the JH-binding pocket while the other (MPD2) in a second cavity. Detailed comparison with the apo-JHBP and JHBP-JH II complex structures previously reported by us led to a number of intriguing findings. First, the JH-binding pocket changes its size in a ligand-dependent manner due to flexibility of the gate α1 helix. Second, MPD1 mimics interactions of the epoxide moiety of JH previously observed in the JHBP-JH complex, and MPD can compete with JH in binding to the JH-binding pocket. We also confirmed that methoprene, which has an MPD-like structure, inhibits the complex formation between JHBP and JH while the unepoxydated JH III (methyl farnesoate) does not. These findings may open the door to the development of novel IGRs targeted against JHBP. Third, binding of MPD to the second cavity of JHBP induces significant conformational changes accompanied with a cavity expansion. This finding, together with MPD2-JHBP interaction mechanism identified in the JHBP-MPD complex, should provide important guidance in the search for the natural ligand of the second cavity. PMID:23437107

  20. 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

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

    SciTech Connect

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

    2005-01-01

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

  2. 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

  3. Crystal structure of zwitterionic 4-(ammonio-methyl)-benzoate: a simple mol-ecule giving rise to a complex supra-molecular structure.

    PubMed

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

    2014-11-01

    The asymmetric unit of the title compound, C8H9NO2·H2O consists of an isolated 4-(ammonio-meth-yl)benzoate zwitterion derived from 4-amino-methyl-benzoic 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.

  4. Shifting the Azo-hydrazone tautomeric equilibrium of methyl yellow in acidic medium by the formation of inclusion complexes with cyclodextrins

    NASA Astrophysics Data System (ADS)

    Ferreira, Ivania R.; Ando, Rômulo A.

    2012-01-01

    The protonation of methyl yellow (MY) leads to a tautomeric equilibrium involving the azo and hydrazone species, where the latter is predominant. Electronic and Raman spectroscopic data show that when MY in acidic medium is included in cyclodextrins, there is an inversion in the relative ratio of tautomers, in which the azo species become the major species. This indicates that the azo bond is included in cyclodextrin precluding its protonation. The understanding of the protonation, tautomeric and inclusion equilibria of these systems plays an important role in the designing of cyclodextrin based molecular machines controlled by light.

  5. 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.

  6. Crystal structure of a dinuclear Co(II) complex with bridging fluoride ligands: di-μ-fluorido-bis-{tris-[(6-methyl-pyridin-2-yl)meth-yl]amine}-dicobalt(II) bis-(tetra-fluorido-borate).

    PubMed

    Inomata, Masataka; Suenaga, Yusaku

    2014-11-01

    Reaction of Co(BF4)2·6H2O with tris-[(6-methyl-pyridin-2-yl)meth-yl]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 Co(II) cation is six-coordinated in a distorted octa-hedral geometry and forms a +II high-spin state. In the crystal, the complex cation and the BF4 (-) anion are connected by C-H⋯F hydrogen bonds, forming a three-dimensional network. An intra-molecular C-H⋯F hydrogen bond is also observed. PMID:25484774

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

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

  9. 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) Å, b=12.8627(12) Å, c=21.683(2) Å, α=90.00, β=114.626(2), γ=90.00 V=4721.8(8) Å, Z=4. The crystal structure of the complex shows Ru(II) atom is six-coordinated, forming a slightly distorted octahedral geometry with two P atoms in axial positions, and three chelating donor atoms of the tridentate Schiff base ligand and one carbonyl group located in the equatorial plane. The molecular structure is stabilized by intramolecular O-H···N interactions. No intermolecular hydrogen bond was observed. The intramolecular hydrogen bond exists between the oxygen atom from salicylic acid moiety and nitrogen from the same moiety. A variety of solution studies were carried out for the determination of DNA binding mode of the complexes. The results suggest that both complexes bind to Herring sperm DNA via non intercalative mode. PMID:21763180

  10. Aerobic oxidation of methyl p-tolyl sulfide catalyzed by a remarkably labile heteroscorpionate RuII-aqua complex, fac-[RuII(H2O)(dpp)(tppm)]2+.

    PubMed

    Huynh, My Hang V; Witham, Laura M; Lasker, Joanne M; Wetzler, Modi; Mort, Brendan; Jameson, Donald L; White, Peter S; Takeuchi, Kenneth J

    2003-01-15

    fac-[RuII(Cl)(dpp)(L3)]+ (L3 = tris(pyrid-2-yl)methoxymethane (tpmm) = [1A]+ and tris(pyrid-2-yl)pentoxymethane (tppm) = [1B]+ and dpp = di(pyrazol-1-yl)propane) rapidly undergo ligand substitution with water to form fac-[RuII(H2O)(dpp)(L3)]2+ (L3 = tpmm = [2A]2+ and tppm = [2B]2+). In the structure of [2A]2+, the distorted octahedral arrangement of ligands around Ru is evident by a long Ru(1)-O(40) of 2.172(3) A and a large angle O(40)-Ru(1)-N(51) of 96.95(14) degrees . The remarkably short distance between O(40) of H2O and H(45a) of dpp confirms the heteroscorpionate ligand effect of dpp on H2O. [2B]2+ aerobically catalyzes methyl p-tolyl sulfide to methyl p-tolyl sulfoxide in 1,2-dichlorobenzene at 25.0 +/- 0.1 degrees C under 11.4 psi of O2. Experimental facts in support of this aerobic sulfide oxidation are the absence of H2O2 and the oxidative reactivity of the putative Ru(IV)-oxo intermediate toward methyl p-tolyl sulfide, 2-propanol, and allyl alcohol. This study provides the first documented example of aerobic-sulfide oxidation catalyzed by the remarkably labile heteroscorpionate Ru(II)-aqua complex without the formation of a highly reactive peroxide as an intermediate.

  11. 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

  12. Effect of persistence length on binding of DNA to polyions and overcharging of their intermolecular complexes in aqueous and in 1-methyl-3-octyl imidazolium chloride ionic liquid solutions.

    PubMed

    Rawat, Kamla; Pathak, Jyotsana; Bohidar, H B

    2013-08-01

    The effect of persistence length on the intermolecular binding of DNA (200 bp, persistence length l(p) = 50 nm, polyanion) with three proteins, gelatin B (GB) (l(p) = 2 nm, polyampholyte chain), bovine serum albumin (BSA) (l(p) = 7 nm, polyampholyte colloid), gelatin A (GA) (l(p) = 10 nm, polyampholyte chain), and a polysaccharide chitosan (l(p) = 17 nm, polycation), was investigated in aqueous and in 1-methyl-3-octyl imidazolium chloride ionic liquid ([C8mim][Cl]) solutions. In DNA-GB and DNA-BSA solutions complexation primarily arises from surface patch binding whereas DNA-chitosan and DNA-GA binding was predominantly governed by electrostatic forces. These occurred at well defined pH values: (i) at pHc associative interactions ensued and soluble complexes were formed, (ii) at pHΦ soluble complexes coalesced to give rise to liquid-liquid phase separation (coacervation) and (iii) at pH(prep) formation of large insoluble complexes drove the solution towards liquid-solid phase separation. A universal phase diagram encapsulating the aforesaid interactions can be made using the persistence length of polyion as an independent variable. DNA formed overcharged intermolecular complexes with all these polyions when the polyion concentration was more than the concentration required to produce charge neutralized complexes (disproportionate binding). In IL solutions maximum binding occurred when 0.075 < [IL] < 0.10% (w/v) and the effect of overcharging was substantially screened. The extent of overcharge was a monotonous increasing function of the polyion persistence length. Results clearly revealed that DNA-polyion binding was hierarchical in polyion concentration and persistence length. Overcharging of the DNA-polyion complex was found to be ubiquitous for the polyions used in the present study.

  13. 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.

  14. Oxygen-assisted excitation of methyl iodide as a test of double spin-flip transition in van der Waals complex CH3I-O2

    NASA Astrophysics Data System (ADS)

    Bogomolov, Alexandr S.; Kochubei, Sergei A.; Baklanov, Alexey V.

    2016-09-01

    Photoexcitation of van der Waals (vdW) complex CH3I-O2 has been studied with velocity map imaging of I atoms arising in photodissociation. A new scheme of resonance-enhanced multiphoton ionization of iodine atoms has been applied with simultaneous use of UV and VIS radiation. The measured kinetic energy of I(2P3/2) atoms indicates photogeneration of precursor CH3I molecules via complex-specific channel with excitation energy expected for double spin-flip transition in complex CH3I-O2. The angular distribution for recoil directions of I(2P3/2) atoms coming from vdW complexes also corresponds to that expected for double spin-flip transition.

  15. Catalysis of methyl acetate formation from methanol alone by ({mu}{sup 5}-C{sub 5}H{sub 5})(PPh{sub 3}){sub 2}RuX (X=Cl, SnCl{sub 3}, SnF{sub 3}): High activity for the SnF{sub 3} complex

    SciTech Connect

    Einaga, Hisahiro; Yamakawa, Tetsu; Shinoda, Sumio

    1994-12-31

    The authors have recently shown that the Ru(II)-Sn(II) bimetallic complex can catalyze the unprecedented one-step formation of acetic acid (or methyl acetate) with methanol used as the sole source. It was suggested that the reaction consists of sequential processes of methanol {r_arrow} formaldehyde (methyl){r_arrow}methyl formate {r_arrow} acetic acid (methyl acetate). While the Ru(II) complexes capable of catalyzing the dehydrogenation of methanol into methyl formate are known, this catalyst system is unique because of its extra ability to isomerize methyl formate to acetic acid without a CO atmosphere (usually high pressure) or an iodide promoter (often corrosive to reaction apparatus). In this communication, the authors examine the cyclopentadienyl bis(triphenylphosphine) ruthenium(II) auxilliary in view of its well defined geometry and configurational stability, and demonstrate that combination with the SnF{sub 3} ligand gives quite high catalytic ability compared to the conventional SnCl{sub 3} ligand. 12 refs., 1 fig.

  16. Constrained photophysics of partially and fully encapsulated charge transfer probe (E)-3-(4-Methylaminophenyl) acrylic acid methyl ester inside cyclodextrin nano-cavities: Evidence of cyclodextrins cavity dependent complex stoichiometry

    NASA Astrophysics Data System (ADS)

    Ghosh, Shalini; Jana, Sankar; Guchhait, Nikhil

    2011-12-01

    The polarity sensitive intra-molecular charge transfer (ICT) emission from (E)-3-(4-Methylaminophenyl) acrylic acid methyl ester (MAPAME) is found to show distinct changes once introduced into the nano-cavities of cyclodextrins in aqueous environment. Movement of the molecule from the more polar aqueous environment to the less polar, hydrophobic cyclodextrin interior is marked by the blue shift of the CT emission band with simultaneous fluorescence intensity enhancement. The emission spectral changes on complexation with the α- and β-CD show different stoichiometries as observed from the Benesi-Hildebrand plots. Fluorescence anisotropy and lifetime measurements were performed to probe the different behaviors of MAPAME in aqueous α- and β-CD solutions.

  17. A DFT/TD DFT study of the structure and spectroscopic properties of 5-methyl-2-(8-quinolinyl)benzoxazole and its complexes with Zn(II) ion.

    PubMed

    Guzow, Katarzyna; Milewska, Magda; Czaplewski, Cezary; Wiczk, Wiesław

    2010-02-01

    The structure and spectroscopic properties of 5-methyl-2-(8-quinolinyl)benzoxazole and its complexes with Zn(II) ion were studied using a DFT and TD DFT methods with def2-TZVP basis set. It was shown that the type of functional used (B3-LYP or pbe0) implemented in TURBOMOLE package does not have essential influence on the geometry (small differences in bond length, valence and dihedral angles) of studied compounds in both ground and excited states. However, significant differences were obtained for the position of vertical absorption and emission transition but not for the oscillator strength of transition. Application of pbe0 functional seems to reproduce better the experimental spectrum.

  18. 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.

  19. Simultaneous determination of Mn2+ and Fe3+ as 4,4'[(4-cholorophenyl)methylene] bis(3-methyl-1-phenyl-1H-pyrazol-5-ol) complexes in some foods, vegetable and water samples by artificial neural networks.

    PubMed

    Abbasi-Tarighat, Maryam; Shahbazi, Elahe; Niknam, Khodabakhsh

    2013-06-01

    A simple and sensitive spectrophotometric method to the simultaneous determination of Mn(2+) and Fe(3+) in foods, vegetable and water sample with the aid of artificial neural networks (ANNs) is described. It relies on the complexation of analytes with recently synthesised bis pyrazol base ligand as 4,4'[(4-cholorophenyl)methylene] bis(3-methyl-1-phenyl-1H-pyrazol-5-ol)(CMBPP). The analytical data show that the ratio of ligand to metal in metal complexes is 1:1 and 1:2 for Fe(3+) and Mn(2+), respectively. It was found that the complexation reactions are completed at pH 6.7 and 5 min after mixing. The results showed that Mn(2+) and Fe(3+) could be determined simultaneously in the range of 0.20-7.5 and 0.30-9.0 mgl(-1), respectively. The analytical characteristics of the method such as the detection limit and the relative standard error predictions were calculated. The data obtained from synthetic mixtures of the metal ions were processed by radial basis function networks (RBFNs) and feed forward neural networks (FFNNs). The optimal conditions of the neural networks were obtained by adjusting various parameters by trial-and-error. Under the working conditions, the proposed methods were successfully applied to the simultaneous determination of elements in different water, tablet, rice, tea leaves, tomato, cabbage and lettuce samples.

  20. Enhanced catalysis and enantioselective resolution of racemic naproxen methyl ester by lipase encapsulated within iron oxide nanoparticles coated with calix[8]arene valeric acid complexes.

    PubMed

    Sayin, Serkan; Akoz, Enise; Yilmaz, Mustafa

    2014-09-14

    In this study, two types of nanoparticles have been used as additives for the encapsulation of Candida rugosa lipase via the sol-gel method. In one case, the nanoparticles were covalently linked with a new synthesized calix[8]arene octa valeric acid derivative (C[8]-C4-COOH) to produce new calix[8]arene-adorned magnetite nanoparticles (NP-C[8]-C4-COOH), and then NP-C[8]-C4-COOH was used as an additive in the sol-gel encapsulation process. In the other case, iron oxide nanoparticles were directly added into the sol-gel encapsulation process in order to interact electrostatically with both C[8]-C4-COOH and Candida rugosa lipase. The catalytic activities and enantioselectivities of two novel encapsulated lipases (Enc-NP-C[8]-C4-COOH and Enc-C[8]-C4-COOH@Fe3O4) in the hydrolysis reaction of racemic naproxen methyl ester were evaluated. The results showed that the activity and enantioselectivity of the lipase were improved when the lipase was encapsulated in the presence of calixarene-based additives. Indeed, the encapsulated lipases have an excellent rate of enantioselectivity, with E = 371 and 265, respectively, as compared to the free enzyme (E = 137). The lipases encapsulated with C[8]-C4-COOH and iron oxide nanoparticles (Enc-C[8]-C4-COOH@Fe3O4) retained more than 86% of their initial activities after 5 repeated uses and 92% with NP-C[8]-C4-COOH.

  1. 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

  2. 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.

  3. Crystal structure, DNA binding studies, nucleolytic property and topoisomerase I inhibition of zinc complex with 1,10-phenanthroline and 3-methyl-picolinic acid.

    PubMed

    Seng, Hoi-Ling; Von, Sze-Tin; Tan, Kong-Wai; Maah, Mohd Jamil; Ng, Seik-Weng; Rahman, Raja Noor Zaliha Raja Abd; Caracelli, Ignez; Ng, Chew-Hee

    2010-02-01

    Crystal structure analysis of the zinc complex establishes it as a distorted octahedral complex, bis(3-methylpicolinato-kappa(2) N,O)(2)(1,10-phenanthroline-kappa(2) N,N)-zinc(II) pentahydrate, [Zn(3-Me-pic)(2)(phen)]x5H(2)O. The trans-configuration of carbonyl oxygen atoms of the carboxylate moieties and orientation of the two planar picolinate ligands above and before the phen ligand plane seems to confer DNA sequence recognition to the complex. It cannot cleave DNA under hydrolytic condition but can slightly be activated by hydrogen peroxide or sodium ascorbate. Circular Dichroism and Fluorescence spectroscopic analysis of its interaction with various duplex polynucleotides reveals its binding mode as mainly intercalation. It shows distinct DNA sequence binding selectivity and the order of decreasing selectivity is ATAT > AATT > CGCG. Docking studies lead to the same conclusion on this sequence selectivity. It binds strongly with G-quadruplex with human tolemeric sequence 5'-AG(3)(T(2)AG(3))(3)-3', can inhibit topoisomerase I efficiently and is cytotoxic against MCF-7 cell line.

  4. Lanthanide complexes containing 5-methyl-1,2,4-triazolo[1,5-a] pyrimidin-7(4H)-one and their therapeutic potential to fight leishmaniasis and Chagas disease.

    PubMed

    Caballero, Ana B; Rodríguez-Diéguez, Antonio; Salas, Juan M; Sánchez-Moreno, Manuel; Marín, Clotilde; Ramírez-Macías, Inmaculada; Santamaría-Díaz, Noelia; Gutiérrez-Sánchez, Ramón

    2014-09-01

    In the last years, numerous and significant advances in lanthanide coordination chemistry have been achieved. The unique chemical nature of these metal ions which is conferred by their f-electrons has led to a wide range of coordination compounds with interesting structural, physical and also biological properties. Consequently, lanthanide complexes have found applications mainly in catalysis, gas adsorption, photochemistry and as diagnostic tools. However, research on their therapeutic potential and the understanding of their mechanism of action is still taking its first steps, and there is a distinct lack of research in the parasitology field. In the present work, we describe the synthesis and physical properties of seven new lanthanide complexes with the anionic form of the bioactive ligand 5-methyl-1,2,4-triazolo[1,5-a]pyrimidin-7(4H)-one (HmtpO), namely [Ln(mtpO)3(H2O)6]·9H2O (Ln=La(III), Nd(III), Eu(III), Gd(III), Tb(III), Dy(III) and Er(III)). In addition, results on the in vitro antiproliferative activity against Leishmania spp. and Trypanosoma cruzi are described. The high activity of the new compounds against parasite proliferation and their low cytotoxicity against reference host cell lines show a great potential of this type of compounds to become a new generation of highly effective and non-toxic antiparasitic agents to fight the so considered neglected diseases leishmaniasis and Chagas disease.

  5. 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.

  6. 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

  7. DNA-gelatin complex coacervation, UCST and first-order phase transition of coacervate to anisotropic ion gel in 1-methyl-3-octylimidazolium chloride ionic liquid solutions.

    PubMed

    Rawat, Kamla; Aswal, V K; Bohidar, H B

    2012-12-27

    Study of kinetics of complex coacervation occurring in aqueous 1-octyl-3-methylimidazolium chloride ionic liquid solution of low charge density polypeptide (gelatin A) and 200 base pair DNA, and thermally activated coacervate into anisotropic gel transition, is reported here. Associative interaction between DNA and gelatin A (GA) having charge ratio (DNA:GA = 16:1) and persistence length ratio (5:1) was studied at fixed DNA (0.005% (w/v)) and varying GA concentration (C(GA) = 0-0.25% (w/v)). The interaction profile was found to be strongly hierarchical and revealed three distinct binding regions: (i) Region I showed DNA-condensation (primary binding) for C(GA) < 0.10% (w/v), the DNA ζ potential decrease from -80 to -5 mV (95%) (partial charge neutralization), and a size decrease by ≈60%. (ii) Region II (0.10 < C(GA) < 0.15% (w/v)) indicated secondary binding, a 4-fold turbidity increase, a ζ potential decrease from -5 to 0 mV (complete charge neutralization), which resulted in the appearance of soluble complexes and initiation of coacervation. (iii) Region III (0.15 < C(GA) < 0.25% (w/v)) revealed growth of insoluble complexes followed by precipitation. The hydration of coacervate was found to be protein concentration specific in Raman studies. The binding profile of DNA-GA complex with IL concentration revealed optimum IL concentration (=0.05% (w/v)) was required to maximize the interactions. Small angle neutron scattering (SANS) data of coacervates gave static structure factor profiles, I(q) versus wave vector q, that were remarkably similar and invariant of protein concentration. This data could be split into two distinct regions: (i) for 0.0173 < q < 0.0353 Å(-1), I(q) ~ q(-α) with α = 1.35-1.67, and (ii) for 0.0353 < q < 0.35 Å(-1), I(q) = I(0)/(1 + q(2)ξ(2)). The correlation length found was ξ = 2 ± 0.1 nm independent of protein concentration. The viscoelastic length (≈8 nm) was found to have value close to the persistence length of the protein

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

    PubMed

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

    2014-07-21

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

  9. 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 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

  10. 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.

  11. Crystal structure, spectroscopic properties and DFT studies on copper (II) complex of bis{(E)-1-[(2-phenoxyphenylimino)methyl]naphthalene-2-ol}chloroform solvate

    NASA Astrophysics Data System (ADS)

    Macit, Mustafa; Alpaslan, Gökhan

    2014-08-01

    Copper (II) complex of the title Schiff base compound was synthesized from the reaction of 2-hydroxy-1-naphthaldehyde with 2-phenoxyaniline. The complex has been characterized by FT-IR, and X-ray single-crystal techniques. The molecular geometry, vibrational frequencies values of the compound in the ground state have been calculated using the density functional theory (DFT/B3LYP) method with the LANL2DZ basis set and compared with the experimental data. The calculated results show that the optimized geometry is compatible with the crystal structure and the theoretical vibrational frequencies are in good agreement with the experimental values. The energetic behavior of the compound in solvent media has been examined using B3LYP method with the LANL2DZ basis set by applying the polarizable continuum model (PCM). In addition, frontier molecular orbital analysis (HOMO-LUMO), natural bond orbital analysis (NBO) and non-linear optical (NLO) properties of the compound were investigated using same theoretical calculations.

  12. 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 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.

  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 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

  14. pH-Dependent Monomer <--> Oligomer Interconversion of Copper(II) Complexes with N-(2-R-imidazol-4-ylmethylidene)-2-aminoethylpyridine (R = Methyl, Phenyl).

    PubMed

    Matsumoto, Naohide; Motoda, Yuri; Matsuo, Toshihiro; Nakashima, Toshio; Re, Nazzareno; Dahan, Francoise; Tuchagues, Jean-Pierre

    1999-03-22

    The monomer <--> oligomer interconversion of the reported metal complexes is generated by proton abstraction/supply as a common external information input. The mononuclear copper(II) complexes 1 and 2 with [CuCl(2)(HL(n)())] chemical formula have been prepared (HL(1) = N-(2-methylimidazol-4-ylmethylidene)-2-aminoethylpyridine; HL(2) = N-(2-phenylimidazol-4-ylmethylidene)-2-aminoethylpyridine). The crystal structures were determined. 1.H(2)O, C(12)H(16)N(4)OCl(2)Cu: a = 13.773(2) Å, b = 8.245(2) Å, c = 13.861(2) Å, beta = 110.10(1) degrees, monoclinic, P2(1)/n, and Z = 4. 2, C(17)H(16)N(4)Cl(2)Cu: a = 7.6659(7) Å, b = 16.287(1) Å, c = 14.103(1) Å, beta = 95.058(7) degrees, monoclinic, P2(1)/c, and Z = 4. Complexes 1.H(2)O and 2 assume a pentacoordinated square pyramidal geometry with a N(3)Cl(2) donor set consisting of the nitrogen atoms of the protonated tridentate ligand and two chloride ions in the solid state, while in aqueous solution the Cu(II) ion is tetracoordinated (N(3)Ow donor set). When 1 and 2 are treated with an equimolar amount of sodium hydroxide or triethylamine, the deprotonation of the imidazole moiety promotes a self-assembly process, arising from coordination of the imidazolate nitrogen atom to a Cu(II) ion of an adjacent unit, to yield compounds 1'.4H(2)O as the perchlorate salt, and 2'a.6H(2)O as the perchlorate salt and( )()2'b as the hexafluorophosphate salt, respectively. 1'.4H(2)O, C(12)H(15)N(4)O(5)ClCu: a = b = 13.966(2) Å, c = 33.689(3) Å, tetragonal, I4(1)/a, and Z = 16. 2'a.6H(2)O, C(51)H(51)N(12)O(15)Cl(3)Cu(3): a = 15.177(3) Å, b = 15.747(3) Å, c = 14.128(3) Å, alpha = 100.06(2) degrees, beta = 110.37(2) degrees, gamma = 63.54(1) degrees, triclinic, P&onemacr;, and Z = 2. 2'b, C(17)H(15)N(9)F(6)PCu: a = b = 29.812(5) Å, c = 11.484(3) Å, trigonal, R&thremacr;, and Z = 18. The nuclearity of the self-assembled molecules and their detailed structure were confirmed to be cyclic imidazolate-bridged tetranuclear for 1'.4H(2)O

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

    PubMed

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

    2014-11-17

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

  16. A series of dinuclear Dy(iii) complexes bridged by 2-methyl-8-hydroxylquinoline: replacement on the periphery coordinated β-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(μ-HMq)2 (1), [Dy(DBM)2]2(μ-HMq)2(n-C6H14) (2), [Dy(hmac)2]2(μ-HMq)2 (3) and [Dy(hfac)3]2(μ-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 β-diketonate ligands complete the coordination sphere by bidentate oxygen atoms. The different substituents on the β-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, τ0 = 1.8 × 10(-5) s and Ueff/kB = 9.2 K, τ0 = 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 β-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

  17. Promoting C–C Bond Coupling of Benzyne and Methyl Ligands in Electron-Deficient (triphos)Pt–CH3+ Complexes

    PubMed Central

    2016-01-01

    In situ generated benzyne reacts at room temperature with (triphos)Pt–CH3+ to form a five-coordinate π-complex (2) that is isolable and stable in solution. Thermolysis of 2 at 60 °C generates (triphos)Pt(o-tolyl)+ (3), which is the product of formal migratory insertion of CH3– onto the coordinated benzyne. The reaction of 2 with the acid Ph2NH2+ yields toluene at room temperature over the course of 8 h, while the same reaction with 3 only proceeds to 40% conversion over 2 days. These data indicate that the protonolysis of 2 does not proceed by CH3 migration onto benzyne to form 3 followed by protodemetalation. Instead, the data suggest either that protonation of 2 is first and is followed by H migration to yield a PtIVPh(Me) dication or that this latter species is generated by direct protonolysis of coordinated benzyne prior to reductive elimination of toluene. PMID:26146438

  18. Synthesis, spectroscopic characterization and X-ray structure determinations and packing of tetralkylammonium trans-diamminetetranitrocobaltate(III) complex salts where alkyl=methyl or ethyl

    NASA Astrophysics Data System (ADS)

    Sharma, Raj Pal; Vermani, Bal Krishan; Sharma, Rajni; Bala, Ritu; Gill, Dip Singh; Salas, Juan M.; Quiros, Miguel

    2006-02-01

    The two cobalt(III) complex salts [(CH 3) 4N][ trans-Co(NH 3) 2(NO 2) 4] ( I) and [(C 2H 5) 4N][ trans-Co(NH 3) 2(NO 2) 4] ( II) have been synthesized in high yields by reacting equimolar quantities of [(CH 3) 4N]Br and [(C 2H 5) 4N]Cl with K[ trans-Co(NH 3) 2(NO 2) 4], respectively in aqueous medium at room temperature. The salt I crystallized with monoclinic space group P 2 1/ m having cell dimensions a=6.1926(7), b=18.248(3), c=6.2335(6) Å, β=90.078(7)°, V=704.41(16) Å 3, Z=2, R=0.0868 and the salt II crystallized with monoclinic space group P 2 1/c having cell dimensions a=10.2635(18), b=9.0480(15), c=9.752(2) Å, β=104.493(12)°, V=876.8(3) Å 3, Z=2, R=0.0408. X-ray structure determination revealed the presence of discrete ions, [(CH 3) 4N] + and [ trans-Co(NH 3) 2(NO 2) 4] - in I and [(C 2H 5) 4N] + and [ trans-Co(NH 3) 2(NO 2) 4] - in II. In the anion, the central metal atom cobalt(III) is octahedrally surrounded in trans geometry. The crystal lattice is stabilized by electrostatic forces of attractions and hydrogen bonding interactions in I. These are the first X-ray structures of salts containing the tetralkylammonium cations and the anion [ trans-Co(NH 3) 2(NO 2) 4] -. The packing diagrams show a layered structures in the two salts.

  19. [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

  20. 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.

  1. [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.

  2. Structural basis for Klf4 recognition of methylated DNA.

    PubMed

    Liu, Yiwei; Olanrewaju, Yusuf Olatunde; Zheng, Yu; Hashimoto, Hideharu; Blumenthal, Robert M; Zhang, Xing; Cheng, Xiaodong

    2014-04-01

    Transcription factor Krüppel-like factor 4 (Klf4), one of the factors directing cellular reprogramming, recognizes the CpG dinucleotide (whether methylated or unmodified) within a specific G/C-rich sequence. The binding affinity of the mouse Klf4 DNA-binding domain for methylated DNA is only slightly stronger than that for an unmodified oligonucleotide. The structure of the C-terminal three Krüppel-like zinc fingers (ZnFs) of mouse Klf4, in complex with fully methylated DNA, was determined at 1.85 Å resolution. An arginine and a glutamate interact with the methyl group. By comparison with two other recently characterized structures of ZnF protein complexes with methylated DNA, we propose a common principle of recognition of methylated CpG by C2H2 ZnF proteins, which involves a spatially conserved Arg-Glu pair. PMID:24520114

  3. 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

  4. 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 1·1.2MeOH·0.6H(2)O and 8·1.2MeOH·0.6H(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 η(1):η(1):η(1):μ 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

  5. DNA methylation biomarkers: cancer and beyond.

    PubMed

    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.

  6. 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

  7. Cytosine methylation profiling of cancer cell lines

    PubMed Central

    Ehrich, Mathias; Turner, Julia; Gibbs, Peter; Lipton, Lara; Giovanneti, Mara; Cantor, Charles; van den Boom, Dirk

    2008-01-01

    DNA-methylation changes in human cancer are complex and vary between the different types of cancer. Capturing this epigenetic variability in an atlas of DNA-methylation changes will be beneficial for basic research as well as translational medicine. Hypothesis-free approaches that interrogate methylation patterns genome-wide have already generated promising results. However, these methods are still limited by their quantitative accuracy and the number of CpG sites that can be assessed individually. Here, we use a unique approach to measure quantitative methylation patterns in a set of >400 candidate genes. In this high-resolution study, we employed a cell-line model consisting of 59 cancer cell lines provided by the National Cancer Institute and six healthy control tissues for discovery of methylation differences in cancer-related genes. To assess the effect of cell culturing, we validated the results from colon cancer cell lines by using clinical colon cancer specimens. Our results show that a large proportion of genes (78 of 400 genes) are epigenetically altered in cancer. Although most genes show methylation changes in only one tumor type (35 genes), we also found a set of genes that changed in many different forms of cancer (seven genes). This dataset can easily be expanded to develop a more comprehensive and ultimately complete map of quantitative methylation changes. Our methylation data also provide an ideal starting point for further translational research where the results can be combined with existing large-scale datasets to develop an approach that integrates epigenetic, transcriptional, and mutational findings. PMID:18353987

  8. Methyl salicylate overdose

    MedlinePlus

    Deep heating rubs overdose; Oil of wintergreen overdose ... These products contain methyl salicylate: Deep-heating creams used to relieve sore muscles and joints (Ben Gay, Icy Hot) Oil of wintergreen Solutions for vaporizers Other products may also ...

  9. 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...

  10. Reconfiguration of DNA methylation in aging.

    PubMed

    Zampieri, Michele; Ciccarone, Fabio; Calabrese, Roberta; Franceschi, Claudio; Bürkle, 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.

  11. Global DNA Methylation of Ischemic Stroke Subtypes

    PubMed Central

    Soriano-Tárraga, Carolina; Jiménez-Conde, Jordi; Giralt-Steinhauer, Eva; Mola, Marina; Ois, Ángel; Rodríguez-Campello, Ana; Cuadrado-Godia, Elisa; Fernández-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

  12. Enzyme mechanisms for sterol C-methylations.

    PubMed

    Nes, W David

    2003-09-01

    The mechanisms by which sterol methyl transferases (SMT) transform olefins into structurally different C-methylated products are complex, prompting over 50 years of intense research. Recent enzymological studies, together with the latest discoveries in the fossil record, functional analyses and gene cloning, establish new insights into the enzymatic mechanisms of sterol C-methylation and form a basis for understanding regulation and evolution of the sterol pathway. These studies suggest that SMTs, originated shortly after life appeared on planet earth. SMTs, including those which ultimately give rise to 24 alpha- and 24 beta-alkyl sterols, align the si(beta)-face pi-electrons of the Delta(24)-double bond with the S-methyl group of AdoMet relative to a set of deprotonation bases in the active site. From the orientation of the conformationally flexible side chain in the SMT Michaelis complex, it has been found that either a single product is formed or cationic intermediates are partitioned into multiple olefins. The product structure and stereochemistry of SMT action is phylogenetically distinct and physiologically significant. SMTs control phytosterol homeostasis and their activity is subject to feedback regulation by specific sterol inserts in the membrane. A unified conceptual framework has been formulated in the steric-electric plug model that posits SMT substrate acceptability on the generation of single or double 24-alkylated side chains, which is the basis for binding order, stereospecificity and product diversity in this class of AdoMet-dependent methyl transferase enzymes. The focus of this review is the mechanism of the C-methylation process which, as discussed, can be altered by point mutations in the enzyme to direct the shape of sterol structure to optimize function.

  13. DNA Methylation Patterns in the Hypothalamus of Female Pubertal Goats

    PubMed Central

    Li, Xiumei; Gao, Xiaoxiao; Zhang, Kaifa; Luo, Lei; Ding, Jianping; Zhang, Yunhai; Li, Yunsheng; Cao, Hongguo; Ling, Yinghui; Zhang, Xiaorong; Liu, Ya; Fang, Fugui

    2016-01-01

    Female pubertal development is tightly controlled by complex mechanisms, including neuroendocrine and epigenetic regulatory pathways. Specific gene expression patterns can be influenced by DNA methylation changes in the hypothalamus, which can in turn regulate timing of puberty onset. In order to understand the relationship between DNA methylation changes and gene expression patterns in the hypothalamus of pubertal goats, whole-genome bisulfite sequencing and RNA-sequencing analyses were carried out. There was a decline in DNA methylation levels in the hypothalamus during puberty and 268 differentially methylated regions (DMR) in the genome, with differential patterns in different gene regions. There were 1049 genes identified with distinct expression patterns. High levels of DNA methylation were detected in promoters, introns and 3′-untranslated regions (UTRs). Levels of methylation decreased gradually from promoters to 5′-UTRs and increased from 5′-UTRs to introns. Methylation density analysis demonstrated that methylation level variation was consistent with the density in the promoter, exon, intron, 5′-UTRs and 3′-UTRs. Analyses of CpG island (CGI) sites showed that the enriched gene contents were gene bodies, intergenic regions and introns, and these CGI sites were hypermethylated. Our study demonstrated that DNA methylation changes may influence gene expression profiles in the hypothalamus of goats during the onset of puberty, which may provide new insights into the mechanisms involved in pubertal onset. PMID:27788248

  14. miRNA and methylation: a multifaceted liaison.

    PubMed

    Chhabra, Ravindresh

    2015-01-19

    miRNAs and DNA methylation are both critical regulators of gene expression. Aberration in miRNA expression or DNA methylation is a causal factor for numerous pathological conditions. DNA methylation can inhibit the transcription of miRNAs, just like coding genes, by methylating the CpG islands in the promoter regions of miRNAs. Conversely, certain miRNAs can directly target DNA methyltransferases and bring about their inhibition, thereby affecting the whole genome methylation pattern. Recently, methylation patterns have also been revealed in mRNA. Surprisingly, the two most commonly studied methylation states in mRNA (m6A and m5C) are found to be enriched in 3'-UTRs (untranslated regions), the target site for the majority of miRNAs. Whereas m5C is reported to stabilise mRNA, m6A has a destabilising effect on mRNA. However, the effect of mRNA methylation on its interaction with miRNAs is largely unexplored. The review highlights the complex interplay between microRNA and methylation at DNA and mRNA level. PMID:25469751

  15. Classification of Epstein-Barr virus-positive gastric cancers by definition of DNA methylation epigenotypes.

    PubMed

    Matsusaka, Keisuke; Kaneda, Atsushi; Nagae, Genta; Ushiku, Tetsuo; Kikuchi, Yasuko; Hino, Rumi; Uozaki, Hiroshi; Seto, Yasuyuki; Takada, Kenzo; Aburatani, Hiroyuki; Fukayama, Masashi

    2011-12-01

    Epstein-Barr virus (EBV) is associated with Burkitt lymphoma, nasopharyngeal carcinoma, opportunistic lymphomas in immunocompromised hosts, and a fraction of gastric cancers. Aberrant promoter methylation accompanies human gastric carcinogenesis, though the contribution of EBV to such somatic methylation changes has not been fully clarified. We analyzed promoter methylation in gastric cancer cases with Illumina's Infinium BeadArray and used hierarchical clustering analysis to classify gastric cancers into 3 subgroups: EBV(-)/low methylation, EBV(-)/high methylation, and EBV(+)/high methylation. The 3 epigenotypes were characterized by 3 groups of genes: genes methylated specifically in the EBV(+) tumors (e.g., CXXC4, TIMP2, and PLXND1), genes methylated both in EBV(+) and EBV(-)/high tumors (e.g., COL9A2, EYA1, and ZNF365), and genes methylated in all of the gastric cancers (e.g., AMPH, SORCS3, and AJAP1). Polycomb repressive complex (PRC) target genes in embryonic stem cells were significantly enriched among EBV(-)/high-methylation genes and commonly methylated gastric cancer genes (P = 2 × 10(-15) and 2 × 10(-34), respectively), but not among EBV(+) tumor-specific methylation genes (P = 0.2), suggesting a different cause for EBV(+)-associated de novo methylation. When recombinant EBV was introduced into the EBV(-)/low-methylation epigenotype gastric cancer cell, MKN7, 3 independently established subclones displayed increases in DNA methylation. The promoters targeted by methylation were mostly shared among the 3 subclones, and the new methylation changes caused gene repression. In summary, DNA methylation profiling classified gastric cancer into 3 epigenotypes, and EBV(+) gastric cancers showed distinct methylation patterns likely attributable to EBV infection.

  16. 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

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

    PubMed

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

    2015-08-15

    Methylated arsenic can be found in virtually all earth surface environments. So far, however, little information has been collected regarding their removal by coagulation. In this study, the removal of monomethylarsenate (MMA) and dimethylarsenate (DMA) from drinking water by coagulation was investigated from the viewpoint of methyl substitution. Results indicated that FeCl3 was more efficient than AlCl3 and polyaluminum chloride (PACl) in methylated As removal. For the initial arsenic concentration of 200 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.

  18. In vitro Methylation Assay to Study Protein Arginine Methylation

    PubMed Central

    Bikkavilli, Rama Kamesh; Avasarala, Sreedevi; Van Scoyk, Michelle; Karuppusamy Rathinam, Manoj Kumar; Tauler, Jordi; Borowicz, Stanley; Winn, Robert A.

    2014-01-01

    Protein arginine methylation is one of the most abundant post-translational modifications in the nucleus. Protein arginine methylation can be identified and/or determined via proteomic approaches, and/or immunoblotting with methyl-arginine specific antibodies. However, these techniques sometimes can be misleading and often provide false positive results. Most importantly, these techniques cannot provide direct evidence in support of the PRMT substrate specificity. In vitro methylation assays, on the other hand, are useful biochemical assays, which are sensitive, and consistently reveal if the identified proteins are indeed PRMT substrates. A typical in vitro methylation assay includes purified, active PRMTs, purified substrate and a radioisotope labeled methyl donor (S-adenosyl-L-[methyl-3H] methionine). Here we describe a step-by-step protocol to isolate catalytically active PRMT1, a ubiquitously expressed PRMT family member. The methyl transferase activities of the purified PRMT1 were later tested on Ras-GTPase activating protein binding protein 1 (G3BP1), a known PRMT substrate, in the presence of S-adenosyl-L-[methyl-3H] methionine as the methyl donor. This protocol can be employed not only for establishing the methylation status of novel physiological PRMT1 substrates, but also for understanding the basic mechanism of protein arginine methylation. PMID:25350748

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. DNA Methylation in Osteoarthritis.

    PubMed

    den Hollander, Wouter; Meulenbelt, Ingrid

    2015-12-01

    Osteoarthritis (OA) is a prevalent disease of articular joints and primarily characterized by degradation and calcification of articular cartilage. Presently, no effective treatment other than pain relief exists and patients ultimately need to undergo replacement surgery of the affected joint. During disease progression articular chondrocytes, the single cell type present in articular cartilage, show altered transcriptional profiles and undergo phenotypic changes that resemble the terminal differentiation route apparent in growth plate chondrocytes. Hence, given its prominent function in both regulating gene expression and maintaining cellular phenotypes, DNA methylation of CpG dinucleotides is intensively studied in the context of OA. An increasing number of studies have been published that employed a targeted approach on genes known to play a role in OA pathophysiology. As of such, it has become clear that OA responsive DNA methylation changes seem to mediate disease associated aberrant gene expression. Furthermore, established OA susceptibility alleles such as GDF5 and DIO2 appear to confer OA risk via DNA methylation and respective pathophysiological expression changes. In more recent years, genome wide profiling of DNA methylation in OA affected articular cartilage has emerged as a powerful tool to address the epigenetic changes in their entirety, which has resulted in the identification of putative patient subgroups as well as generic OA associated pathways. PMID:27019616

  6. Kenaf methyl esters

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  7. Abiotic Formation of Methyl Halides in the Terrestrial Environment

    NASA Astrophysics Data System (ADS)

    Keppler, F.

    2011-12-01

    include a consideration on how stable isotope studies assisted advancements in this subject area. For example, it has been shown that the methoxyl groups of lignin and pectin which together constitute the bulk of the C1 plant pool have a carbon isotope signature significantly depleted in 13C. Plant-derived C1 volatile organic compounds (VOCs) are also highly depleted in 13C compared with Cn+1 VOCs. These observations suggest that the plant methoxyl pool is the predominant source of methyl halides released from senescent and dead plant litter. The distinct 13C depletion of plant methoxyl groups and naturally produced methyl halides may provide a helpful tool in constraining complex environmental processes and therefore improve our understanding of the global cycles of atmospheric methyl halides.

  8. DNA Methylation and Cancer Diagnosis

    PubMed Central

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

    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

  9. A Study on Spectro-Analytical Aspects, DNA - Interaction, Photo-Cleavage, Radical Scavenging, Cytotoxic Activities, Antibacterial and Docking Properties of 3 - (1 - (6 - methoxybenzo [d] thiazol - 2 - ylimino) ethyl) - 6 - methyl - 3H - pyran - 2, 4 - dione and its Metal Complexes.

    PubMed

    Ravi, Mudavath; Chennam, Kishan Prasad; Ushaiah, B; Eslavath, Ravi Kumar; Perugu, Shyam; Ajumeera, Rajanna; Devi, Ch Sarala

    2015-09-01

    The focus of the present work is on the design, synthesis, characterization, DNA-interaction, photo-cleavage, radical scavenging, in-vitro cytotoxicity, antimicrobial, docking and kinetic studies of Cu (II), Cd (II), Ce (IV) and Zr (IV) metal complexes of an imine derivative, 3 - (1 - (6 - methoxybenzo [d] thiazol - 2 - ylimino) ethyl) - 6 - methyl - 3H - pyran - 2, 4 - dione. The investigation of metal ligand interactions for the determination of composition of metal complexes, corresponding kinetic studies and antioxidant activity in solution was carried out by spectrophotometric methods. The synthesized metal complexes were characterized by EDX analysis, Mass, IR, (1)H-NMR, (13)C-NMR and UV-Visible spectra. DNA binding studies of metal complexes with Calf thymus (CT) DNA were carried out at room temperature by employing UV-Vis electron absorption, fluorescence emission and viscosity measurement techniques. The results revealed that these complexes interact with DNA through intercalation. The results of in vitro antibacterial studies showed the enhanced activity of chelating agent in metal chelated form and thus inferring scope for further development of new therapeutic drugs. Cell viability experiments indicated that all complexes showed significant dose dependent cytotoxicity in selected cell lines. The molecular modeling and docking studies were carried out with energy minimized structures of metal complexes to identify the receptor to metal interactions. PMID:26315729

  10. Predicting DNA methylation level across human tissues.

    PubMed

    Ma, Baoshan; Wilker, Elissa H; Willis-Owen, Saffron A G; Byun, Hyang-Min; Wong, Kenny C C; Motta, Valeria; Baccarelli, Andrea A; Schwartz, Joel; Cookson, William O C M; Khabbaz, Kamal; Mittleman, Murray A; Moffatt, Miriam F; Liang, Liming

    2014-04-01

    Differences in methylation across tissues are critical to cell differentiation and are key to understanding the role of epigenetics in complex diseases. In this investigation, we found that locus-specific methylation differences between tissues are highly consistent across individuals. We developed a novel statistical model to predict locus-specific methylation in target tissue based on methylation in surrogate tissue. The method was evaluated in publicly available data and in two studies using the latest IlluminaBeadChips: a childhood asthma study with methylation measured in both peripheral blood leukocytes (PBL) and lymphoblastoid cell lines; and a study of postoperative atrial fibrillation with methylation in PBL, atrium and artery. We found that our method can greatly improve accuracy of cross-tissue prediction at CpG sites that are variable in the target tissue [R(2) increases from 0.38 (original R(2) between tissues) to 0.89 for PBL-to-artery prediction; from 0.39 to 0.95 for PBL-to-atrium; and from 0.81 to 0.98 for lymphoblastoid cell line-to-PBL based on cross-validation, and confirmed using cross-study prediction]. An extended model with multiple CpGs further improved performance. Our results suggest that large-scale epidemiology studies using easy-to-access surrogate tissues (e.g. blood) could be recalibrated to improve understanding of epigenetics in hard-to-access tissues (e.g. atrium) and might enable non-invasive disease screening using epigenetic profiles. PMID:24445802

  11. Is There a Relationship between DNA Methylation and Phenotypic Plasticity in Invertebrates?

    PubMed Central

    Roberts, Steven B.; Gavery, Mackenzie R.

    2011-01-01

    There is a significant amount of variation in DNA methylation characteristics across organisms. Likewise, the biological role of DNA methylation varies across taxonomic lineages. The complexity of DNA methylation patterns in invertebrates has only recently begun to be characterized in-depth. In some invertebrate species that have been examined to date, methylated DNA is found primarily within coding regions and patterning is closely associated with gene function. Here we provide a perspective on the potential role of DNA methylation in these invertebrates with a focus on how limited methylation may contribute to increased phenotypic plasticity in highly fluctuating environments. Specifically, limited methylation could facilitate a variety of transcriptional opportunities including access to alternative transcription start sites, increasing sequence mutations, exon skipping, and transient methylation. PMID:22232607

  12. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks

    PubMed Central

    Zilberman, Daniel; Coleman-Derr, Devin; Ballinger, Tracy; Henikoff, Steven

    2010-01-01

    Eukaryotic chromatin is separated into functional domains differentiated by posttranslational histone modifications, histone variants, and DNA methylation1–6. Methylation is associated with repression of transcriptional initiation in plants and animals, and is frequently found in transposable elements. Proper methylation patterns are critical for eukaryotic development4,5, and aberrant methylation-induced silencing of tumor suppressor genes is a common feature of human cancer7. In contrast to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1 ATPase complex near 5′ ends of genes where it promotes transcriptional competence8–20. How DNA methylation and H2A.Z influence transcription remains largely unknown. Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of DNA methylation in the bodies of actively transcribed genes and in methylated transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses and gains of DNA methylation4,5, engenders opposite changes in H2A.Z deposition, while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads to genome-wide hypermethylation. Our findings indicate that DNA methylation can influence chromatin structure and effect gene silencing by excluding H2A.Z, and that H2A.Z protects genes from DNA methylation. PMID:18815594

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

    PubMed Central

    Walker, E L

    1998-01-01

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

  14. DNA methylation: conducting the orchestra from exposure to phenotype?

    PubMed

    Leenen, Fleur A D; Muller, Claude P; Turner, Jonathan D

    2016-01-01

    DNA methylation, through 5-methyl- and 5-hydroxymethylcytosine (5mC and 5hmC), is considered to be one of the principal interfaces between the genome and our environment, and it helps explain phenotypic variations in human populations. Initial reports of large differences in methylation level in genomic regulatory regions, coupled with clear gene expression data in both imprinted genes and malignant diseases, provided easily dissected molecular mechanisms for switching genes on or off. However, a more subtle process is becoming evident, where small (<10 %) changes to intermediate methylation levels are associated with complex disease phenotypes. This has resulted in two clear methylation paradigms. The latter "subtle change" paradigm is rapidly becoming the epigenetic hallmark of complex disease phenotypes, although we are currently hampered by a lack of data addressing the true biological significance and meaning of these small differences. Our initial expectation of rapidly identifying mechanisms linking environmental exposure to a disease phenotype led to numerous observational/association studies being performed. Although this expectation remains unmet, there is now a growing body of literature on specific genes, suggesting wide ranging transcriptional and translational consequences of such subtle methylation changes. Data from the glucocorticoid receptor (NR3C1) has shown that a complex interplay between DNA methylation, extensive 5'UTR splicing, and microvariability gives rise to the overall level and relative distribution of total and N-terminal protein isoforms generated. Additionally, the presence of multiple AUG translation initiation codons throughout the complete, processed mRNA enables translation variability, hereby enhancing the translational isoforms and the resulting protein isoform diversity, providing a clear link between small changes in DNA methylation and significant changes in protein isoforms and cellular locations. Methylation changes in

  15. 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

  16. 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.

  17. DNA Methylation Screening and Analysis

    PubMed Central

    Sant, Karilyn E.; Nahar, Muna S.; Dolinoy, Dana C.

    2013-01-01

    DNA methylation is an epigenetic form of gene regulation that is universally important throughout the life course, especially during in utero and postnatal development. DNA methylation aids in cell cycle regulation and cellular differentiation processes. Previous studies have demonstrated that DNA methylation profiles may be altered by diet and the environment, and that these profiles are especially vulnerable during development. Thus, it is important to understand the role of DNA methylation in developmental governance and subsequent disease progression. A variety of molecular methods exist to assay for global, gene-specific, and epigenome-wide methylation. Here we describe these methods and discuss their relative strengths and limitations. PMID:22669678

  18. 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.

  19. 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.

  20. Boryl-assisted hydrogenolysis of a nickel-methyl bond.

    PubMed

    Curado, Natalia; Maya, Celia; López-Serrano, Joaquín; Rodríguez, Amor

    2014-12-25

    A stable nickel(II) methyl complex containing a diphosphino-boryl (PBP) pincer ligand is described. Mechanistic studies on the hydrogenolysis of the Ni-Me bond suggest a metal ligand cooperation mechanism that involves the intermediacy of a σ-B-H Ni(0) species that further undergoes B-H oxidative addition to form a Ni(II) hydride complex.

  1. 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

  2. Direct DNA Methylation Profiling Using Methyl Binding Domain Proteins

    PubMed Central

    Yu, Yinni; Blair, Steve; Gillespie, David; Jensen, Randy; Myszka, David G.; Badran, Ahmed H.; Ghosh, Indraneel; Chagovetz, Alexander

    2010-01-01

    Methylation of DNA is responsible for gene silencing by establishing heterochromatin structure that represses transcription, and studies have shown that cytosine methylation of CpG islands in promoter regions acts as a precursor to early cancer development. The naturally occurring methyl binding domain (MBD) proteins from mammals are known to bind to the methylated CpG dinucleotide (mCpG), and subsequently recruit other chromatin-modifying proteins to suppress transcription. Conventional methods of detection for methylated DNA involve bisulfite treatment or immunoprecipitation prior to performing an assay. We focus on proof-of-concept studies for a direct microarray-based assay using surface-bound methylated probes. The recombinant protein 1xMBD-GFP recognizes hemi-methylation and symmetric methylation of the CpG sequence of hybridized dsDNA, while displaying greater affinity for the symmetric methylation motif, as evaluated by SPR. From these studies, for symmetric mCpG, the KD for 1xMBD-GFP ranged from 106 nM to 870 nM, depending upon the proximity of the methylation site to the sensor surface. The KD values for non-symmetrical methylation motifs were consistently greater (> 2 µM), but the binding selectivity between symmetric and hemi-methylation motifs ranged from 4 to 30, with reduced selectivity for sites close to the surface or multiple sites in proximity, which we attribute to steric effects. Fitting skew normal probability density functions to our data, we estimate an accuracy of 97.5% for our method in identifying methylated CpG loci, which can be improved through optimization of probe design and surface density. PMID:20507169

  3. The Reaction Mechanism of Methyl-Coenzyme M Reductase

    PubMed Central

    Wongnate, Thanyaporn; Ragsdale, Stephen W.

    2015-01-01

    Methyl-coenzyme M reductase (MCR) is a nickel tetrahydrocorphinoid (coenzyme F430) containing enzyme involved in the biological synthesis and anaerobic oxidation of methane. MCR catalyzes the conversion of methyl-2-mercaptoethanesulfonate (methyl-SCoM) and N-7-mercaptoheptanoylthreonine phosphate (CoB7SH) to CH4 and the mixed disulfide CoBS-SCoM. In this study, the reaction of MCR from Methanothermobacter marburgensis, with its native substrates was investigated using static binding, chemical quench, and stopped-flow techniques. Rate constants were measured for each step in this strictly ordered ternary complex catalytic mechanism. Surprisingly, in the absence of the other substrate, MCR can bind either substrate; however, only one binary complex (MCR·methyl-SCoM) is productive whereas the other (MCR·CoB7SH) is inhibitory. Moreover, the kinetic data demonstrate that binding of methyl-SCoM to the inhibitory MCR·CoB7SH complex is highly disfavored (Kd = 56 mm). However, binding of CoB7SH to the productive MCR·methyl-SCoM complex to form the active ternary complex (CoB7SH·MCR(NiI)·CH3SCoM) is highly favored (Kd = 79 μm). Only then can the chemical reaction occur (kobs = 20 s−1 at 25 °C), leading to rapid formation and dissociation of CH4 leaving the binary product complex (MCR(NiII)·CoB7S−·SCoM), which undergoes electron transfer to regenerate Ni(I) and the final product CoBS-SCoM. This first rapid kinetics study of MCR with its natural substrates describes how an enzyme can enforce a strictly ordered ternary complex mechanism and serves as a template for identification of the reaction intermediates. PMID:25691570

  4. 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

  5. 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.

  6. DNA methylation in spermatogenesis and male infertility

    PubMed Central

    Cui, Xiangrong; Jing, Xuan; Wu, Xueqing; Yan, Meiqin; Li, Qiang; Shen, Yan; Wang, Zhenqiang

    2016-01-01

    Infertility is a significant problem for human reproduction, with males and females equally affected. However, the molecular mechanisms underlying male infertility remain unclear. Spermatogenesis is a highly complex process involving mitotic cell division, meiosis cell division and spermiogenesis; during this period, unique and extensive chromatin and epigenetic modifications occur to bring about specific epigenetic profiles in spermatozoa. It has recently been suggested that the dysregulation of epigenetic modifications, in particular the methylation of sperm genomic DNA, may serve an important role in the development of numerous diseases. The present study is a comprehensive review on the topic of male infertility, aiming to elucidate the association between sperm genomic DNA methylation and poor semen quality in male infertility. In addition, the current status of the genetic and epigenetic determinants of spermatogenesis in humans is discussed. PMID:27698683

  7. DNA methylation in spermatogenesis and male infertility

    PubMed Central

    Cui, Xiangrong; Jing, Xuan; Wu, Xueqing; Yan, Meiqin; Li, Qiang; Shen, Yan; Wang, Zhenqiang

    2016-01-01

    Infertility is a significant problem for human reproduction, with males and females equally affected. However, the molecular mechanisms underlying male infertility remain unclear. Spermatogenesis is a highly complex process involving mitotic cell division, meiosis cell division and spermiogenesis; during this period, unique and extensive chromatin and epigenetic modifications occur to bring about specific epigenetic profiles in spermatozoa. It has recently been suggested that the dysregulation of epigenetic modifications, in particular the methylation of sperm genomic DNA, may serve an important role in the development of numerous diseases. The present study is a comprehensive review on the topic of male infertility, aiming to elucidate the association between sperm genomic DNA methylation and poor semen quality in male infertility. In addition, the current status of the genetic and epigenetic determinants of spermatogenesis in humans is discussed.

  8. 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

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

  10. 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.

  11. 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

  12. 2-Methyl-L-tryptophan is a substrate of tryptophanase.

    PubMed

    Faleev, N G; Gogoleva, O I; Dementieva, I S; Zakomirdina, L N; Belikov, V M

    1995-04-01

    Tryptophanase was generally considered to be inactive towards tryptophan derivatives substituted at 2-position of the indole ring. We have shown that cells containing tryptophanase catalyze the formation of 2-methyl-L-tryptophan from 2-methylindole and L-serine, and from 2-methylindole, pyruvate and ammonium ion. The kinetics of pyruvate formation from 2-methyl-L-tryptophan and its alpha-deuterated analogue catalyzed by homogeneous tryptophanase were examined. The primary deuterium isotope effect (kH/kD = 4.0) as well as the absorption spectrum of tryptophanase complex with 2-methyl-L-tryptophan indicate that the rate of enzymatic reaction of 2-methyl-L-tryptophan is in a considerable degree determined by the stage of removal of alpha-proton.

  13. 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

  14. 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.

  15. Quantitative reconstruction of leukocyte subsets using DNA methylation

    PubMed Central

    2014-01-01

    Background Cell lineage-specific DNA methylation patterns distinguish normal human leukocyte subsets and can be used to detect and quantify these subsets in peripheral blood. We have developed an approach that uses DNA methylation to simultaneously quantify multiple leukocyte subsets, enabling investigation of immune modulations in virtually any blood sample including archived samples previously precluded from such analysis. Here we assess the performance characteristics and validity of this approach. Results Using Illumina Infinium HumanMethylation27 and VeraCode GoldenGate Methylation Assay microarrays, we measure DNA methylation in leukocyte subsets purified from human whole blood and identify cell lineage-specific DNA methylation signatures that distinguish human T cells, B cells, NK cells, monocytes, eosinophils, basophils and neutrophils. We employ a bioinformatics-based approach to quantify these cell types in complex mixtures, including whole blood, using DNA methylation at as few as 20 CpG loci. A reconstruction experiment confirms that the approach could accurately measure the composition of mixtures of human blood leukocyte subsets. Applying the DNA methylation-based approach to quantify the cellular components of human whole blood, we verify its accuracy by direct comparison to gold standard immune quantification methods that utilize physical, optical and proteomic characteristics of the cells. We also demonstrate that the approach is not affected by storage of blood samples, even under conditions prohibiting the use of gold standard methods. Conclusions Cell mixture distributions within peripheral blood can be assessed accurately and reliably using DNA methylation. Thus, precise immune cell differential estimates can be reconstructed using only DNA rather than whole cells. PMID:24598480

  16. Electrochemical strategy for sensing DNA methylation and DNA methyltransferase activity.

    PubMed

    Wang, Gang Lin; Zhou, Long Yin; Luo, Hong Qun; Li, Nian Bing

    2013-03-20

    The present work demonstrates a novel signal-off electrochemical method for the determination of DNA methylation and the assay of methyltransferase activity using the electroactive complex [Ru(NH3)6](3+) (RuHex) as a signal transducer. The assay exploits the electrostatic interactions between RuHex and DNA strands. Thiolated single strand DNA1 was firstly self-assembled on a gold electrode via Au-S bonding, followed by hybridization with single strand DNA2 to form double strand DNA containing specific recognition sequence of DNA adenine methylation MTase and methylation-responsive restriction endonuclease Dpn I. The double strand DNA may adsorb lots of electrochemical species ([Ru(NH3)6](3+)) via the electrostatic interaction, thus resulting in a high electrochemical signal. In the presence of DNA adenine methylation methyltransferase and S-adenosyl-l-methionine, the formed double strand DNA was methylated by DNA adenine methylation methyltransferase, then the double strand DNA can be cleaved by methylation-responsive restriction endonuclease Dpn I, leading to the dissociation of a large amount of signaling probes from the electrode. As a result, the adsorption amount of RuHex reduced, resulting in a decrease in electrochemical signal. Thus, a sensitive electrochemical method for detection of DNA methylation is proposed. The proposed method yielded a linear response to concentration of Dam MTase ranging from 0.25 to 10UmL(-1) with a detection limit of 0.18UmL(-1) (S/N=3), which might promise this method as a good candidate for monitoring DNA methylation in the future. PMID:23473252

  17. Genomics of CpG methylation in developing and developed zebrafish.

    PubMed

    McGaughey, David M; Abaan, Hatice Ozel; Miller, Ryan M; Kropp, Peter A; Brody, Lawrence C

    2014-05-01

    DNA methylation is a dynamic process through which specific chromatin modifications can be stably transmitted from parent to daughter cells. A large body of work has suggested that DNA methylation influences gene expression by silencing gene promoters. However, these conclusions were drawn from data focused mostly on promoter regions. Regarding the entire genome, it is unclear how methylation and gene transcription patterns are related during vertebrate development. To identify the genome-wide distribution of CpG methylation, we created series of high-resolution methylome maps of Danio rerio embryos during development and in mature, differentiated tissues. We found that embryonic and terminal tissues have unique methylation signatures in CpG islands and repetitive sequences. Fully differentiated tissues have increased CpG and LTR methylation and decreased SINE methylation relative to embryonic tissues. Unsupervised clustering analyses reveal that the embryonic and terminal tissues can be classified solely by their methylation patterning. Novel analyses also identify a previously undescribed genome-wide exon methylation signature. We also compared whole genome methylation with genome-wide mRNA expression levels using publicly available RNA-seq datasets. These comparisons revealed previously unrecognized relationships between gene expression, alternative splicing, and exon methylation. Surprisingly, we found that exonic methylation is a better predictor of mRNA expression level than promoter methylation. We also found that transcriptionally skipped exons have significantly less methylation than retained exons. Our integrative analyses reveal highly complex interplay between gene expression, alternative splicing, development, and methylation patterning in zebrafish. PMID:24657902

  18. Antagonism between DNA and H3K27 Methylation at the Imprinted Rasgrf1 Locus

    PubMed Central

    McLean, Chelsea M.; Dokshin, Gregoriy A.; Persson, Jenna M.; Herman, Herry; Pasini, Diego; Miró, Xavier; Donohoe, Mary E.; Lee, Jeannie T.; Helin, Kristian; Soloway, Paul D.

    2008-01-01

    At the imprinted Rasgrf1 locus in mouse, a cis-acting sequence controls DNA methylation at a differentially methylated domain (DMD). While characterizing epigenetic marks over the DMD, we observed that DNA and H3K27 trimethylation are mutually exclusive, with DNA and H3K27 methylation limited to the paternal and maternal sequences, respectively. The mutual exclusion arises because one mark prevents placement of the other. We demonstrated this in five ways: using 5-azacytidine treatments and mutations at the endogenous locus that disrupt DNA methylation; using a transgenic model in which the maternal DMD inappropriately acquired DNA methylation; and by analyzing materials from cells and embryos lacking SUZ12 and YY1. SUZ12 is part of the PRC2 complex, which is needed for placing H3K27me3, and YY1 recruits PRC2 to sites of action. Results from each experimental system consistently demonstrated antagonism between H3K27me3 and DNA methylation. When DNA methylation was lost, H3K27me3 encroached into sites where it had not been before; inappropriate acquisition of DNA methylation excluded normal placement of H3K27me3, and loss of factors needed for H3K27 methylation enabled DNA methylation to appear where it had been excluded. These data reveal the previously unknown antagonism between H3K27 and DNA methylation and identify a means by which epigenetic states may change during disease and development. PMID:18670629

  19. 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.

  20. 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.

  1. 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.

  2. Selectivity in metal-carbon bond protonolysis in p-tolyl- (or methyl)-cycloplatinated(II) complexes: kinetics and mechanism of the uncatalyzed isomerization of the resulting Pt(II) products.

    PubMed

    Haghighi, Mohsen Golbon; Nabavizadeh, S Masoud; Rashidi, Mehdi; Kubicki, Maciej

    2013-10-01

    Reaction of each of the known starting complexes [PtR(C^N)(SMe2)], 1, in which R = Me or p-MeC6H4 and C^N is either ppy (deprotonated 2-phenylpyridine) or bhq (deprotonated benzo[h]quinoline), with one equivalent of CF3CO2H, gave the complexes [Pt(C^N)(CF3CO2)(SMe2)], 3 (C^N = ppy, 3a; bhq, 3b). The bis-chelate complexes [Pt(C^N)(P^P)](CF3CO2), 4, were obtained by reaction of complexes 3 with one equivalent of either of the P^P bisphosphine reagents, dppf = 1,1'-bis(diphenylphosphino)ferrocene or dppe = bis(diphenylphosphino)ethane. Complexes 4 were alternatively made by reaction of the complexes [PtMe(κ(1)C-C^N)(P^P)], 2, with one equivalent of CF3CO2H. When the complex 3b was reacted with 0.5 equivalents of dppe, 0.5 equivalents of the related bis-chelate product, 4d, formed along with 0.5 equivalents of the unreacted starting complex 3b. In contrast, when the complex 3b was reacted with 0.5 equivalents of dppf, then the dimeric complex [Pt2(bhq)2(CF3CO2)2(μ-dppf)], 5, formed in pure form. In all the above-mentioned acid reactions, the M-R bond rather than the M-C bond of the cycloplatinated complex is cleaved. When the PPh3 analogues of complexes 1, i.e. the complexes [PtR(C^N)(PPh3)], 6, in which C^N is ppy or tpy = deprotonated 2-p-tolylpyridine, were reacted with one equivalent of CF3CO2H, the course of the reaction reversed and the M-C bonds of the cycloplatinated complexes are cleaved rather than the M-R bonds. The latter reaction gave [PtR(κ(1)N-HC^N)(PPh3)(CF3CO2)], as an equilibrium mixture of two isomers 7 and 8. Crystal structures of the typical complexes show a variety of extensive intermolecular hydrogen bonding involving C-H bonds from the different ligands and electronegative atoms (O or F) from the CF3CO2 moiety. On the basis of data obtained from kinetic studies (using (1)H NMR spectroscopy), a dissociative mechanism is proposed for the case of the 7c/8c isomerization process, involving dissociation of the κ(1)N-Htpy neutral ligand, rather

  3. DNA methylation and carcinogenesis.

    PubMed

    Lichtenstein, A V; Kisseljova, N P

    2001-03-01

    In the world of easy things truth is opposed to lie; in the world of complicated things one profound truth is opposed to another not less profound than the first. Neils Bohr The hypothesis of the exclusively genetic origin of cancer ("cancer is a disease of genes, a tumor without any damage to the genome does not exist") dominated in the oncology until recently. A considerable amount of data confirming this hypothesis was accumulated during the last quarter of the last century. It was demonstrated that the accumulation of damage of specific genes lies at the origin of a tumor and its following progression. The damage gives rise to structural changes in the respective proteins and, consequently, to inappropriate mitogenic stimulation of cells (activation of oncogenes) or to the inactivation of tumor suppressor genes that inhibit cell division, or to the combination of both (in most cases). According to an alternative (epigenetic) hypothesis that was extremely unpopular until recently, a tumor is caused not by a gene damage, but by an inappropriate function of genes ("cancer is a disease of gene regulation and differentiation"). However, recent studies led to the convergence of these hypotheses that initially seemed to be contradictory. It was established that both factors--genetic and epigenetic--lie at the origin of carcinogenesis. The relative contribution of each varies significantly in different human tumors. Suppressor genes and genes of repair are inactivated in tumors due to their damage or methylation of their promoters (in the latter case an "epimutation", an epigenetic equivalent of a mutation, occurs, producing the same functional consequences). It is becoming evident that not only the mutagens, but various factors influencing cell metabolism, notably methylation, should be considered as carcinogens.

  4. Neural Tube Defects, Folic Acid and Methylation

    PubMed Central

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

    2013-01-01

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

  5. 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.

  6. 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)}]2·THF 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 μ(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.

  7. 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.

  8. Ternary Copper(II) Complexes With Indomethacin, a Potent Non-Steroidal Antiinflammatory Drug. Crystal Structure of Bis (Dimethylformamide)-Tetrakis[1-(4-Chlorobenzoyl)-5-Methoxy-2-Methyl-1-H-Indole-3-Acetato]Dicopper(II). Antiinflammatory Properties and Prevention of Gastrointestinal Side Effects by Nanocapsules

    PubMed Central

    Guessous, Fadila; Daran, Jean-Claude; Viossat, Bernard; Morgant, Georges; Labouze, Xavier; Leroy, Anne Laure; Roch-Arveiller, Monique

    1998-01-01

    Two ternary copper(ll) complexes of indomethacin [1-(4-chlorobenzoyl)-5-methoxy-2- methyl-1-H-indole-3-acetic acid] called hereafter lndo, were prepared and characterized by single crystal X-ray diffraction. The first complex Cu2(Indo)4(DMF)2 I crystallizes in space group P-1 (a = 10.829(2), b = 13.379(2), c = 16.491(3) Å; α = 105.58(2), β = 101.06(2), γ = 106.96(2)°; V= 2104.6(6) Å3, Z= 1). The title molecule is a centrosymmetric binuclear complex, with Cu atoms bridged by the carboxylate moieties of four indomethacinate ligands. The four nearest O atoms around each Cu atom form a square planar arrangement with the square pyramidal coordination completed by the O atom of N,N′-dimethylformamide. Daily administration for seven days of 1 mg/kg of indomethacin, I and I encapsulated into liposomes induces a weak inflammation of rat gastrointestinal tract. I was less inflammatory than indomethacin but the better protection was brought by encapsulation of the compound. This might be of interest in sustained therapies of chronic inflammatory diseases. PMID:18475870

  9. Crystal structure of a tetranuclear Cu(II) complex with an O,N,N'-donor Schiff base ligand: hexa-μ2-acetato-bis-(2-{[(2,2,6,6-tetra-methyl-piperidin-4-yl)imino]-meth-yl}phenolato-κ(3) O,N,N')tetra-copper(II).

    PubMed

    Huang, Guohui; Liu, Xiaoxuan

    2016-04-01

    The title compound, [Cu4(CH3COO)6(C16H23N2O)2], lies across a twofold rotation axis. The asymmetric unit contains two independent Cu(II) ions. The symmetry-unique terminal Cu(II) ion is O,N,N'-coordinated by a 2-{[(2,2,6,6-tetra-methyl-piperidin-4-yl)imino]-meth-yl}phenolate ligand and an O atom from an acetate group in a slightly distorted square-planar coordination environment. The symmetry-unique central Cu(II) ion is coordinated by a different O atom from the same acetate group and by four bridging acetate ligands, which connect the asymmetric unit into a dimeric complex and form a distorted square-pyramidal coordination environment. Within the complex there are two symmetry-equivalent intra-molecular N-H⋯O hydrogen bonds. In the crystal, weak C-H⋯O hydrogen bonds link the complex mol-ecules, forming a three-dimensional network. PMID:27375896

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-10-01

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

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

    NASA Technical Reports Server (NTRS)

    Robbins, D. E.

    1976-01-01

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

  13. 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

  14. Synthesis, structure and catalase-like activity of dimanganese(III) complexes of 1,5-bis(X-salicylidenamino)pentan-3-ol (X = 3- and 5-methyl). Influence of phenyl-ring substituents on catalytic activity.

    PubMed

    Moreno, Diego; Palopoli, Claudia; Daier, Verónica; Shova, Sergiu; Vendier, Laure; Sierra, Manuel González; Tuchagues, Jean-Pierre; Signorella, Sandra

    2006-11-21

    The diMn(III) complexes [Mn2(5-Me-salpentO)(mu-MeO)(mu-AcO)(H2O)Br] (1) and [Mn2(3-Me-salpentO)(mu-MeO)(mu-AcO)(MeOH)2]Br (2), where salpentOH = 1,5-bis(salicylidenamino)pentan-3-ol, were synthesised and structurally characterized. The two complexes include a bis(micro-alkoxo)(micro-acetato) triply-bridged diMn(III) core with an Mn...Mn separation of 2.93-2.94 A, the structure of which is retained upon dissolution. Complexes 1 and 2 show catalytic activity toward disproportionation of H2O2, with first-order dependence on the catalyst, and saturation kinetics on [H2O2], in methanol and DMF. In DMF, the two complexes are able to disproportionate at least 1500 eq. of H2O2 without significant decomposition, while in methanol, they rapidly lose activity with formation of a non-coupled Mn(II) species. Electrospray ionisation mass spectrometry, EPR and UV/vis spectroscopy used to monitor the reaction suggest that the major active form of the catalyst occurs in the Mn2(III) oxidation state during cycling. The correlation between log(k(cat)) and the redox potentials of 1, 2 and analogous complexes of other X-salpentOH derivatives indicates that, in this series, the oxidation of the catalyst is probably the rate-limiting step in the catalytic cycle. It is also noted that formation of the catalyst-peroxide adduct is more sensitive to steric effects in DMF than in methanol. Overall, kinetics and spectroscopic studies of H2O2 dismutation by these complexes converge at a catalytic cycle that involves the Mn2(III) and Mn2(IV) oxidation states. PMID:17077889

  15. Histone lysine methylation: critical regulator of memory and behavior.

    PubMed

    Jarome, Timothy J; Lubin, Farah D

    2013-01-01

    Histone lysine methylation is a well-established transcriptional mechanism for the regulation of gene expression changes in eukaryotic cells and is now believed to function in neurons of the central nervous system to mediate the process of memory formation and behavior. In mature neurons, methylation of histone proteins can serve to both activate and repress gene transcription. This is in stark contrast to other epigenetic modifications, including histone acetylation and DNA methylation, which have largely been associated with one transcriptional state in the brain. In this review, we discuss the evidence for histone methylation mechanisms in the coordination of complex cognitive processes such as long-term memory formation and storage. In addition, we address the current literature highlighting the role of histone methylation in intellectual disability, addiction, schizophrenia, autism, depression, and neurodegeneration. Further, we discuss histone methylation within the context of other epigenetic modifications and the potential advantages of exploring this newly identified mechanism of cognition, emphasizing the possibility that this molecular process may provide an alternative locus for intervention in long-term psychopathologies that cannot be clearly linked to genes or environment alone.

  16. The potential role of DNA methylation in abdominal aortic aneurysms.

    PubMed

    Ryer, Evan J; Ronning, Kaitryn E; Erdman, Robert; Schworer, Charles M; Elmore, James R; Peeler, Thomas C; Nevius, Christopher D; Lillvis, John H; Garvin, Robert P; Franklin, David P; Kuivaniemi, Helena; Tromp, Gerard

    2015-01-01

    Abdominal aortic aneurysm (AAA) is a complex disorder that has a significant impact on the aging population. While both genetic and environmental risk factors have been implicated in AAA formation, the precise genetic markers involved and the factors influencing their expression remain an area of ongoing investigation. DNA methylation has been previously used to study gene silencing in other inflammatory disorders and since AAA has an extensive inflammatory component, we sought to examine the genome-wide DNA methylation profiles in mononuclear blood cells of AAA cases and matched non-AAA controls. To this end, we collected blood samples and isolated mononuclear cells for DNA and RNA extraction from four all male groups: AAA smokers (n = 11), AAA non-smokers (n = 9), control smokers (n = 10) and control non-smokers (n = 11). Methylation data were obtained using the Illumina 450k Human Methylation Bead Chip and analyzed using the R language and multiple Bioconductor packages. Principal component analysis and linear analysis of CpG island subsets identified four regions with significant differences in methylation with respect to AAA: kelch-like family member 35 (KLHL35), calponin 2 (CNN2), serpin peptidase inhibitor clade B (ovalbumin) member 9 (SERPINB9), and adenylate cyclase 10 pseudogene 1 (ADCY10P1). Follow-up studies included RT-PCR and immunostaining for CNN2 and SERPINB9. These findings are novel and suggest DNA methylation may play a role in AAA pathobiology. PMID:25993294

  17. Aberrant DNA Methylation in Keratoacanthoma

    PubMed Central

    Nakagawa, Hidemi

    2016-01-01

    Background Keratoacanthoma (KA) is a self-limiting epidermal tumor for which histopathological examination sometimes suggests malignancy. Based on inconsistent clinical views, KA can be regarded as both a benign tumor and a variant of squamous cell carcinoma (SCC). Aberrant DNA methylation frequently occurs in malignant tumors but it scarcely occurs in benign tumors. Whether aberrant methylation occurs in KA has not been previously examined. Objective The aim is to elucidate whether aberrant methylation of CpG islands (CGI) containing a high density of cytosine-guanine dinucleotide (CpG) sites occurs in KA. Methods Five SCC cell lines, two cultured samples of normal human epidermal keratinocytes (NHEKs), 18 clinical SCC samples, and 21 clinical KA samples were analyzed with Infinium HumanMethylation450 BeadChips, quantitative real-time methylation-specific PCR (RT-MSP) and/or bisulfite sequencing. Results Genome-wide analyses of NHEK, KA, and SCC indicated that there was a greater number of aberrantly hypermethylated CGIs in SCC than in KA and there were aberrantly hypermethylated CGIs which are common in both. Among the common hypermethylated CGIs, RT-MSP and bisulfite sequencing targeting CGIs located on CCDC17, PVR, and MAP3K11 gene bodies also showed that methylation levels were significantly higher in KA than in normal epidermis. Statistical analyses suggested that the methylation level of CGI located on PVR in SCC might be correlated to lymph node metastasis (P = 0.013, Mann-Whitney U test) and that the methylation level of CGI in MAP3K11 in KA might be correlated to age (P = 0.031, linear regression analysis). Conclusion Aberrant DNA methylation occurs in KA. PMID:27788211

  18. 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.

  19. [DNA methylation in thyroid carcinoma].

    PubMed

    Song, Xianyun; Shang, Xiaoling; Zhang, Yutuo

    2015-03-01

    Cancer has become clear that not merely gene variations but also epigenetic modifications may contribute to it. Epigenetic changes refer to stable alterations in gene expression with unrelated to changes in the underlying genetic sequence,resulting in heritable. DNA methylation is one of the common epigenetic changes. It control the gene expression through changing DNA conformation and stability, chromatin structer, DNA-protein interaction. The reversal of dysregulated DNA methylation has emerged as a potential strategy for the treatment of thyroid carcinoma. The artical will provide an overview of how DNA methylation contribute to thyroid carcinoma dissemination,invasion and metastasis and we will summarize the latest epigenetic therapies for thyroid carcinoma.

  20. Accounting for population stratification in DNA methylation studies.

    PubMed

    Barfield, Richard T; Almli, Lynn M; Kilaru, Varun; Smith, Alicia K; Mercer, Kristina B; Duncan, Richard; Klengel, Torsten; Mehta, Divya; Binder, Elisabeth B; Epstein, Michael P; Ressler, Kerry J; Conneely, Karen N

    2014-04-01

    DNA methylation is an important epigenetic mechanism that has been linked to complex diseases and is of great interest to researchers as a potential link between genome, environment, and disease. As the scale of DNA methylation association studies approaches that of genome-wide association studies, issues such as population stratification will need to be addressed. It is well-documented that failure to adjust for population stratification can lead to false positives in genetic association studies, but population stratification is often unaccounted for in DNA methylation studies. Here, we propose several approaches to correct for population stratification using principal components (PCs) from different subsets of genome-wide methylation data. We first illustrate the potential for confounding due to population stratification by demonstrating widespread associations between DNA methylation and race in 388 individuals (365 African American and 23 Caucasian). We subsequently evaluate the performance of our PC-based approaches and other methods in adjusting for confounding due to population stratification. Our simulations show that (1) all of the methods considered are effective at removing inflation due to population stratification, and (2) maximum power can be obtained with single-nucleotide polymorphism (SNP)-based PCs, followed by methylation-based PCs, which outperform both surrogate variable analysis and genomic control. Among our different approaches to computing methylation-based PCs, we find that PCs based on CpG sites chosen for their potential to proxy nearby SNPs can provide a powerful and computationally efficient approach to adjust for population stratification in DNA methylation studies when genome-wide SNP data are unavailable.

  1. Accounting for population stratification in DNA methylation studies.

    PubMed

    Barfield, Richard T; Almli, Lynn M; Kilaru, Varun; Smith, Alicia K; Mercer, Kristina B; Duncan, Richard; Klengel, Torsten; Mehta, Divya; Binder, Elisabeth B; Epstein, Michael P; Ressler, Kerry J; Conneely, Karen N

    2014-04-01

    DNA methylation is an important epigenetic mechanism that has been linked to complex diseases and is of great interest to researchers as a potential link between genome, environment, and disease. As the scale of DNA methylation association studies approaches that of genome-wide association studies, issues such as population stratification will need to be addressed. It is well-documented that failure to adjust for population stratification can lead to false positives in genetic association studies, but population stratification is often unaccounted for in DNA methylation studies. Here, we propose several approaches to correct for population stratification using principal components (PCs) from different subsets of genome-wide methylation data. We first illustrate the potential for confounding due to population stratification by demonstrating widespread associations between DNA methylation and race in 388 individuals (365 African American and 23 Caucasian). We subsequently evaluate the performance of our PC-based approaches and other methods in adjusting for confounding due to population stratification. Our simulations show that (1) all of the methods considered are effective at removing inflation due to population stratification, and (2) maximum power can be obtained with single-nucleotide polymorphism (SNP)-based PCs, followed by methylation-based PCs, which outperform both surrogate variable analysis and genomic control. Among our different approaches to computing methylation-based PCs, we find that PCs based on CpG sites chosen for their potential to proxy nearby SNPs can provide a powerful and computationally efficient approach to adjust for population stratification in DNA methylation studies when genome-wide SNP data are unavailable. PMID:24478250

  2. A/T Run Geometry of B-form DNA Is Independent of Bound Methyl-CpG Binding Domain, Cytosine Methylation and Flanking Sequence.

    PubMed

    Chia, Jyh Yea; Tan, Wen Siang; Ng, Chyan Leong; Hu, Nien-Jen; Foo, Hooi Ling; Ho, Kok Lian

    2016-08-09

    DNA methylation in a CpG context can be recognised by methyl-CpG binding protein 2 (MeCP2) via its methyl-CpG binding domain (MBD). An A/T run next to a methyl-CpG maximises the binding of MeCP2 to the methylated DNA. The A/T run characteristics are reported here with an X-ray structure of MBD A140V in complex with methylated DNA. The A/T run geometry was found to be strongly stabilised by a string of conserved water molecules regardless of its flanking nucleotide sequences, DNA methylation and bound MBD. New water molecules were found to stabilise the Rett syndrome-related E137, whose carboxylate group is salt bridged to R133. A structural comparison showed no difference between the wild type and MBD A140V. However, differential scanning calorimetry showed that the melting temperature of A140V constructs in complex with methylated DNA was reduced by ~7 °C, although circular dichroism showed no changes in the secondary structure content for A140V. A band shift analysis demonstrated that the larger fragment of MeCP2 (A140V) containing the transcriptional repression domain (TRD) destabilises the DNA binding. These results suggest that the solution structure of MBD A140V may differ from the wild-type MBD although no changes in the biochemical properties of X-ray A140V were observed.

  3. A/T Run Geometry of B-form DNA Is Independent of Bound Methyl-CpG Binding Domain, Cytosine Methylation and Flanking Sequence

    PubMed Central

    Chia, Jyh Yea; Tan, Wen Siang; Ng, Chyan Leong; Hu, Nien-Jen; Foo, Hooi Ling; Ho, Kok Lian

    2016-01-01

    DNA methylation in a CpG context can be recognised by methyl-CpG binding protein 2 (MeCP2) via its methyl-CpG binding domain (MBD). An A/T run next to a methyl-CpG maximises the binding of MeCP2 to the methylated DNA. The A/T run characteristics are reported here with an X-ray structure of MBD A140V in complex with methylated DNA. The A/T run geometry was found to be strongly stabilised by a string of conserved water molecules regardless of its flanking nucleotide sequences, DNA methylation and bound MBD. New water molecules were found to stabilise the Rett syndrome-related E137, whose carboxylate group is salt bridged to R133. A structural comparison showed no difference between the wild type and MBD A140V. However, differential scanning calorimetry showed that the melting temperature of A140V constructs in complex with methylated DNA was reduced by ~7 °C, although circular dichroism showed no changes in the secondary structure content for A140V. A band shift analysis demonstrated that the larger fragment of MeCP2 (A140V) containing the transcriptional repression domain (TRD) destabilises the DNA binding. These results suggest that the solution structure of MBD A140V may differ from the wild-type MBD although no changes in the biochemical properties of X-ray A140V were observed. PMID:27502833

  4. A/T Run Geometry of B-form DNA Is Independent of Bound Methyl-CpG Binding Domain, Cytosine Methylation and Flanking Sequence.

    PubMed

    Chia, Jyh Yea; Tan, Wen Siang; Ng, Chyan Leong; Hu, Nien-Jen; Foo, Hooi Ling; Ho, Kok Lian

    2016-01-01

    DNA methylation in a CpG context can be recognised by methyl-CpG binding protein 2 (MeCP2) via its methyl-CpG binding domain (MBD). An A/T run next to a methyl-CpG maximises the binding of MeCP2 to the methylated DNA. The A/T run characteristics are reported here with an X-ray structure of MBD A140V in complex with methylated DNA. The A/T run geometry was found to be strongly stabilised by a string of conserved water molecules regardless of its flanking nucleotide sequences, DNA methylation and bound MBD. New water molecules were found to stabilise the Rett syndrome-related E137, whose carboxylate group is salt bridged to R133. A structural comparison showed no difference between the wild type and MBD A140V. However, differential scanning calorimetry showed that the melting temperature of A140V constructs in complex with methylated DNA was reduced by ~7 °C, although circular dichroism showed no changes in the secondary structure content for A140V. A band shift analysis demonstrated that the larger fragment of MeCP2 (A140V) containing the transcriptional repression domain (TRD) destabilises the DNA binding. These results suggest that the solution structure of MBD A140V may differ from the wild-type MBD although no changes in the biochemical properties of X-ray A140V were observed. PMID:27502833

  5. Supramolecular Affinity Chromatography for Methylation-Targeted Proteomics.

    PubMed

    Garnett, Graham A E; Starke, Melissa J; Shaurya, Alok; Li, Janessa; Hof, Fraser

    2016-04-01

    Proteome-wide studies of post-translationally methylated species using mass spectrometry are complicated by high sample diversity, competition for ionization among peptides, and mass redundancies. Antibody-based enrichment has powered methylation proteomics until now, but the reliability, pan-specificity, polyclonal nature, and stability of the available pan-specific antibodies are problematic and do not provide a standard, reliable platform for investigators. We have invented an anionic supramolecular host that can form host-guest complexes selectively with methyllysine-containing peptides and used it to create a methylysine-affinity column. The column resolves peptides on the basis of methylation-a feat impossible with a comparable commercial cation-exchange column. A proteolyzed nuclear extract was separated on the methyl-affinity column prior to standard proteomics analysis. This experiment demonstrates that such chemical methyl-affinity columns are capable of enriching and improving the analysis of methyllysine residues from complex protein mixtures. We discuss the importance of this advance in the context of biomolecule-driven enrichment methods. PMID:26973166

  6. Conservation of DNA Methylation Programming Between Mouse and Human Gametes and Preimplantation Embryos.

    PubMed

    White, Carlee R; MacDonald, William A; Mann, Mellissa R W

    2016-09-01

    In mice, assisted reproductive technologies (ARTs) applied during gametogenesis and preimplantation development can result in disruption of genomic imprinting. In humans, these technologies and/or subfertility have been linked to perturbations in genomic imprinting. To understand how ARTs and infertility affect DNA methylation, it is important to understand DNA methylation dynamics and the role of regulatory factors at these critical stages. Recent genome studies performed using mouse and human gametes and preimplantation embryos have shed light onto these processes. Here, we comprehensively review the current state of knowledge regarding global and imprinted DNA methylation programming in the mouse and human. Available data highlight striking similarities in mouse and human DNA methylation dynamics during gamete and preimplantation development. Just as fascinating, these studies have revealed sex-, gene-, and allele-specific differences in DNA methylation programming, warranting future investigation to untangle the complex regulation of DNA methylation dynamics during gamete and preimplantation development.

  7. 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

  8. Synthesis, crystal structures, and biological evaluation of Cu(II) and Zn(II) complexes of 2-benzoylpyridine Schiff bases derived from S-methyl- and S-phenyldithiocarbazates.

    PubMed

    Li, Ming Xue; Zhang, Li Zhi; Chen, Chun Ling; Niu, Jing Yang; Ji, Bian Sheng

    2012-01-01

    Two NNS tridentate Schiff base ligands of 2-benzoylpyridine S-methyldithiocarbazate (HL(1)) and 2-benzoylpyridine S-phenyldithiocarbazate (HL(2)) and their transition metal complexes [Cu(2)(L(1))(2)(CH(3)COO)](ClO(4)) (1), [Zn(2)(L(1))(2)(ClO(4))(2)] (2), [Zn(L(2))(2)](3) have been prepared and characterized by elemental analysis, IR, MS, NMR and single-crystal X-ray diffraction studies. In the solid state, each of two Schiff bases remains in its thione tautomeric form with the thione sulfur atom trans to the azomethine nitrogen atom. Under similar prepared conditions, three new complexes showed distinctly different coordination modes depending on their coordinating preferences. Each copper atom in S-bridged dinuclear complex [Cu(2)(L(1))(2)(CH(3)COO)](ClO(4)) (1) is surrounded by five donor atoms in a square-pyramidal fashion (4+1). [Zn(2)(L(1))(2)(ClO(4))(2)] (2) is a dimer in which each zinc atom adopts a seven-coordinate distorted pentagonal bipyramidal geometry, while mononuclear [Zn(L(2))(2)] (3) has octahedral coordination geometry. Biological studies, carried out in vitro against selected bacteria, fungi, and K562 leukaemia cell line, respectively, have shown that different substituted groups attached at the dithiocarbazate moieties and metals showed distinctive differences in the biological property. Zinc(II) complexes 2 and 3 could distinguish K562 leukaemia cell line from normal hepatocyte QSG7701 cell line. Effect of the title compounds on Mitochondria membrane potential (MMP) and PI-associated fluorescence intensity in K562 leukaemia cell line are also studied. The title compounds may exert their cytotoxicity activity via induced loss of MMP. PMID:22112848

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

    SciTech Connect

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

    2015-01-20

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

  10. Density functional theory study of oxygen-atom insertion into metal-methyl bonds of iron(II), ruthenium(II), and osmium(II) complexes: study of metal-mediated C-O bond formation.

    PubMed

    Pardue, Daniel B; Mei, Jiajun; Cundari, Thomas R; Gunnoe, T Brent

    2014-03-17

    Metal-mediated C-O bond formation is a key step in hydrocarbon oxygenation catalytic cycles; however, few examples of this reaction have been reported for low-oxidation-state complexes. Oxygen insertion into a metal-carbon bond of Cp*M(CO)(OPy)R (Cp* = η(5)-pentamethylcyclopentadienyl; R = Me, Ph; OPy = pyridine-N-oxide; M = Fe, Ru, Os) was analyzed via density functional theory calculations. Oxygen-atom insertions through a concerted single-step organometallic Baeyer-Villiger pathway and a two-step pathway via a metal-oxo intermediate were studied; calculations predict that the former pathway was lower in energy. The results indicated that functionalization of M-R to M-OR (R = Me, Ph) is plausible using iron(II) complexes. Starting from Cp*Fe(CO)(OPy)Ph, the intermediate Fe-oxo showed oxyl character and, thus, is best considered an Fe(III)O(•-) complex. Oxidation of the π-acid ancillary ligand CO was facile. Substitutions of CO with dimethylamide and NH3 were calculated to lower the activation barrier by ∼1-2 kcal/mol for formation of the Fe(III)O(•-) intermediate, whereas a chloride ligand raised the activation barrier to 26 kcal/mol from 22.9 kcal/mol. PMID:24571202

  11. Short and efficient synthetic route to methyl α-trioxacarcinoside B and anomerically activated derivatives.

    PubMed

    Magauer, Thomas; Myers, Andrew G

    2011-10-21

    A 9-step synthetic route to the complex carbohydrate methyl α-trioxacarcinoside B from 2-acetylfuran is described. Anomerically activated forms, including 1-phenylthio, 1-O-(4'-pentenyl), 1-fluoro, and 1-O-acetyl derivatives are also prepared.

  12. 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.

  13. 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

  14. CpG methylation increases the DNA binding of 9-aminoacridine carboxamide Pt analogues.

    PubMed

    Kava, Hieronimus W; Murray, Vincent

    2016-10-01

    This study investigated the effect of CpG methylation on the DNA binding of cisplatin analogues with an attached aminoacridine intercalator. DNA-targeted 9-aminoacridine carboxamide Pt complexes are known to bind at 5'-CpG sequences. Their binding to methylated and non-methylated 5'-CpG sequences was determined and compared with cisplatin. The damage profiles of each platinum compound were quantified via a polymerase stop assay with fluorescently labelled primers and capillary electrophoresis. Methylation at 5'-CpG was shown to significantly increase the binding intensity for the 9-aminoacridine carboxamide compounds, whereas no significant increase was found for cisplatin. 5'-CpG methylation had the largest effect on the 9-ethanolamine-acridine carboxamide Pt complex, followed by the 9-aminoacridine carboxamide Pt complex and the 7-fluoro complex. The methylation state of a cell's genome is important in maintaining normal gene expression, and is often aberrantly altered in cancer cells. An analogue of cisplatin which differentially targets methylated DNA may be able to improve its therapeutic activity, or alter its range of targets and evade the chemoresistance which hampers cisplatin efficacy in clinical use. PMID:27567075

  15. 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.

  16. Genetic and environmental impacts on DNA methylation levels in twins.

    PubMed

    Yet, Idil; Tsai, Pei-Chien; Castillo-Fernandez, Juan E; Carnero-Montoro, Elena; Bell, Jordana T

    2016-01-01

    Epigenetics describes the study of cellular modifications that can modify the expression of genes without changing the DNA sequence. DNA methylation is one of the most stable and prevalent epigenetic mechanisms. Twin studies have been a valuable model for unraveling the genetic and epigenetic epidemiology of complex traits, and now offer a potential to dissect the factors that impact DNA methylation variability and its biomedical significance. The twin design specifically allows for the study of genetic, environmental and lifestyle factors, and their potential interactions, on epigenetic profiles. Furthermore, genetically identical twins offer a unique opportunity to assess nongenetic impacts on epigenetic profiles. Here, we summarize recent findings from twin studies of DNA methylation profiles across tissues, to define current knowledge regarding the genetic and nongenetic factors that influence epigenetic variation. PMID:26678685

  17. DNA methylation in inflammatory bowel disease and beyond

    PubMed Central

    Low, Daren; Mizoguchi, Atsushi; Mizoguchi, Emiko

    2013-01-01

    Inflammatory bowel disease (IBD) is a consequence of the complex, dysregulated interplay between genetic predisposition, environmental factors, and microbial composition in the intestine. Despite a great advancement in identifying host-susceptibility genes using genome-wide association studies (GWAS), the majority of IBD cases are still underrepresented. The immediate challenge in post-GWAS era is to identify other causative genetic factors of IBD. DNA methylation has received increasing attention for its mechanistical role in IBD pathogenesis. This stable, yet dynamic DNA modification, can directly affect gene expression that have important implications in IBD development. The alterations in DNA methylation associated with IBD are likely to outset as early as embryogenesis all the way until old-age. In this review, we will discuss the recent advancement in understanding how DNA methylation alterations can contribute to the development of IBD. PMID:23983426

  18. Synthesis, spectral and quantum chemical studies and use of (E)-3-[(3,5-bis(trifluoromethyl)phenylimino)methyl]benzene-1,2-diol and its Ni(II) and Cu(II) complexes as an anion sensor, DNA binding, DNA cleavage, anti-microbial, anti-mutagenic and anti-cancer agent

    NASA Astrophysics Data System (ADS)

    Ünver, Hüseyin; Boyacıoğlu, Bahadır; Zeyrek, Celal Tuğrul; Yıldız, Mustafa; Demir, Neslihan; Yıldırım, Nuray; Karaosmanoğlu, Oğuzhan; Sivas, Hülya; Elmalı, Ayhan

    2016-12-01

    We report the synthesis of a novel Schiff base (E)-3-[(3,5-bis(trifluoromethyl) phenylimino)methyl] benzene-1,2-diol from the reaction of 2,3-dihydroxybenzaldehyde with 3,5-bis(trifluoromethyl)aniline, and its Ni(II) and Cu(II) complexes. The molecular structure of the Schiff base was experimentally determined using X-ray single-crystal data and was compared to the structure predicted by theoretical calculations using density functional theory (DFT), Hartree-Fock (HF) and Möller-Plesset second-order perturbation (MP2). In addition, nonlinear optical (NLO) effects of the compound was predicted using DFT. The antimicrobial activities of the compounds were investigated for their minimum inhibitory concentration. UV-Vis spectroscopy studies of the interactions between the compounds and calf thymus DNA (CT-DNA) showed that the compounds interacts with CT-DNA via intercalative binding. A DNA cleavage study showed that the Cu(II) complex cleaved DNA without any external agents. The compounds inhibited the base pair mutation in the absence of S9 with high inhibition rate. In addition, in vitro cytotoxicity of the Ni(II) complex towards HepG2 cell line was assayed by the MTT method. Also, the colorimetric response of the Schiff base in DMSO to the addition of equivalent amount of anions (F-, Br-, I-, CN-, SCN-, ClO4-, HSO4-, AcO-, H2PO4-, N3- and OH-) was investigated. In this regard, while the addition of F-, CN-, AcO- and OH- anions into the solution containing Schiff base resulted in a significant color change, the addition of Br-, I-, SCN-, ClO4-, HSO4-, H2PO4- and N3- anions resulted in no color change. The most discernable color change in the Schiff base was caused by CN-, which demonstrated that the ligand can be used to selectively detect CN-.

  19. 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.

  20. 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

  1. 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

  2. Anticancer activity of methyl-substituted oxaliplatin analogs.

    PubMed

    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

    2012-05-01

    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.

  3. 3-Methyl-1-butanol Biosynthesis in an Engineered Corynebacterium glutamicum.

    PubMed

    Xiao, Shiyuan; Xu, Jingliang; Chen, Xiaoyan; Li, Xiekun; Zhang, Yu; Yuan, Zhenhong

    2016-05-01

    Biofuel offers a promising solution to the adverse environmental problems and depletion in reserves of fossil fuels. Higher alcohols including 3-methyl-1-butanol were paid much more attention as fuel substitute in recent years, due to its similar properties to gasoline. In the present work, 3-methyl-1-butanol production in engineered Corynebacterium glutamicum was studied. α-Ketoisovalerate decarboxylase gene (kivd) from Lactococcus lactis combined with alcohol dehydrogenase gene (adh2, adhA, and adh3) from three organisms were overexpressed in C. glutamicum. Enzymatic assay and alcohol production results showed that adh3 from Zymomonas mobilis was the optimum candidate for 3-methyl-1-butanol production in C. glutamicum. The recombinant with kivd and adh3 could produce 0.182 g/L of 3-methyl-1-butanol and 0.144 g/L of isobutanol after 12 h of incubation. Further inactivation of the E1 subunit of pyruvate dehydrogenase complex gene (aceE) and lactic dehydrogenase gene (ldh) in the above C. glutamicum strain would improve the 3-Methyl-1-butanol titer to 0.497 g/L after 12 h of incubation. PMID:26961908

  4. SNP-Based Quantification of Allele-Specific DNA Methylation Patterns by Pyrosequencing®.

    PubMed

    Busato, Florence; Tost, Jörg

    2015-01-01

    The analysis of allele-specific DNA methylation patterns has recently attracted much interest as loci of allele-specific DNA methylation overlap with known risk loci for complex diseases and the analysis might contribute to the fine-mapping and interpretation of non-coding genetic variants associated with complex diseases and improve the understanding between genotype and phenotype. In the presented protocol, we present a method for the analysis of DNA methylation patterns on both alleles separately using heterozygous Single Nucleotide Polymorphisms (SNPs) as anchor for allele-specific PCR amplification followed by analysis of the allele-specific DNA methylation patterns by Pyrosequencing(®). Pyrosequencing is an easy-to-handle, quantitative real-time sequencing method that is frequently used for genotyping as well as for the analysis of DNA methylation patterns. The protocol consists of three major steps: (1) identification of individuals heterozygous for a SNP in a region of interest using Pyrosequencing; (2) analysis of the DNA methylation patterns surrounding the SNP on bisulfite-treated DNA to identify regions of potential allele-specific DNA methylation; and (3) the analysis of the DNA methylation patterns associated with each of the two alleles, which are individually amplified using allele-specific PCR. The enrichment of the targeted allele is re-enforced by modification of the allele-specific primers at the allele-discriminating base with Locked Nucleic Acids (LNA). For the proof-of-principle of the developed approach, we provide assay details for three imprinted genes (IGF2, IGF2R, and PEG3) within this chapter. The mean of the DNA methylation patterns derived from the individual alleles corresponds well to the overall DNA methylation patterns and the developed approach proved more reliable compared to other protocols for allele-specific DNA methylation analysis.

  5. Identification and Functional Relevance of de novo DNA Methylation in Cancerous B-Cell Populations

    PubMed Central

    Wang, Xiao-Ming; Greiner, Timothy C.; Bibikova, Marina; Pike, Brian L.; Siegmund, Kimberly D.; Sinha, Uttam K.; Müschen, Markus; Jaeger, Erich B.; Weisenburger, Dennis J.; Chan, Wing C.; Shibata, Darryl; Fan, Jian-Bing; Hacia, Joseph G.

    2011-01-01

    Epigenetic remodeling is a hallmark of cancer, with the frequent acquisition of de novo DNA methylation in CpG islands. However, the functional relevance of de novo DNA methylation in cancer is less well-defined. To begin to address this issue in B-cells, we used BeadArray assays to survey the methylation status of 1,500 cancer-related CpG loci in two molecular subtypes of diffuse large B-cell lymphoma (ABC-DLBCL and GCB-DLBCL) and cognate normal B-cell populations. We identified 81 loci that showed frequent de novo DNA methylation in GCB-DLBCL and 67 loci that showed frequent de novo DNA methylation in ABC-DLBCL. These de novo methylated CpG loci included reported targets of polycomb repressive complexes (PRC) in stem cells. All candidate loci in GCB-DLBCL are proximal to genes that are poorly expressed or silent in purified normal germinal center (GC) B-cells. This is consistent with the hypothesis that de novo DNA methylation in cancer is more frequently involved in the maintenance rather than the initiation of gene silencing (de novo repression). This suggests that epigenetic switching occurs during tumorigenesis with de novo DNA methylation locking in gene silencing normally mediated by transcriptional repressors. Furthermore, we propose that similar to de novo genetic mutations, the majority of de novo DNA methylation events observed in tumors are passengers not causally involved in tumorigenesis. PMID:20069569

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

    PubMed

    Brady, Pamlea N; Macnaughtan, Megan A

    2015-12-15

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

  7. 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.

  8. Corruption of the intra-gene DNA methylation architecture is a hallmark of cancer.

    PubMed

    Bartlett, Thomas E; Zaikin, Alexey; Olhede, Sofia C; West, James; Teschendorff, Andrew E; Widschwendter, Martin

    2013-01-01

    Epigenetic processes--including DNA methylation--are increasingly seen as having a fundamental role in chronic diseases like cancer. It is well known that methylation levels at particular genes or loci differ between normal and diseased tissue. Here we investigate whether the intra-gene methylation architecture is corrupted in cancer and whether the variability of levels of methylation of individual CpGs within a defined gene is able to discriminate cancerous from normal tissue, and is associated with heterogeneous tumour phenotype, as defined by gene expression. We analysed 270985 CpGs annotated to 18272 genes, in 3284 cancerous and 681 normal samples, corresponding to 14 different cancer types. In doing so, we found novel differences in intra-gene methylation pattern across phenotypes, particularly in those genes which are crucial for stem cell biology; our measures of intra-gene methylation architecture are a better determinant of phenotype than measures based on mean methylation level alone (K-S test [Formula: see text] in all 14 diseases tested). These per-gene methylation measures also represent a considerable reduction in complexity, compared to conventional per-CpG beta-values. Our findings strongly support the view that intra-gene methylation architecture has great clinical potential for the development of DNA-based cancer biomarkers.

  9. Water mediated ligand functional group cooperativity: the contribution of a methyl group to binding affinity is enhanced by a COO(-) group through changes in the structure and thermodynamics of the hydration waters of ligand-thermolysin complexes.

    PubMed

    Nasief, Nader N; Tan, Hongwei; Kong, Jing; Hangauer, David

    2012-10-11

    Ligand functional groups can modulate the contributions of one another to the ligand-protein binding thermodynamics, producing either positive or negative cooperativity. Data presented for four thermolysin phosphonamidate inhibitors demonstrate that the differential binding free energy and enthalpy caused by replacement of a H with a Me group, which binds in the well-hydrated S2' pocket, are more favorable in presence of a ligand carboxylate. The differential entropy is however less favorable. Dissection of these differential thermodynamic parameters, X-ray crystallography, and density-functional theory calculations suggest that these cooperativities are caused by variations in the thermodynamics of the complex hydration shell changes accompanying the H→Me replacement. Specifically, the COO(-) reduces both the enthalpic penalty and the entropic advantage of displacing water molecules from the S2' pocket and causes a subsequent acquisition of a more enthalpically, less entropically, favorable water network. This study contributes to understanding the important role water plays in ligand-protein binding.

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

    NASA Astrophysics Data System (ADS)

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

    2009-02-01

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

  11. 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

  12. 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.

  13. 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

  14. Photoaffinity labelling of methyltransferase enzymes with S-adenosylmethionine: effects of methyl acceptor substrates.

    PubMed

    Hurst, J H; Billingsley, M L; Lovenberg, W

    1984-07-31

    Radioactivity from 3H-[methyl]-S-adenosyl-L-methionine (AdoMet) was covalently bound to protein-O-carboxylmethyltransferase and phenylethanolamine N-methyltransferase following 10-15 min irradiation by short-wave ultraviolet light. This photoaffinity binding of 3H-[methyl]-AdoMet was blocked by S-adenosylhomocysteine and sinefungin, but was not affected by 5 mM dithiothreitol. The binding was also inhibited by including methyl acceptors such as calmodulin (protein-O-carboxylmethyltransferase) or phenylethanolamine (phenylethanolamine N-methyltransferase) in the photoaffinity incubation. Staphlococcus V8 protease digests of 3H-[methyl]-AdoMet/enzyme complexes revealed that the primary structure around the AdoMet binding site is different in these two enzymes. Thus, protein-O-carboxylmethyltransferase, a large molecule methyltransferase, can covalently bind 3H-[methyl]-AdoMet in a manner similar to that of phenylethanolamine-N-methyltransferase.

  15. Exploring genome wide bisulfite sequencing for DNA methylation analysis in livestock: a technical assessment.

    PubMed

    Doherty, Rachael; Couldrey, Christine

    2014-01-01

    Recent advances made in "omics" technologies are contributing to a revolution in livestock selection and breeding practices. Epigenetic mechanisms, including DNA methylation are important determinants for the control of gene expression in mammals. DNA methylation research will help our understanding of how environmental factors contribute to phenotypic variation of complex production and health traits. High-throughput sequencing is a vital tool for the comprehensive analysis of DNA methylation, and bisulfite-based strategies coupled with DNA sequencing allows for quantitative, site-specific methylation analysis at the genome level or genome wide. Reduced representation bisulfite sequencing (RRBS) and more recently whole genome bisulfite sequencing (WGBS) have proven to be effective techniques for studying DNA methylation in both humans and mice. Here we report the development of RRBS and WGBS for use in sheep, the first application of this technology in livestock species. Important technical issues associated with these methodologies including fragment size selection and sequence depth are examined and discussed. PMID:24860595

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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....

  2. 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...

  3. Conversion of polyhydroxyalkanoates to methyl crotonate using whole cells.

    PubMed

    Spekreijse, J; Holgueras Ortega, J; Sanders, J P M; Bitter, J H; Scott, E L

    2016-07-01

    Isolated polyhydroxyalkanoates (PHA) can be used to produce biobased bulk chemicals. However, isolation is complex and costly. To circumvent this, whole cells containing PHA may be used. Here, PHA containing 3-hydroxybutyrate and small amounts of 3-hydroxyvalerate was produced from wastewater and used in the conversion of the 3-hydroxybutyrate monomer to methyl crotonate. Due to the increased complexity of whole cell reaction mixtures compared to pure PHA, the effect of 3-hydroxyvalerate content, magnesium salts and water content was studied in order to evaluate the need for downstream processing. A water content up to 20% and the presence of 3-hydroxyvalerate have no influence on the conversion of the 3-hydroxybutyrate to methyl crotonate. The presence of Mg(2+)-ions resulted either in an increased yield or in byproduct formation depending on the counter ion. Overall, it is possible to bypass a major part of the downstream processing of PHA for the production of biobased chemicals. PMID:27023381

  4. Electronic transport in methylated fragments of DNA

    SciTech Connect

    Almeida, M. L. de; 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.; Moura, F. A. B. F. de; Lyra, M. L.

    2015-11-16

    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.

  5. 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.

  6. 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…

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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.

  14. 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.

  15. ELUCIDATING THE PATHWAY FOR ARSENIC METHYLATION

    EPA Science Inventory

    Enzymatically-catalyzed methylation of arsenic is part of a metabolic pathway that converts inorganic arsenic into methylated products. Hence, in humans chronically exposed to inorganic arsenic, methyl and dimethyl arsenic account for most of the arsenic that is excreted in the ...

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

    PubMed Central

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

    2015-01-01

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

  17. 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

  18. The relationship between DNA methylation and telomere length in dyskeratosis congenita.

    PubMed

    Gadalla, Shahinaz M; Katki, Hormuzd A; Shebl, Fatma M; Giri, Neelam; Alter, Blanche P; Savage, Sharon A

    2012-02-01

    The regulation of telomere length (TL) is a complex process, requiring the telomerase enzyme complex and numerous regulatory proteins. Epigenetic regulation may also be important in telomere maintenance. Specifically, methylation at subtelomeres is associated with changes in TL in vitro and in mouse models. Dyskeratosis congenita (DC) is an inherited bone marrow failure syndrome characterized by exceedingly short telomeres and mutations in telomere biology genes. To understand the interaction between methylation and TL in humans, we measured LINE-1, pericentromeric (NBL2), and subtelomeric (D4Z4) methylation in peripheral blood DNA derived from 40 patients with DC and 51 mutation-negative relatives. Pearson's correlation coefficient and linear regression models were used to evaluate the relationship between age-standardized lymphocyte TL measured by flow FISH and % DNA methylation. No differences in % subtelomeric, LINE-1, or pericentromeric methylation between patients with DC and relatives were noted except for an increase in % subtelomeric methylation in DC patients with a telomerase-complex mutation (TERC, TERT, DKC1, or TCAB1) (63.0% in DC vs. 61.8% in relatives, P = 0.03). Positive correlations between TL and DNA methylation at LINE-1 (r = 0.39, P = 0.01) and subtelomeric (r = 0.32, P = 0.05) sites were present in patients with DC. The positive correlation between TL and % LINE-1 methylation was restricted to TINF2 mutations. In contrast, statistically nonsignificant inverse correlations between TL and % LINE-1 (r = -0.17), subtelomeric (r = -0.20) were present in unaffected relatives. This study suggests an interaction between TL and both subtelomeric and LINE-1 methylation, which may be altered based on mutation status of telomere biology genes. PMID:21981348

  19. Crystal structure of tris-(di-methyl-amido-κN)-bis-(di-methyl-amine-κN)-zirconium(IV) iodide.

    PubMed

    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 mol-ecular structure of tris-(di-methyl-amido)-bis-(di-methyl-amine)-zirconium(IV) iodide, [Zr(C2H6N)3(C2H7N)2]I. The bond lengths and bond angles are consistent with a slightly distorted trigonal-bipyramidal coordination geometry around the metal atom. N⋯I contacts of 3.6153 (15) and 3.5922 (14) Å are consistent with the presence of N-H⋯I inter-actions. These N-H⋯I inter-actions link the complex cations and iodide anions into extended chains that propagate parallel to the a axis. PMID:26870590

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

    PubMed

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

    2014-04-01

    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.

  1. Genome-Wide DNA Methylation Patterns and Transcription Analysis in Sheep Muscle

    PubMed Central

    Couldrey, Christine; Brauning, Rudiger; Bracegirdle, Jeremy; Maclean, Paul; Henderson, Harold V.; McEwan, John C.

    2014-01-01

    DNA methylation plays a central role in regulating many aspects of growth and development in mammals through regulating gene expression. The development of next generation sequencing technologies have paved the way for genome-wide, high resolution analysis of DNA methylation landscapes using methodology known as reduced representation bisulfite sequencing (RRBS). While RRBS has proven to be effective in understanding DNA methylation landscapes in humans, mice, and rats, to date, few studies have utilised this powerful method for investigating DNA methylation in agricultural animals. Here we describe the utilisation of RRBS to investigate DNA methylation in sheep Longissimus dorsi muscles. RRBS analysis of ∼1% of the genome from Longissimus dorsi muscles provided data of suitably high precision and accuracy for DNA methylation analysis, at all levels of resolution from genome-wide to individual nucleotides. Combining RRBS data with mRNAseq data allowed the sheep Longissimus dorsi muscle methylome to be compared with methylomes from other species. While some species differences were identified, many similarities were observed between DNA methylation patterns in sheep and other more commonly studied species. The RRBS data presented here highlights the complexity of epigenetic regulation of genes. However, the similarities observed across species are promising, in that knowledge gained from epigenetic studies in human and mice may be applied, with caution, to agricultural species. The ability to accurately measure DNA methylation in agricultural animals will contribute an additional layer of information to the genetic analyses currently being used to maximise production gains in these species. PMID:25010796

  2. Regulation of DNA methylation of Rasgrf1

    PubMed Central

    Yoon, Bong June; Herman, Herry; Sikora, Aimee; Smith, Laura T.; Plass, Christoph; Soloway, Paul D.

    2009-01-01

    In mammals, DNA is methylated at cytosines within CpG dinucleotides. Properly regulated methylation is crucial for normal development1,2. Inappropriate methylation may contribute to tumorigenesis by silencing tumor-suppressor genes3-10 or by activating growth-stimulating genes11-13. Although many genes have been identified that acquire methylation and whose expression is methylation-sensitive14,15, little is known about how DNA methylation is controlled16. We have identified a DNA sequence that regulates establishment of DNA methylation in the male germ line at Rasgrf1. In mice, the imprinted Rasgrf1 locus is methylated on the paternal allele within a differentially methylated domain (DMD) 30 kbp 5′ of the promoter. Expression is exclusively from the paternal allele in neonatal brain17. Methylation is regulated by a repeated sequence, consisting of a 41-mer repeated 40 times, found immediately 3′ of the DMD. This sequence is present in organisms in which Rasgrf1 is imprinted18. In addition, DMD methylation is required for imprinted Rasgrf1 expression. Together the DMD and repeat element constitute a binary switch that regulates imprinting at the locus. PMID:11753386

  3. Increased DNA methylation in the suicide brain.

    PubMed

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

    2014-09-01

    Clinical studies find that childhood adversity and stressful 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 < 2.2 x 10(-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.

  4. Microbial mercury methylation in Antarctic sea ice.

    PubMed

    Gionfriddo, Caitlin M; Tate, Michael T; Wick, Ryan R; Schultz, Mark B; Zemla, Adam; Thelen, Michael P; Schofield, Robyn; Krabbenhoft, David P; Holt, Kathryn E; Moreau, John W

    2016-01-01

    Atmospheric deposition of mercury onto sea ice and circumpolar sea water provides mercury for microbial methylation, and contributes to the bioaccumulation of the potent neurotoxin methylmercury in the marine food web. Little is known about the abiotic and biotic controls on microbial mercury methylation in polar marine systems. However, mercury methylation is known to occur alongside photochemical and microbial mercury reduction and subsequent volatilization. Here, we combine mercury speciation measurements of total and methylated mercury with metagenomic analysis of whole-community microbial DNA from Antarctic snow, brine, sea ice and sea water to elucidate potential microbially mediated mercury methylation and volatilization pathways in polar marine environments. Our results identify the marine microaerophilic bacterium Nitrospina as a potential mercury methylator within sea ice. Anaerobic bacteria known to methylate mercury were notably absent from sea-ice metagenomes. We propose that Antarctic sea ice can harbour a microbial source of methylmercury in the Southern Ocean. PMID:27670112

  5. Role of the pks15/1 gene in the biosynthesis of phenolglycolipids in the Mycobacterium tuberculosis complex. Evidence that all strains synthesize glycosylated p-hydroxybenzoic methyl esters and that strains devoid of phenolglycolipids harbor a frameshift mutation in the pks15/1 gene.

    PubMed

    Constant, Patricia; Perez, Esther; Malaga, Wladimir; Lanéelle, Marie-Antoinette; Saurel, Olivier; Daffé, Mamadou; Guilhot, Christophe

    2002-10-11

    Diesters of phthiocerol and phenolphthiocerol are important virulence factors of Mycobacterium tuberculosis and Mycobacterium leprae, the two main mycobacterial pathogens in humans. They are both long-chain beta-diols, and their biosynthetic pathway is beginning to be elucidated. Although the two classes of molecules share a common lipid core, phthiocerol diesters have been found in all the strains of the M. tuberculosis complex examined although phenolphthiocerol diesters are produced by only a few groups of strains. To address the question of the origin of this diversity 8 reference strains and 10 clinical isolates of M. tuberculosis were analyzed. We report the presence of glycosylated p-hydroxybenzoic acid methyl esters, structurally related to the type-specific phenolphthiocerol glycolipids, in the culture media of all reference strains of M. tuberculosis, suggesting that the strains devoid of phenolphthiocerol derivatives are unable to elongate the putative p-hydroxybenzoic acid precursor. We also show that all the strains of M. tuberculosis examined and deficient in the production of phenolphthiocerol derivatives are natural mutants with a frameshift mutation in pks15/1 whereas a single open reading frame for pks15/1 is found in Mycobacterium bovis BCG, M. leprae, and strains of M. tuberculosis that produce phenolphthiocerol derivatives. Complementation of the H37Rv strain of M. tuberculosis, which is devoid of phenolphthiocerol derivatives, with the fused pks15/1 gene from M. bovis BCG restored phenolphthiocerol glycolipids production. Conversely, disruption of the pks15/1 gene in M. bovis BCG led to the abolition of the synthesis of type-specific phenolphthiocerol glycolipid. These data indicate that Pks15/1 is involved in the elongation of p-hydroxybenzoic acid to give p-hydroxyphenylalkanoates, which in turn are converted, presumably by the PpsA-E synthase, to phenolphthiocerol derivatives.

  6. Predicting aberrant CpG island methylation

    PubMed Central

    Feltus, F. A.; Lee, E. K.; Costello, J. F.; Plass, C.; Vertino, P. M.

    2003-01-01

    Epigenetic silencing associated with aberrant methylation of promoter region CpG islands is one mechanism leading to loss of tumor suppressor function in human cancer. Profiling of CpG island methylation indicates that some genes are more frequently methylated than others, and that each tumor type is associated with a unique set of methylated genes. However, little is known about why certain genes succumb to this aberrant event. To address this question, we used Restriction Landmark Genome Scanning to analyze the susceptibility of 1,749 unselected CpG islands to de novo methylation driven by overexpression of DNA cytosine-5-methyltransferase 1 (DNMT1). We found that although the overall incidence of CpG island methylation was increased in cells overexpressing DNMT1, not all loci were equally affected. The majority of CpG islands (69.9%) were resistant to de novo methylation, regardless of DNMT1 overexpression. In contrast, we identified a subset of methylation-prone CpG islands (3.8%) that were consistently hypermethylated in multiple DNMT1 overexpressing clones. Methylation-prone and methylation-resistant CpG islands were not significantly different with respect to size, C+G content, CpG frequency, chromosomal location, or promoter association. We used DNA pattern recognition and supervised learning techniques to derive a classification function based on the frequency of seven novel sequence patterns that was capable of discriminating methylation-prone from methylation-resistant CpG islands with 82% accuracy. The data indicate that CpG islands differ in their intrinsic susceptibility to de novo methylation, and suggest that the propensity for a CpG island to become aberrantly methylated can be predicted based on its sequence context. PMID:14519846

  7. First evidence of DNA methylation in insect Tribolium castaneum: environmental regulation of DNA methylation within heterochromatin.

    PubMed

    Feliciello, Isidoro; Parazajder, Josip; Akrap, Ivana; Ugarković, Durđica

    2013-05-01

    DNA methylation has been studied in many eukaryotic organisms, in particular vertebrates, and was implicated in developmental and phenotypic variations. Little is known about the role of DNA methylation in invertebrates, although insects are considered as excellent models for studying the evolution of DNA methylation. In the red flour beetle, Tribolium castaneum (Tenebrionidae, Coleoptera), no evidence of DNA methylation has been found till now. In this paper, a cytosine methylation in Tribolium castaneum embryos was detected by methylation sensitive restriction endonucleases and immuno-dot blot assay. DNA methylation in embryos is followed by a global demethylation in larvae, pupae and adults. DNA demethylation seems to proceed actively through 5-hydroxymethylcytosine, most probably by the action of TET enzyme. Bisulfite sequencing of a highly abundant satellite DNA located in pericentromeric heterochromatin revealed similar profile of cytosine methylation in adults and embryos. Cytosine methylation was not only restricted to CpG sites but was found at CpA, CpT and CpC sites. In addition, complete cytosine demethylation of heterochromatic satellite DNA was induced by heat stress. The results reveal existence of DNA methylation cycling in T. castaneum ranging from strong overall cytosine methylation in embryos to a weak DNA methylation in other developmental stages. Nevertheless, DNA methylation is preserved within heterochromatin during development, indicating its role in heterochromatin formation and maintenance. It is, however, strongly affected by heat stress, suggesting a role for DNA methylation in heterochromatin structure modulation during heat stress response.

  8. 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.

  9. The vegetarian lifestyle and DNA methylation.

    PubMed

    Geisel, Jürgen; Schorr, Heike; Bodis, Marion; Isber, Sonia; Hübner, Ulrich; Knapp, Jean-Pierre; Obeid, Rima; Herrmann, Wolfgang

    2005-01-01

    Vegetarians have a lower intake of vitamin B12 than omnivores do. Vitamin B12 deficiency (holotranscobalamin II <35 pmol/L or methylmalonic acid >271 nmol/L) was found in 58% of 71 vegetarians studied. Higher homocysteine levels (>12 micromol/L) found in 45% indicate disturbed remethylation of homocysteine to methionine. The methylation of DNA is strongly linked to homocysteine metabolism. Since DNA methylation is an important epigenetic factor in the regulation of gene expression, alteration of the methylation pattern has been associated with aging, cancer, atherosclerosis and other diseases. Three observations indicate that DNA methylation could be diminished by a vegetarian lifestyle. The vegetarian diet has a low content of methionine, remethylation of homocysteine is reduced by vitamin B12 deficiency and elevated homocysteine levels can induce the generation of S-adenosylhomocysteine (SAH), a potent inhibitor of methyltransferases. In our study we observed a significant correlation between SAH and whole-genome methylation (r=-0.36, p<0.01). This observation underlines the role of SAH as a potent inhibitor of methyltransferases. The methylation status was not correlated with homocysteine or S-adenosylemethionine (SAM). These results indicate that the degree of methylation does not depend on the supply of methyl groups and that the reverse generation of SAH has no influence. In addition to whole-genome methylation, the specific promoter methylation of the p66Shc gene was studied. However, the latter did not correlate with SAH, SAM or homocysteine. Obviously, the promoter methylation of the p66Shc gene is controlled in a specific way, without following the general regulating influence of SAH. In conclusion, an inhibitory effect of SAH on whole-genome methylation was found, but from our data no interaction between vegetarian lifestyle and DNA methylation could be determined.

  10. 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.

  11. Regulation of HIF-1α stability by lysine methylation

    PubMed Central

    Baek, Sung Hee; Kim, Keun Il

    2016-01-01

    The level and activity of critical regulatory proteins in cells are tightly controlled by several tiers of post-translational modifications. HIF-1α is maintained at low levels under normoxia conditions by the collaboration between PHD proteins and the VHL-containing E3 ubiquitin ligase complex. We recently identified a new physiologically relevant mechanism that regulates HIF-1α stability in the nucleus in response to cellular oxygen levels. This mechanism is based on the collaboration between the SET7/9 methyltransferase and the LSD1 demethylase. SET7/9 adds a methyl group to HIF-1α, which triggers degradation of the protein by the ubiquitin-proteasome system, whereas LSD1 removes the methyl group, leading to stabilization of HIF-1α under hypoxia conditions. In cells from knock-in mice with a mutation preventing HIF-1α methylation (Hif1αKA/KA), HIF-1α levels were increased in both normoxic and hypoxic conditions. Hif1αKA/KA knock-in mice displayed increased hematological parameters, such as red blood cell count and hemoglobin concentration. They also displayed pathological phenotypes; retinal and tumor-associated angiogenesis as well as tumor growth were increased in Hif1αKA/KA knock-in mice. Certain human cancer cells exhibit mutations that cause defects in HIF-1α methylation. In summary, this newly identified methylation-based regulation of HIF-1α stability constitutes another layer of regulation that is independent of previously identified mechanisms. [BMB Reports 2016; 49(5): 245-246] PMID:26973343

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

    PubMed Central

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

    2014-01-01

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

  13. The genetic basis for bacterial mercury methylation.

    PubMed

    Parks, Jerry M; Johs, Alexander; Podar, Mircea; Bridou, Romain; Hurt, Richard A; Smith, Steven D; Tomanicek, Stephen J; Qian, Yun; Brown, Steven D; Brandt, Craig C; Palumbo, Anthony V; Smith, Jeremy C; Wall, Judy D; Elias, Dwayne A; Liang, Liyuan

    2013-03-15

    Methylmercury is a potent neurotoxin produced in natural environments from inorganic mercury by anaerobic bacteria. However, until now the genes and proteins involved have remained unidentified. Here, we report a two-gene cluster, hgcA and hgcB, required for mercury methylation by Desulfovibrio desulfuricans ND132 and Geobacter sulfurreducens PCA. In either bacterium, deletion of hgcA, hgcB, or both genes abolishes mercury methylation. The genes encode a putative corrinoid protein, HgcA, and a 2[4Fe-4S] ferredoxin, HgcB, consistent with roles as a methyl carrier and an electron donor required for corrinoid cofactor reduction, respectively. Among bacteria and archaea with sequenced genomes, gene orthologs are present in confirmed methylators but absent in nonmethylators, suggesting a common mercury methylation pathway in all methylating bacteria and archaea sequenced to date.

  14. Wp specific methylation of highly proliferated LCLs.

    PubMed

    Park, Jung-Hoon; Jeon, Jae-Pil; Shim, Sung-Mi; Nam, Hye-Young; Kim, Joon-Woo; Han, Bok-Ghee; Lee, Suman

    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.

  15. 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

  16. DNA methylation: old dog, new tricks?

    PubMed

    Spruijt, Cornelia G; Vermeulen, Michiel

    2014-11-01

    DNA methylation is an epigenetic modification that is generally associated with repression of transcription initiation at CpG-island promoters. Here we argue that, on the basis of recent high-throughput genomic and proteomic screenings, DNA methylation can also have different outcomes, including activation of transcription. This is evidenced by the fact that transcription factors can interact with methylated DNA sequences. Furthermore, in certain cellular contexts, genes containing methylated promoters are highly transcribed. Interestingly, this uncoupling between methylated DNA and repression of transcription seems to be particularly evident in germ cells and pluripotent cells. Thus, contrary to previous assumptions, DNA methylation is not exclusively associated with repression of transcription initiation. PMID:25372310

  17. (State resolved studies of the methyl radical)

    SciTech Connect

    Houston, P.L.

    1991-01-01

    Reactions of methyl radicals play a major role in the combustion of nearly all hydrocarbon fuels. During the past three years, the objectives of our DOE supported research have been (1) to examine photodissociations producing methyl radicals in order to learn the internal and translational energy distributions of the products, and (2) to develop a capability to investigate important combustion reactions using these methyl radicals as reagents are summarized. The sources for methyl (and other) radicals that have been examined in our laboratory, and our progress in constructing an apparatus to investigate their reactions. Our group has performed detailed examination of four methyl sources: methyl iodide, acetone, acetaldehyde, and nitromethane. 24 refs., 9 figs.

  18. 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.

  19. Infant sex-specific placental cadmium and DNA methylation associations

    SciTech Connect

    Mohanty, April F.; Farin, Fred M.; Bammler, Theo K.; MacDonald, James W.; Afsharinejad, Zahra; Burbacher, Thomas M.; Siscovick, David S.; and others

    2015-04-15

    Background: Recent evidence suggests that maternal cadmium (Cd) burden and fetal growth associations may vary by fetal sex. However, mechanisms contributing to these differences are unknown. Objectives: Among 24 maternal-infant pairs, we investigated infant sex-specific associations between placental Cd and placental genome-wide DNA methylation. Methods: We used ANOVA models to examine sex-stratified associations of placental Cd (dichotomized into high/low Cd using sex-specific Cd median cutoffs) with DNA methylation at each cytosine-phosphate-guanine site or region. Statistical significance was defined using a false discovery rate cutoff (<0.10). Results: Medians of placental Cd among females and males were 5 and 2 ng/g, respectively. Among females, three sites (near ADP-ribosylation factor-like 9 (ARL9), siah E3 ubiquitin protein ligase family member 3 (SIAH3), and heparin sulfate (glucosamine) 3-O-sulfotransferase 4 (HS3ST4) and one region on chromosome 7 (including carnitine O-octanoyltransferase (CROT) and TP5S target 1 (TP53TG1)) were hypomethylated in high Cd placentas. Among males, high placental Cd was associated with methylation of three sites, two (hypomethylated) near MDS1 and EVI1 complex locus (MECOM) and one (hypermethylated) near spalt-like transcription factor 1 (SALL1), and two regions (both hypomethylated, one on chromosome 3 including MECOM and another on chromosome 8 including rho guanine nucleotide exchange factor (GEF) 10 (ARHGEF10). Differentially methylated sites were at or close to transcription start sites of genes involved in cell damage response (SIAH3, HS3ST4, TP53TG1) in females and cell differentiation, angiogenesis and organ development (MECOM, SALL1) in males. Conclusions: Our preliminary study supports infant sex-specific placental Cd-DNA methylation associations, possibly accounting for previously reported differences in Cd-fetal growth associations across fetal sex. Larger studies are needed to replicate and extend these

  20. N6-adenosine methylation in MiRNAs.

    PubMed

    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

  1. 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

  2. Notes on the role of dynamic DNA methylation in mammalian development.

    PubMed

    Bestor, Timothy H; Edwards, John R; Boulard, Mathieu

    2015-06-01

    It has been nearly 40 y since it was suggested that genomic methylation patterns could be transmitted via maintenance methylation during S phase and might play a role in the dynamic regulation of gene expression during development [Holliday R, Pugh JE (1975) Science 187(4173):226-232; Riggs AD (1975) Cytogenet Cell Genet 14(1):9-25]. This revolutionary proposal was justified by "... our almost complete ignorance of the mechanism for the unfolding of the genetic program during development" that prevailed at the time. Many correlations between transcriptional activation and demethylation have since been reported, but causation has not been demonstrated and to date there is no reasonable proof of the existence of a complex biochemical system that activates and represses genes via reversible DNA methylation. Such a system would supplement or replace the conserved web of transcription factors that regulate cellular differentiation in organisms that have unmethylated genomes (such as Caenorhaditis elegans and the Dipteran insects) and those that methylate their genomes. DNA methylation does have essential roles in irreversible promoter silencing, as in the monoallelic expression of imprinted genes, in the silencing of transposons, and in X chromosome inactivation in female mammals. Rather than reinforcing or replacing regulatory pathways that are conserved between organisms that have either methylated or unmethylated genomes, DNA methylation endows genomes with the ability to subject specific sequences to irreversible transcriptional silencing even in the presence of all of the factors required for their expression, an ability that is generally unavailable to organisms that have unmethylated genomes.

  3. 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

  4. Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1).

    PubMed

    Takeshita, Kohei; Suetake, Isao; Yamashita, Eiki; Suga, Michihiro; Narita, Hirotaka; Nakagawa, Atsushi; Tajima, Shoji

    2011-05-31

    Methylation of cytosine in DNA plays a crucial role in development through inheritable gene silencing. The DNA methyltransferase Dnmt1 is responsible for the propagation of methylation patterns to the next generation via its preferential methylation of hemimethylated CpG sites in the genome; however, how Dnmt1 maintains methylation patterns is not fully understood. Here we report the crystal structure of the large fragment (291-1620) of mouse Dnmt1 and its complexes with cofactor S-adenosyl-L-methionine and its product S-adenosyl-L-homocystein. Notably, in the absence of DNA, the N-terminal domain responsible for targeting Dnmt1 to replication foci is inserted into the DNA-binding pocket, indicating that this domain must be removed for methylation to occur. Upon binding of S-adenosyl-L-methionine, the catalytic cysteine residue undergoes a conformation transition to a catalytically competent position. For the recognition of hemimethylated DNA, Dnmt1 is expected to utilize a target recognition domain that overhangs the putative DNA-binding pocket. Taking into considerations the recent report of a shorter fragment structure of Dnmt1 that the CXXC motif positions itself in the catalytic pocket and prevents aberrant de novo methylation, we propose that maintenance methylation is a multistep process accompanied by structural changes. PMID:21518897

  5. 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.

  6. Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1)

    PubMed Central

    Takeshita, Kohei; Suetake, Isao; Yamashita, Eiki; Suga, Michihiro; Narita, Hirotaka; Nakagawa, Atsushi; Tajima, Shoji

    2011-01-01

    Methylation of cytosine in DNA plays a crucial role in development through inheritable gene silencing. The DNA methyltransferase Dnmt1 is responsible for the propagation of methylation patterns to the next generation via its preferential methylation of hemimethylated CpG sites in the genome; however, how Dnmt1 maintains methylation patterns is not fully understood. Here we report the crystal structure of the large fragment (291–1620) of mouse Dnmt1 and its complexes with cofactor S-adenosyl-L-methionine and its product S-adenosyl-L-homocystein. Notably, in the absence of DNA, the N-terminal domain responsible for targeting Dnmt1 to replication foci is inserted into the DNA-binding pocket, indicating that this domain must be removed for methylation to occur. Upon binding of S-adenosyl-L-methionine, the catalytic cysteine residue undergoes a conformation transition to a catalytically competent position. For the recognition of hemimethylated DNA, Dnmt1 is expected to utilize a target recognition domain that overhangs the putative DNA-binding pocket. Taking into considerations the recent report of a shorter fragment structure of Dnmt1 that the CXXC motif positions itself in the catalytic pocket and prevents aberrant de novo methylation, we propose that maintenance methylation is a multistep process accompanied by structural changes. PMID:21518897

  7. Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1).

    PubMed

    Takeshita, Kohei; Suetake, Isao; Yamashita, Eiki; Suga, Michihiro; Narita, Hirotaka; Nakagawa, Atsushi; Tajima, Shoji

    2011-05-31

    Methylation of cytosine in DNA plays a crucial role in development through inheritable gene silencing. The DNA methyltransferase Dnmt1 is responsible for the propagation of methylation patterns to the next generation via its preferential methylation of hemimethylated CpG sites in the genome; however, how Dnmt1 maintains methylation patterns is not fully understood. Here we report the crystal structure of the large fragment (291-1620) of mouse Dnmt1 and its complexes with cofactor S-adenosyl-L-methionine and its product S-adenosyl-L-homocystein. Notably, in the absence of DNA, the N-terminal domain responsible for targeting Dnmt1 to replication foci is inserted into the DNA-binding pocket, indicating that this domain must be removed for methylation to occur. Upon binding of S-adenosyl-L-methionine, the catalytic cysteine residue undergoes a conformation transition to a catalytically competent position. For the recognition of hemimethylated DNA, Dnmt1 is expected to utilize a target recognition domain that overhangs the putative DNA-binding pocket. Taking into considerations the recent report of a shorter fragment structure of Dnmt1 that the CXXC motif positions itself in the catalytic pocket and prevents aberrant de novo methylation, we propose that maintenance methylation is a multistep process accompanied by structural changes.

  8. 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.

  9. 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

  10. 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.

  11. Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more

    PubMed Central

    Marinus, Martin G.; Casadesus, Josep

    2010-01-01

    The Dam methylase of gamma-proteobacteria and the CcrM methylase of alpha-proteobacteria catalyze an identical reaction (methylation of adenosine moieties using S-adenosyl-methionine as methyl donor) at similar DNA targets (GATC and GANTC, respectively). Dam and CcrM are of independent evolutionary origin. Each may have evolved from an ancestral restriction-modification system that lost its restriction component, leaving an “orphan” methylase devoted solely to epigenetic genome modification. Formation of 6-methyladenine lowers the thermodynamic stability of DNA and changes DNA curvature. As a consequence, the methylation state of specific adenosine moieties can affect DNA-protein interactions. Well known examples include binding of the replication initiation complex to the methylated oriC, recognition of hemimethylated GATCs in newly replicated DNA by the MutHLS mismatch repair complex, and discrimination of methylation states in promoters and regulatory DNA motifs by RNA polymerase and transcription factors. In recent years, Dam and CcrM have been shown to play roles in host-pathogen interactions. These roles are diverse and only partially understood. Especially intriguing is the evidence that Dam methylation regulates virulence genes in E. coli, Salmonella, and Yersinia at the postranscriptional level. PMID:19175412

  12. 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.

  13. 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

  14. Determining DNA methylation profiles using sequencing.

    PubMed

    Feng, Suhua; Rubbi, Liudmilla; Jacobsen, Steven E; Pellegrini, Matteo

    2011-01-01

    Cytosine methylation is an epigenetic mark that has a significant impact on the regulation of transcription and replication of DNA. DNA methylation patterns are highly conserved across cell divisions and are therefore highly heritable. Furthermore, in multicellular organisms, DNA methylation patterning is a key determinant of cellular differentiation and tissue-specific expression patterns. Lastly, DNA demethylases can affect global levels of DNA methylation during specific stages of development. Bisulfite sequencing is considered the gold standard for measuring the methylation state of cytosines. Sodium bisulfite -converts unmethylated cytosines to uracils (which after PCR are converted to thymines), while leaving methylated cytosines unconverted. By mapping bisulfite treated DNA back to the original reference genome, it is then possible to determine the methylation state of individual cytosines. With the advent of next-generation sequencers during the past few years, it is now possible to determine the methylation state of an entire genome. Here, we describe in detail two protocols for preparing bisulfite treated libraries, which may be sequenced using Illumina GAII sequencers. The first of these uses premethylated adapters, which are not affected by bisulfite treatments, while the second uses a two-stage adapter strategy and does not require premethylation of the adapters. We also describe the specialized protocol for mapping bisulfite converted reads. These approaches allow one to determine the methylation state of each cytosine in the genome. PMID:21431774

  15. DNA Methylation Landscapes of Human Fetal Development.

    PubMed

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

    2015-10-01

    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.

  16. Methylation patterns of immunoglobulin genes in lymphoid cells: correlation of expression and differentiation with undermethylation.

    PubMed

    Storb, U; Arp, B

    1983-11-01

    Different states of eukaryotic gene expression are often correlated with different levels of methylation of DNA sequences containing structural genes and their flanking regions. To assess the potential role of DNA methylation in the expression of immunoglobulin genes, which require complex rearrangements prior to expression, methylation patterns were examined in cell lines representing different stages of lymphocyte maturation. Methylation of the second cytosine in the sequence 5' C-C-G-G 3' was determined by using Hpa II/Msp I endonuclease digestion. Four CH genes (C mu, C delta, C gamma 2b, and C alpha), C kappa, V kappa, C lambda, and V lambda genes were analyzed. The results lead to the following conclusions: (i) transcribed immunoglobulin genes are undermethylated; (ii) the C gene allelic to an expressed C gene is always also undermethylated; and (iii) all immunoglobulin loci tend to become increasingly undermethylated as B cells mature.

  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. A recyclable perfluoroalkylated PCP pincer palladium complex.

    PubMed

    Duncan, Daniel; Hope, Eric G; Singh, Kuldip; Stuart, Alison M

    2011-03-01

    A new fluorous PCP pincer ligand has been coordinated to Ni(II), Pd(II) and Pt(II). The air stable palladium complex, which promotes Heck reactions between methyl acrylate and either aryl bromides or iodides, can be recovered intact by fluorous solid-phase extraction and was reused four times in the Heck reaction between methyl acrylate and 4-bromoacetophenone without loss in catalytic activity. PMID:21264422

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

    PubMed

    Suckert, Stefan; Wöhlert, Susanne; Jess, Inke; Näther, 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.

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

    PubMed

    Suckert, Stefan; Wöhlert, Susanne; Jess, Inke; Näther, 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

  1. 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...

  2. 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...

  3. 21 CFR 177.2000 - Vinylidene chloride/methyl acrylate/methyl methacrylate polymers.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

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

  4. Phenyltrimethylammonium Salts as Methylation Reagents in the Nickel-Catalyzed Methylation of C-H Bonds.

    PubMed

    Uemura, Takeshi; Yamaguchi, Mao; Chatani, Naoto

    2016-02-24

    Methylation of C(sp(2))-H bonds was achieved through the Ni(II)-catalyzed reaction of benzamides with phenyltrimethylammonium bromide or iodide as the source of the methyl group. The reaction has a broad scope and shows high functional-group compatibility. The reaction is also applicable to the methylation of C(sp(3))-H bonds in aliphatic amides. PMID:26821872

  5. 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...

  6. 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...

  7. 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

  8. Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome

    PubMed Central

    Gu, Junchen; Stevens, Michael; Xing, Xiaoyun; Li, Daofeng; Zhang, Bo; Payton, Jacqueline E.; Oltz, Eugene M.; Jarvis, James N.; Jiang, Kaiyu; Cicero, Theodore; Costello, Joseph F.; Wang, Ting

    2016-01-01

    DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Many studies have mapped DNA methylation changes associated with embryogenesis, cell differentiation, and cancer at a genome-wide scale. Our understanding of genome-wide DNA methylation changes in a developmental or disease-related context has been steadily growing. However, the investigation of which CpGs are variably methylated in different normal cell or tissue types is still limited. Here, we present an in-depth analysis of 54 single-CpG-resolution DNA methylomes of normal human cell types by integrating high-throughput sequencing-based methylation data. We found that the ratio of methylated to unmethylated CpGs is relatively constant regardless of cell type. However, which CpGs made up the unmethylated complement was cell-type specific. We categorized the 26,000,000 human autosomal CpGs based on their methylation levels across multiple cell types to identify variably methylated CpGs and found that 22.6% exhibited variable DNA methylation. These variably methylated CpGs formed 660,000 variably methylated regions (VMRs), encompassing 11% of the genome. By integrating a multitude of genomic data, we found that VMRs enrich for histone modifications indicative of enhancers, suggesting their role as regulatory elements marking cell type specificity. VMRs enriched for transcription factor binding sites in a tissue-dependent manner. Importantly, they enriched for GWAS variants, suggesting that VMRs could potentially be implicated in disease and complex traits. Taken together, our results highlight the link between CpG methylation variation, genetic variation, and disease risk for many human cell types. PMID:26888867

  9. 2-Amino-5-methyl-pyridinium 4-methyl-benzoate.

    PubMed

    Thanigaimani, Kaliyaperumal; Farhadikoutenaei, Abbas; Arshad, Suhana; Razak, Ibrahim Abdul

    2013-01-01

    The 4-methyl-benzoate anion of the title salt, C6H9N2(+)·C8H7O2(-), is nearly planar, with a dihedral angle of 6.26 (10)° between the benzene ring and the carboxyl-ate group. In the crystal, the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxyl-ate O atoms of the anion via a pair of N-H⋯O hydrogen bonds with an R2(2)(8) ring motif, forming an approximately planar ion pair with a dihedral angle of 9.63 (4)° between the pyridinium and benzene rings. The ion pairs are further connected via N-H⋯O and weak C-H⋯O hydrogen bonds, forming a two-dimensional network parallel to the bc plane. PMID:23476474

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

    Yang, Jun; Sharma, Sunny; Kötter, 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

  12. 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; Dalprà, 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.

  13. 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

  14. Conformation-selective methylation of geminivirus DNA.

    PubMed

    Paprotka, T; Deuschle, K; Metzler, V; Jeske, H

    2011-11-01

    Geminiviruses with small circular single-stranded DNA genomes replicate in plant cell nuclei by using various double-stranded DNA (dsDNA) intermediates: distinct open circular and covalently closed circular as well as heterogeneous linear DNA. Their DNA may be methylated partially at cytosine residues, as detected previously by bisulfite sequencing and subsequent PCR. In order to determine the methylation patterns of the circular molecules, the DNAs of tomato yellow leaf curl Sardinia virus (TYLCSV) and Abutilon mosaic virus were investigated utilizing bisulfite treatment followed by rolling circle amplification. Shotgun sequencing of the products yielded a randomly distributed 50% rate of C maintenance after the bisulfite reaction for both viruses. However, controls with unmethylated single-stranded bacteriophage DNA resulted in the same level of C maintenance. Only one short DNA stretch within the C2/C3 promoter of TYLCSV showed hyperprotection of C, with the protection rate exceeding the threshold of the mean value plus 1 standard deviation. Similarly, the use of methylation-sensitive restriction enzymes suggested that geminiviruses escape silencing by methylation very efficiently, by either a rolling circle or recombination-dependent replication mode. In contrast, attempts to detect methylated bases positively by using methylcytosine-specific antibodies detected methylated DNA only in heterogeneous linear dsDNA, and methylation-dependent restriction enzymes revealed that the viral heterogeneous linear dsDNA was methylated preferentially. PMID:21835804

  15. 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.

  16. 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

  17. Fully methylated, atomically flat (111) silicon surface

    NASA Astrophysics Data System (ADS)

    Fidélis, A.; Ozanam, F.; Chazalviel, J.-N.

    2000-01-01

    The atomically flat hydrogenated (111) silicon surface has been methylated by anodization in a Grignard reagent and the surface obtained characterized by infrared spectroscopy. 100% substitution of the hydrogen atoms by methyl groups is observed. The resulting surface exhibits preserved ordering and superior chemical stability.

  18. Methylation-sensitive polymerase chain reaction.

    PubMed

    Moore, Hannah R; Meehan, Richard R; Young, Lorraine E

    2006-01-01

    Here, we describe a robust and reproducible methylation-sensitive polymerase chain reaction (MS-PCR) method to detect the percentage methylation in repeat sequences of individual pre-implantation ovine embryos produced by different embryo technologies. This method allows the comparison of embryos produced by nuclear transfer with other production and embryo culture methods, accounting for the heterogeneity between embryos within a single treatment. DNA extracted from single embryos is digested with a methylation-sensitive restriction enzyme to determine the percentage methylation after PCR amplification in comparison with an undigested control. The undigested control represents 100% methylation because methylation-sensitive enzymes do not cut methylated DNA, allowing the entire sample to be amplified by PCR. Image analysis quantification of the digested subsample PCR product on an ethidium bromide-stained agarose gel is proportional to the amount of methylated DNA in each embryo. By comparing quadruplicate values obtained for each embryo against a standard curve, we are able to ensure the validity of our results for each individual embryo. Compared with bisulphite sequencing methods, the method described is rapid, inexpensive, and relatively high-throughput. PMID:16761730

  19. 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)

  20. 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 π-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.

  1. 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.

  2. 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.

  3. 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

  4. Arginine methylation of G3BP1 in response to Wnt3a regulates β-catenin mRNA

    PubMed Central

    Bikkavilli, Rama Kamesh; Malbon, Craig C.

    2011-01-01

    Wnt/β-catenin signaling is essential for normal mammalian development. Wnt3a activates the Wnt/β-catenin pathway through stabilization of β-catenin; a process in which the phosphoprotein Dishevelled figures prominently. Protein arginine methylation in signaling complexes containing Dishevelled was investigated. Mass spectrometry of a prominent arginine-methylated, Dishevelled-associated protein identified the Ras GTPase activating protein-binding protein 1 G3BP1. Stimulation of totipotent mouse embryonic F9 cells with Wnt3a provoked increased methylation of G3BP1. We show that G3BP1 is a novel Ctnnb1 mRNA binding protein. Methylation of G3BP1 constitutes a molecular switch that regulates Ctnnb1 mRNA in response to Wnt3a. Thus, the protein arginine methylation that targets G3BP1 acts as a novel regulator of Ctnnb1 mRNA. PMID:21652632

  5. One-pot approach for examining the DNA methylation patterns using an engineered methyl-probe.

    PubMed

    Kim, Seong-Eun; Chang, Matthew; Yuan, Chongli

    2014-08-15

    Aberrant DNA methylation is a common observation in various types of human cancers, i.e., breast and lung cancers. Nevertheless, the current DNA methylation detection approaches require bisulfite treatments and are laborious or costly to perform. To address these challenges, we developed a methyl-probe based on the MBD1 protein. Combined with fluorescence correlation spectroscopy, our probe can sensitively detect the existence of DNA methylation at concentrations above 20nM in a one-pot assay. The probe can quantify the total amount of methylated CG dinucleotides above ~20nM, independent of DNA sequence contexts, concentrations (20-1900nM) and methylation levels (5-100%). Our detection platform offers a simple and cheap alternative DNA methylation detection approach.

  6. Peptide quantitation with methyl iodide isotopic tags and mass spectrometry.

    PubMed

    Blagojevic, Voislav; Zhidkov, Nickholas; Tharmaratnam, Samuel; Pham, Van Thong; Kaplan, Harvey; Bohme, Diethard K

    2010-06-01

    A novel method is presented for the quantitation of peptides based on their methylation by in vacuo chemical reaction with methyl iodide. Samples of two small peptides, hexaglycine and pentaalanine, were labeled with CH(3)I and CD(3)I, representing the "unknown" and "standard" respectively, and then subjected to a series of tests using mass spectrometry to ascertain the suitability of the isotopic labels for peptide quantitation. The experiments show methyl iodide to be a very quantitative label, exhibiting a linear relationship in concentration over the dynamic range of the mass spectrometer used in the analysis (up to 4 orders of magnitude) both as pure samples and in a complex mixture of peptides. The tendency of trimethylated peptides to preferentially form a(2) fragment ions in MS(2) produces a significant increase in sensitivity, especially when the mass spectrometer is used in the MRM mode. Tests were also performed to verify the stability of the label against H/D exchange and its suitability for long-term storage, showing little degradation while in solution and during subsequent chemical processing.

  7. 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

  8. 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.

  9. Maternal Methyl-Group Donor Intake and Global DNA (Hydroxy)Methylation before and during Pregnancy

    PubMed Central

    Pauwels, Sara; Duca, Radu Corneliu; Devlieger, Roland; Freson, Kathleen; Straetmans, Dany; Van Herck, Erik; Huybrechts, Inge; Koppen, Gurdun; Godderis, Lode

    2016-01-01

    It is still unclear to which extent methyl-group intake during pregnancy can affect maternal global DNA (hydroxyl)methylation. Pregnancy methylation profiling and its link with methyl-group intake in a healthy population could enhance our understanding of the development of pregnancy related disorders. One hundred forty-eight women were enrolled in the MANOE (MAternal Nutrition and Offspring’s Epigenome) study. Thiry-four women were enrolled before pregnancy and 116 during the first trimester of pregnancy. Global DNA (hydroxy)methylation in blood using LC-MS/MS and dietary methyl-group intake (methionine, folate, betaine, and choline) using a food-frequency questionnaire were estimated pre-pregnancy, during each trimester, and at delivery. Global DNA (hydroxy)methylation levels were highest pre-pregnancy and at weeks 18–22 of pregnancy. We observed a positive relation between folic acid and global DNA methylation (p = 0.04) and hydroxymethylation (p = 0.04). A high intake of methionine pre-pregnancy and in the first trimester showed lower (hydroxy)methylation percentage in weeks 11–13 and weeks 18–22, respectively. Choline and betaine intake in the first weeks was negatively associated with hydroxymethylation. Women with a high intake of these three methyl groups in the second and third trimester showed higher hyrdoxymethylation/methylation levels in the third trimester. To conclude, a time trend in DNA (hydroxy)methylation was found and women with higher methyl-group intake showed higher methylation in the third trimester, and not in earlier phases of pregnancy. PMID:27509522

  10. Maternal Methyl-Group Donor Intake and Global DNA (Hydroxy)Methylation before and during Pregnancy.

    PubMed

    Pauwels, Sara; Duca, Radu Corneliu; Devlieger, Roland; Freson, Kathleen; Straetmans, Dany; Van Herck, Erik; Huybrechts, Inge; Koppen, Gurdun; Godderis, Lode

    2016-01-01

    It is still unclear to which extent methyl-group intake during pregnancy can affect maternal global DNA (hydroxyl)methylation. Pregnancy methylation profiling and its link with methyl-group intake in a healthy population could enhance our understanding of the development of pregnancy related disorders. One hundred forty-eight women were enrolled in the MANOE (MAternal Nutrition and Offspring's Epigenome) study. Thiry-four women were enrolled before pregnancy and 116 during the first trimester of pregnancy. Global DNA (hydroxy)methylation in blood using LC-MS/MS and dietary methyl-group intake (methionine, folate, betaine, and choline) using a food-frequency questionnaire were estimated pre-pregnancy, during each trimester, and at delivery. Global DNA (hydroxy)methylation levels were highest pre-pregnancy and at weeks 18-22 of pregnancy. We observed a positive relation between folic acid and global DNA methylation (p = 0.04) and hydroxymethylation (p = 0.04). A high intake of methionine pre-pregnancy and in the first trimester showed lower (hydroxy)methylation percentage in weeks 11-13 and weeks 18-22, respectively. Choline and betaine intake in the first weeks was negatively associated with hydroxymethylation. Women with a high intake of these three methyl groups in the second and third trimester showed higher hyrdoxymethylation/methylation levels in the third trimester. To conclude, a time trend in DNA (hydroxy)methylation was found and women with higher methyl-group intake showed higher methylation in the third trimester, and not in earlier phases of pregnancy. PMID:27509522

  11. Folic acid, methylation and neural tube closure in humans.

    PubMed

    Blom, Henk J

    2009-04-01

    This review provides a brief description of folate use and folic acid metabolism in relation to neural tube defect (NTD) risk. First, a meta-analysis of reduction in NTD recurrence and occurrence risk with periconceptional folic acid supplementation is presented. Second, an overview of the complex folate metabolism is given. Third, SNPs for genes involved in folate and homocysteine metabolism that have been studied in relation to NTD riskare discussed. Fourth, the questions whether folate receptor autoantibodies or hampered methylation are mechanisms underlying NTDs are briefly discussed.

  12. High-frequency aberrantly methylated targets in pancreatic adenocarcinoma identified via global DNA methylation analysis using methylCap-seq

    PubMed Central

    2014-01-01

    Background Extensive reprogramming and dysregulation of DNA methylation is an important characteristic of pancreatic cancer (PC). Our study aimed to characterize the genomic methylation patterns in various genomic contexts of PC. The methyl capture sequencing (methylCap-seq) method was used to map differently methylated regions (DMRs) in pooled samples from ten PC tissues and ten adjacent non-tumor (PN) tissues. A selection of DMRs was validated in an independent set of PC and PN samples using methylation-specific PCR (MSP), bisulfite sequencing PCR (BSP), and methylation sensitive restriction enzyme-based qPCR (MSRE-qPCR). The mRNA and expressed sequence tag (EST) expression of the corresponding genes was investigated using RT-qPCR. Results A total of 1,131 PC-specific and 727 PN-specific hypermethylated DMRs were identified in association with CpG islands (CGIs), including gene-associated CGIs and orphan CGIs; 2,955 PC-specific and 2,386 PN-specific hypermethylated DMRs were associated with gene promoters, including promoters containing or lacking CGIs. Moreover, 1,744 PC-specific and 1,488 PN-specific hypermethylated DMRs were found to be associated with CGIs or CGI shores. These results suggested that aberrant hypermethylation in PC typically occurs in regions surrounding the transcription start site (TSS). The BSP, MSP, MSRE-qPCR, and RT-qPCR data indicated that the aberrant DNA methylation in PC tissue and in PC cell lines was associated with gene (or corresponding EST) expression. Conclusions Our study characterized the genome-wide DNA methylation patterns in PC and identified DMRs that were distributed among various genomic contexts that might influence the expression of corresponding genes or transcripts to promote PC. These DMRs might serve as diagnostic biomarkers or therapeutic targets for PC. PMID:25276247

  13. 40 CFR 180.439 - Thifensulfuron methyl; tolerances for residues.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... residues of thifensulfuron methyl, including its metabolites and degradates, in or on the commodities... established for residues of thifensulfuron methyl, including its metabolites and degradates, in or on...

  14. 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

  15. 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

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

    PubMed Central

    Tsai, Pei-Chien; Bell, Jordana T

    2015-01-01

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

  17. A Semiautomated Assignment Protocol for Methyl Group Side Chains in Large Proteins.

    PubMed

    Kim, Jonggul; Wang, Yingjie; Li, Geoffrey; Veglia, Gianluigi

    2016-01-01

    The developments of biosynthetic specific labeling strategies for side-chain methyl groups have allowed structural and dynamic characterization of very large proteins and protein complexes. However, the assignment of the methyl-group resonances remains an Achilles' heel for NMR, as the experiments designed to correlate side chains to the protein backbone become rather insensitive with the increase of the transverse relaxation rates. In this chapter, we outline a semiempirical approach to assign the resonances of methyl-group side chains in large proteins. This method requires a crystal structure or an NMR ensemble of conformers as an input, together with NMR data sets such as nuclear Overhauser effects (NOEs) and paramagnetic relaxation enhancements (PREs), to be implemented in a computational protocol that provides a probabilistic assignment of methyl-group resonances. As an example, we report the protocol used in our laboratory to assign the side chains of the 42-kDa catalytic subunit of the cAMP-dependent protein kinase A. Although we emphasize the labeling of isoleucine, leucine, and valine residues, this method is applicable to other methyl group side chains such as those of alanine, methionine, and threonine, as well as reductively methylated cysteine side chains.

  18. 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.

  19. 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.

  20. Genome-wide profiles of methylation, microRNAs, and gene expression in chemoresistant breast cancer

    PubMed Central

    He, Dong-Xu; Gu, Feng; Gao, Fei; Hao, Jun-jun; Gong, Desheng; Gu, Xiao-Ting; Mao, Ai-Qin; Jin, Jian; Fu, Li; Ma, Xin

    2016-01-01

    Cancer chemoresistance is regulated by complex genetic and epigenetic networks. In this study, the features of gene expression, methylation, and microRNA (miRNA) expression were investigated with high-throughput sequencing in human breast cancer MCF-7 cells resistant to adriamycin (MCF-7/ADM) and paclitaxel (MCF-7/PTX). We found that: ① both of the chemoresistant cell lines had similar, massive changes in gene expression, methylation, and miRNA expression versus chemosensitive controls. ② Pairwise integration of the data highlighted sets of genes that were regulated by either methylation or miRNAs, and sets of miRNAs whose expression was controlled by DNA methylation in chemoresistant cells. ③ By combining the three sets of high-throughput data, we obtained a list of genes whose expression was regulated by both methylation and miRNAs in chemoresistant cells; ④ Expression of these genes was then validated in clinical breast cancer samples to generate a 17-gene signature that showed good predictive and prognostic power in triple-negative breast cancer patients receiving anthracycline-taxane-based neoadjuvant chemotherapy. In conclusion, our results have generated a new workflow for the integrated analysis of the effects of miRNAs and methylation on gene expression during the development of chemoresistance. PMID:27094684

  1. 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.

  2. 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.

  3. Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana.

    PubMed

    Meng, Dazhe; Dubin, Manu; Zhang, Pei; Osborne, Edward J; Stegle, Oliver; Clark, Richard M; Nordborg, Magnus

    2016-07-01

    The extent to which epigenetic variation affects complex traits in natural populations is not known. We addressed this question using transcriptome and DNA methylation data from a sample of 135 sequenced A. thaliana accessions. Across individuals, expression was significantly associated with cis-methylation for hundreds of genes, and many of these associations remained significant after taking SNP effects into account. The pattern of correlations differed markedly between gene body methylation and transposable element methylation. The former was usually positively correlated with expression, and the latter usually negatively correlated, although exceptions were found in both cases. Finally, we developed graphical models of causality that adapt to a sample with heavy population structure, and used them to show that while methylation appears to affect gene expression more often than expression affects methylation, there is also strong support for both being independently controlled. In conclusion, although we find clear evidence for epigenetic regulation, both the number of loci affected and the magnitude of the effects appear to be small compared to the effect of SNPs. PMID:27398721

  4. Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana

    PubMed Central

    Zhang, Pei; Osborne, Edward J.; Stegle, Oliver; Clark, Richard M.

    2016-01-01

    The extent to which epigenetic variation affects complex traits in natural populations is not known. We addressed this question using transcriptome and DNA methylation data from a sample of 135 sequenced A. thaliana accessions. Across individuals, expression was significantly associated with cis-methylation for hundreds of genes, and many of these associations remained significant after taking SNP effects into account. The pattern of correlations differed markedly between gene body methylation and transposable element methylation. The former was usually positively correlated with expression, and the latter usually negatively correlated, although exceptions were found in both cases. Finally, we developed graphical models of causality that adapt to a sample with heavy population structure, and used them to show that while methylation appears to affect gene expression more often than expression affects methylation, there is also strong support for both being independently controlled. In conclusion, although we find clear evidence for epigenetic regulation, both the number of loci affected and the magnitude of the effects appear to be small compared to the effect of SNPs. PMID:27398721

  5. On your histone mark, SET, methylate!

    PubMed Central

    Binda, Olivier

    2013-01-01

    Lysine methylation of histones and non-histone proteins has emerged in recent years as a posttranslational modification with wide-ranging cellular implications beyond epigenetic regulation. The molecular interactions between lysine methyltransferases and their substrates appear to be regulated by posttranslational modifications surrounding the lysine methyl acceptor. Two very interesting examples of this cross-talk between methyl-lysine sites are found in the SET (Su(var)3–9, Enhancer-of-zeste, Trithorax) domain-containing lysine methyltransferases SET7 and SETDB1, whereby the histone H3 trimethylated on lysine 4 (H3K4me3) modification prevents methylation by SETDB1 on H3 lysine 9 (H3K9) and the histone H3 trimethylated on lysine 9 (H3K9me3) modification prevents methylation by SET7 on H3K4. A similar cross-talk between posttranslational modifications regulates the functions of non-histone proteins such as the tumor suppressor p53 and the DNA methyltransferase DNMT1. Herein, in cis effects of acetylation, phosphorylation, as well as arginine and lysine methylation on lysine methylation events will be discussed. PMID:23625014

  6. Targeting DNA methylation with green tea catechins.

    PubMed

    Yiannakopoulou, Eugenia C

    2015-01-01

    Aberrant epigenetic alterations in the genome such as DNA methylation play a significant role in cancer development. Green tea catechins have been reported to modulate epigenetic processes. This review aims to synthesize evidence on the modulation of DNA methylation by green tea catechins. Green tea catechins have been reported to reverse DNA methylation of tumor suppressor genes and increase transcription of these genes. Green tea catechins and especially epigallocatechin gallate modulate DNA methylation by attenuating the effect of DNA methyltransferase 1 (DNMT1). However, the exact mechanism of DNMT1 inhibition is not delineated. Suggested mechanisms include direct enzymatic inhibition, indirect enzymatic inhibition, reduced DNMT1 expression and translation. The possible effect of green tea catechins on other pathways of DNA methylation, i.e. methyl-CpG binding domain proteins, has not been investigated. Furthermore, the link between redox properties and epigenetic modulation by green tea catechins has not been defined either. Since green tea catechins are natural compounds with a rather acceptable safety profile, further research on their action as inhibitors of DNA methylation seems worthwhile.

  7. 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

  8. 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

  9. DNA methylation and body temperature in fishes.

    PubMed

    Varriale, Annalisa; Bernardi, Giorgio

    2006-12-30

    Previous investigations from our laboratory [Jabbari, K., Cacciò, S., Pais de Barros, J.P., Desgres, J., Bernardi G., 1997. Evolutionary changes in CpG and methylation levels in the genome of vertebrates. Gene 205, 109-118.] led to the discovery of two different methylation levels in the genomes of vertebrates, a higher one exhibited by fishes and amphibians and a lower one shown by mammals and birds. It was also noted that data from the literature indicated a higher CpG level in fishes and amphibians compared to mammals and birds. Such observations led to suggesting the existence of two equilibria and to speculate that the transitions between the two equilibria in DNA methylation and CpG levels were due to a higher deamination rate in warm-blooded vertebrates related to their higher body temperature. Here we used Reverse-Phase High-Performance Liquid Chromatography (RP-HPLC) analysis to study methylation levels in a number of fish genomes living at different temperatures. We found that polar fishes exhibit DNA methylation levels that are higher than those of tropical and temperate fishes, the latter being in turn higher than the methylation levels of warm-blooded vertebrates, as expected from previous work. A closer analysis of the data revealed that, among Antarctic fishes, the Channichthyidae (the icefishes, deprived of haemoglobin) had the highest methylation level, and that, among temperate and tropical fishes the latter showed the lowest methylation level. These results confirm the existence of an inverse relationship between DNA methylation and body temperature, when the latter is maintained over evolutionary times.

  10. Postnatal epigenetic regulation of intestinal stem cells requires DNA methylation and is guided by the microbiome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA methylation is an epigenetic mechanism central to the development and maintenance of complex mammalian tissues, but our understanding of its role in intestinal development is limited. We used whole genome bisulfite sequencing, and found that differentiation of mouse colonic intestinal stem cell...

  11. A Short and Efficient Synthetic Route to Methyl α-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 methyl α-trioxacarcinoside B from 2-acetylfuran is described. Anomerically activated forms, including 1-phenylthio, 1-O-(4’f-pentenyl), 1-fluoro, and 1-O-acetyl derivatives are also prepared. PMID:21958151

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

    PubMed Central

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

    2015-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  15. Sunflower oil methyl ester as diesel fuel

    SciTech Connect

    Hassett, D.J.; Hasan, R.A.

    1982-01-01

    Methyl ester formation represents one approach to overcome the problems associated with the relatively high viscosity of sunflower oil when used as a diesel fuel replacement. Sunflower oil methyl ester is being prepared at the University of North Dakota Engieering Experiment Station. Physical and chemical properties of this material at varying levels of refinement and purity will be used to define fuel properties. Engine testing is being carried out to determine if the fouling characteristics of methyl ester are significantly less than those of sunflower oil. 1 figure, 1 table.

  16. DNA methylation changes in the postmortem dorsolateral prefrontal cortex of patients with schizophrenia

    PubMed Central

    Numata, Shusuke; Ye, Tianzhang; Herman, Mary; Lipska, Barbara K.

    2014-01-01

    Background: Schizophrenia is a complex psychiatric disorder with a lifetime morbidity rate of 0.5–1.0%. The pathophysiology of schizophrenia still remains obscure. Accumulating evidence indicates that DNA methylation, which is the addition of a methyl group to the cytosine in a CpG dinucleotide, might play an important role in the pathogenesis of schizophrenia. Methods: To gain further insight into the molecular mechanisms underlying schizophrenia, a genome-wide DNA methylation profiling (27,578 CpG dinucleotides spanning 14,495 genes) of the human dorsolateral prefrontal cortex (DLPFC) was conducted in a large cohort (n = 216) of well characterized specimens from individuals with schizophrenia and non-psychiatric controls, combined with an analysis of genetic variance at ~880,000 SNPs. Results: Aberrant DNA methylation in schizophrenia was identified at 107 CpG sites at 5% Bonferroni correction (p < 1.99 × 10−6). Of these significantly altered sites, hyper-DNA methylation was observed at 79 sites (73.8%), mostly in the CpG islands (CGIs) and in the regions flanking CGIs (CGI: 31 sites; CGI shore: 35 sites; CGI shelf: 3 sites). Furthermore, a large number of cis-methylation quantitative trait loci (mQTL) were identified, including associations with risk SNPs implicated in schizophrenia. Conclusions: These results suggest that altered DNA methylation might be involved in the pathophysiology and/or treatment of schizophrenia, and that a combination of epigenetic and genetic approaches will be useful to understanding the molecular mechanism of this complex disorder. PMID:25206360

  17. Conformations and Barriers to Methyl Group Internal Rotation in Two Asymmetric Ethers: Propyl Methyl Ether and Butyl Methyl Ether

    NASA Astrophysics Data System (ADS)

    Long, B. E.; Dechirico, F.; Cooke, S. A.

    2012-06-01

    The conformational preferences of the O-C-C-C unit are important in many biological systems with the unit generally preferring a gauche configuration compared to an anti configuration. Butyl methyl ether and propyl methyl ether provide very simple systems for this phenomenom to manifest. Pure rotational spectra of the title molecules have been recorded using chirped pulse Fourier transform microwave spectroscopy (CP-FTMW). In the case of butyl methyl ether, only one conformer has been observed. This conformer has torsional angles of COCC = 180°, OCCC = 62° and CCCC = 180° (anti-gauche-anti) and rotational constants of A = 10259.4591(33) MHz, B = 1445.6470(13) MHz, and C = 1356.2944(14) MHz. The rotational spectrum was doubled and has been analyzed to produce an effective barrier to methyl group internal rotation of 780(35) cm-1. A prior rotational spectroscopic study on propyl methyl ether had focused only on the high energy anti-anti conformer. We have analyzed spectra from the lowest energy anti-gauche conformer and the spectroscopic constants will be presented. A summary of the differences in conformational energies and methyl group internal rotation barriers for the class of aliphatic asymmetric ethers will be presented. K. N. Houk, J. E. Eksterowicz, Y.-D. Wu, C. D. Fuglesang, D. B. Mitchell. J. Am. Chem. Soc. 115 (4170), 1993. Hiroshi Kato, Jun Nakagawa, Michiro Hayashi. J. Mol. Spectrosc. 80 (272), 1980.

  18. Transparent and luminescent ionogels composed of Eu(3+)-coordinated ionic liquids and poly(methyl methacrylate).

    PubMed

    Zhou, Fan; Wang, Tianren; Li, Zhiqiang; Wang, Yige

    2015-12-01

    We report here on transparent and luminescent ionogels that consist of ionic ternary europium (III) complexes and the inexpensive non-toxic compound, poly(methyl methacrylate) (PMMA) and that were formed by dissolving these complexes in methacrylate (MMA) monomers followed by in situ polymerization. The resulting ionogels show a bright red emission under near-UV light irradiation. Luminescence data confirm the energy transfer from terpyridine-functionalized ionic liquid to Eu(3+) ions.

  19. Hydrogen exchange between hydride and methyl ligands in [Cp*Os(dmpm)(CH{sub 3})H{sup +}

    SciTech Connect

    Martin, R.L.

    1999-10-13

    Very recently Gross and Girolami described the first report of a transition metal methyl/hydride complex in which the hydrogens of the alkyl and hydride are exchanging at a rate sufficient to be dynamic on the NMR time scale. The results suggest that an alkane complex L{sub x}M(CH{sub 4}) is formed reversibly from the methyl/hydride complex. This communication reports density functional theory (DFT) calculations on a model of the Os(IV) methyl/hydride studied by Gross and Girolami. A bound methane complex is indeed found which lies {approx} 6 kcal/mol above the methyl/hydride. The theoretical barrier height connecting the two is in good agreement with the experimental kinetic data reported for hydrogen exchange. Once formed, the methane complex can scramble the hydrogen bound to the metal through a lower-lying transition state involving {eta}{sup 2}-H,H coordination to the metal. The larger barrier measured for the reductive elimination of CH{sub 4} may be a measure of the stability of the methyl/hydride.

  20. Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes.

    PubMed

    Gaspin, C; Cavaillé, J; Erauso, G; Bachellerie, J P

    2000-04-01

    Ribose methylation is a prevalent type of nucleotide modification in rRNA. Eukaryotic rRNAs display a complex pattern of ribose methylations, amounting to 55 in yeast Saccharomyces cerevisiae and about 100 in vertebrates. Ribose methylations of eukaryotic rRNAs are each guided by a cognate small RNA, belonging to the family of box C/D antisense snoRNAs, through transient formation of a specific base-pairing at the rRNA modification site. In prokaryotes, the pattern of rRNA ribose methylations has been fully characterized in a single species so far, Escherichia coli, which contains only four ribose methylated rRNA nucleotides. However, the hyperthermophile archaeon Sulfolobus solfataricus contains, like eukaryotes, a large number of (yet unmapped) rRNA ribose methylations and homologs of eukaryotic box C/D small nucleolar ribonuclear proteins have been identified in archaeal genomes. We have therefore searched archaeal genomes for potential homologs of eukaryotic methylation guide small nucleolar RNAs, by combining searches for structured motifs with homology searches. We have identified a family of 46 small RNAs, conserved in the genomes of three hyperthermophile Pyrococcus species, which we have experimentally characterized in Pyrococcus abyssi. The Pyrococcus small RNAs, the first reported homologs of methylation guide small nucleolar RNAs in organisms devoid of a nucleus, appear as a paradigm of minimalist box C/D antisense RNAs. They differ from their eukaryotic homologs by their outstanding structural homogeneity, extended consensus box motifs and the quasi-systematic presence of two (instead of one) rRNA antisense elements. Remarkably, for each small RNA the two antisense elements always match rRNA sequences close to each other in rRNA structure, suggesting an important role in rRNA folding. Only a few of the predicted P. abyssi rRNA ribose methylations have been detected so far. Further analysis of these archaeal small RNAs could provide new insights into

  1. Chirped Pulse Microwave Spectroscopy on Methyl Butanoate

    NASA Astrophysics Data System (ADS)

    Hernandez-Castillo, Alicia O.; Hays, Brian M.; Abeysekera, Chamara; Zwier, Timothy S.

    2016-06-01

    The microwave spectrum of methyl butanoate has been taken from 8-18 GHz using a chirped pulse spectrometer. This molecule is a model biofuel, and its thermal decomposition products are of interest due to its many dissociation channels. As a preliminary step before such pyrolysis studies, we have examined the jet cooled spectrum of methyl butanoate in a chirped pulse spectrometer, which shows a very rich spectrum. Several conformers have been identified, each with tunneling splittings in the methyl ester group due to internal rotation. These spectra have been fit to obtain rotational constants, relative populations, and methyl rotor barriers for each conformational isomer. The results of these studies are compared to high level calculations.

  2. Degradation of methyl bromide in anaerobic sediments

    USGS Publications Warehouse

    Oremland, R.S.; Miller, L.G.; Strohmaler, F.E.

    1994-01-01

    Methyl bromide (MeBr) was anaerobically degraded in saltmarsh sediments after reaction with sulfide. The product of this nucleophilic substitution reaction was methanethiol, which underwent further chemical and bacterial reactions to form dimethyl sulfide. These two gases appeared transiently during sediment incubations because they were metabolized by methanogenic and sulfate-reducing bacteria. A second, less significant reaction of MeBr was the exchange with chloride, forming methyl chloride, which was also susceptible to attack by sulfide. Incubation of 14C-labeled methyl iodide as an analogue of MeBr resulted in the formation of 14CH4 and 14CO2 and also indicated that sulfate-reducing bacteria as well as methanogens metabolized the methylated sulfur intermediates. These results suggest that exposed sediments with abundant free sulfide, such as coastal salt-marshes, may constitute a sink for atmospheric MeBr.

  3. Emission of methyl bromide from biomass burning

    SciTech Connect

    Manoe, S.; Andreae, M.O. )

    1994-03-04

    Bromine is, per atom, far more efficient than chlorine in destroying stratospheric ozone, and methyl bromide is the single largest source of stratospheric bromine. The two main previously known sources of this compound are emissions from the ocean and from the compound's use as an agricultural pesticide. Laboratory biomass combustion experiments showed that methyl bromide was emitted in the smoke from various fuels tested. Methyl bromide was also found in smoke plumes from wildfires in savannas, chaparral, and boreal forest. Global emissions of methyl bromide from biomass burning are estimated to be in the range of 10 to 50 gigagrams per year, which is comparable to the amount produced by ocean emission and pesticide use and represents a major contribution ([approximately]30 percent) to the stratospheric bromine budget.

  4. Targeting DNA Methylation for Epigenetic Therapy

    PubMed Central

    Yang, Xiaojing; Lay, Fides; Han, Han; Jones, Peter A.

    2010-01-01

    DNA methylation patterns are established during embryonic development and faithfully copied through somatic cell divisions. Based on our understanding of DNA methylation and other interrelated epigenetic modifications, a comprehensive view of the epigenetic landscape and cancer epigenome is evolving. The cancer methylome is highly disrupted, making DNA methylation an excellent target for anti-cancer therapies. During the last few decades, an increasing number of drugs targeting DNA methylation have been developed in an effort to increase efficacy, stability and to decrease toxicity. The earliest and the most successful epigenetic drug to date, 5-Azacytidine, is currently recommended as the first-line treatment for high risk myelodysplastic syndromes (MDS) patients. Encouraging results from clinical trials have prompted further efforts to elucidate epigenetic alterations in cancer and subsequently develop new epigenetic therapies. This review delineates the latest cancer epigenetic models, recent discovery of hypomethylation agents and their application in the clinic. PMID:20846732

  5. Oxidative carbonylation of styrene to methyl cinnamate

    SciTech Connect

    Hsu, C.Y.

    1987-04-01

    Oxidative carbonylation technology is used for making methyl cinnamate from styrene as an alternative to Claisen condensation of benzaldehyde with methyl acetate. Using this approach, the optimum yield of cinnamate is greater than 90%, with CO{sub 2}, acetophenone, and phenylsuccinate as the major by-products. The conversion of styrene and the selectivity to cinnamate depend upon the types of catalysts and reaction conditions used. A plausible reaction mechanism is proposed to account for the selective formation of cinnamate.

  6. Epigenetic genome-wide association methylation in aging and longevity.

    PubMed

    Ben-Avraham, Danny; Muzumdar, Radhika H; Atzmon, Gil

    2012-10-01

    The aging phenotype is the result of a complex interaction between genetic, epigenetic and environmental factors. Evidence suggests that epigenetic changes (i.e., a set of reversible, heritable changes in gene function or other cell phenotype that occurs without a change in DNA sequence) may affect the aging process and may be one of the central mechanisms by which aging predisposes to many age-related diseases. The total number of altered methylation sites increases with increasing age, such that they could serve as marker for chronological age. This article systematically highlights the advances made in the field of epigenomics and their contribution to the understanding of the complex physiology of aging, lifespan and age-associated diseases.

  7. Methyl-CpG island-associated genome signature tags

    SciTech Connect

    Dunn, John J

    2014-05-20

    Disclosed is a method for analyzing the organismic complexity of a sample through analysis of the nucleic acid in the sample. In the disclosed method, through a series of steps, including digestion with a type II restriction enzyme, ligation of capture adapters and linkers and digestion with a type IIS restriction enzyme, genome signature tags are produced. The sequences of a statistically significant number of the signature tags are determined and the sequences are used to identify and quantify the organisms in the sample. Various embodiments of the invention described herein include methods for using single point genome signature tags to analyze the related families present in a sample, methods for analyzing sequences associated with hyper- and hypo-methylated CpG islands, methods for visualizing organismic complexity change in a sampling location over time and methods for generating the genome signature tag profile of a sample of fragmented DNA.

  8. Selenophene transition metal complexes

    SciTech Connect

    White, C.J.

    1994-07-27

    This research shows that selenophene transition metal complexes have a chemistry that is similar to their thiophene analogs. Selenophene coordination has been demonstrated and confirmed by molecular structure in both the {eta}{sup 5}- and the {eta}{sup 1}(Se)-coordination modes. The reaction chemistry of selenophene complexes closely resembles that of the analogous thiophene complexes. One major difference, however, is that selenophene is a better donor ligand than thiophene making the selenophene complexes more stable than the corresponding thiophene complexes. The {sup 77}Se NMR chemical shift values for selenophene complexes fall within distinct regions primarily depending on the coordination mode of the selenophene ligand. In the final paper, the C-H bond activation of {eta}{sup 1}(S)-bound thiophenes, {eta}{sup 1}(S)-benzothiophene and {eta}{sup 1}(Se)-bound selenophenes has been demonstrated. The deprotonation and rearrangement of the {eta}{sup 1}(E)-bound ligand to the carbon bound L-yl complex readily occurs in the presence of base. Reprotonation with a strong acid gives a carbene complex that is unreactive towards nucleophilic attack at the carbene carbon and is stable towards exposure to air. The molecular structure of [Cp(NO)(PPh{sub 3})Re(2-benzothioenylcarbene)]O{sub 3}SCF{sub 3} was determined and contains a Re-C bond with substantial double bond character. Methyl substitution for the thienylcarbene or selenylcarbene gives a carbene that rearranges thermally to give back the {eta}{sup 1}(E)-bound complex. Based on these model reactions, a new mechanism for the H/D exchange of thiophene over the hydrodesulfurization catalyst has been proposed.

  9. Function and evolution of DNA methylation in Nasonia vitripennis.

    PubMed

    Wang, Xu; Wheeler, David; Avery, Amanda; Rago, Alfredo; Choi, Jeong-Hyeon; Colbourne, John K; Clark, Andrew G; Werren, John H

    2013-01-01

    The parasitoid wasp Nasonia vitripennis is an emerging genetic model for functional analysis of DNA methylation. Here, we characterize genome-wide methylation at a base-pair resolution, and compare these results to gene expression across five developmental stages and to methylation patterns reported in other insects. An accurate assessment of DNA methylation across the genome is accomplished using bisulfite sequencing of adult females from a highly inbred line. One-third of genes show extensive methylation over the gene body, yet methylated DNA is not found in non-coding regions and rarely in transposons. Methylated genes occur in small clusters across the genome. Methylation demarcates exon-intron boundaries, with elevated levels over exons, primarily in the 5' regions of genes. It is also elevated near the sites of translational initiation and termination, with reduced levels in 5' and 3' UTRs. Methylated genes have higher median expression levels and lower expression variation across development stages than non-methylated genes. There is no difference in frequency of differential splicing between methylated and non-methylated genes, and as yet no established role for methylation in regulating alternative splicing in Nasonia. Phylogenetic comparisons indicate that many genes maintain methylation status across long evolutionary time scales. Nasonia methylated genes are more likely to be conserved in insects, but even those that are not conserved show broader expression across development than comparable non-methylated genes. Finally, examination of duplicated genes shows that those paralogs that have lost methylation in the Nasonia lineage following gene duplication evolve more rapidly, show decreased median expression levels, and increased specialization in expression across development. Methylation of Nasonia genes signals constitutive transcription across developmental stages, whereas non-methylated genes show more dynamic developmental expression patterns. We

  10. Function and Evolution of DNA Methylation in Nasonia vitripennis

    PubMed Central

    Wang, Xu; Wheeler, David; Avery, Amanda; Rago, Alfredo; Choi, Jeong-Hyeon; Colbourne, John K.; Clark, Andrew G.; Werren, John H.

    2013-01-01

    The parasitoid wasp Nasonia vitripennis is an emerging genetic model for functional analysis of DNA methylation. Here, we characterize genome-wide methylation at a base-pair resolution, and compare these results to gene expression across five developmental stages and to methylation patterns reported in other insects. An accurate assessment of DNA methylation across the genome is accomplished using bisulfite sequencing of adult females from a highly inbred line. One-third of genes show extensive methylation over the gene body, yet methylated DNA is not found in non-coding regions and rarely in transposons. Methylated genes occur in small clusters across the genome. Methylation demarcates exon-intron boundaries, with elevated levels over exons, primarily in the 5′ regions of genes. It is also elevated near the sites of translational initiation and termination, with reduced levels in 5′ and 3′ UTRs. Methylated genes have higher median expression levels and lower expression variation across development stages than non-methylated genes. There is no difference in frequency of differential splicing between methylated and non-methylated genes, and as yet no established role for methylation in regulating alternative splicing in Nasonia. Phylogenetic comparisons indicate that many genes maintain methylation status across long evolutionary time scales. Nasonia methylated genes are more likely to be conserved in insects, but even those that are not conserved show broader expression across development than comparable non-methylated genes. Finally, examination of duplicated genes shows that those paralogs that have lost methylation in the Nasonia lineage following gene duplication evolve more rapidly, show decreased median expression levels, and increased specialization in expression across development. Methylation of Nasonia genes signals constitutive transcription across developmental stages, whereas non-methylated genes show more dynamic developmental expression

  11. DNA methylation and application in forensic sciences.

    PubMed

    Kader, Farzeen; Ghai, Meenu

    2015-04-01

    DNA methylation of cytosine residues is a stable epigenetic alteration, beginning as early as foetal development in the uterus and continuously evolving throughout life. DNA methylation as well as other epigenetic modifications such as chromatin remodelling and histone modifications are indispensable in mammalian development. Methylation is to a large extent influenced by the ageing process, diets and lifestyle choices. Our understanding of this crucial modification may even contribute to the treatment and prevention of age-related illnesses in the very near future. Genome-wide methylation analysis using high throughput DNA technologies has discovered numerous differentially methylated regions (tDMRs) which differ in levels of methylation in various cell types and tissues. TDMRs have been useful in various applications, particularly medicine and forensic sciences. Forensic scientists are constantly seeking exciting and novel methods to aid in the reconstruction of crime scenes, and the analysis of tDMRs represents a new and reliable technique to identify biological fluids and tissues found at the scene of a violent act. Not only has research been able to unequivocally identify various fluids and tissues, but methods to determine the sex, age and phenotype of donors has been developed. New tDMRs in genes are being searched for consistently to serve as novel markers in forensic DNA analysis. PMID:25732744

  12. Editing DNA Methylation in the Mammalian Genome.

    PubMed

    Liu, X Shawn; Wu, Hao; Ji, Xiong; Stelzer, Yonatan; Wu, Xuebing; Czauderna, Szymon; Shu, Jian; Dadon, Daniel; Young, Richard A; Jaenisch, Rudolf

    2016-09-22

    Mammalian DNA methylation is a critical epigenetic mechanism orchestrating gene expression networks in many biological processes. However, investigation of the functions of specific methylation events remains challenging. Here, we demonstrate that fusion of Tet1 or Dnmt3a with a catalytically inactive Cas9 (dCas9) enables targeted DNA methylation editing. Targeting of the dCas9-Tet1 or -Dnmt3a fusion protein to methylated or unmethylated promoter sequences caused activation or silencing, respectively, of an endogenous reporter. Targeted demethylation of the BDNF promoter IV or the MyoD distal enhancer by dCas9-Tet1 induced BDNF expression in post-mitotic neurons or activated MyoD facilitating reprogramming of fibroblasts into myoblasts, respectively. Targeted de novo methylation of a CTCF loop anchor site by dCas9-Dnmt3a blocked CTCF binding and interfered with DNA looping, causing altered gene expression in the neighboring loop. Finally, we show that these tools can edit DNA methylation in mice, demonstrating their wide utility for functional studies of epigenetic regulation. PMID:27662091

  13. DNA methylation and application in forensic sciences.

    PubMed

    Kader, Farzeen; Ghai, Meenu

    2015-04-01

    DNA methylation of cytosine residues is a stable epigenetic alteration, beginning as early as foetal development in the uterus and continuously evolving throughout life. DNA methylation as well as other epigenetic modifications such as chromatin remodelling and histone modifications are indispensable in mammalian development. Methylation is to a large extent influenced by the ageing process, diets and lifestyle choices. Our understanding of this crucial modification may even contribute to the treatment and prevention of age-related illnesses in the very near future. Genome-wide methylation analysis using high throughput DNA technologies has discovered numerous differentially methylated regions (tDMRs) which differ in levels of methylation in various cell types and tissues. TDMRs have been useful in various applications, particularly medicine and forensic sciences. Forensic scientists are constantly seeking exciting and novel methods to aid in the reconstruction of crime scenes, and the analysis of tDMRs represents a new and reliable technique to identify biological fluids and tissues found at the scene of a violent act. Not only has research been able to unequivocally identify various fluids and tissues, but methods to determine the sex, age and phenotype of donors has been developed. New tDMRs in genes are being searched for consistently to serve as novel markers in forensic DNA analysis.

  14. Native DNA repeats and methylation in Ascobolus.

    PubMed Central

    Goyon, C; Rossignol, J L; Faugeron, G

    1996-01-01

    We identified two classes of native dispersed DNA repeats in the Ascobolus genome. The first class consisted of several kilobase long, methylated repeats. These repeats, named Mars (methylated Ascobolus repeated sequences), fell in one family of LINE-like elements and in three families of LTR-containing retrotransposable elements. The methylation features of Mars elements were those expected if they were natural targets for the MIP (methylation induced premeiotically) previously discovered in Ascobolus. The second class consisted of short repeats, approximately 100 bp long, corresponding to 5S rRNA and tRNA genes. As expected from their size, which was too small to allow MIP to occur, they were unmethylated, as were 26 kb of unique sequences tested. These observations are consistent with the hypothesis that MIP is targeted at natural DNA repeats and constitutes a defensive process against the detrimental consequences of the spreading of mobile elements throughout the genome. The 9 kb tandem repeats harbouring the 28S, 18S and 5.8S rRNA genes displayed methylation features suggesting that rDNA methylation proceeds through a process other than MIP. PMID:8811089

  15. 21 CFR 173.250 - Methyl alcohol residues.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Methyl alcohol residues. 173.250 Section 173.250... and Related Substances § 173.250 Methyl alcohol residues. Methyl alcohol may be present in the... specifies the presence of methyl alcohol and provides for the use of the hops extract only as prescribed...

  16. 21 CFR 173.385 - Sodium methyl sulfate.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... pectin by sulfuric acid and methyl alcohol and subsequent treatment with sodium bicarbonate. (b) It does... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Sodium methyl sulfate. 173.385 Section 173.385... CONSUMPTION Specific Usage Additives § 173.385 Sodium methyl sulfate. Sodium methyl sulfate may be present...

  17. 21 CFR 173.385 - Sodium methyl sulfate.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... pectin by sulfuric acid and methyl alcohol and subsequent treatment with sodium bicarbonate. (b) It does... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Sodium methyl sulfate. 173.385 Section 173.385... CONSUMPTION Specific Usage Additives § 173.385 Sodium methyl sulfate. Sodium methyl sulfate may be present...

  18. 21 CFR 173.385 - Sodium methyl sulfate.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... pectin by sulfuric acid and methyl alcohol and subsequent treatment with sodium bicarbonate. (b) It does... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Sodium methyl sulfate. 173.385 Section 173.385... CONSUMPTION Specific Usage Additives § 173.385 Sodium methyl sulfate. Sodium methyl sulfate may be present...

  19. 21 CFR 173.385 - Sodium methyl sulfate.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... sulfuric acid and methyl alcohol and subsequent treatment with sodium bicarbonate. (b) It does not exceed 0... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Sodium methyl sulfate. 173.385 Section 173.385 Food... Specific Usage Additives § 173.385 Sodium methyl sulfate. Sodium methyl sulfate may be present in pectin...

  20. Integrated Genetic and Epigenetic Analysis Identifies Haplotype-Specific Methylation in the FTO Type 2 Diabetes and Obesity Susceptibility Locus

    PubMed Central

    Wilson, Gareth A.; Rakyan, Vardhman K.; Teschendorff, Andrew E.; Akan, Pelin; Stupka, Elia; Down, Thomas A.; Prokopenko, Inga; Morison, Ian M.; Mill, Jonathan; Pidsley, Ruth; Deloukas, Panos; Frayling, Timothy M.; Hattersley, Andrew T.; McCarthy, Mark I.; Beck, Stephan; Hitman, Graham A.

    2010-01-01

    Recent multi-dimensional approaches to the study of complex disease have revealed powerful insights into how genetic and epigenetic factors may underlie their aetiopathogenesis. We examined genotype-epigenotype interactions in the context of Type 2 Diabetes (T2D), focussing on known regions of genomic susceptibility. We assayed DNA methylation in 60 females, stratified according to disease susceptibility haplotype using previously identified association loci. CpG methylation was assessed using methylated DNA immunoprecipitation on a targeted array (MeDIP-chip) and absolute methylation values were estimated using a Bayesian algorithm (BATMAN). Absolute methylation levels were quantified across LD blocks, and we identified increased DNA methylation on the FTO obesity susceptibility haplotype, tagged by the rs8050136 risk allele A (p = 9.40×10−4, permutation p = 1.0×10−3). Further analysis across the 46 kb LD block using sliding windows localised the most significant difference to be within a 7.7 kb region (p = 1.13×10−7). Sequence level analysis, followed by pyrosequencing validation, revealed that the methylation difference was driven by the co-ordinated phase of CpG-creating SNPs across the risk haplotype. This 7.7 kb region of haplotype-specific methylation (HSM), encapsulates a Highly Conserved Non-Coding Element (HCNE) that has previously been validated as a long-range enhancer, supported by the histone H3K4me1 enhancer signature. This study demonstrates that integration of Genome-Wide Association (GWA) SNP and epigenomic DNA methylation data can identify potential novel genotype-epigenotype interactions within disease-associated loci, thus providing a novel route to aid unravelling common complex diseases. PMID:21124985

  1. Nitrogen fixation revisited on iron(0) dinitrogen phosphine complexes.

    PubMed

    Field, Leslie D; Hazari, Nilay; Li, Hsiu L

    2015-05-18

    A reinvestigation of the treatment of [Fe(N2)(PP)2] (PP = depe, dmpe) with acid revealed no ammonium formation. Instead, rapid protonation at the metal center to give hydride complexes was observed. Treatment of [Fe(N2)(dmpe)2] with methylating agents such as methyl triflate or methyl tosylate resulted in methylation of the metal center to afford [FeMe(N2)(dmpe)2](+). Treatment of [Fe(N2)(dmpe)2] with trimethylsilyl triflate, however, resulted in reaction at dinitrogen affording NH4(+) on subsequent treatment with acid. The side-on bound hydrazine complex [Fe(N2H4)(dmpe)2](2+) and bis(ammonia) complex [Fe(NH3)2(dmpe)2](2+) were identified by (15)N NMR spectroscopy as other species formed in the reaction mixture.

  2. Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma

    PubMed Central

    Decock, Anneleen; Ongenaert, Maté; Cannoodt, Robrecht; Verniers, Kimberly; De Wilde, Bram; Laureys, Geneviève; Van Roy, Nadine; Berbegall, Ana P.; Bienertova-Vasku, Julie; Bown, Nick; Clément, Nathalie; Combaret, Valérie; Haber, Michelle; Hoyoux, Claire; Murray, Jayne; Noguera, Rosa; Pierron, Gaelle; Schleiermacher, Gudrun; Schulte, Johannes H.; Stallings, Ray L.; Tweddle, Deborah A.; De Preter, Katleen; Speleman, Frank; Vandesompele, Jo

    2016-01-01

    Accurate assessment of neuroblastoma outcome prediction remains challenging. Therefore, this study aims at establishing novel prognostic tumor DNA methylation biomarkers. In total, 396 low- and high-risk primary tumors were analyzed, of which 87 were profiled using methyl-CpG-binding domain (MBD) sequencing for differential methylation analysis between prognostic patient groups. Subsequently, methylation-specific PCR (MSP) assays were developed for 78 top-ranking differentially methylated regions and tested on two independent cohorts of 132 and 177 samples, respectively. Further, a new statistical framework was used to identify a robust set of MSP assays of which the methylation score (i.e. the percentage of methylated assays) allows accurate outcome prediction. Survival analyses were performed on the individual target level, as well as on the combined multimarker signature. As a result of the differential DNA methylation assessment by MBD sequencing, 58 of the 78 MSP assays were designed in regions previously unexplored in neuroblastoma, and 36 are located in non-promoter or non-coding regions. In total, 5 individual MSP assays (located in CCDC177, NXPH1, lnc-MRPL3-2, lnc-TREX1-1 and one on a region from chromosome 8 with no further annotation) predict event-free survival and 4 additional assays (located in SPRED3, TNFAIP2, NPM2 and CYYR1) also predict overall survival. Furthermore, a robust 58-marker methylation signature predicting overall and event-free survival was established. In conclusion, this study encompasses the largest DNA methylation biomarker study in neuroblastoma so far. We identified and independently validated several novel prognostic biomarkers, as well as a prognostic 58-marker methylation signature. PMID:26646589

  3. 40 CFR 721.10326 - 2-Propenoic acid, 2-methyl-, methyl ester, polymer with butyl 2-propenoate, ethyl 2-propenoate...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... ester, polymer with butyl 2-propenoate, ethyl 2-propenoate, zinc 2-methyl-2-propenoate (1:2) and zinc 2... 2-Propenoic acid, 2-methyl-, methyl ester, polymer with butyl 2-propenoate, ethyl 2-propenoate, zinc 2-methyl-2-propenoate (1:2) and zinc 2-propenoate (1:2), 2,2'-(1,2-diazenediyl)bis - and...

  4. Measurement of Mercury Methylation in Lake Water and Sediment Samples

    PubMed Central

    Furutani, Akira; Rudd, John W. M.

    1980-01-01

    Biological mercury methylation was assayed by a new radiochemical technique in the water column and sediments of a mercury-contaminated lake. In 24 weeks during 1979, there were three episodes of methylating activity in surface floc and in water, each lasting 3 to 5 weeks. Periods of methylation in the water column coincided with surface sediment methylation and appeared to be related to overall microbial activity. Mercury was actively methylated in the presence of bound sulfide. PMID:16345649

  5. Crystal structure of tris­(di­methyl­amido-κN)­bis­(di­methyl­amine-κN)­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 trigonal–bipyramidal coordination geometry around the metal atom. N⋯I contacts of 3.6153 (15) and 3.5922 (14) Å are consistent with the presence of N—H⋯I inter­actions. These N—H⋯I inter­actions link the complex cations and iodide anions into extended chains that propagate parallel to the a axis. PMID:26870590

  6. Methylation interactions in Arabidopsis hybrids require RNA-directed DNA methylation and are influenced by genetic variation.

    PubMed

    Zhang, Qingzhu; Wang, Dong; Lang, Zhaobo; He, Li; Yang, Lan; Zeng, Liang; Li, Yanqiang; Zhao, Cheng; Huang, Huan; Zhang, Heng; Zhang, Huiming; Zhu, Jian-Kang

    2016-07-19

    DNA methylation is a conserved epigenetic mark in plants and many animals. How parental alleles interact in progeny to influence the epigenome is poorly understood. We analyzed the DNA methylomes of Arabidopsis Col and C24 ecotypes, and their hybrid progeny. Hybrids displayed nonadditive DNA methylation levels, termed methylation interactions, throughout the genome. Approximately 2,500 methylation interactions occurred at regions where parental DNA methylation levels are similar, whereas almost 1,000 were at differentially methylated regions in parents. Methylation interactions were characterized by an abundance of 24-nt small interfering RNAs. Furthermore, dysfunction of the RNA-directed DNA methylation pathway abolished methylation interactions but did not affect the increased biomass observed in hybrid progeny. Methylation interactions correlated with altered genetic variation within the genome, suggesting that they may play a role in genome evolution. PMID:27382183

  7. Global Analysis of H3K4 Methylation Defines MLL Family Member Targets and Points to a Role for MLL1-Mediated H3K4 Methylation in the Regulation of Transcriptional Initiation by RNA Polymerase II ▿ †

    PubMed Central

    Wang, Pengfei; Lin, Chengqi; Smith, Edwin R.; Guo, Hong; Sanderson, Brian W.; Wu, Min; Gogol, Madelaine; Alexander, Tara; Seidel, Christopher; Wiedemann, Leanne M.; Ge, Kai; Krumlauf, Robb; Shilatifard, Ali

    2009-01-01

    A common landmark of activated genes is the presence of trimethylation on lysine 4 of histone H3 (H3K4) at promoter regions. Set1/COMPASS was the founding member and is the only H3K4 methylase in Saccharomyces cerevisiae; however, in mammals, at least six H3K4 methylases, Set1A and Set1B and MLL1 to MLL4, are found in COMPASS-like complexes capable of methylating H3K4. To gain further insight into the different roles and functional targets for the H3K4 methylases, we have undertaken a genome-wide analysis of H3K4 methylation patterns in wild-type Mll1+/+ and Mll1−/− mouse embryonic fibroblasts (MEFs). We found that Mll1 is required for the H3K4 trimethylation of less than 5% of promoters carrying this modification. Many of these genes, which include developmental regulators such as Hox genes, show decreased levels of RNA polymerase II recruitment and expression concomitant with the loss of H3K4 methylation. Although Mll1 is only required for the methylation of a subset of Hox genes, menin, a component of the Mll1 and Mll2 complexes, is required for the overwhelming majority of H3K4 methylation at Hox loci. However, the loss of MLL3/MLL4 and/or the Set1 complexes has little to no effect on the H3K4 methylation of Hox loci or their expression levels in these MEFs. Together these data provide insight into the redundancy and specialization of COMPASS-like complexes in mammals and provide evidence for a possible role for Mll1-mediated H3K4 methylation in the regulation of transcriptional initiation. PMID:19703992

  8. Biodegradation-inspired bioproduction of methylacetoin and 2-methyl-2,3-butanediol

    PubMed Central

    Jiang, Xinglin; Zhang, Haibo; Yang, Jianming; Zheng, Yanning; Feng, Dexin; Liu, Wei; Xu, Xin; Cao, Yujin; Zou, Huibin; Zhang, Rubin; Cheng, Tao; Jiao, Fengjiao; Xian, Mo

    2013-01-01

    Methylacetoin (3-hydroxy-3-methylbutan-2-one) and 2-methyl-2,3-butanediol are currently obtained exclusively via chemical synthesis. Here, we report, to the best of our knowledge, the first alternative route, using engineered Escherichia coli. The biological synthesis of methylacetoin was first accomplished by reversing its biodegradation, which involved modifying the enzyme complex involved, switching the reaction substrate, and coupling the process to an exothermic reaction. 2-Methyl-2,3-butanediol was then obtained by reducing methylacetoin by exploiting the substrate promiscuity of acetoin reductase. A complete biosynthetic pathway from renewable glucose and acetone was then established and optimized via in vivo enzyme screening and host metabolic engineering, which led to titers of 3.4 and 3.2 g l−1 for methylacetoin and 2-methyl-2,3-butanediol, respectively. This work presents a biodegradation-inspired approach to creating new biosynthetic pathways for small molecules with no available natural biosynthetic pathway. PMID:23945710

  9. Dispersion characteristics and sinks for methyl bromide vapors downwind of treated agricultural fields

    SciTech Connect

    Seiber, J.N.; Woodrow, J.E.; Dowling, K.

    1995-12-31

    A study of methyl bromide volatilization and fate from a treated agricultural field was conducted in Monterey County, California, in 1994. Air concentrations were measured above and downwind from the field with the objective of comparing vertical and horizontal flux terms. Another objective was to compare observed downwind concentrations with those predicted by the Industrial Source Complex model, to begin the process of identifying potential sinks which might scavenge methyl bromide from the atmosphere. The final objective was to determine the limit of detection of our analytical method for airborne methyl bromide using field samples representing a wide range of concentrations. A description of the methods and results of the study will be presented, along with a discussion of data quality and interpretation.

  10. Formation of methyl formate in comets by irradiation of methanol-bearing ices

    NASA Astrophysics Data System (ADS)

    Modica, P.; Palumbo, M. E.; Strazzulla, G.

    2012-12-01

    Methyl formate is a complex organic molecule considered potentially relevant as precursor of biologically active molecules. It has been observed in several astrophysical environments, such as hot cores, hot corinos, and comets. The processes that drive the formation of molecules in cometary ices are poorly understood. In particular it is not yet clear if molecules are directly accreted from the pre-solar nebula to form comets or are formed after accretion. The present work analyzes the possible role of cosmic ion irradiation and radioactive decay in methyl formate formation in methanol-bearing ices. The results indicate that cosmic ion irradiation can account for about 12% of the methyl formate observed in comet Hale-Bopp, while radioactive decay can account for about 6% of this amount. The need of new data coming from earth based and space observational projects as well as from laboratory experiments is outlined.

  11. Biodegradation-inspired bioproduction of methylacetoin and 2-methyl-2,3-butanediol.

    PubMed

    Jiang, Xinglin; Zhang, Haibo; Yang, Jianming; Zheng, Yanning; Feng, Dexin; Liu, Wei; Xu, Xin; Cao, Yujin; Zou, Huibin; Zhang, Rubin; Cheng, Tao; Jiao, Fengjiao; Xian, Mo

    2013-01-01

    Methylacetoin (3-hydroxy-3-methylbutan-2-one) and 2-methyl-2,3-butanediol are currently obtained exclusively via chemical synthesis. Here, we report, to the best of our knowledge, the first alternative route, using engineered Escherichia coli. The biological synthesis of methylacetoin was first accomplished by reversing its biodegradation, which involved modifying the enzyme complex involved, switching the reaction substrate, and coupling the process to an exothermic reaction. 2-Methyl-2,3-butanediol was then obtained by reducing methylacetoin by exploiting the substrate promiscuity of acetoin reductase. A complete biosynthetic pathway from renewable glucose and acetone was then established and optimized via in vivo enzyme screening and host metabolic engineering, which led to titers of 3.4 and 3.2 g l(-1) for methylacetoin and 2-methyl-2,3-butanediol, respectively. This work presents a biodegradation-inspired approach to creating new biosynthetic pathways for small molecules with no available natural biosynthetic pathway.

  12. Evidence for methyl group transfer between the methyl-accepting chemotaxis proteins in Bacillus subtilis

    SciTech Connect

    Bedale, W.A.; Nettleton, D.O.; Sopata, C.S.; Thoelke, M.S.; Ordal, G.W.

    1988-01-01

    The authors present evidence for methyl (as methyl or methoxy) transfer from the methyl-accepting chemotaxis proteins H1 and possibly H3 of Bacillus subtilis to the methyl-accepting chemotaxis protein H2. This methyl transfer, which has been observed in vitro was strongly stimulated by the chemoattractant aspartate and thus may plan an important role in the sensory processing system of this organism. Although radiolabeling of H1 and H3 began at once after the addition of (/sup 3/H) methionine, radiolabeling of H2 showed a lag. Furthermore, the addition of excess nonradioactive methionine caused immediate exponential delabeling of H1 and H3 while labeling of H2 continued to increase. Methylation of H2 required the chemotactic methyltransferase, probably to first methylate H1 and H3. Aspartate caused increased labeling of H2 and strongly decreased labeling of H1 and H3 after the addition of nonradioactive methionine. Without the addition of nonradioactive methionine, aspartate caused demethylation of H1 and to a lesser extent H3, with an approximately equal increase of methylation of H2.

  13. Methyl N-phenyl carbamate synthesis from aniline and methyl formate: carbon recycling to chemical products.

    PubMed

    Yalfani, Mohammad S; Lolli, Giulio; Müller, Thomas E; Wolf, Aurel; Mleczko, Leslaw

    2015-02-01

    Methyl N-phenyl carbamate was synthesized from aniline by using methyl formate as a green and efficient carbonylating agent. High yields were obtained at milder reaction conditions compared to the conventional CO/CH3 OH route. Studies on the reaction sequence led to suggest an alternative and more efficient route to the carbamate via formanilide as intermediate.

  14. MethylAction: detecting differentially methylated regions that distinguish biological subtypes.

    PubMed

    Bhasin, Jeffrey M; Hu, Bo; Ting, Angela H

    2016-01-01

    DNA methylation differences capture substantial information about the molecular and gene-regulatory states among biological subtypes. Enrichment-based next generation sequencing methods such as MBD-isolated genome sequencing (MiGS) and MeDIP-seq are appealing for studying DNA methylation genome-wide in order to distinguish between biological subtypes. However, current analytic tools do not provide optimal features for analyzing three-group or larger study designs. MethylAction addresses this need by detecting all possible patterns of statistically significant hyper- and hypo- methylation in comparisons involving any number of groups. Crucially, significance is established at the level of differentially methylated regions (DMRs), and bootstrapping determines false discovery rates (FDRs) associated with each pattern. We demonstrate this functionality in a four-group comparison among benign prostate and three clinical subtypes of prostate cancer and show that the bootstrap FDRs are highly useful in selecting the most robust patterns of DMRs. Compared to existing tools that are limited to two-group comparisons, MethylAction detects more DMRs with strong differential methylation measurements confirmed by whole genome bisulfite sequencing and offers a better balance between precision and recall in cross-cohort comparisons. MethylAction is available as an R package at http://jeffbhasin.github.io/methylaction.

  15. High-Throughput Analysis of Global DNA Methylation Using Methyl-Sensitive Digestion

    PubMed Central

    Feinweber, Carmen; Knothe, Claudia; Lötsch, Jörn; Thomas, Dominique; Geisslinger, Gerd; Parnham, Michael J.; Resch, Eduard

    2016-01-01

    DNA methylation is a major regulatory process of gene transcription, and aberrant DNA methylation is associated with various diseases including cancer. Many compounds have been reported to modify DNA methylation states. Despite increasing interest in the clinical application of drugs with epigenetic effects, and the use of diagnostic markers for genome-wide hypomethylation in cancer, large-scale screening systems to measure the effects of drugs on DNA methylation are limited. In this study, we improved the previously established fluorescence polarization-based global DNA methylation assay so that it is more suitable for application to human genomic DNA. Our methyl-sensitive fluorescence polarization (MSFP) assay was highly repeatable (inter-assay coefficient of variation = 1.5%) and accurate (r2 = 0.99). According to signal linearity, only 50–80 ng human genomic DNA per reaction was necessary for the 384-well format. MSFP is a simple, rapid approach as all biochemical reactions and final detection can be performed in one well in a 384-well plate without purification steps in less than 3.5 hours. Furthermore, we demonstrated a significant correlation between MSFP and the LINE-1 pyrosequencing assay, a widely used global DNA methylation assay. MSFP can be applied for the pre-screening of compounds that influence global DNA methylation states and also for the diagnosis of certain types of cancer. PMID:27749902

  16. DNA methylation profiling for a confirmatory test for blood, saliva, semen, vaginal fluid and menstrual blood.

    PubMed

    Lee, Hwan Young; Jung, Sang-Eun; Lee, Eun Hee; Yang, Woo Ick; Shin, Kyoung-Jin

    2016-09-01

    The ability to predict the type of tissues or cells from molecular profiles of crime scene samples has important practical implications in forensics. A previously reported multiplex assay using DNA methylation markers could only discriminate between 4 types of body fluids: blood, saliva, semen, and the body fluid which originates from female reproductive organ. In the present study, we selected 15 menstrual blood-specific CpG marker candidates based on analysis of 12 genome-wide DNA methylation profiles of vaginal fluid and menstrual blood. The menstrual blood-specificity of the candidate markers was confirmed by comparison with HumanMethylation450 BeadChip array data obtained for 58 samples including 12 blood, 12 saliva, 12 semen, 3 vaginal fluid, and 19 skin epidermis samples. Among 15CpG marker candidates, 3 were located in the promoter region of the SLC26A10 gene, and 2 of them (cg09696411 and cg18069290) showed high menstrual blood specificity. DNA methylation at the 2CpG markers was further tested by targeted bisulfite sequencing of 461 additional samples including 49 blood, 52 saliva, 34 semen, 125 vaginal fluid, and 201 menstrual blood. Because the 2 markers showed menstrual blood-specific methylation patterns, we modified our previous multiplex methylation SNaPshot reaction to include these 2 markers. In addition, a blood marker cg01543184 with cross reactivity to semen was replaced with cg08792630, and a semen-specific unmethylation marker cg17621389 was removed. The resultant multiplex methylation SNaPshot allowed positive identification of blood, saliva, semen, vaginal fluid and menstrual blood using the 9CpG markers which show a methylation signal only in the target body fluids. Because of the complexity in cell composition, menstrual bloods produced DNA methylation profiles that vary with menstrual cycle and sample collection methods, which are expected to provide more insight into forensic menstrual blood test. Moreover, because the developed

  17. Dissolved Organic Matter Enhances Hg Bioavailability to a Hg-Methylating Bacterium Under Mildly Sulfidic Conditions

    NASA Astrophysics Data System (ADS)

    Graham, A. M.; Gilmour, C. C.

    2011-12-01

    Field studies have demonstrated a strong linkage between dissolved organic matter (DOM) quantity and quality and in-situ methylmercury (MeHg) production. The biogeochemical basis for these field observations is unknown however. Here, we investigate the roles of DOM and sulfide in controlling Hg bioavailability to the Hg-methylating bacterium Desulfovibrio desulfuricans ND132 in short-term washed cell assays. At environmentally relevant Hg/DOM ratios (2-4300 ng Hg/mg DOM), MeHg production increased linearly with increasing Suwannee River humic acid (SRHA) concentration, even in the presence of sulfide concentrations (5-10 μM) sufficient to outcompete SRHA for inorganic Hg. The DOM-dependent enhancement in Hg-methylation cannot be attributed to an enhancement of ND132 metabolic activity or alteration of Hg sorption to cells or bottle walls. Equilibrium speciation calculations indicated that cell suspensions were supersaturated with respect to metacinnabar (β-HgS(s)) and that Hg-DOM thiol complexes were relatively minor species. Notably, SRHA addition had no effect on Hg methylation in solutions where Hg-cysteine species predominated and β-HgS(s) precipitation was not predicted. We hypothesize that DOM enhances Hg-methylation by stabilizing HgS(s) colloids or nanoparticles against aggregation and/or by reducing the crystallinty of HgS(s) particles, and that such HgS(s) colloids are bioavailable to Hg-methylating bacteria. Ongoing work in the laboratory is evaluating the role of DOM character (size, aromaticity, reduced S content, etc.) in controlling the extent of the enhancement in MeHg production. These findings highlight the limits of equilibrium speciation approaches to predicting Hg bioavailability to methylating bacteria given the demonstrated significance of Hg-DOM-sulfide interactions in the anoxic environments where methylation occurs. Our laboratory experiments provide additional insight into the role that DOM plays in determining spatial and temporal

  18. Emerging Molecular and Biological Functions of MBD2, a Reader of DNA Methylation

    PubMed Central

    Wood, Kathleen H.; Zhou, Zhaolan

    2016-01-01

    DNA methylation is an epigenetic mark that is essential for many biological processes and is linked to diseases such as cancer. Methylation is usually associated with transcriptional silencing, but new research has challenged this model. Both transcriptional activation and repression have recently been found to be associated with DNA methylation in a context-specific manner. How DNA methylation patterns are interpreted into different functional output remains poorly understood. One mechanism involves the protein ‘readers’ of methylation, which includes the methyl-CpG binding domain (MBD) family of proteins. This review examines the molecular and biological functions of MBD2, which binds to CpG methylation and is an integral part of the nucleosome remodeling and histone deacetylation (NuRD) complex. MBD2 has been linked to immune system function and tumorigenesis, yet little is known about its functions in vivo. Recent studies have found the MBD2 protein is ubiquitously expressed, with relatively high levels in the lung, liver, and colon. Mbd2 null mice surprisingly show relatively mild phenotypes compared to mice with loss of function of other MBD proteins. This evidence has previously been interpreted as functional redundancy between the MBD proteins. Here, we examine and contextualize research that suggests MBD2 has unique properties and functions among the MBD proteins. These functions translate to recently described roles in the development and differentiation of multiple cell lineages, including pluripotent stem cells and various cell types of the immune system, as well as in tumorigenesis. We also consider possible models for the dynamic interactions between MBD2 and NuRD in different tissues in vivo. The functions of MBD2 may have direct therapeutic implications for several areas of human disease, including autoimmune conditions and cancer, in addition to providing insights into the actions of NuRD and chromatin regulation. PMID:27303433

  19. Notes on the role of dynamic DNA methylation in mammalian development

    PubMed Central

    Bestor, Timothy H.; Edwards, John R.; Boulard, Mathieu

    2015-01-01

    It has been nearly 40 y since it was suggested that genomic methylation patterns could be transmitted via maintenance methylation during S phase and might play a role in the dynamic regulation of gene expression during development [Holliday R, Pugh JE (1975) Science 187(4173):226–232; Riggs AD (1975) Cytogenet Cell Genet 14(1):9–25]. This revolutionary proposal was justified by “... our almost complete ignorance of the mechanism for the unfolding of the genetic program during development” that prevailed at the time. Many correlations between transcriptional activation and demethylation have since been reported, but causation has not been demonstrated and to date there is no reasonable proof of the existence of a complex biochemical system that activates and represses genes via reversible DNA methylation. Such a system would supplement or replace the conserved web of transcription factors that regulate cellular differentiation in organisms that have unmethylated genomes (such as Caenorhaditis elegans and the Dipteran insects) and those that methylate their genomes. DNA methylation does have essential roles in irreversible promoter silencing, as in the monoallelic expression of imprinted genes, in the silencing of transposons, and in X chromosome inactivation in female mammals. Rather than reinforcing or replacing regulatory pathways that are conserved between organisms that have either methylated or unmethylated genomes, DNA methylation endows genomes with the ability to subject specific sequences to irreversible transcriptional silencing even in the presence of all of the factors required for their expression, an ability that is generally unavailable to organisms that have unmethylated genomes. PMID:25368180

  20. Hidden among the crowd: differential DNA methylation-expression correlations in cancer occur at important oncogenic pathways

    PubMed Central

    Mosquera Orgueira, Adrián

    2015-01-01

    DNA methylation is a frequent epigenetic mechanism that participates in transcriptional repression. Variations in DNA methylation with respect to gene expression are constant, and, for unknown reasons, some genes with highly methylated promoters are sometimes overexpressed. In this study we have analyzed the expression and methylation patterns of thousands of genes in five groups of cancer and normal tissue samples in order to determine local and genome-wide differences. We observed significant changes in global methylation-expression correlation in all the neoplasms, which suggests that differential correlation events are frequent in cancer. A focused analysis in the breast cancer cohort identified 1662 genes whose correlation varies significantly between normal and cancerous breast, but whose DNA methylation and gene expression patterns do not change substantially. These genes were enriched in cancer-related pathways and repressive chromatin features across various model cell lines, such as PRC2 binding and H3K27me3 marks. Substantial changes in methylation-expression correlation indicate that these genes are subject to epigenetic remodeling, where the differential activity of other factors break the expected relationship between both variables. Our findings suggest a complex regulatory landscape where a redistribution of local and large-scale chromatin repressive domains at differentially correlated genes (DCGs) creates epigenetic hotspots that modulate cancer-specific gene expression. PMID:26029238