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1

PAF1-complex-mediated histone methylation of FLOWERING  

E-print Network

PAF1-complex-mediated histone methylation of FLOWERING LOCUS C chromatin is required for exposure to the cold of winter to flower in the spring) in Arabidopsis thaliana is mainly due to the repression of flowering by relatively high levels of FLC expression. Exposure to prolonged cold attenuates

Raines, Ronald T.

2

A proteomic analysis of arginine-methylated protein complexes.  

PubMed

Arginine methylation is a post-translational modification that results in the formation of asymmetrical and symmetrical dimethylated arginines (a- and sDMA). This modification is catalyzed by type I and II protein-arginine methyltransferases (PRMT), respectively. The two major enzymes PRMT1 (type I) and PRMT5 (type II) preferentially methylate arginines located in RG-rich clusters. Arginine methylation is a common modification, but the reagents for detecting this modification have been lacking. Thus, fewer than 20 proteins have been identified in the last 40 years as containing dimethylated arginines. We have generated previously four arginine methyl-specific antibodies; ASYM24 and ASYM25 are specific for aDMA, whereas SYM10 and SYM11 recognize sDMA. All of these antibodies were generated by using peptides with aDMA or sDMA in the context of different RG-rich sequences. HeLa cell extracts were used to purify the protein complexes recognized by each of the four antibodies, and the proteins were identified by microcapillary reverse-phase liquid chromatography coupled on line with electrospray ionization tandem mass spectrometry. The analysis of two tandem mass spectra for each methyl-specific antibody resulted in the identification of over 200 new proteins that are putatively arginine-methylated. The major protein complexes that were purified include components required for pre-mRNA splicing, polyadenylation, transcription, signal transduction, and cytoskeleton and DNA repair. These findings provide a basis for the identification of the role of arginine methylation in many cellular processes. PMID:14534352

Boisvert, François-Michel; Côté, Jocelyn; Boulanger, Marie-Chloé; Richard, Stéphane

2003-12-01

3

Azacytidine causes complex DNA methylation responses in myeloid leukemia.  

PubMed

Aberrant DNA methylation patterns play an important role in the pathogenesis of hematologic malignancies. The DNA methyltransferase inhibitors azacytidine and decitabine have shown significant clinical benefits in the treatment of myelodysplastic syndrome (MDS), but their precise mode of action remains to be established. Both drugs have been shown the ability to deplete DNA methyltransferase enzymes and to induce DNA demethylation and epigenetic reprogramming in vitro. However, drug-induced methylation changes have remained poorly characterized in patients and therapy-related models. We have now analyzed azacytidine-induced demethylation responses in myeloid leukemia cell lines. These cells showed remarkable differences in the drug-induced depletion of DNA methyltransferases that coincided with their demethylation responses. In agreement with these data, DNA methylation analysis of blood and bone marrow samples from MDS patients undergoing azacytidine therapy also revealed substantial differences in the epigenetic responses of individual patients. Significant, transient demethylation could be observed in 3 of 6 patients and affected many hypermethylated loci in a complex pattern. Our results provide important proof-of-mechanism data for the demethylating activity of azacytidine in MDS patients and provide detailed insight into drug-induced demethylation responses. PMID:18790780

Stresemann, Carlo; Bokelmann, Imke; Mahlknecht, Ulrich; Lyko, Frank

2008-09-01

4

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

E-print Network

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

Jones, William D.

5

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

PubMed

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

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

2014-10-23

6

Crystal and solution structure of oxo rhenium(V) complexes with cysteine and cysteine methyl ester.  

PubMed

The monooxo rhenium(V) complexes of cysteine (complex 1) and cysteine methyl ester (complex 2) were synthesised via a ligand exchange reaction starting from gluconatooxorhenium(V). Unexpectedly, the obtained oxorhenium(V) complex with cysteine methyl ester (2) was partially saponified. Both complexes were characterised by common analytical techniques in their solid state. Thus, an octahedral complex structure with 2(NH2,S) co-ordination in the equatorial plane and one carboxyl group bound trans to the oxo group is proven for complex 2 by X-ray diffraction. Furthermore, the existence of a dioxo species at higher pH was proven for the first time with this type of ligand by determining the nearest co-ordination sphere of the rhenium centre in solution at a pH of 12 using extended X-ray absorption fine structure spectroscopy. PMID:10499102

Kirsch, S; Jankowsky, R; Leibnitz, P; Spies, H; Johannsen, B

1999-02-01

7

SMYD2-dependent HSP90 methylation promotes cancer cell proliferation by regulating the chaperone complex formation.  

PubMed

Heat shock protein 90 (HSP90) is a highly conserved molecular chaperone that facilitates the maturation of a wide range of proteins, and it has been recognized as a crucial facilitator of oncogene addiction and cancer cell survival. Although HSP90 function is regulated by a variety of post-translational modifications, the physiological significance of methylation has not fully been elucidated. Here we demonstrate that HSP90AB1 is methylated by the histone methyltransferase SMYD2 and that it plays a critical role in human carcinogenesis. HSP90AB1 and SMYD2 can interact through the C-terminal region of HSP90AB1 and the SET domain of SMYD2. Both in vitro and in vivo methyltransferase assays revealed that SMYD2 could methylate HSP90AB1 and mass spectrometry analysis indicated lysines 531 and 574 of HSP90AB1 to be methylated. These methylation sites were shown to be important for the dimerization and chaperone complex formation of HSP90AB1. Furthermore, methylated HSP90AB1 accelerated the proliferation of cancer cells. Our study reveals a novel mechanism for human carcinogenesis via methylation of HSP90AB1 by SMYD2, and additional functional studies may assist in developing novel strategies for cancer therapy. PMID:24880080

Hamamoto, Ryuji; Toyokawa, Gouji; Nakakido, Makoto; Ueda, Koji; Nakamura, Yusuke

2014-08-28

8

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

PubMed Central

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. PMID:22592791

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.

2012-01-01

9

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

PubMed

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. PMID:22592791

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

2012-05-29

10

Histone H3 lysine 36 methylation targets the Isw1b remodeling complex to chromatin.  

PubMed

Histone H3 lysine 36 methylation is a ubiquitous hallmark of productive transcription elongation. Despite the prevalence of this histone posttranslational modification, however, the downstream functions triggered by this mark are not well understood. In this study, we showed that H3K36 methylation promoted the chromatin interaction of the Isw1b chromatin-remodeling complex in Saccharomyces cerevisiae. Similar to H3K36 methylation, Isw1b was found at the mid- and 3' regions of transcribed genes genome wide, and its presence at active genes was dependent on H3K36 methylation and the PWWP domain of the Isw1b subunit, Ioc4. Moreover, purified Isw1b preferentially interacted with recombinant nucleosomes that were methylated at lysine 36, and this interaction also required the Ioc4 PWWP domain. While H3K36 methylation has been shown to regulate the binding of numerous factors, this is the first time that it has been shown to facilitate targeting of a chromatin-remodeling complex. PMID:22751925

Maltby, Vicki E; Martin, Benjamin J E; Schulze, Julia M; Johnson, Ian; Hentrich, Thomas; Sharma, Aishwariya; Kobor, Michael S; Howe, LeAnn

2012-09-01

11

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

SciTech Connect

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.

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. (UCLA); (MSKCC); (Delaware)

2012-10-23

12

The methanol·HCl complex: structure and methyl group internal rotation barrier  

Microsoft Academic Search

The rotational spectra of the methanol·HCl complex and several of its isotopomers were reinvestigated by Fourier transform-microwave spectroscopy. An ambiguity in the assignment of the ground state rotational spectrum was clarified. New E state transitions were measured and fit to determine the potential barrier that hinders the methyl group internal rotation for all species. A dramatic reduction in this torsional

Xue-Qing Tan; Ioannis I. Ioannou; Robert L. Kuczkowski

1995-01-01

13

The Methanol · Ar Complex: Apparent Reduction of the Methyl Group Internal Rotation Barrier  

Microsoft Academic Search

The rotational spectra of the methanol · Ar complex and five of its isotopomers were reinvestigated by Fourier transform microwave spectroscopy. New E internal rotation state transitions were measured and fit to determine the potential barrier that hinders the methyl group internal rotation for all the species. A dramatic reduction of this torsional barrier height determined using the conventional internal

X. Q. Tan; L. H. Sun; R. L. Kuczkowski

1995-01-01

14

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

PubMed Central

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

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

2010-01-01

15

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

PubMed

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

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

2010-05-25

16

Fixation of atmospheric carbon dioxide by ruthenium complexes bearing an NHC-based pincer ligand: formation of a methylcarbonato complex and its methylation.  

PubMed

A methylcarbonato ruthenium complex was prepared by capture of CO2 from air using the (CNC)(bpy)Ru scaffold. The methylcarbonato complex was relatively inert to decarboxylation. Treatments with methylating reagents released dimethylcarbonate. PMID:25711491

Arikawa, Yasuhiro; Nakamura, Takuo; Ogushi, Shinji; Eguchi, Kazushige; Umakoshi, Keisuke

2015-03-10

17

Signaling within a coactivator complex: methylation of SRC-3/AIB1 is a molecular switch for complex disassembly.  

PubMed

Recent studies indicate that steroid receptor-mediated transcriptional initiation is a cyclical process involving multiple rounds of coactivator assembly and disassembly. Steroid receptor coactivator 3 (SRC-3) coactivator phosphorylation has been shown to regulate coactivator complex assembly, but the mechanisms by which coactivator disassembly is triggered are not well understood. In this study, we provide in vitro and in vivo evidence that members of the SRC coactivator family serve as substrates for the enzymatic coactivator coactivator-associated arginine methyltransferase 1 (CARM1). Methylation of SRC-3 was localized to an arginine in its CARM1 binding region and correlated with decreased estrogen receptor alpha-mediated transcription, as seen with both cell-based and in vitro transcription assays. Consistent with this finding, we demonstrated that methylation promotes dissociation of the SRC-3/CARM1 coactivator complex. Methylation of SRC-3 is regulated by estrogen signaling in MCF7 cells and serves as a molecular switch for disassembly of the SRC-3 transcriptional coactivator complex. We propose that CARM1 is a dual-function coactivator, as it not only activates transcription by modifying core histone tails but also terminates hormone signaling by disassembly of the coactivator complex. PMID:16923966

Feng, Qin; Yi, Ping; Wong, Jiemin; O'Malley, Bert W

2006-11-01

18

A novel structural motif for calix[4]arene dihydrophosphonic acid in its complex with di-methyl ammonium and tetra-methyl ammonium cations  

NASA Astrophysics Data System (ADS)

The structure of calix[4]arene dihydrophosphonic acid in its complex with di-methyl ammonium and tetra-methyl ammonium cations shows a novel dimeric structural motifs for the calixarene assembly, with one calixarene unit showing distal aromatic rings inclined into the cavity and then both of the rings partially included into the cavity of a second molecule present in the flattened cone conformation.

Danylyuk, Oksana; Lazar, Adina N.; Coleman, Anthony W.; Suwinska, Kinga

2008-11-01

19

A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder.  

PubMed

Epigenetic studies of DNA and histone modifications represent a new and important activity in molecular investigations of human disease. Our previous epigenome-wide scan identified numerous DNA methylation differences in post-mortem brain samples from individuals affected with major psychosis. In this article, we present the results of fine mapping DNA methylation differences at the human leukocyte antigen (HLA) complex group 9 gene (HCG9) in bipolar disorder (BPD). Sodium bisulfite conversion coupled with pyrosequencing was used to interrogate 28 CpGs spanning ?700 bp region of HCG9 in 1402 DNA samples from post-mortem brains, peripheral blood cells and germline (sperm) of bipolar disease patients and controls. The analysis of nearly 40?000 CpGs revealed complex relationships between DNA methylation and age, medication as well as DNA sequence variation (rs1128306). Two brain tissue cohorts exhibited lower DNA methylation in bipolar disease patients compared with controls at an extended HCG9 region (P=0.026). Logistic regression modeling of BPD as a function of rs1128306 genotype, age and DNA methylation uncovered an independent effect of DNA methylation in white blood cells (odds ratio (OR)=1.08, P=0.0077) and the overall sample (OR=1.24, P=0.0011). Receiver operating characteristic curve A prime statistics estimated a 69-72% probability of correct BPD prediction from a case vs control pool. Finally, sperm DNA demonstrated a significant association (P=0.018) with BPD at one of the regions demonstrating epigenetic changes in the post-mortem brain and peripheral blood samples. The consistent multi-tissue epigenetic differences at HCG9 argue for a causal association with BPD. PMID:21647149

Kaminsky, Z; Tochigi, M; Jia, P; Pal, M; Mill, J; Kwan, A; Ioshikhes, I; Vincent, J B; Kennedy, J L; Strauss, J; Pai, S; Wang, S-C; Petronis, A

2012-07-01

20

CCR4/NOT complex associates with the proteasome and regulates histone methylation.  

PubMed

The proteasome regulates histone lysine methylation and gene transcription, but how it does so is poorly understood. To better understand this process, we used the epistatic miniarray profile (E-MAP) approach to identify factors that genetically interact with proteasomal subunits. In addition to members of the Set1 complex that mediate histone H3 lysine 4 methylation (H3K4me), we found that deleting members of the CCR4/NOT mRNA processing complex exhibit synthetic phenotypes when combined with proteasome mutants. Further biochemical analyses revealed physical associations between CCR4/NOT and the proteasome in vivo. Consistent with the genetic and biochemical interactions linking CCR4/NOT with proteasome and Set1-mediated methylation, we find that loss of Not4 decreases global and gene-specific H3K4 trimethylation (H3K4me3) and decreases 19S proteasome recruitment to the PMA1 gene. Similar to proteasome regulation of histone methylation, loss of CCR4/NOT members does not affect ubiquitinated H2B. Mapping of Not4 identified the RING finger domain as essential for H3K4me3, suggesting a role for ubiquitin in this process. Consistent with this idea, loss of the Not4-interacting protein Ubc4, a known ubiquitin-conjugating enzyme, decreases H3K4me3. These studies implicate CCR4/NOT in the regulation of H3K4me3 through a ubiquitin-dependent pathway that likely involves the proteasome. PMID:17389396

Laribee, R Nicholas; Shibata, Yoichiro; Mersman, Douglas P; Collins, Sean R; Kemmeren, Patrick; Roguev, Assen; Weissman, Jonathan S; Briggs, Scott D; Krogan, Nevan J; Strahl, Brian D

2007-04-01

21

On the complexation of quercetin with methyl-?-cyclodextrin: photostability and antioxidant studies  

Microsoft Academic Search

Quercetin, a plant-derived flavonoid, has been extensively investigated for a wide range of potential health benefits linked\\u000a to its antioxidant properties. Unfortunately the topical administration of this molecule is restricted by its fast photodegradation.\\u000a In the attempt to overcome this limitation the inclusion complex between quercetin (Q) and methyl-?-cyclodextrin (Me-?-CD)\\u000a was prepared and previously investigated by a molecular modelling study,

M. E. Carlotti; S. Sapino; E. Ugazio; G. Caron

2011-01-01

22

Structural studies of MeCP2 in complex with methylated DNA   

E-print Network

DNA methylation is a common epigenetic mark that affects gene regulation, genomic stability and chromatin structure. In mammals, methylation is mainly found in the CpG dinucleotides. The CpG methylation signals can be recognised by the Methyl...

Ho, Kok Lian

2009-01-01

23

Methylated Trivalent Arsenic-Glutathione Complexes are More Stable than their Arsenite Analog  

PubMed Central

The trivalent arsenic glutathione complexes arsenic triglutathione, methylarsonous diglutathione, and dimethylarsinous glutathione are key intermediates in the mammalian metabolism of arsenite and possibly represent the arsenic species that are transported from the liver to the kidney for urinary excretion. Despite this, the comparative stability of the arsenic-sulfur bonds in these complexes has not been investigated under physiological conditions resembling hepatocyte cytosol. Using size-exclusion chromatography and a glutathione-containing phosphate buffered saline mobile phase (5 or 10 mM glutathione, pH 7.4) in conjunction with an arsenic-specific detector, we chromatographed arsenite, monomethylarsonous acid, and dimethylarsinous acid. The on-column formation of the corresponding arsenic-glutathione complexes between 4 and 37°C revealed that methylated arsenic-glutathione complexes are more stable than arsenic triglutathione. The relevance of these results with regard to the metabolic fate of arsenite in mammals is discussed. PMID:18509491

Percy, Andrew J.; Gailer, Jürgen

2008-01-01

24

Complexes of polyadenylic acid and the methyl esters of amino acids  

NASA Technical Reports Server (NTRS)

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.

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

1983-01-01

25

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

PubMed

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

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

2015-01-01

26

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

SciTech Connect

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.

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

27

Spectroscopy and dynamics of methyl-4-hydroxycinnamate: the influence of isotopic substitution and water complexation.  

PubMed

High-resolution Resonance Enhanced MultiPhoton Ionization (REMPI) and Laser Induced Fluorescence (LIF) excitation spectra of jet-cooled methyl-4-hydroxycinnamate, methyl-4-OD-cinnamate, and of their water clusters have been recorded. Whereas water complexation leads to significant linewidth narrowing, isotopic substitution does for all practical purposes not influence the excited-state dynamics. In this light, we evaluate two previously proposed decay channels of the photoexcited ??* state involving the dissociative ??* state (analogous to phenol) and involving the optically dark n?* state (as concluded for para-coumaric acid). To come to an unambiguous interpretation of the REMPI studies, it has been necessary to determine ionization thresholds. For methyl-4-hydroxycinnamate and its water cluster values of 8.078 and 7.636 eV have been found. Apart from the electronic excitation studies, IR absorption studies have been performed as well. These studies provide important vibrational markers for the assignment of the various conformations that are present under molecular beam conditions, and offer a direct measure of the influence of hydrogen bonding on the properties of the hydroxyl group. PMID:21246114

Smolarek, Szymon; Vdovin, Alexander; Tan, Eric M M; de Groot, Mattijs; Buma, Wybren Jan

2011-03-14

28

Preparation and characterization of uranyl complexes with three isomeric methyl-pyridine-N-oxide ligands  

Microsoft Academic Search

The synthesis and characterization of complexes of uranyl nitrate with methyl-pyridine-N-oxide isomers (picoline-N-oxide (2-picNO), 3-picoline-N-oxide (3-picNO) and 4-picoline-N-oxide (4-picNO)) as ligands (L) are described. They were prepared by reaction of hydrated uranyl nitrate with ligands in ethanolic solution (molar ratio 1:2). The compounds were characterized by CHN microanalytical procedures, infrared spectroscopy, X-ray powder diffraction, and TG\\/DTG. The analytical results suggest

M. G Alvarenga; L. B Zinner; C. A Fantin; J. R Matos; G Vicentini

2004-01-01

29

Methyl Dynamics of a Ca2+-Calmodulin-Peptide Complex from NMR/SRLS  

PubMed Central

We developed the slowly relaxing local structure (SRLS) approach for analyzing NMR spin relaxation in proteins. SRLS accounts for dynamical coupling between the tumbling of the protein and the local motion of the probe, and for general tensorial properties. It is the generalization of the traditional model-free (MF) method, which does not account for mode-coupling and treats only simple tensiorial properties. SRLS is applied herein to 2H relaxation of 13CDH2 groups in the complex of Ca2+?calmodulin with the peptide smMLCKp. Literature data comprising 2H T1 and T2 acquired at 14.1 and 17.6 T, and 288, 295, 308 and 320 K, are used. We find that mode-coupling is a small effect for methyl dynamics. On the other hand, general tensorial properties are important. In particular, it is important to allow for the asymmetry of the local spatial restrictions, which can be represented in SRLS by a rhombic local ordering tensor with components S02 and S22. Here, we find that ?0.2?S02?0.5 and ?0.4?S22?0. MF features a single "generalized" order parameter, S, confined to the 0–0.316 range. The parameter S is inaccurate, having absorbed unaccounted for effects, notably S22?0. We find that the methionine methyls (the other methyl types) reorient with rates of 8.6×109–21.4×109 (0.67×109–6.5×109) 1/s. The corresponding activation energies are 10 (10–27) kJ/mol. By contrast, MF yields inaccurate effective local motional correlation times, ?e, with non-physical temperature-dependence. Thus, the problematic S-, and ?e-based MF picture of methyl dynamics has been replaced with an insightful physical picture based on a local ordering tensor related to structural features, and a local diffusion tensor that yields accurate activation energies. PMID:21166433

Shapiro, Yury E.; Polimeno, Antonino; Freed, Jack H.; Meirovitch, Eva

2011-01-01

30

Environmental significance of the diclofop-methyl and cyclodextrin inclusion complexes.  

PubMed

Cyclodextrins (CDs) possess a hydrophilic external surface and a hydrophobic cavity. They are thus highly soluble and, in the meantime, effectively form inclusion complexes with hydrophobic organic compounds to enhance their solubilities. In this study, the complexation between modified beta-CDs and the herbicide diclofop-methyl (DM), (2-(4-(2,4-dichlorophenoxy)-phenoxy) propionate), was investigated. The complexation was confirmed by the shifts in the wavelengths of maximum ultra violet (UV) absorption and fluorescence excitation/emission. The deuterium isotope effects indicate that in the presence of beta-CDs the solubility of DM was lower while that of diclofop was higher in D2O than in H2O, suggesting the primary role of hydrophobic interactions in complexation. The solubility of DM was enhanced in the presence of beta-CDs, the extent of which depended on the modification of beta-CDs. The complexation reduced the hydrolysis of DM and hence increased its stability. The small inconsistency in the power of beta-CDs between hydrolysis retardation and solubilization suggests that hydrolysis was affected by the properties of beta-CDs and the configuration of DM in the complexes. Use of beta-CDs may thus result in the mobilization of soil DM. Properly modified beta-CDs may be utilized as formulation additives for improved delivery of DM and for enhanced environmental remediation. PMID:16923595

Cai, Xiyun; Zhang, Anping; Liu, Weiping

2006-01-01

31

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

NASA Astrophysics Data System (ADS)

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

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

2014-04-01

32

MBD2MBD3 complex binds to hemi-methylated DNA and forms a complex containing DNMT1 at the replication foci in late S phase  

Microsoft Academic Search

Background: In vertebrates and plants, DNA methy- lation is one of the major mechanisms regulating gene expression. Recently, a family of methyl-CpG- binding proteins has been identified, and some members, such as MeCP2 and MBD2, were shown to mediate gene repression by recruiting histone deacetylase complexes to methylated genes. How- ever, the function of another member of this family, MBD3,

Ken-ichiro Tatematsu; Tetsu Yamazaki; Fuyuki Ishikawa

2000-01-01

33

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

NASA Astrophysics Data System (ADS)

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

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

2003-10-01

34

Raman spectroscopy of neutral and doped poly(3-methyl thienylene) and poly(3-methyl thienylene)-heteropolyanion complexes  

Microsoft Academic Search

In the first part of this paper is reported a Raman study performed on several electrochemically prepared poly(3-methyl thienylene) (P3MeT) films. The sample dependence of the Raman spectra is analysed. A correlation between the intensity, the frequency and the width of the Raman lines and the nature of the films under consideration (defined in terms of thickness, conjugation length, amount

J. L. Sauvajol; J. P. Lere-Porte; C. Chorro; G. Poussigue

1992-01-01

35

NDUFAF7 Methylates Arginine 85 in the NDUFS2 Subunit of Human Complex I*  

PubMed Central

Complex I (NADH ubiquinone oxidoreductase) in mammalian mitochondria is an L-shaped assembly of 44 subunits. One arm is embedded in the inner membrane with the other protruding ?100 ? into the matrix of the organelle. The extrinsic arm contains binding sites for NADH and the primary electron acceptor FMN, and it provides a scaffold for seven iron-sulfur clusters that form an electron pathway linking FMN to the terminal electron acceptor, ubiquinone, which is bound in the region of the junction between the arms. The membrane arm contains four antiporter-like domains, probably energetically coupled to the quinone site and involved in pumping protons from the matrix into the intermembrane space contributing to the proton motive force. Complex I is put together from preassembled subcomplexes. Their compositions have been characterized partially, and at least 12 extrinsic assembly factor proteins are required for the assembly of the complex. One such factor, NDUFAF7, is predicted to belong to the family of S-adenosylmethionine-dependent methyltransferases characterized by the presence in their structures of a seven-?-strand protein fold. In the present study, the presence of NDUFAF7 in the mitochondrial matrix has been confirmed, and it has been demonstrated that it is a protein methylase that symmetrically dimethylates the ?-NG,NG? atoms of residue Arg-85 in the NDUFS2 subunit of complex I. This methylation step occurs early in the assembly of complex I and probably stabilizes a 400-kDa subcomplex that forms the initial nucleus of the peripheral arm and its juncture with the membrane arm. PMID:24089531

Rhein, Virginie F.; Carroll, Joe; Ding, Shujing; Fearnley, Ian M.; Walker, John E.

2013-01-01

36

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

PubMed

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

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

2015-01-01

37

Aberration in DNA Methylation in B-Cell Lymphomas Has a Complex Origin and Increases with Disease Severity  

E-print Network

Aberration in DNA Methylation in B-Cell Lymphomas Has a Complex Origin and Increases with Disease in normal B-cell populations and subtypes of B-cell non-Hodgkin lymphoma: follicular lymphoma and diffuse large B-cell lymphomas. These lymphomas display striking and progressive intra-tumor heterogeneity

38

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...

39

Nonstoichiometric polyelectrolyte complex of carboxymethylcellulose andN-methylated poly(2-vinylpyridine): Formation of a gel-like structure  

Microsoft Academic Search

The formation of polyelectrolyte complexes between carboxymethylcellu- lose and N-methylated poly(2-vinylpyridine), at a nonstoichiometric mixing ratio, was studied. Various methods, such as viscometry, turbidimetry, electrophoresis, and opti- cal spectroscopy, were used to investigate the complexes with respect to their compo- sition, structure, and stability in aqueous systems of different ionic strengths. A gel-like structure was proposed for the nonstoichiometric polyelectrolyte

B. Vishalakshi; Soumyadeb Ghosh

2003-01-01

40

Beta-Phosphinoethylboranes as Ambiphilic Ligands in Nickel-Methyl Complexes  

SciTech Connect

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).

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

2007-10-28

41

Ab initio and semiempirical investigations of the complexation of methyl pyruvate by ammonia and the ammonium cation  

NASA Astrophysics Data System (ADS)

The optimal structures and energies of the methyl pyruvate system complexed by NH 3 and NH +4 have been calculated using the ab initio method at various levels of theory. The results indicate that both complexes are stable, with a much larger complexation energy for the second one due to the stabilizing electrostatic interactions. These conclusions, which are in agreement with semiempirical calculations performed using reaction potentials, provide valuable information concerning the interaction occurring between the substrate and the nitrogen atom of the stereogenic centre of cinchona alkaloids, which are used for chiral induction in the enantioselective hydrogenation of ?-ketoesters.

Schwalm, Olivier; Weber, Jacques; Margitfalvi, József; Baiker, Alfons

1993-08-01

42

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

PubMed

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

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

2013-12-26

43

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

PubMed Central

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

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

2014-01-01

44

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

SciTech Connect

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

Ikin, A.F.; Kloog, Y.; Sokolovsky, M. (Tel Aviv Univ. (Israel))

1990-03-06

45

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

Microsoft Academic Search

A simple, rapid and sensitive spectrophotometric method has been proposed for the assay of benzydamine HCl (BENZ), levamisole HCl (LEV) and mebeverine HCl (MBV) in bulk and pharmaceutical formulations. The method based on the reaction of the selected drugs with methyl orange (MO) in buffered aqueous solution at pH 3.6. The formed yellow ion-pair complexes were extracted with dichloromethane and

Akram M. El-Didamony

2008-01-01

46

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

NASA Astrophysics Data System (ADS)

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

Sampath, Krishnan; Sathiyaraj, Subbaiyan; Jayabalakrishnan, Chinnasamy

2013-03-01

47

Rheological comparison of organogelators based on iron and aluminum complexes of dodecylmethylphosphinic acid and methyl dodecanephosphonic acid.  

PubMed

Organogels were prepared from a 1:3 molar ratio of metal/ligand complexes of iron(III) or aluminum(III) with methyl dodecanephosphonic acid or dodecylmethylphosphinic acid at a concentration of 10 mM in dodecane. Gelation occurs spontaneously upon dissolution of the solid complex. Dynamic oscillatory measurements over the temperature range of 100-150 degrees C indicate that these materials behave as living polymers. Both reptation and reversible chain scission contribute to stress relaxation. The phosphonate ester complex gels are stronger than the corresponding dialkylphosphinate complex gels. Even at 150 degrees C, the phosphonate ester complexes maintained significant structure. Zero-shear viscosity activation energies are in the range of 26.5-61.2 kJ/mol, comparable to that for typical polymer melts. PMID:19334730

Funkhouser, Gary P; Tonmukayakul, Narongsak; Liang, Feng

2009-08-01

48

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

PubMed

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

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

49

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

PubMed Central

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

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

50

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

PubMed Central

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

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

51

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

E-print Network

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

Do, Loi H.

52

Effects of methyl group substitution on metal-coordinated cyclopentadienyl rings. The core and valence ionizations of methylated tricarbonyl(eta/sup 5/-cyclopentadienyl)metal complexes  

SciTech Connect

Gas-phase He I, He II, and Mg K..cap alpha.. photoelectron spectra are reported for molecules of the type (eta/sup 5/-C/sub 5/H/sub 5-n/-(CH/sub 3/)/sub n/)M(CO)/sub 3/ where n = 0, 1, 5 and M = Mn, Re. The influence of methyl groups on the cyclopentadienyl ring is monitored by shifts in both core and valence ionization energies. This enables effective separation of electron density transfer (inductive) and ring-methyl orbital overlap (hyperconjugative) effects. While the shift in the ring e/sub 1/'' ionization is found to be primarily a hyperconjugative effect, the shift in the metal valence ionizations is caused essentially entirely by a shift of electron density toward the metal atom. A great proportion of this increased density is transferred to the carbonyls in the rhenium complexes than in the manganese complexes, indicating the greater back-bonding ability of the third-row atom. Further evidence of extensive Re-CO back-bonding is provided by the presence of vibrational fine structure on one of the predominantly metal ionizations of the rhenium complexes. This structure is the vibrational progression of the symmetric metal-carbon(CO) stretching mode. The long vibrational progression observed in this band and the frequency of the M-C stretch in the positive ion are direct evidence of considerable ..pi.. back-bonding from the metal to the carbonyls. The observed vibrational structure in the spin-orbit split rhenium d ionizations also leads to a definitive interpretation of the pattern of metal ionizations in such complexes. The origin of the characteristic splitting of the predominantly ring e/sub 1/'' ionization is also considered in detail. The data suggest that the carbon-carbon bond distances in the ring are distorted an average of 0.01 to 0.02 A from fivefold symmetry when coordinated to a d/sup 6/ ML/sub 3/ species. This is the first indication from gas-phase spectroscopy for such distortions.

Calabro, D.C.; Hubbard, J.L.; Blevins, C.H. II; Campbell, A.C.; Lichtenberger, D.L.

1981-11-18

53

Transcription-Coupled Methylation of Histone H3 at Lysine 36 Regulates Dosage Compensation by Enhancing Recruitment of the MSL Complex in Drosophila melanogaster  

Microsoft Academic Search

In Drosophila melanogaster, dosage compensation relies on the targeting of the male-specific lethal (MSL) complex to hundreds of sites along the male X chromosome. Transcription-coupled methylation of histone H3 lysine 36 is enriched toward the 3 end of active genes, similar to the MSL proteins. Here, we have studied the link between histone H3 methylation and MSL complex targeting using

Oliver Bell; Thomas Conrad; Jop Kind; Christiane Wirbelauer; Asifa Akhtar; Dirk Schubeler

2008-01-01

54

Anionic lanthanide complexes with 3-methyl-1-phenyl-4-formylpyrazole-5-one and hydroxonium as counter ion  

PubMed Central

A series of [H3O]+[LnL4]?·nH2O complexes (n = 1–3, Ln = Nd, (1), Sm (2), Eu (3), Tb (4); HL = 3-methyl-1-phenyl-4-formylpyrazole-5-one) were synthesized and characterized. The structures of the SmIII and EuIII complexes were investigated by X-ray diffraction. The isostructutal crystalls 2 and 3 consist the tetrakis [LnL4]? anions which are linked by H-bonding with the hydroxonium counter-ion and water molecules. The lanthanide ion is situated in the center of distorted tetragonal antiprism formed by eight oxygen atoms of 4-formyl-5-hydroxypyrazolonate anions. The TbIII and SmIII complexes show strong luminescence in solid state, whereas the EuIII and NdIII complexes show low luminescence activity. PMID:23805004

Shul’gin, Victor F.; Konnik, Oleg V.; Abkhairova, Susana V.; Gusev, Alexey N.; Meshkova, Svetlana B.; Kiriyak, Anna V.; Rusanov, Eduard B.; Hasegawa, Miki; Linert, Wolfgang

2013-01-01

55

Iridium(I) PNP complexes in the sp³ C-H bond activation of methyl propanoate and related esters.  

PubMed

The utilisation of the PNP iridium pincer complex [Ir(PNP)(COE)][BF4] [PNP = 2,6-bis{(di-tert-butylphosphino)methyl}pyridine; COE = cyclooctene] in the sp(3) C-H activation of methyl propanoate and other related esters was explored. In particular, this study provides further insight into the factors that govern the regioselectivity of such reactions. These included factors such as the steric demands of the substrate, the formation of favourable ring systems as well as the electronic effects that may influence the pKa values of protons. In particular, the effects of water on the outcome of these reactions were of great interest, since earlier literature reports have shown the presence of water to promote selective C-H activation in the ?-position of ketones. PMID:25482307

Coetzee, Jacorien; Eastham, Graham R; Slawin, Alexandra M Z; Cole-Hamilton, David J

2015-01-28

56

Mononuclear and Dinuclear Manganese(II) Complexes from the Use of Methyl(2-pyridyl)ketone Oxime  

PubMed Central

The reactions of methyl(2-pyridyl)ketone oxime, (py)C(Me)NOH, with manganese(II) sulfate monohydrate have been investigated. The reaction between equimolar quantities of MnSO4 · H2O and (py)C(Me)NOH in H2O lead to the dinuclear complex [Mn2(SO4)2{(py)C(Me)NOH}4] · (py)C(Me)NOH, 1 · (py)C(Me)NOH, while employment of NaOMe as base affords the compound [Mn(HCO2)2{(py)C(Me)NOH}2] (2). The structures of both compounds have been determined by single crystal X-ray diffraction. In both complexes, the organic ligand chelates through its nitrogen atoms. The IR data are discussed in terms of the nature of bonding and the structures of the two complexes. PMID:20671965

Efthymiou, Constantinos G.; Nastopoulos, Vassilios; Raptopoulou, Catherine; Tasiopoulos, Anastasios; Perlepes, Spyros P.; Papatriantafyllopoulou, Constantina

2010-01-01

57

Solution structure of the YTH domain in complex with N6-methyladenosine RNA: a reader of methylated RNA  

PubMed Central

N6A methylation is the most abundant RNA modification occurring within messenger RNA. Impairment of methylase or demethylase functions are associated with severe phenotypes and diseases in several organisms. Beside writer and eraser enzymes of this dynamic RNA epigenetic modification, reader proteins that recognize this modification are involved in numerous cellular processes. Although the precise characterization of these reader proteins remains unknown, preliminary data showed that most potential reader proteins contained a conserved YT521-B homology (YTH) domain. Here we define the YTH domain of rat YT521-B as a N6-methylated adenosine reader domain and report its solution structure in complex with a N6-methylated RNA. The structure reveals a binding preference for NGANNN RNA hexamer and a deep hydrophobic cleft for m6A recognition. These findings establish a molecular function for YTH domains as m6A reader domains and should guide further studies into the biological functions of YTH-containing proteins in m6A recognition. PMID:25389274

Theler, Dominik; Dominguez, Cyril; Blatter, Markus; Boudet, Julien; Allain, Frédéric H.-T.

2014-01-01

58

Rapid reduction and complexation of vanadium by 1-phenyl-3-methyl-4-toluoyl-5-pyrazolone: Spectroscopic characterization and structure modelling  

Microsoft Academic Search

The reduction of oxovanadium(V) by 1-phenyl-3-methyl-4-toluoyl-5-pyrazolone (Hpmtp) over the pH range 1.0–7.0 has been assessed by cyclicvoltammetry, electron paramagnetic resonance spectroscopy, magnetic susceptibility, FT-IR, electronic spectroscopy, high-resolution mass spectroscopy and elemental analyses. The reaction proceeds by the transfer of one electron from Hpmtp to oxovanadium(V) via the formation of a free-radical intermediate, and subsequently the reduced oxovanadium(IV) species rapidly complexes

P. N. Remya; C. H. Suresh; M. L. P. Reddy

2007-01-01

59

Synthesis and crystal structure of complex of Ce(NO 3 ) 3 with N-(3-methyl-pyridin-2-yl)formimidoyl(3-methyl-pyridin-2-yl) hydrazone  

Microsoft Academic Search

The reaction of 3,6-di-(3-methyl-pyridin-2-yI)-s-tetrazine (DMPTZ, II) with CeIII salt [Ce(NO3)3 · 6H2O] generates a new ligand, N-(3-methyl-pyridin-2-yl)-formimidoyl-(3-methyl-pyridin-2-yl) hydrazone (L), and forms a new complex:\\u000a a mononuclear complex [Ce(L)(NO3)2 (H2O)3] · NO3 (III). Crystal data for III: space group P-1, with a = 0.7133(4) nm, b = 1.1139(2) nm, c = 1.4572(3) nm, ?= 102.13(2)°, ?=\\u000a 99.81(3)°, ?= 91.10(3)°, Z =

Jiang Yinzhi; Hu Weixiao

2004-01-01

60

Nitric oxide-forming reaction between the iron-N-methyl-D-glucamine dithiocarbamate complex and nitrite.  

PubMed

The objective of this study was to elucidate the origin of the nitric oxide-forming reactions from nitrite in the presence of the iron-N-methyl-D-glucamine dithiocarbamate complex ((MGD)(2)Fe(2+)). The (MGD)(2)Fe(2+) complex is commonly used in electron paramagnetic resonance (EPR) spectroscopic detection of NO both in vivo and in vitro. Although it is widely believed that only NO can react with (MGD)(2)Fe(2+) complex to form the (MGD)(2)Fe(2+).NO complex, a recent article reported that the (MGD)(2)Fe(2+) complex can react not only with NO, but also with nitrite to produce the characteristic triplet EPR signal of (MGD)(2)Fe(2+).NO (Hiramoto, K., Tomiyama, S., and Kikugawa, K. (1997) Free Radical Res. 27, 505-509). However, no detailed reaction mechanisms were given. Alternatively, nitrite is considered to be a spontaneous NO donor, especially at acidic pH values (Samouilov, A., Kuppusamy, P., and Zweier, J. L. (1998) Arch Biochem. Biophys. 357, 1-7). However, its production of nitric oxide at physiological pH is unclear. In this report, we demonstrate that the (MGD)(2)Fe(2+) complex and nitrite reacted to form NO as follows: 1) (MGD)(2)Fe(2).NO complex was produced at pH 7.4; 2) concomitantly, the (MGD)(3)Fe(3+) complex, which is the oxidized form of (MGD)(2)Fe(2+), was formed; 3) the rate of formation of the (MGD)(2)Fe(2+).NO complex was a function of the concentration of [Fe(2+)](2), [MGD], [H(+)] and [nitrite]. PMID:10636843

Tsuchiya, K; Yoshizumi, M; Houchi, H; Mason, R P

2000-01-21

61

Homogeneous solvation controlled photoreduction of cobalt(III) complexes in aqueous 2-methyl-2-propanol solutions  

Microsoft Academic Search

The effect of solvent participation on the ligand-to-metal charge transfer (LMCT, L?CoIII) reduction of the of CoIII(en)2Br(RC6H4NH2)2+ where R=m-OCH3, p-F, H, m-CH3, p-CH3,p-OC2H5 and p-OCH3 were examined in aqueous 2-methyl-2-propanol (ButOH) solutions. The change in the reduction behavior of CoIII centre was also examined through cyclic voltammetric studies. The observed reduction in quantum yield due to LMCT excitation can mainly

K. Anbalagan; I. Sharmila Lydia

2008-01-01

62

Synthesis, crystal structure, antioxidation and DNA-binding properties of the Ln complexes with 1-phenyl-3-methyl-5-hydroxypyrazole-4-carbaldhyde-(benzoyl)hydrazone  

Microsoft Academic Search

Two lanthanide complexes (Ln=La, Pr) with a PMFP Schiff-base, 1-phenyl-3-methyl-5-hydroxypyrazole-4-carbaldhyde-(benzoyl)hydrazone (H2L) were synthesized and characterized. The crystal structure of the La complex was determined by single-crystal X-ray diffraction, the coordination polyhedron is a tricapped trigonal prism configuration with the nine-coordinate atoms composed of three nitrogens and six oxygens from three ligands. The complex crystallized in the monoclinic lattice with a

Hong-Ge Li; Zheng-Yin Yang; Bao-Dui Wang; Jin-Cai Wu

2010-01-01

63

Nonradiative Decay Dynamics of METHYL-4-HYDROXYCINNAMATE and its Monohydrated Complex Revealed by Picosecond Pump-Probe Spectroscopy  

NASA Astrophysics Data System (ADS)

The lifetimes of methyl 4-hydroxycinnamate (OMpCA) and its mono-hydrated complex (OMpCA-H_2O) in the S_1 state have been measured by picosecond pump-probe spectroscopy in a supersonic beam. For OMpCA, the lifetime of the S_1 - S_0 origin is 8 - 9 ps. On the other hand, the lifetime of OMpCA-H_2O complex at the origin is 930 ps, which is 100 times longer than that. Furthermore, in the complex the S_1 lifetime shows rapid decrease at an energy of 200 cm-1 above the origin and becomes as short as 9 ps at 500 cm-1. Theoretical calculations with symmetry-adapted cluster-configuration interaction (SAC-CI) method suggest that in OMpCA, the trans - cis isomerization occurs smoothly without a barrier on the S_1surface, while in OMpCA-H_2O complex, there exists a barrier along the isomerization coordinate. The calculated barrier height of OMpCA-H_2O is in good agreement with that estimated from the lifetime measurements.

Ebata, T.; Shimada, D.; Kusaka, R.; Inokuchi, Y.; Ehara, M.

2012-06-01

64

Biological and cytoselective anticancer properties of copper(II)-polypyridyl complexes modulated by auxiliary methylated glycine ligand.  

PubMed

A series of ternary copper(II)-1,10-phenanthroline complexes with glycine and methylated glycine derivatives, [Cu(phen)(aa)(H(2)O)]NO(3)·xH(2)O 1-4 (amino acid (aa): glycine (gly), 1; DL: -alanine (DL: -ala), 2; 2,2-dimethylglycine (C-dmg), 3; sarcosine (sar), 4), were synthesized and characterized by FTIR, elemental analysis, electrospray ionization-mass spectra (ESI-MS), UV-visible spectroscopy and molar conductivity measurement. The determined X-ray crystallographic structures of 2 and 3 show each to consist of distorted square pyramidal [Cu(phen)(aa)(H(2)O)](+) cation, a nitrate counter anion, and with or without lattice water, similar to previously reported structure of [Cu(phen)(gly)(H(2)O)]NO(3)·1½H(2)O. It is found that 1-4 exist as 1:1 electrolytes in aqueous solution, and the cationic copper(II) complexes are at least stable up to 24 h. Positive-ion ESI-MS spectra show existence of only undissociated [Cu(phen)(aa)](+) species. Electron paramagnetic resonance, gel electrophoresis, fluorescence quenching, and restriction enzyme inhibition assay were used to study the binding interaction, binding affinity and selectivity of these complexes for various types of B-form DNA duplexes and G-quadruplex. All complexes can bind selectively to DNA by intercalation and electrostatic forces, and inhibit topoisomerase I. The effect of the methyl substituents of the coordinated amino acid in the above complexes on these biological properties are presented and discussed. The IC(50) values (24 h) of 1-4 for nasopharyngeal cancer cell line HK1 are in the range 2.2-5.2 ?M while the corresponding values for normal cell line NP69 are greater than 13.0 ?M. All complexes, at 5 ?M, induced 41-60 % apoptotic cell death in HK1 cells but no significant cell death in NP69 cells. PMID:22836829

Seng, Hoi-Ling; Wang, Wai-San; Kong, Siew-Ming; Alan Ong, Han-Kiat; Win, Yip-Foo; Raja Abd Rahman, Raja Noor Zaliha; Chikira, Makoto; Leong, Weng-Kee; Ahmad, Munirah; Khoo, Alan Soo-Beng; Ng, Chew-Hee

2012-10-01

65

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

Microsoft Academic Search

The inclusion complexes of ?-cyclodextrin (?-CD) and HP-?-cyclodextrin (HP-?-CD) with caffeine, theophylline and theobromine were investigated by fluorimetry. Various factors affecting the formation of inclusion complexes were discussed in detail including forming time, pH effect and temperature. The results indicate that inclusion process was affected seriously by laying time and pH. The forming time of ?-CD inclusion complexes is much

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

2003-01-01

66

C-H activation and C=C double bond formation reactions in iridium ortho-methyl arylphosphane complexes.  

PubMed

The Vaska-type iridium(I) complex [IrCl(CO){PPh(2)(2-MeC(6)H(4))}(2)] (1), characterized by an X-ray diffraction study, was obtained from iridium(III) chloride hydrate and PPh(2)(2,6-MeRC(6)H(3)) with R=H in DMF, whereas for R=Me, activation of two ortho-methyl groups resulted in the biscyclometalated iridium(III) compound [IrCl(CO){PPh(2)(2,6-CH(2)MeC(6)H(3))}(2)] (2). Conversely, for R=Me the iridium(I) compound [IrCl(CO){PPh(2)(2,6-Me(2)C(6)H(3))}(2)] (3) can be obtained by treatment of [IrCl(COE)(2)](2) (COE=cyclooctene) with carbon monoxide and the phosphane in acetonitrile. Compound 3 in CH(2)Cl(2) undergoes intramolecular C-H oxidative addition, affording the cyclometalated hydride iridium(III) species [IrHCl(CO){PPh(2)(2,6-CH(2)MeC(6)H(3))}{PPh(2)(2,6-Me(2)C(6)H(3))}] (4). Treatment of 2 with Na[BAr(f) (4)] (Ar(f)=3,5-C(6)H(3)(CF(3))(2)) gives the fluxional cationic 16-electron complex [Ir(CO){PPh(2)(2,6-CH(2)MeC(6)H(3))}(2)][BAr(f) (4)] (5), which reversibly reacts with dihydrogen to afford the delta-agostic complex [IrH(CO){PPh(2)(2,6-CH(2)MeC(6)H(3))}{PPh(2)(2,6-Me(2)C(6)H(3))}][BAr(f)(4)] (6), through cleavage of an Ir-C bond. This species can also be formed by treatment of 4 with Na[BAr(f)(4)] or of 2 with Na[BAr(f)(4)] through C-H oxidative addition of one ortho-methyl group, via a transient 14-electron iridium(I) complex. Heating of the coordinatively unsaturated biscyclometalated species 5 in toluene gives the trans-dihydride iridium(III) complex [IrH(2)(CO){PPh(2)(2,6-MeC(6)H(3)CH=CHC(6)H(3)Me-2,6)PPh(2)}][BAr(f) (4)] (7), containing a trans-stilbene-type terdentate ligand, as result of a dehydrogenative carbon-carbon double bond coupling reaction, possibly through an iridium carbene species. PMID:17535000

Baratta, Walter; Ballico, Maurizio; Del Zotto, Alessandro; Zangrando, Ennio; Rigo, Pierluigi

2007-01-01

67

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

SciTech Connect

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

Tretiak, Sergei [Los Alamos National Laboratory

2008-01-01

68

Redox cycling of iron complexes of N-(dithiocarboxy)sarcosine and N-methyl-D-glucamine dithiocarbamate.  

PubMed

Iron(II)-dithiocarbamate complexes are used to trap nitrogen monoxide in biological samples, and the resulting nitrosyliron(II)-dithiocarbamate is detected and quantified by ESR. As the chemical properties of these compounds have been little studied, we investigated whether iron dithiocarbamate complexes can redox cycle. The electrode potentials of iron complexes of N-(dithiocarboxy)sarcosine (dtcs) and N-methyl-d-glucamine dithiocarbamate (mgd) are 56 and -25 mV at pH 7.4, respectively, as measured by cyclic voltammetry. The autoxidation and Fenton reaction of iron(II)-dtcs and iron(II)-mgd were studied by stopped-flow spectrophotometry with both iron(II) complexes and dioxygen or hydrogen peroxide in excess. In the case of excess iron(II)-dtcs and -mgd complexes, the rate constants of the autoxidation and the Fenton reaction are (1.6-3.2) x 10(4) and (0.7-1.1) x 10(5) M(-1) s(-1), respectively. In the presence of nitrogen monoxide, the oxidation of iron(II)-dtcs and iron(II)-mgd by hydrogen peroxide is significantly slower (ca. 10-15 M(-1) s(-1)). The physiological reductants ascorbate, cysteine, and glutathione efficiently reduce iron(III)-dtcs and iron(III)-mgd. Therefore, iron bound to dtcs and mgd can redox cycle between iron(II) and iron(III). The ligands dtcs and mgd are slowly oxidized by hydrogen peroxide with rate constants of 5.0 and 3.8 M(-1) s(-1), respectively. PMID:16298683

Lu, Changyuan; Koppenol, Willem H

2005-12-15

69

DNA Methylation Profiling of the Human Major Histocompatibility Complex: A Pilot Study for the Human Epigenome Project  

Microsoft Academic Search

The Human Epigenome Project aims to identify, catalogue, and interpret genome-wide DNA methylation phenomena. Occurring naturally on cytosine bases at cytosine–guanine dinucleotides, DNA methylation is intimately involved in diverse biological processes and the aetiology of many diseases. Differentially methylated cytosines give rise to distinct profiles, thought to be specific for gene activity, tissue type, and disease state. The identification of

Vardhman K Rakyan; Thomas Hildmann; Karen L Novik; Jörn Lewin; Jörg Tost; Antony V Cox; T. Dan Andrews; Kevin L Howe; Thomas Otto; Alexander Olek; Judith Fischer; Ivo G Gut; Kurt Berlin; Stephan Beck

2004-01-01

70

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

PubMed Central

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

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

2015-01-01

71

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

PubMed

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

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

2015-03-01

72

Structural Basis for the Recognition of Methylated Histone H3K36 by the Eaf3 Subunit of Histone Deacetylase Complex Rpd3S  

PubMed Central

SUMMARY Deacetylation of nucleosomes by the Rpd3S histone deacetylase along the path of transcribing RNA polymerase II regulates access to DNA, contributing to faithful gene transcription. The association of Rpd3S with chromatin requires its Eaf3 subunit, which binds histone H3 methylated at lysine 36 (H3K36). Eaf3 is also part of NuA4 acetyltransferase that recognizes methylated H3K4. Here we show that Eaf3 in Saccharomyces cerevisiae contains a chromo barrel-related domain that binds methylated peptides, including H3K36 and H3K4, with low specificity and millimolar-range affinity. Nuclear magnetic resonance structure determination of Eaf3 bound to methylated H3K36 was accomplished by engineering a linked Eaf3-H3K36 molecule with a chemically incorporated methyllysine analog. Our study uncovers the molecular details of Eaf3-methylated H3K36 complex formation, and suggests that, in the cell, Eaf3 can only function within a framework of combinatorial interactions. This work also provides a general method for structure determination of low-affinity protein complexes implicated in methyllysine recognition. PMID:18818090

Xu, Chao; Cui, Gaofeng; Botuyan, Maria Victoria; Mer, Georges

2008-01-01

73

Synthesis of palladium(II) complexes with 3-amino-5-methyl-5-(4-pyridyl)-hydantoin: cytotoxic and antimicrobial investigations and comparison with their platinum analogues  

Microsoft Academic Search

Two new Pd(II) complexes with 3-amino-5-methyl-5-(4-pyridyl)-hydantoin (AMPH) were synthesized: cis-[Pd(AMPH)2Cl2]·2H2O and cis-[Pd(AMPH)2Br2]·H2O. The complexes were characterized by physico-chemical and spectroscopic methods. The determination of crystal water content\\u000a in the complexes was defined by Karl Fisher titration. The cytotoxic effects of these complexes were examined on a panel of\\u000a human tumor cell lines. Qualitative antimicrobial assays on three pathogenic microorganisms of

H. VarbanovA; A. Bakalova; R. Buyukliev; G. Momekov; R. Baykushev

2010-01-01

74

Synthesis, characterization, and studies on DNA binding of a new Mg(II) complex with N1,N8-bis(1-methyl-4-nitropyrrole-2-carbonyl)triethylenetetramine.  

PubMed

A new Mg(II) complex of MgL(NO3)2 (here L = N(1),N(8)-bis(1-methyl-4-nitropyrrole-2-carbonyl)triethylenetetramine) has been synthesized and characterized. The interactions between the Mg(II) complex and calf thymus DNA has been investigated using UV spectra, fluorescent spectra, viscosity, thermal denaturation, and molecular modeling. The cleavage reaction on plasmid DNA has been monitored by agarose gel electrophoresis. The experimental results show that the mode of binding of the complex to DNA is non-classical electrostatic action and the complex can cleave pBR322 DNA. PMID:18393758

Zhou, Cheng-Yong; Wu, Yan-Bo; Yang, Pin

2008-03-01

75

Anion binding to a ferric porphyrin complexed with per-O-methylated beta-cyclodextrin in aqueous solution.  

PubMed

5,10,15,20-Tetrakis(4-sulfonatophenyl)porphinato iron(III) (Fe(III)TPPS) forms a very stable 1:2 complex with heptakis(2,3,6-tri-O-methyl)-beta-cyclodextrin (TMe-beta-CD), whose iron(III) center is located at a hydrophobic cleft formed by two face-to-face TMe-beta-CD molecules. Various inorganic anions (X(-)) such as F(-), Cl(-), Br(-), I(-), N(3)(-), and SCN(-) coordinate to Fe(III)TPPS(TMe-beta-CD)(2) to form five-coordinate high-spin Fe(III)TPPS(X)(TMe-beta-CD)(2), while no coordination occurs with ClO(4)(-), H(2)PO(4)(-), NO(3)(-), and HSO(4)(-). Except for F(-), none of the anions investigated coordinate to Fe(III)TPPS in the absence of TMe-beta-CD due to extensive hydration to the anions as well as to Fe(III)TPPS. The present system shows a high selectivity toward the N(3)(-) anion. The thermodynamics suggests that Lewis basicity, hydrophilicity, and shape of an X(-) anion are the main factors to determine the stability of the Fe(III)TPPS(X)(TMe-beta-CD)(2) complex. PMID:15548017

Kano, Koji; Kitagishi, Hiroaki; Tamura, Shigeto; Yamada, Akihisa

2004-11-24

76

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

PubMed

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

El-Didamony, Akram M

2008-03-01

77

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

NASA Astrophysics Data System (ADS)

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

El-Didamony, Akram M.

2008-03-01

78

Anomalous dielectric dispersion in glycol chitosan—carboxy methyl cellulose polyelectrolyte complex containing alkali ions  

Microsoft Academic Search

In films of the polyelectrolyte complexes of glycol chitosan (gc) with alginic acid (aa) and hyaluronic acid (ha) anomalously large dielectric dispersion was observed in the range 1 to 100 kHz above 50‡C. This was attributed to the formation\\u000a of electrical double layers around the polyanion by the sodium ions inevitably present in the films.\\u000a \\u000a To test this hypothesis films

R. Srinivasan; Pushpa Viswanathan

1983-01-01

79

Effects of methyl group substitution on metal-coordinated cyclopentadienyl rings. The core and valence ionizations of methylated tricarbonyl(eta⁵-cyclopentadienyl)metal complexes  

Microsoft Academic Search

Gas-phase He I, He II, and Mg K..cap alpha.. photoelectron spectra are reported for molecules of the type (eta⁵-CâH\\/sub 5-n\\/-(CHâ)\\/sub n\\/)M(CO)â where n = 0, 1, 5 and M = Mn, Re. The influence of methyl groups on the cyclopentadienyl ring is monitored by shifts in both core and valence ionization energies. This enables effective separation of electron density transfer

David C. Calabro; John L. Hubbard; Charles H. Blevins; Andrew C. Campbell; Dennis L. Lichtenberger

1981-01-01

80

Two-reactant Fukui function and molecular electrostatic potential analysis of the methyl acrylate binding mode in the complexes with the Ni- and Pd-diimine catalysts  

NASA Astrophysics Data System (ADS)

Two-reactant Fukui function (FF) and molecular electrostatic potential (MEP) have been used to investigate the origin of the differences in the polar monomer binding mode observed in the complexes with the Pd- and Ni-based catalysts for the ethylene/methyl acrylate copolymerization. The ?-coordination is energetically preferred for the Pd-system (active catalyst), while in the Ni-case (inactive) the ?-complex with methyl acrylate bound by its carbonyl oxygen has lower energy. The results demonstrate that the preference of the O-coordination in the Ni-complexes has electrostatic origin. MEP displays larger positive values for the Ni-catalyst, while the two-reactant FF exhibit similar features for both catalysts.

Michalak, Artur

2004-03-01

81

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

NASA Astrophysics Data System (ADS)

The crystal structures of {4-bromo-2-[(2-hydroxyethylimino)-methyl]phenolo}aquacopper(II) nitrate hemihydrate ( I), chloro-{4-bromo-2-[(2-hydroxyethylimino)-methyl]phenolo}copper hemihydrate ( II), and chloro-{4-bromo-2-[(2-hydroxyethylimino)-methyl]phenolo}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 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.

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

2008-07-01

82

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

PubMed Central

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.Hha I) 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.Hha I 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. PMID:12206775

Zhou, L.; Connolly, B.A.; Dickman, M.J.; Hurd, P.J.

2009-01-01

83

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

SciTech Connect

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.

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

2009-01-01

84

Synthesis, spectroscopic characterization and biological evaluation studies of Schiff's base derived from naphthofuran-2-carbohydrazide with 8-formyl-7-hydroxy-4-methyl coumarin and its metal complexes  

NASA Astrophysics Data System (ADS)

Metal complexes of the type ML2, where M = Co(II), Ni(II), Cu(II), Zn(II), Cd(II), Hg(II) and L = Schiff's base derived from the condensation of naphthofuran-2-carbohydrazide with 8-formyl-7-hydroxy-4-methyl coumarin have been synthesized. The chelation of the complexes have been elucidated in the light of analytical, IR, UV-vis, 1H NMR, mass, ESR spectral data, thermal and magnetic studies. The measured molar conductance values indicate that, the complexes are non-electrolytic in nature. The redox behavior of one of the synthesized metal complexes was investigated by cyclic voltammetry. The Schiff's base and its metal complexes have been screened for their in vitro antibacterial and antifungal activities by MIC method. The DNA cleavage activities of all the complexes were studied by agarose gel electrophoresis method. In addition, the free ligand along with its complexes has been studied for their antioxidant activity.

Halli, M. B.; Sumathi, R. B.; Kinni, Mallikarjun

2012-12-01

85

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

PubMed Central

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

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

2014-01-01

86

(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)

(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.

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

2015-02-01

87

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

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 ?,?-unsaturated carboxylic acid moiety leading to increase in the length of ?-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

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

2012-01-01

88

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

SciTech Connect

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

Chumakov, Yu. M., E-mail: chumakov.xray@phys.asm.md [Academy of Sciences of Moldova, Institute of Applied Physics (Moldova, Republic of); Tsapkov, V. I. [State University of Moldova (Moldova, Republic of); Petrenko, P. A. [Academy of Sciences of Moldova, Institute of Applied Physics (Moldova, Republic of); Popovski, L. G. [State University of Moldova (Moldova, Republic of); Simonov, Yu. A. [Academy of Sciences of Moldova, Institute of Applied Physics (Moldova, Republic of); Bocelli, G. [National Research Council (IMEM-CNR), Institute of Materials for Electronics and Magnetism (Italy); Gulea, A. P. [State University of Moldova (Moldova, Republic of)

2009-03-15

89

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

NASA Astrophysics Data System (ADS)

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

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

2009-03-01

90

Light-on fluorescent chemosensor for fluoride in aqueous solution based on ternary complex of Zr-EDTA and 4?- N, N-dimethylamino-6-methyl-3-hydroxylflavone  

Microsoft Academic Search

A ternary complex, composed of Zr-EDTA and 4?-N,N-dimethylamino-6-methyl-3-hydroxylflavone (L), was developed as an efficient fluoride chemosensor in aqueous solution with a good selectivity and sensitivity. Fluorescence intensity of the solution of Zr-EDTA-L was increased significantly upon addition of fluoride anion, which was interpreted by the ligand exchange between L coordinated to Zr-EDTA and fluoride anion.

Jia-Sheng Wu; Fang Wang; Wei-Min Liu; Peng-Fei Wang; Shi-Kang Wu; Xiaohua Wu; Xiao-Hong Zhang

2007-01-01

91

Cloud Point Extraction Preconcentration of Trace Cadmium as 1Phenyl3-methyl-4-benzoyl-5-pyrazolone Complex and Determination by Flame Atomic Absorption Spectrometry  

Microsoft Academic Search

A new method for the determination of trace cadmium in water samples by flame atomic absorption spectrometry (FAAS) after cloud point extraction (CPE) is proposed. The method is based on the complexation of Cd with 1-phenyl-3-methyl-4-benzoyl-5-pyrazolone (PMBP) in the presence of non-ionic micelles of Triton X-100. The effect of experimental conditions such as pH, concentration of chelating agent and surfactant,

Pei Liang; Jing Li; Xiaoying Yang

2005-01-01

92

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

E-print Network

Prior to each titration, an acid-base titration withby Gran’s titration. 15 N-methyl- iminodiacetic acid (MIDA,titration with IDA (left), Stage I consisted of only the first addition because little free acid (

Rao, Linfeng

2011-01-01

93

[Enzymatic synthesis of a conducting complex of polyaniline and poly(2-arcylamido-2-methyl-1-propanesulfonic ACID) using palm tree peroxidase and its properties].  

PubMed

An enzymatic method of producing a conducting polyelectrolyte complex of polyaniline (PANI) and poly(2-acrylamido-2-methyl-1-propanesulfonic acid) (PAMPS) was developed. Acidic stable peroxidase isolated from royal palm tree (Roystonea regia L.) leaves was used as a catalyst in the oxidative polymerization of aniline at pH 2.8. The synthesis procedure was optimized. Spectroscopic and electrochemical characteristics of nanoparticles of obtained PANI/PAMPS complexes at different pH were studied. It was shown that the acidity of the medium affects their properties. PMID:15977787

Mazhugo, Iu M; Karamyshev, A V; Shleev, S V; Sakharov, I Iu; Iaropolov, A I

2005-01-01

94

A novel mixed valence copper(I) copper(II) bis(antipyryl-methyl)-piperazine complex: synthesis, molecular structure and spectroscopic characterization  

NASA Astrophysics Data System (ADS)

This paper describes a new case of the bis(antipyryl-methyl)-piperazine [BAMP] ligand being in the "boat"-conformation and acting as a tetradentate. But unlike in Co(BAMP)(NCS) 2, which is the only complex with BAMP acting as tetradentate known so far, the coordinated copper(II) is connected via a iodo-bridge to a Cu II 2-moiety. The synthesis, elemental analysis, spectroscopic (far- and mid-FTIR, UV-Vis) and structural characterization (X-ray diffraction) as well as magnetochemical and conductivity data of this novel mixed valence binuclear complex Cu ICu II(BAMP)I 3 are presented.

Weinberger, P.; Costisor, O.; Tudose, R.; Baumgartner, O.; Linert, W.

2000-02-01

95

Lanthanide complex of 1-phenyl-3-methyl-5-hydroxypyrazole-4-carbaldehyde-(isonicotinoyl) hydrazone: crystal structure and DNA-binding properties  

Microsoft Academic Search

A Schiff-base ligand derived from 1-phenyl-3-methyl-4-formyl-2-pyrazolin-5-one (PMFP) and isoniazid was prepared and its La(III) complex was characterized by X-ray single crystal diffraction. The La(III) is nine-coordinate in a space group P21\\/n. DNA-binding was investigated by UV-Vis, fluorescence titration, ethidium bromide displacement experiments, and viscosity measurements, which indicated that the ligand and La(III) complex strongly binds to calf thymus DNA presumably

Mingfang Wang; Zhengyin Yang; Yong Li; Hongge Li

2011-01-01

96

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

PubMed

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

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

2014-06-01

97

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

NASA Astrophysics Data System (ADS)

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

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

2013-04-01

98

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

SciTech Connect

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

Bellachioma, G.; Cardaci, G.; Macchioni, A.; Madami, A. (Universita di Perugia (Italy))

1993-03-03

99

Synthesis, Spectroscopic, DNA Binding and Antimicrobial Studies on bis (1-amidino-O-alkylurea) Cu(II) tartrate complexes where alkyl = methyl, ethyl, n-propyl, n- or iso-butyl  

Microsoft Academic Search

Five New Cu(II) complexes, [bis(1-amidino-O-alkylurea)Cu(II)tartrate], where alkyl = methyl (1), ethyl (2), n-propyl (3), n-butyl (4) or iso-butyl (5) have been synthesized and characterized. The EPR spectra of complexes 1 and 2 showed features of mononuclear species whereas complexes 3, 4 and 5 in frozen DMSO solution show the existence of mononuclear and binuclear species in these complexes. Complexes crystallize

R. K. Hemakumar Singh; N. Shantibala Devi; L. Reena Devi; R. M. Kadam

2012-01-01

100

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

PubMed

We report the synthesis of the ligand, salicilaldehyde-N-methyl p-toluenesulfonylhydrazone (salptsmh) derived from p-toluenesulfonicacid-1-methylhydrazide (ptsmh) and its Pd(II) and Co(II) metal complexes were synthesized for the first time. The structure of the ligand and their complexes were investigated using elemental analysis, magnetic susceptibility, molar conductance and spectral (IR, NMR and LC-MS) measurements. Salptsmh has also been characterized by single crystal X-ray diffraction. (1)H and (13)C shielding tensors for crystal structure were calculated with GIAO/DFT/B3LYP/6-311++G(d,p) methods in CDCl3. The complexes were found to have general composition [ML2]. The results of elemental analysis showed 1:2 (metal/ligand) stoichiometry for all the complex. Magnetic and spectral data indicate a square planar geometry for Pd(II) complex and a distorted tetrahedral geometry for Co(II) complexes. The ligand and its metal chelates have been screened for their antimicrobial activities using the disk diffusion method against the selected Gram positive bacteria: Bacillus subtilis, Bacillus cereus, Staphylococcus aureus, Enterococcus faecalis, Gram negative bacteria: Eschericha coli, Pseudomonas aeruginosa, Klebsiella pneumonia. The inhibition activities of these compounds on carbonic anhydrase II (CA II) and carbonic anhydrase I (CA I) have been investigated by comparing IC50 and Ki values and it has been found that Pd(II) complex have more enzyme inhibition efficiency than salptsmh and Co(II) complex. PMID:24835932

Alyar, Saliha; Adem, ?evki

2014-10-15

101

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)

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.

Chandra, Sulekh; Vandana; Kumar, Suresh

2015-01-01

102

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)

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.

Alyar, Saliha; Adem, ?evki

2014-10-01

103

Histone methyltransferases G9a and GLP form heteromeric complexes and are both crucial for methylation of euchromatin at H3-K9  

PubMed Central

Histone H3 Lys 9 (H3-K9) methylation is a crucial epigenetic mark for transcriptional silencing. G9a is the major mammalian H3-K9 methyltransferase that targets euchromatic regions and is essential for murine embryogenesis. There is a single G9a-related methyltransferase in mammals, called GLP/Eu-HMTase1. Here we show that GLP is also important for H3-K9 methylation of mouse euchromatin. GLP-deficiency led to embryonic lethality, a severe reduction of H3-K9 mono- and dimethylation, the induction of Mage-a gene expression, and HP1 relocalization in embryonic stem cells, all of which were phenotypes of G9a-deficiency. Furthermore, we show that G9a and GLP formed a stoichiometric heteromeric complex in a wide variety of cell types. Biochemical analyses revealed that formation of the G9a/GLP complex was dependent on their enzymatic SET domains. Taken together, our new findings revealed that G9a and GLP cooperatively exert H3-K9 methyltransferase function in vivo, likely through the formation of higher-order heteromeric complexes. PMID:15774718

Tachibana, Makoto; Ueda, Jun; Fukuda, Mikiko; Takeda, Naoki; Ohta, Tsutomu; Iwanari, Hiroko; Sakihama, Toshiko; Kodama, Tatsuhiko; Hamakubo, Takao; Shinkai, Yoichi

2005-01-01

104

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

PubMed Central

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

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

2014-01-01

105

Genome-wide analysis of histone methylation reveals chromatin state-based complex regulation of differential gene transcription and function of CD8 memory T cells  

PubMed Central

Summary Memory lymphocytes are characterized by their ability to exhibit a rapid response to the recall antigen, in which differential transcription plays a significant role, yet the underlying mechanism is not understood. We report here a genome-wide analysis of histone methylation on two histone H3 lysine residues (H3K4me3 and H3K27me3) and gene expression profiles in naïve and memory CD8 T cells. We found that a general correlation exists between the levels of gene expression and the levels of H3K4me3 (positive correlation) and H3K27me3 (negative correlation) across the gene body. These correlations display four distinct modes: repressive, active, poised, and bivalent, reflecting different functions of these genes. Furthermore, a permissive chromatin state of each gene is established by a combination of different histone modifications. Our findings reveal a complex regulation by histone methylation in differential gene expression and suggest that histone methylation may be responsible for memory CD8 T cell function. PMID:19523850

Araki, Yasuto; Wang, Zhibin; Zang, Chongzhi; Wood, William H.; Schones, Dustin; Cui, Kairong; Roh, Tae-Young; Lhotsky, Brad; Wersto, Robert P.; Peng, Weiqun; Becker, Kevin G.; Zhao, Keji; Weng, Nan-ping

2009-01-01

106

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)

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.

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

2014-12-01

107

Ir(2-Phenylpyridine)2(benzene-1,2-dithiolate) Anion as a Diastereoselective Metalloligand and Nucleophile: Stereoelectronic Effect, Spectroscopy, and Computational Study of the Methylated and Aurated Complexes and their Oxygenation Products.  

PubMed

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

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

2015-03-01

108

Synthesis, Spectroscopic, DNA Binding, and Antimicrobial Studies on bis (1-amidino-O-alkylurea) Cu(II) Tartrate Complexes Where Alkyl = Methyl, Ethyl, n-Propyl, n-, or IsoButyl  

Microsoft Academic Search

Five New Cu(II) complexes, [bis(1-amidino-O-alkylurea) Cu(II)tartrate], where alkyl= methyl (1), ethyl (2), n-propyl (3), n-butyl (4), or iso-butyl (5) have been synthesized and characterized. The electron paramagnetic resonance spectra of complexes 1 and 2 showed features of mononuclear species whereas complexes 3, 4, and 5 in frozen DMSO solution show the existence of mononuclear and binuclear species in these complexes.

R. K. Hemakumar Singh; N. Shantibala Devi; L. Reena Devi; R. M. Kadam

2012-01-01

109

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)

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.

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

2013-08-01

110

Complex formed in the system hydrophobically modified polyethylene glycol\\/methylated ?-cyclodextrin\\/water. An NMR diffusometry study  

Microsoft Academic Search

In aqueous solutions hydrophobically modified polyethylene glycol (HM-PEG) forms a transient polymer network held together by intermolecular hydrophobic associations. In the present investigation we have used NMR-diffusometry to study how the addition of methylated ?-cyclodextrin (M-?-CD) influences the polymer network. The addition of M-?-CD resulted in an increased mean self-diffusion of HM-PEG, DHM-PEG, which is referred to a degradation of

L. Karlson; C. Malmborg; K. Thuresson; O. Söderman

2003-01-01

111

Synthesis, Characterization and Crystal Structure of a Mononuclear Zinc(II) Complex Derived from 2-[(2-Propylaminoethylimino)methyl]phenol  

Microsoft Academic Search

\\u000a Abstract  A new zinc(II) complex, [Zn(C12H18N2O)Cl2]·CH3CN, derived from the Schiff base ligand 2-[(2-propylaminoethylimino)methyl]phenol, has been synthesized and characterized\\u000a by elemental analysis, IR spectra, and X-ray crystallography. The complex crystallizes in the orthorhombic space group Pbcn with unit cell dimensions a = 26.387(9) Å, b = 7.389(2) Å, c = 18.731(6) Å, V = 3,652(2) Å3, Z = 8, R\\u000a 1 = 0.0455 and wR\\u000a 2 = 0.1143. The asymmetric unit of the compound contains a

Xiao-Fang Li; Zhong-Lu You; Peng Hou; Cheng-Lu Zhang

2010-01-01

112

Methylation matters  

PubMed Central

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

Costello, J.; Plass, C.

2001-01-01

113

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

PubMed Central

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

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

2002-01-01

114

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

PubMed

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

Tyagi, Nidhi; Mathur, Pavan

2012-10-01

115

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)

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.

Tyagi, Nidhi; Mathur, Pavan

2012-10-01

116

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

PubMed

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

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

2002-11-01

117

Cellular selectivity and biological impact of cytotoxic rhodium(III) and iridium(III) complexes containing methyl-substituted phenanthroline ligands.  

PubMed

The antiproliferative properties and biological impact of octahedral iridium(III) complexes of the type fac-[IrCl3 (DMSO)(pp)] containing pp=phenanthroline (1) and its 4- and 5-methyl (2, 3) and 4,7- and 5,6-dimethyl derivatives (4, 5) were investigated for both adherent and non-adherent cells. A series of similar rhodium(III) complexes were studied for comparison purposes. The antiproliferative activity toward MCF-7 cancer cells increases eightfold from IC50=4.6 for 1 to IC50=0.60??M for 5, and an even more pronounced 18-fold improvement was established for the analogous rhodium complexes 6 and 8, the respective IC50 values for which are 1.1 and 0.06??M. Annexin?V/propidium iodide assays demonstrated that the 5,6-dimethylphenanthroline complexes 5 and 8 both cause significant inhibition of Jurkat leukemia cell proliferation and invoke extensive apoptosis but negligible necrosis. The percentages of Jurkat cells exhibiting high levels of reactive oxygen species correlate with the percentages of cells undergoing apoptosis. The antiproliferative activity of 5 and 8 is strongly selective toward MCF-7 and HT-29 cancer cells over normal HFF-1 and immortalized HEK-293 cells. Complex 5 also exhibits high selectivity toward BJAB lymphoma cells relative to healthy leukocytes. Both 5 and 8 invoke permanent decreases in the adhesion and respiration of MCF-7 cells. PMID:21337523

Geldmacher, Yvonne; Kitanovic, Igor; Alborzinia, Hamed; Bergerhoff, Katharina; Rubbiani, Riccardo; Wefelmeier, Pascal; Prokop, Aram; Gust, Ronald; Ott, Ingo; Wölfl, Stefan; Sheldrick, William S

2011-03-01

118

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

NASA Astrophysics Data System (ADS)

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

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

2015-01-01

119

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

E-print Network

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

Lisal, Martin

120

Photodegradation of methyl orange and photoinactivation of bacteria by visible light activation of persulphate using a tris(2,2'-bipyridyl)ruthenium(II) complex.  

PubMed

Persulphate is an emerging oxidant in the field of advanced oxidation processes for the degradation of environmentally persistent organic compounds. The present study shows that visible light activation of persulphate (2 mM) using tris(2,2'-bipyridyl)ruthenium(II) (complex 1) (1 ?M) caused rapid degradation (98%) of model azo dye methyl orange (MO) (12 mg L(-1)) with significant mineralization (76%), and also complete inactivation of both Gram negative and positive bacteria (?10(7) CFU mL(-1)). BacLight LIVE/DEAD assay, scanning electron microscopy and genomic DNA analysis revealed cell membrane damage and loss of chromosomal DNA, indicating oxidative stress caused to E. coli during photoinactivation. The effect of concentration of complex 1 : persulphate ratio and presence of inorganic ions (0.1 M), such as sodium hydrogen phosphate, sodium sulphate, and sodium hydrogen carbonate, on the photodegradation of MO and photoinactivation of E. coli were studied. In addition, the effect of the presence of the organic contaminant resorcinol on the photoinactivation of E. coli was also studied. Significant degradation of MO and complete inactivation of bacteria were observed in simulated ground water. The present study is the first to reveal that activation of persulphate using a visible light absorbing metal complex in aqueous media has the ability to cause degradation of organic contaminants as well as complete inactivation of bacteria. PMID:23183999

Subramanian, Gokulakrishnan; Parakh, Priyadarshini; Prakash, Halan

2013-03-01

121

Novel Square Arrangements in Tetranuclear and Octanuclear Iron(III) Complexes with Asymmetric Iron Environments Created by the Unsymmetric Bridging Ligand N,N,N'-Tris((N-methyl)-2-benzimidazolylmethyl)-N'-methyl-1,3-diamino-2-propanol.  

PubMed

The synthesis and characterization of novel tetranuclear and octanuclear iron(III) complexes with structures based on a nearly square arrangement of four iron ions are reported. Reaction of ferric nitrate, sodium acetate, and the unsymmetrical binucleating ligand HBMDP, where HBMDP is N,N,N'-tris((N-methyl)-2-benzimidazolylmethyl)-N'-methyl-1,3-diamino-2-propanol, in acetone/water yields the tetranuclear iron complex [Fe(4)(&mgr;-O)(2)(&mgr;-BMDP)(2)(&mgr;-OAc)(2)](4+), which exhibits coordination number asymmetry. The structure of [Fe(4)(&mgr;-O)(2)(&mgr;-BMDP)(2)(&mgr;-OAc)(2)](NO(3))(3)(OH).12H(2)O has been determined by single-crystal X-ray diffraction. Each (&mgr;-BMDP) ligand spans two iron(III) ions and causes these ions to become structurally distinct. Within this binuclear unit one iron atom is five-coordinate with distorted square pyramidal geometry and an N(2)O(3) donor set, while the other iron is six-coordinate with distorted octahedral geometry and an N(3)O(3) donor set. Two of these binuclear units are linked through a pair of oxo and acetato bridges to form the centrosymmetric tetranuclear complex. The coordinatively nonequivalent iron atoms exhibit distinct Mössbauer spectroscopic parameters and produce a pair of doublets at 80 K. The iron(III) centers are coupled antiferromagnetically with a room-temperature moment of 1.9 &mgr;(B) per iron with J = -103.3 cm(-)(1), zJ' = -105.9 cm(-)(1). The properties of the unsymmetric cation [Fe(4)(&mgr;-O)(2)(&mgr;-BMDP)(2)(&mgr;-OAc)(2)](4+) are similar to those observed for binuclear iron proteins with comparable coordinative inequivalence. Efforts to increase the solubility of [Fe(4)(&mgr;-O)(2)(&mgr;-BMDP)(2)(&mgr;-OAc)(2)](4+) by metathesis with sodium tetrafluoroborate resulted in the isolation of crystals of a new octanuclear iron species, [Fe(8)(&mgr;-O)(4)(&mgr;-BMDP)(4)(OH)(4)(&mgr;-OAc)(4)](BF(4))(3)(OH).2CH(3)CN.8H(2)O( )()(2), which has also been characterized by single-crystal X-ray diffraction. The asymmetric unit consists of an Fe(2)(&mgr;-O)(&mgr;-BMDP)(&mgr;-OAc)(OH) group which is externally bridged via the oxo ions to form a molecular square with four of the eight iron ions at the corners. Both iron sites are six-coordinate with distorted octahedral geometry. One has an N(2)O(4) donor set; the other has an N(3)O(3) donor set. PMID:11670809

Satcher, Joe H.; Olmstead, Marilyn M.; Droege, Michael W.; Parkin, Sean R.; Noll, Bruce C.; May, Leopold; Balch, Alan L.

1998-12-28

122

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

Microsoft Academic Search

This paper reports the synthesis of five new hexa-coordinated mixed-ligand dinitrosyl complexes of molybdenum(0) of the composition [Mo(NO)2(L)(OH)], where LH=N-(3?-methyl-1?-phenyl-4?-valerylidene-2?-pyrazolin-5?-one)-4-aminoantipyrine (mphvp-aapH), N-(4?-benzoylidene-3?-methyl-1?-phenyl-2 ?-pyrazolin-5?-one)-4-aminoantipyrine (bmphp-aapH), N-(3?-methyl-1?-phenyl-4?-propionylidene-2?-pyrazolin-5?-one)-4-aminoantipyrine (mphpp-aapH), N-(4?-acetylidene-3?-methyl-1?-phenyl-2?-pyrazolin-5 ?-one)-4-aminoantipyrine (amphp-aapH) or N-(-4?-iso-butyrylidene-3?-methyl-1?-phenyl-2?-pyrazolin-5?-one)-4-aminoantipyrine (iso-bumphp-aapH) directly from molybdate (VI) in a single step and in a single pot. The compounds so obtained have been characterized by elemental analyses, molar conductance, decomposition temperature and

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

2006-01-01

123

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

E-print Network

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

Dutta, Prabir K.

124

DNA methylation program during development  

PubMed Central

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

ZHOU, Feng C.

2013-01-01

125

Interbiopolymer complexing between ?-lactoglobulin and low- and high-methylated pectin measured by potentiometric titration and ultrafiltration  

Microsoft Academic Search

The interactions between proteins and polysaccharides are of great interest to the food industry. Few studies have been carried out on diluted ?-lactoglobulin\\/pectin systems and none has provided a complete investigation on the nature of the interactions involved. The two main objectives of this study were to determine the conditions for the formation of complexes and to identify the type

Maude Girard; Sylvie L Turgeon; Sylvie F Gauthier

2002-01-01

126

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

PubMed Central

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

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

2013-01-01

127

Copper(II) complexes of schiff bases derived of 2-hydroxy-3-naphthaldehyde. The crystal and molecular structures of bis-{(phenyl)[(2-oxo-3 H -naphth-3-ylidene)methyl]aminato}copper(II) and bis-{(benzene-4-trifluoromethyl)[(2-oxo-3 H -naphth-3-ylidene)-methyl]aminato}copper(II)  

Microsoft Academic Search

The Schiff base ligands, 3-[(Phenyl)-2-hydroxy-3H-Naphth-3-ylidene)methyl]aldamine (1) and 3-[(benzene-4-trifluoromethyl)-2-hydroxy-3H-naphth-3-ylidene)methyl]aldamine (2), and their corresponding Cu(II) complexes (I andII were synthesized. The crystal and molecular structures ofI andII were determined. CompoundI crystallizes in the triclinic crystal systema=10.804(5),b=12.589(5), andc=10.369(3) (Å), ?=107.72(3), ?=95.75(3), and ?=76.32(4)(°), in the space group P\\u000a

J. M. Fernández; J. J. Lembrino-Canales; R. Villena-I

1994-01-01

128

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

NASA Astrophysics Data System (ADS)

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

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

2015-01-01

129

Characterization of albendazole-randomly methylated-?-cyclodextrin inclusion complex and in vivo evaluation of its antihelmitic activity in a murine model of Trichinellosis.  

PubMed

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

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

2014-01-01

130

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

PubMed Central

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

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

2014-01-01

131

CG methylation  

PubMed Central

A striking feature of mammalian genomes is the paucity of the CG dinucleotide. There are approximately 20,000 regions termed CpG islands where CGs cluster. This represents 5% of all CGs and 1% of the genome. CpG islands are typically unmethylated and are often promoters for housekeeping genes. The remaining 95% of CG dinucleotides are disposed throughout 99% of the genome and are typically methylated and found in half of all promoters. CG methylation facilitates binding of the C/EBP family of transcription factors, proteins critical for differentiation of many tissues. This allows these proteins to localize in the methylated CG poor regions of the genome where they may produce advantageous changes in gene expression at nearby or more distant regions of the genome. In this review, our growing understanding of the consequences of CG methylation will be surveyed. PMID:23244310

Vinson, Charles; Chatterjee, Raghunath

2013-01-01

132

Multifaceted Genome Control by Set1 Dependent and Independent of H3K4 Methylation and the Set1C/COMPASS Complex  

PubMed Central

Histone modifiers are critical regulators of chromatin-based processes in eukaryotes. The histone methyltransferase Set1, a component of the Set1C/COMPASS complex, catalyzes the methylation at lysine 4 of histone H3 (H3K4me), a hallmark of euchromatin. Here, we show that the fission yeast Schizosaccharomyces pombe Set1 utilizes distinct domain modules to regulate disparate classes of repetitive elements associated with euchromatin and heterochromatin via H3K4me-dependent and -independent pathways. Set1 employs its RNA-binding RRM2 and catalytic SET domains to repress Tf2 retrotransposons and pericentromeric repeats while relying on its H3K4me function to maintain transcriptional repression at the silent mating type (mat) locus and subtelomeric regions. These repressive functions of Set1 correlate with the requirement of Set1C components to maintain repression at the mat locus and subtelomeres while dispensing Set1C in repressing Tf2s and pericentromeric repeats. We show that the contributions of several Set1C subunits to the states of H3K4me diverge considerably from those of Saccharomyces cerevisiae orthologs. Moreover, unlike S. cerevisiae, the regulation of Set1 protein level is not coupled to the status of H3K4me or histone H2B ubiquitination by the HULC complex. Intriguingly, we uncover a genome organization role for Set1C and H3K4me in mediating the clustering of Tf2s into Tf bodies by antagonizing the acetyltransferase Mst1-mediated H3K4 acetylation. Our study provides unexpected insights into the regulatory intricacies of a highly conserved chromatin-modifying complex with diverse roles in genome control. PMID:25356590

Lorenz, David R.; Cam, Hugh P.

2014-01-01

133

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

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

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

134

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

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

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

135

Reporter molecules as probes of DNA conformation: structure of a crystalline complex containing 2-methyl-4-nitro-aniline ethylene dimethylammonium hydrobromide - 5-iodocytidylyl(3'-5')guanosine  

SciTech Connect

2-Methyl-4-nitroaniline ethylene dimethylammonium hydrobromide forms a crystalline complex with the self-complementary dinucleoside monophosphate, 5-iodocytidylyl(3'-5')guanosine. The crystals are tetragonal, with a = b = 32.192 A and c = 23.964 A, space group P4/sub 3/2/sub 1/2. The structure has been solved to atomic resolution by Patterson and Fourier methods, and refined by full matrix least squares. 5-Iodocytidylyl(3'-5')guanosine molecules are held together in pairs through Watson-Crick base-pairing, forming an antiparallel duplex structure. Nitroaniline molecules stack above and below guanine-cytosine pairs in this duplex structure. In addition, a third nitroaniline molecule stacks on one of the other two nitroaniline molecules. The asymmetric unit contains two 5-iodocytidylyl(3'-5')guanosine molecules, three nitroaniline molecules, one bromide ion and thirty-one water molecules, at total of 160 atoms. Details of the structure are described. 15 references, 4 figures, 2 tables.

Vyas, N.K.; Nyas, M.N.; Jain, S.C.; Sobell, H.M.

1984-05-31

136

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

PubMed

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

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

2014-11-12

137

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

SciTech Connect

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.

Szigethy, Geza; Raymond, Kenneth

2010-04-22

138

Ultrasensitive Biosensor for Detection of Organophosphorus Pesticides Based on a Macrocycle Complex/Carbon Nanotubes Composite and 1-Methyl-3-octylimidazolium Tetrafluoroborate as Binder Compound.  

PubMed

This work describes the highly sensitive detection of organophosphorus pesticides employing the cobalt(II) 4,4,4,4-tetrasulfo-phthalocyanine (CoTSPc) macrocycle complex, carbon nanotubes (CNT), and 1-methyl-3-octylimidazolium tetrafluoroborate (OMIM[BF4]). The technique is based on enzyme acetylcholinesterase (AChE) inhibition. The composite was characterized by scanning electron microscopy (SEM), Fourier transform infrared (FT-IR) spectroscopy, and amperometry. The AChE was immobilized on the composite electrode surface by cross-linking with glutaraldehyde and chitosan. The synergistic action of the CoTSPc/CNT/OMIM[BF4] composite showed excellent electrocatalytic activity, with a low applied potential for the amperometric detection of thiocholine (TCh) at 0.0 V vs. Ag/AgCl. The calculated catalytic rate constant, kcat, was 3.67 × 10(3) mol(-1) L s(-1). Under the optimum conditions, the inhibition rates of these pesticides were proportional to their concentrations in the ranges of 1.0 pmol L(-1) to 1.0 nmol L(-1) (fenitrothion), 2.0 pmol L(-1) to 8.0 nmol L(-1) (dichlorvos), and 16 pmol L(-1) to 5.0 nmol L(-1) (malathion). PMID:25792271

Pereira, Neuma das Mercês; Oliveira, Fernando Mota de; Pereira, Nara Rúbia; Verly, Rodrigo Moreira; Souto, Dênio Emanuel Pires; Kubota, Lauro Tatsuo; Tanaka, Auro Atsushi; Damos, Flavio Santos; Luz, Rita de Cássia Silva

2015-01-01

139

Insight into the binding mode between N-methyl pyrimidones and prototype foamy virus integrase-DNA complex by QM-polarized ligand docking and molecular dynamics simulations.  

PubMed

Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme in the viral replication cycle as it catalyzes the insertion of the reverse transcribed viral DNA into host chromosome. The structure of prototype foamy virus (PFV) IN has structural and functional homology with HIV-1 IN (no full-length structure available). In this study, we have used PFV IN-DNA complex as a surrogate model for HIV-1 IN-DNA complex to investigate the binding modes of N-methyl pyrimidones (NMPs) by QM-polarized ligand docking (QPLD), binding free energy calculations and molecular dynamics simulations. The O,O,O donor atom triad of NMPs show metal chelation with divalent Mg(2+) ions in the active site of PFV IN, in perfect agreement with the proposed mechanism of IN strand transfer inhibitors (INSTIs). The results also show that the benzyl group of compounds fit into a pocket to displace the 3'-terminal adenosine of viral DNA from the IN active site making it unavailable for the nucleophile to attack the target DNA in the strand transfer (ST) reaction. The halobenzyl moiety show hydrophobic interactions with conserved PFV IN Tyr212 and Pro214 residues, corresponding to HIV-1 IN Tyr143 and Pro145, respectively. Molecular dynamics (MD) simulations gave important insights into the structural and chemical basis involved in ST inhibition. Based on MD results, hydrogen bond with Tyr212, coordinate bonds with Mg(2+) ions, and hydrophobic interactions play an important role in the stabilization of compounds. Our results provide additional insight into the possible mechanism of action and binding mode of NMPs, and might have implications for rational design of specific HIV-1 INSTIs with improved affinity and selectivity. PMID:25579571

Reddy, Karnati Konda; Singh, Sanjeev Kumar

2015-01-01

140

The Effect of Methylated Vitamin B Complex on Depressive and Anxiety Symptoms and Quality of Life in Adults with Depression  

PubMed Central

Depression, the most common type of mental illness, is the second leading cause of disability and is increasing among Americans. The effect of improved nutrition, particularly with dietary supplements, on depression may provide an alternative to standard medical treatment. Some studies have shown that certain nutrients (e.g., inositol and S-adenosyl methionine) are effective at improving depressed mood, although the results are not unequivocal. The current study was a randomized, double-blind, placebo-controlled trial to evaluate the efficacy of a vitamin B complex nutritional supplement (Max Stress B) for improving depressive and anxiety symptoms according to the Beck Depression and Anxiety Inventories (BDI and BAI) in 60 adults diagnosed with major depression or other forms of depressive disorders. Secondary outcomes included quality of life according to the SF-36. Participants were assessed at baseline and 30- and 60-day followups. Max Stress B showed significant and more continuous improvements in depressive and anxiety symptoms, compared to placebo. Additionally, Max Stress B showed significant improvement on the mental health scale of the SF-36 compared to placebo. Thus, we showed modest utility of Max Stress B to improve mood symptoms and mental health quality of life in adults with depression. PMID:23738221

Lewis, John E.; Tiozzo, Eduard; Melillo, Angelica B.; Leonard, Susanna; Chen, Lawrence; Mendez, Armando; Woolger, Judi M.; Konefal, Janet

2013-01-01

141

DNA Methylation  

PubMed Central

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

Marinus, M.G.; Løbner-Olesen, A.

2014-01-01

142

Combined application of dazomet and Trichoderma asperellum as an efficient alternative to methyl bromide in controlling the soil-borne disease complex of bell pepper  

Microsoft Academic Search

Bell pepper (Capsicum annuum) is an important greenhouse crop in central Europe. However, due to its monoculture cultivation soil-borne pathogens, especially Verticillium dahliae, are a significant yield-limiting factor. Apart from treatment with methyl bromide (MB) phytopathogens can be controlled by several alternative soil treatments. However, a universal control agent such as methyl bromide does not exist and there is crop

Czeslaw ?lusarski; Stanislaw J. Pietr

2009-01-01

143

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

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

Huggins, John Mitchell

1980-06-01

144

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)

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).

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

2014-11-01

145

A three-dimensional zinc(II) interpenetrating network and a ? ? induced silver(I) zigzag complex connected by 1,3-di(imidazole-1-yl-methyl)-5-methylbenzene  

NASA Astrophysics Data System (ADS)

A 3D zinc(II) threefold interpenetrating network {[Zn(dimb) 2](ClO 4) 2} n ( 1) and a ?-? induced silver(I) double zigzag polymer {[Ag(dimb)](NO 3)·(H 2O)} n ( 2) were synthesized via a functional bidentate ligand 1,3-di(imidazole-1-yl-methyl)-5-methyl-benzene (dimb). The X-ray single crystal structural study indicated that the former complex represents an example of 3D interpenetrating network with a diamond topology in which aromatic ligands serve as the connector, while the latter is the first double zigzag polymer that has been formed by two adjacent infinite 1D zigzags through ?-? interactions between benzene rings of the ligand.

Ma, Yonglin; Huang, Wei; Yao, Jingcai; Li, Bin; Gou, Shaohua; Fun, Hoong-Kun

2003-09-01

146

DNA methylation in endometrial cancer  

PubMed Central

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

Freudenheim, Jo L

2010-01-01

147

Synthesis and spectral characterization of mono- and binuclear copper(II) complexes derived from 2-benzoylpyridine-N(4)-methyl-3-thiosemicarbazone: Crystal structure of a novel sulfur bridged copper(II) box-dimer.  

PubMed

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

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

2015-03-15

148

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

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

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

2014-01-01

149

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

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. PMID:24810030

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

2014-09-15

150

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)

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.

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

2014-09-01

151

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)

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 ?- and ?-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 ?- and ?-CD solutions.

Ghosh, Shalini; Jana, Sankar; Guchhait, Nikhil

2011-12-01

152

Automethylation Activities within the Mixed Lineage Leukemia-1 (MLL1) Core Complex Reveal Evidence Supporting a “Two-active Site” Model for Multiple Histone H3 Lysine 4 Methylation*  

PubMed Central

The mixed lineage leukemia-1 (MLL1) core complex predominantly catalyzes mono- and dimethylation of histone H3 at lysine 4 (H3K4) and is frequently altered in aggressive acute leukemias. The molecular mechanisms that account for conversion of mono- to dimethyl H3K4 (H3K4me1,2) are not well understood. In this investigation, we report that the suppressor of variegation, enhancer of zeste, trithorax (SET) domains from human MLL1 and Drosophila Trithorax undergo robust intramolecular automethylation reactions at an evolutionarily conserved cysteine residue in the active site, which is inhibited by unmodified histone H3. The location of the automethylation in the SET-I subdomain indicates that the MLL1 SET domain possesses significantly more conformational plasticity in solution than suggested by its crystal structure. We also report that MLL1 methylates Ash2L in the absence of histone H3, but only when assembled within a complex with WDR5 and RbBP5, suggesting a restraint for the architectural arrangement of subunits within the complex. Using MLL1 and Ash2L automethylation reactions as probes for histone binding, we observed that both automethylation reactions are significantly inhibited by stoichiometric amounts of unmethylated histone H3, but not by histones previously mono-, di-, or trimethylated at H3K4. These results suggest that the H3K4me1 intermediate does not significantly bind to the MLL1 SET domain during the dimethylation reaction. Consistent with this hypothesis, we demonstrate that the MLL1 core complex assembled with a catalytically inactive SET domain variant preferentially catalyzes H3K4 dimethylation using the H3K4me1 substrate. Taken together, these results are consistent with a “two-active site” model for multiple H3K4 methylation by the MLL1 core complex. PMID:24235145

Patel, Anamika; Vought, Valarie E.; Swatkoski, Stephen; Viggiano, Susan; Howard, Benny; Dharmarajan, Venkatasubramanian; Monteith, Kelsey E.; Kupakuwana, Gillian; Namitz, Kevin E.; Shinsky, Stephen A.; Cotter, Robert J.; Cosgrove, Michael S.

2014-01-01

153

Automethylation activities within the mixed lineage leukemia-1 (MLL1) core complex reveal evidence supporting a "two-active site" model for multiple histone H3 lysine 4 methylation.  

PubMed

The mixed lineage leukemia-1 (MLL1) core complex predominantly catalyzes mono- and dimethylation of histone H3 at lysine 4 (H3K4) and is frequently altered in aggressive acute leukemias. The molecular mechanisms that account for conversion of mono- to dimethyl H3K4 (H3K4me1,2) are not well understood. In this investigation, we report that the suppressor of variegation, enhancer of zeste, trithorax (SET) domains from human MLL1 and Drosophila Trithorax undergo robust intramolecular automethylation reactions at an evolutionarily conserved cysteine residue in the active site, which is inhibited by unmodified histone H3. The location of the automethylation in the SET-I subdomain indicates that the MLL1 SET domain possesses significantly more conformational plasticity in solution than suggested by its crystal structure. We also report that MLL1 methylates Ash2L in the absence of histone H3, but only when assembled within a complex with WDR5 and RbBP5, suggesting a restraint for the architectural arrangement of subunits within the complex. Using MLL1 and Ash2L automethylation reactions as probes for histone binding, we observed that both automethylation reactions are significantly inhibited by stoichiometric amounts of unmethylated histone H3, but not by histones previously mono-, di-, or trimethylated at H3K4. These results suggest that the H3K4me1 intermediate does not significantly bind to the MLL1 SET domain during the dimethylation reaction. Consistent with this hypothesis, we demonstrate that the MLL1 core complex assembled with a catalytically inactive SET domain variant preferentially catalyzes H3K4 dimethylation using the H3K4me1 substrate. Taken together, these results are consistent with a "two-active site" model for multiple H3K4 methylation by the MLL1 core complex. PMID:24235145

Patel, Anamika; Vought, Valarie E; Swatkoski, Stephen; Viggiano, Susan; Howard, Benny; Dharmarajan, Venkatasubramanian; Monteith, Kelsey E; Kupakuwana, Gillian; Namitz, Kevin E; Shinsky, Stephen A; Cotter, Robert J; Cosgrove, Michael S

2014-01-10

154

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 Central

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 ?1 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

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

2013-01-01

155

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

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

Onwudiwe, Damian C.; Ajibade, Peter A.

2011-01-01

156

Determination of aminoglutethimide enantiomers in pharmaceutical formulations by capillary electrophoresis using methylated-?-cyclodextrin as a chiral selector and computational calculation for their respective inclusion complexes  

Microsoft Academic Search

A capillary electrophoretic method for the separation of the aminoglutethimide (AGT) enantiomers using methylated-?-cyclodextrin (M-?-CD) as chiral selector is described. Several parameters affecting the separation were studied, including the type and concentration of chiral selector, buffer pH, voltage and temperature. Good chiral separation of the racemic mixture was achieved in less than 9min with resolution factor Rs=2.1, using a fused-silica

Abdalla A. Elbashir; Fakhr Eldin O. Suliman; Bahruddin Saad; Hassan Y. Aboul-Enein

2009-01-01

157

Mass spectrometric behavior of functionalized calix[4]arenes: the screening ability of host–guest complex formation with amino acid methyl esters  

Microsoft Academic Search

The ESI–MS and MS\\/MS behavior of functionalized calix[4]arenes (1–5) has been studied in both positive and negative-ion mode. Liquid chromatography coupled to ESI–MS has been successfully used\\u000a for separation of the byproducts issuing from the functionalization pathways, through the application of a simple reversed\\u000a phase mechanism. The ability of (1–5) to host methyl esters of amino acids, tyrosine, tryptophan, phenylalanine,

Andrei Medvedovici; Florin Albu; Abdelwaheb Hamdi; Rachid Souane; Lidia Kim; Lucia Mutihac; Jacques Vicens

158

Production of methyl-oxonium ion and its complexes in the core-excited (HC(O)OCH3)n clusters: H/H+ transfer from the ? carbonyl  

NASA Astrophysics Data System (ADS)

Dissociation of free methyl-formate (MF), HC(O )OCH3, and its clusters (MF)n, (HC(O)OCH3)n, induced by core-level excitation was studied near the oxygen K edge by time-of-flight fragment-mass spectroscopy. Besides the protonated clusters, (MF)nH+ with n ?15, we identified the production for another series of (MF)mCH3OH2+ with m ?14 as well as methyl-oxonium ion, CH3OH2+, characteristic of hydrogen transfer reactions in the cationic clusters. Here, specifically labeled methyl-formate-d (MFD), DC(O )OCH3 was also used to examine the core-excited dissociation mechanisms. Deuterium-labeled experiments indicated that MFD+ with low internal energies, partially generated after the core excitation, produces CH3OD+ via a site-specific deuterium transfer from the ? carbonyl in the molecular cation and that CH3OD2+ can be formed via the successive transfer of another deuterium from the neighbor molecule in the clusters. The deuteron (proton) transfer was also found to take place preferentially from the ? carbonyl of the neighbor molecule for the production of deuteronated (MFD )nD+, (protonated (MF)nH+), clusters. The minimal energy requirement paths were examined for dimer (MF)2+ cation to support the present dissociation mechanisms of core-excited (MF)n clusters using ab initio molecular-orbital calculations.

Tada, S.; Harada, C.; Yoshida, H.; Wada, S.; Hiraya, A.; Tanaka, K.; Tabayashi, K.

2005-09-01

159

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

PubMed

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

Inomata, Masataka; Suenaga, Yusaku

2014-11-01

160

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)

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.

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

2015-01-01

161

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)

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

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

2011-10-01

162

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

NASA Astrophysics Data System (ADS)

A template condensation of ?-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.

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

2011-12-01

163

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

SciTech Connect

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

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

2005-01-01

164

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

SciTech Connect

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

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

2005-01-01

165

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

PubMed

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

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

2014-11-01

166

Significance of cholesterol methyl groups.  

PubMed

Cholesterol is an indispensable molecule in mammalian cell membranes. To truly understand its role in the functions of membranes, it is essential to unravel cholesterol's structure-function relationship determined by underlying molecular interactions. For this purpose, we elaborate on this issue by considering the previously proposed idea that cholesterol's effects on a number of physical properties of membranes have been optimized during the evolution by removal of its excess methyl groups from the alpha-face of cholesterol, thus "smoothening" the structure. Consequently, the methyl groups still attached to cholesterol are one of the most intriguing structural features of the molecule. An obvious question arises: Why do these methyl groups still exist, and could cholesterol properties be further optimized by their removal? Because of the nature of the biosynthetic pathways of cholesterol, and the evidence of decreased interactions between sterols and lipid acyl chains when methyl groups are present, it seems plausible that removal of the methyl groups might indeed lead to stronger ordering and condensing effects of the cholesterol molecule. Atomic-scale molecular dynamics simulations of numerous modified sterols embedded in saturated lipid bilayers demonstrate, however, that the issue is more subtle. The analysis reveals a complex interplay between the lipid acyl chains and the structural details of cholesterol. Changes in cholesterol structure typically do not improve its performance in terms of promoting membrane order. This view is substantiated by a detailed analysis of the simulation data. In particular, it highlights the importance of the methyl group C18 for cholesterol properties. The C18 group resides between the third and fourth ring of cholesterol on its "rough" beta-side, and the results provide compelling evidence that C18 is crucial for the proper orientation of the sterol. More generally, the data provide insight into the role of the methyl groups of cholesterol. PMID:18278902

Pöyry, Sanja; Róg, Tomasz; Karttunen, Mikko; Vattulainen, Ilpo

2008-03-13

167

DNA methylation patterns in lung carcinomas.  

PubMed

The genome of epithelial tumors is characterized by numerous chromosomal aberrations, DNA base sequence changes, and epigenetic abnormalities. The epigenome of cancer cells has been most commonly studied at the level of DNA CpG methylation. In squamous cell carcinomas of the lung, CpG methylation patterns undergo substantial changes relative to normal lung epithelium. Using a genome-scale mapping technique for CpG methylation (MIRA-chip), we characterized CpG island methylation and methylation patterns of entire chromosome arms at a level of resolution of approximately 100 bp. In individual stage I lung carcinomas, several hundred and probably up to a thousand CpG islands become methylated. Interestingly, a large fraction (almost 80%) of the tumor-specifically methylated sequences are targets of the Polycomb complex in embryonic stem cells. Homeobox genes are particularly overrepresented and all four HOX gene loci on chromosomes 2, 7, 12, and 17 are hotspots for tumor-associated methylation because of the presence of multiple methylated CpG islands within these loci. DNA hypomethylation at CpGs in squamous cell tumors preferentially affects repetitive sequence classes including SINEs, LINEs, subtelomeric repeats, and segmental duplications. Since these epigenetic changes are found in early stage tumors, their contribution to tumor etiology as well as their potential usefulness as diagnostic or prognostic biomarkers of the disease should be considered. PMID:19429482

Pfeifer, Gerd P; Rauch, Tibor A

2009-06-01

168

Coordination chemistry and bioactivity of Ni 2+, Cu 2+, Cd 2+ and Zn 2+ complexes containing bidentate Schiff bases derived from S-benzyldithiocarbazate and the X-ray crystal structure of bis[ S-benzyl-?- N-(5-methyl-2-furylmethylene)dithiocarbazato]cadmium(II)  

Microsoft Academic Search

New bidentate isomeric NS and NS? Schiff bases were derived from the condensation of S-benzyldithiocarbazate (SBDTC) with 5-methyl-2-furyldehyde and 2-furyl-methylketone. Reaction of NS ligand with Ni(II), Cu(II), Cd(II) and Zn(II) salts gave solid complexes. Only the Ni(II) complex of the NS? ligand was isolated. All complexes were characterized by a variety of physico-chemical techniques, viz. elemental analyses, molar conductivity, i.r.

M. T. H Tarafder; Khoo Teng Jin; Karen A Crouse; A. M Ali; B. M Yamin; H.-K Fun

2002-01-01

169

Structural rearrangement in the formation of jet-cooled complexes of chiral (S)-1,2,3,4-tetrahydro-3-isoquinolinemethanol with methyl lactate: chirality effect in conformer selection.  

PubMed

The jet-cooled complexes between the two enantiomers of methyl lactate (ML) and (S)-1,2,3,4-tetrahydro-3-isoquinolinemethanol (THIQM) are studied by double resonance spectroscopy combined with ab initio calculations. Both diastereomer complexes exist in different isomers, involving either direct addition of THIQM on ML with no structural rearrangement of the subunits or formation of very stable structures involving multiple intermolecular hydrogen bonds and extensive deformation of the subunits. Competition between these two processes and its dependence upon chirality are discussed. It is shown that the most stable form of the chromophore (THIQMI with an OH···N hydrogen bond) prefers to directly stick to ML to form the addition complex whereas the second conformer (THIQMII with NH···O hydrogen bond) rearranges to form a strongly bound structure. The two structures are formed for the homochiral as well the heterochiral complex, however with different relative abundance. This shows an enantioselective binding preference of ML for one of the conformers of the chromophore. PMID:23496094

Mahjoub, Ahmed; Le Barbu-Debus, Katia; Zehnacker, Anne

2013-04-11

170

Estimation of nitric oxide level in vivo by microdialysis with water-soluble iron-N-methyl-D-dithiocarbamate complexes as NO traps: a novel approach to nitric oxide spin trapping in animal tissues.  

PubMed

It was found that microdialysis, i.e., passage of aqueous solutions of iron-N-methyl-D-glucamine dithiocarbamate complexes through dialysis fibers implanted into heart, kidney and liver tissues of narcotized rats, was accompanied by effective binding of the complexes to nitric oxide from interstitial fluid. The walls of dialysis fibers used in this study were permeable for compounds with molecular weight not exceeding 5 kDa. The dialyzate samples collected every 20 min and containing diamagnetic nitrosyl Fe3+-MGD adducts were reduced to the paramagnetic state with sodium dithionite; their concentration was measured by the EPR method. The basic level of the adducts, which represented mononitrosyl iron complexes with MGD (MNIC-MGD), in the dialyzate samples of all tested organs were similar (1 microM). Treatment of animals with the water-soluble nitroglycerine analog Isoket or a low-molecular dinitrosyl iron thiosulfate complex as a NO donor increased the concentration of MNIC-MGD with going out into a plateau. The novel approach allows determination of nitric oxide levels in tissue interstitial fluid from concentration of MNIC-MGD formed during microdialysis. PMID:18664386

Timoshin, Alexander A; Drobotova, Diana Yu; Lakomkin, Vladimir L; Ruuge, Enno K; Vanin, Anatoly F

2008-12-01

171

DNA Methylation, Nuclear Structure, Gene Expression and Cancer  

Microsoft Academic Search

DNA methylation, chromatin structure, transcription, and cancer have traditionally been studied as separate phenomena. Recent data provide now direct physical and functional links between these processes revealing a complex network of interactions and mutual dependences. Methylated DNA is bound by methyl-CpG binding protein (MeCP) complexes that include histone deacetylases (HDACs). This recruitment of HDACs is suggested to promote local chromatin

Heinrich Leonhardt; M. Cristina Cardoso

2001-01-01

172

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.  

PubMed

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 ?- and ?-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 ?- and ?-CD solutions. PMID:21996591

Ghosh, Shalini; Jana, Sankar; Guchhait, Nikhil

2011-12-15

173

Reactions of benzene based half sandwich ruthenium(II) complex with 2,6-bis((phenylseleno)methyl)pyridine: Preferential substitution of ring resulting in a catalyst of high activity for oxidation of alcohols  

Microsoft Academic Search

[2,6-Bis((phenylseleno)methyl)pyridine] (L) a (Se, N, Se) pincer ligand synthesized by reacting PhSe? (in situ generated) with 2,6-bis(chloromethyl)pyridine reacts with [{(?6-C6H6)RuCl(?-Cl)}2] (2:1 molar ratio) by preferential substitution of ring resulting in the first Ru-(Se, N, Se) pincer ligand complex, mer-[Ru(CH3CN)2Cl(L)][PF6](1).H2O. Similar reaction in 4:1 molar ratio results in mer-[Ru(L)2][ClO4]2(2). The 1H, 13C{1H} and 77Se{1H} NMR spectra of L, 1 and 2

Dipanwita Das; Pradhumn Singh; Om Prakash; Ajai K. Singh

2010-01-01

174

Pd(II)– N-heterocyclic carbene complexes of 2,6- bis{ N-methyl-(imidazolium\\/benzimidazolium)}pyrazinechloride: Synthesis, structure, catalysis and theoretical studies  

Microsoft Academic Search

The multitopic pyrazine functionalized pro-ligand 2,6-bis(N-methylimidazolium)pyrazinedichloride, L-1; 2,6-bis(N-methylbenzimidazolium)pyrazinedichloride, L-2 and their respective Pd(II)–NHC complexes 1 and 2 have been synthesised and characterized by different spectroscopic methods and have been analyzed within a conceptual DFT framework. Single crystal X-ray structures of (L-1)PF6 and complex 1 have been determined. X-ray structure revels that 1 form a 12 member palladacycle. Both complex 1

Gourisankar Roymahapatra; Santanab Giri; Anders A. Danopoulos; Pratim Kumar Chattaraj; Ambikesh Mahapatra; Valerio Bertolasi; Joydev Dinda

175

Methyl nutrients, DNA methylation, and cardiovascular disease.  

PubMed

Diet plays an important role in the development and prevention of cardiovascular disease (CVD), but the molecular mechanisms are not fully understood. DNA methylation has been implicated as an underlying molecular mechanism that may account for the effect of dietary factors on the development and prevention of CVD. DNA methylation is an epigenetic process that provides "marks" in the genome by which genes are set to be transcriptionally activated or silenced. Epigenomic marks are heritable but are also responsive to environmental shifts, such as changes in nutritional status, and are especially vulnerable during development. S-adenosylmethionine is the methyl group donor for DNA methylation and several nutrients are required for the production of S-adenosylmethionine. These methyl nutrients include vitamins (folate, riboflavin, vitamin B12, vitamin B6, choline) and amino acids (methionine, cysteine, serine, glycine). As such, imbalances in the metabolism of these nutrients have the potential to affect DNA methylation. The focus of this review is to provide an overview on the current understanding of the relationship between methyl nutrient status and DNA methylation patterns and the potential role of this interaction in CVD pathology. PMID:23661599

Glier, Melissa B; Green, Timothy J; Devlin, Angela M

2014-01-01

176

Application of microarrays for DNA methylation profiling.  

PubMed

Comprehensive analyses of the human epigenome may be of critical importance in understanding the molecular mechanisms of complex diseases, development, aging, tissue specificity, parental origin effects, and sex differences, among other systemic aspects of human biology. However, traditional DNA methylation methods allowed for screening of only relatively short DNA fragments. The advent of microarrays has provided new possibilities in DNA methylation analysis, because this technology is able to interrogate a very large number of loci in a highly parallel fashion. There are several permutations of the microarray application in DNA methylation profiling, and such include microarray analysis of bisulfite modified DNA and also the enriched unmethylated or hypermethylated DNA fractions using methylation-sensitive restriction enzymes or antibodies against methylated cytosines. The method described in detail here is based on the analysis of the enriched unmethylated DNA fraction, using a series of treatments with methylation-sensitive restriction enzymes, adaptor ligation, PCR amplification, and quantitative mapping of unmethylated DNA sequences using microarrays. The key advantages of this approach are the ability to investigate DNA methylation patterns using very small DNA amounts and relatively high informativeness in comparison to the other restriction-enzyme- based strategies for DNA methylation profiling [1]. PMID:18370099

Schumacher, Axel; Weinhäusl, Andreas; Petronis, Arturas

2008-01-01

177

Establishment of histone H3 methylation on the inactive X chromosome requires transient recruitment of Eed-Enx1 polycomb group complexes  

Microsoft Academic Search

Previous studies have implicated the Eed-Enx1 Polycomb group complex in the maintenance of imprinted X inactivation in the trophectoderm lineage in mouse. Here we show that recruitment of Eed-Enx1 to the inactive X chromosome (Xi) also occurs in random X inactivation in the embryo proper. Localization of Eed-Enx1 complexes to Xi occurs very early, at the onset of Xist expression,

Jose Silva; Winifred Mak; Ilona Zvetkova; Ruth Appanah; Tatyana B Nesterova; Zoe Webster; Antoine H. F. M Peters; Thomas Jenuwein; Arie P Otte; Neil Brockdorff

2003-01-01

178

Protolytic Cleavage of Hg-C Bonds Induced by 1-Methyl-1,3-dihydro-2H-benzimidazole-2-selone: Synthesis and Structural Characterization of Mercury Complexes.  

PubMed

Multinuclear ((1)H, (77)Se, and (199)Hg) NMR spectroscopy demonstrates that 1-methyl-1,3-dihydro-2H-benzimidazole-2-selone, H(sebenzim(Me)), a structural analogue of the selenoamino acid, selenoneine, binds rapidly and reversibly to the mercury centers of HgX2 (X = Cl, Br, I), while X-ray diffraction studies provide evidence for the existence of adducts of composition [H(sebenzim(Me))]xHgX2 (X = Cl, x = 2, 3, 4; X = I, x = 2) in the solid state. H(sebenzim(Me)) also reacts with methylmercury halides, but the reaction is accompanied by elimination of methane resulting from protolytic cleavage of the Hg-C bond, an observation that is of relevance to the report that selenoneine demethylates CysHgMe, thereby providing a mechanism for mercury detoxification. Interestingly, the structures of [H(sebenzim(Me))]xHgX2 exhibit a variety of different hydrogen bonding patterns resulting from the ability of the N-H groups to form hydrogen bonds with chlorine, iodine, and selenium. PMID:25822075

Palmer, Joshua H; Parkin, Gerard

2015-04-01

179

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

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.

Assefa, Zerihun [Transuranium Chemistry Group, Chemical Sciences Division, Oak Ridge National Laboratory, MS 6375, Oak Ridge, TN 37831-6375 (United States)]. E-mail: assefaz@ornl.gov; Yaita, T. [Department of Materials Science, Japan Atomic Energy Research Institute, Tokai (Japan); Haire, R.G. [Transuranium Chemistry Group, Chemical Sciences Division, Oak Ridge National Laboratory, MS 6375, Oak Ridge, TN 37831-6375 (United States); Tachimori, S. [Department of Materials Science, Japan Atomic Energy Research Institute, Tokai (Japan)

2005-02-15

180

Modeling of the oxidation of methyl esters--Validation for methyl hexanoate, methyl heptanoate, and methyl decanoate in a  

E-print Network

-temperature range are similar to that of alkanes. Keywords: Methyl esters; Oxidation; Detailed kinetic model; MethylModeling of the oxidation of methyl esters--Validation for methyl hexanoate, methyl heptanoate Abstract The modeling of the oxidation of methyl esters was investigated and the specific chemistry, which

Paris-Sud XI, Université de

181

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

PubMed

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

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

2014-05-01

182

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

NASA Astrophysics Data System (ADS)

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

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

183

On how mammalian transcription factors recognize methylated DNA  

PubMed Central

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

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

2013-01-01

184

Synthesis, spectroscopic studies and structures of square-planar nickel(II) and copper(II) complexes derived from 2-{(Z)-[furan-2-ylmethyl]imino]methyl}-6-methoxyphenol.  

PubMed

Two new nickel(II) [Ni(L)(2)] and copper(II) [Cu(L)(2)] complexes have been synthesized with bidentate NO donor Schiff base ligand (2-{(Z)-[furan-2-ylmethyl]imino]methyl}-6-methoxyphenol) (HL) and both complexes Ni(L)(2) and Cu(L)(2) have been characterized by elemental analyses, IR, UV-vis, (1)H, (13)C NMR, mass spectroscopy and room temperature magnetic susceptibility measurement. The tautomeric equilibria (phenol-imine, O-H...N and keto-amine, O...H-N forms) have been systemetically studied by using UV-vis absorption spectra for the ligand HL. The UV-vis spectra of this ligand HL were recorded and commented in polar, non-polar, acidic and basic media. The crystal structures of these complexes have also been determined by using X-ray crystallographic techniques. The complexes Ni(L)(2) and Cu(L)(2) crystallize in the monoclinic space group P2(1)/n and P2(1)/c with unit cell parameters: a=10.4552(3)A and 12.1667(4)A, b=8.0121(3)A and 10.4792(3)A, c=13.9625(4)A and 129.6616(3)A, V=1155.22(6)A(3) and 1155.22(6)A(3), D(x)=1.493 and 1.476 g cm(-3) and Z=2 and 2, respectively. The crystal structures were solved by direct methods and refined by full-matrix least squares to a find R=0.0377 and 0.0336 of for 2340 and 2402 observed reflections, respectively. PMID:20047854

Unver, Hüseyin; Hayvali, Zeliha

2010-02-01

185

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

186

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

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. PMID:24861807

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

187

Structural Basis for Methyl Transfer by a Radical SAM Enzyme  

SciTech Connect

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.

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

2014-10-02

188

Structural basis for Klf4 recognition of methylated DNA  

PubMed Central

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

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

2014-01-01

189

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

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.

Roth, S.; Ramamoorthy, V.; Sharp, P.R. (Univ. of Missouri, Columbia (USA))

1990-09-05

190

Synthesis, spectral and structural studies of a Mn(II) complex of [N?-(pyridine-4-carbonyl)-hydrazine]-carbodithioic acid ethyl ester and Mn(II) and Ni(II) complexes of [N?-(pyridine-4-carbonyl)-hydrazine]-carbodithioic acid methyl ester  

Microsoft Academic Search

The new complexes [Mn(Hpchce)2(o-phen)], {2[Mn(pchcm)(o-phen)2]}·7H2O and [Ni(Hpchcm)(o-phen)2]Cl·CH3OH with [N?-(pyridine-4-carbonyl)-hydrazine]-carbodithioic acid ethyl ester (H2pchce) and [N?-(pyridine-4-carbonyl)-hydrazine]-carbodithioic acid methyl ester (H2pchcm) have been synthesized, containing o-phenanthroline (o-phen) as a coligand. These ligands and their complexes have been characterized by elemental analyses, IR, magnetic susceptibility and single crystal X-ray data. H2pchce (2), [Mn(Hpchce)2(o-phen)] (3) {2[Mn(pchcm)(o-phen)2]}·7H2O (4) and [Ni(Hpchcm)(o-phen)2]Cl·CH3OH (5) crystallized in the monoclinic

N. K. Singh; M. K. Bharty; S. K. Kushawaha; U. P. Singh; Pooja Tyagi

2010-01-01

191

DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes  

Microsoft Academic Search

Cytosine DNA methylation in vertebrates is widespread, but methylation in plants is found almost exclusively at transposable elements and repetitive DNA [1]. Within regions of methylation, methylcytosines are typically found in CG, CNG, and asymmetric contexts. CG sites are maintained by a plant homolog of mammalian Dnmt1 acting on hemi-methylated DNA after replication. Methylation of CNG and asymmetric sites appears

Robert K. Tran; Jorja G. Henikoff; Daniel Zilberman; Renata F. Ditt; Steven E. Jacobsen; Steven Henikoff

2005-01-01

192

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

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 ? 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 ? 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(-?) with ? = 1.35-1.67, and (ii) for 0.0353 < q < 0.35 Å(-1), I(q) = I(0)/(1 + q(2)?(2)). The correlation length found was ? = 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 (?10 nm). Rheology data indicated that the coacervate phase resided close to the gelation state of the protein. Thus, on a heating-cooling cycle (heating to 50 °C followed by cooling to 20 °C), the heterogeneous coacervate exhibited an irreversible first-order phase transition to an anisotropic ion gel. This established a coacervate-ion gel phase diagram having a well-defined UCST. PMID:23194173

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

2012-12-27

193

Methylating agents and DNA repair responses: methylated bases and sources of strand breaks  

PubMed Central

The chemical methylating agents methylmethane sulfonate (MMS) and N-methyl-N?-nitro-N-nitrosoguanidine (MNNG) have been used for decades as classical DNA damaging agents. These agents have been utilized to uncover and explore pathways of DNA repair, DNA damage response, and mutagenesis. MMS and MNNG modify DNA by adding methyl groups to a number of nucleophilic sites on the DNA bases, although MNNG produces a greater percentage of O-methyl adducts. There has been substantial progress elucidating direct reversal proteins that remove methyl groups and base excision repair (BER), which removes and replaces methylated bases. Direct reversal proteins and BER thus counteract the toxic, mutagenic and clastogenic effects of methylating agents. Despite recent progress, the complexity of DNA damage responses to methylating agents is still being discovered. In particular, there is growing understanding of pathways such as homologous recombination, lesion bypass, and mismatch repair that react when the response of direct reversal proteins and BER is insufficient. Furthermore, the importance of proper balance within the steps in BER has been uncovered with the knowledge that DNA structural intermediates during BER are deleterious. A number of issues complicate elucidating the downstream responses when direct reversal is insufficient or BER is imbalanced. These include inter-species differences, cell-type specific differences within mammals and between cancer cell lines, and the type of methyl damage or BER intermediate encountered. MMS also carries a misleading reputation of being a ‘radiomimetic,’ i.e., capable of directly producing strand breaks. This review focuses on the DNA methyl damage caused by MMS and MNNG for each site of potential methylation to summarize what is known about the repair of such damage and the downstream responses and consequences if not repaired. PMID:17173371

Wyatt, Michael D.; Pittman, Douglas L.

2008-01-01

194

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)

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.

Macit, Mustafa; Alpaslan, Gökhan

2014-08-01

195

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

PubMed

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

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

2014-07-21

196

DNA methylation and cancer.  

PubMed

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

Kulis, Marta; Esteller, Manel

2010-01-01

197

Iron(0) and ruthenium(0) complexes with tridentate phosphonite ligands and their potential for ketene formation from methyl iodide, CO and a base  

Microsoft Academic Search

An efficient route to the novel tridentate phosphine ligands RP[CH2CH2CH2P(OR?)2]2 (I: R=Ph; R?=i-Pr; II: R=Cy; R?=i-Pr; III: R=Ph; R?=Me and IV: R=Cy; R?=Me) has been developed. The corresponding ruthenium and iron dicarbonyl complexes M(triphos)(CO)2 (1: M=Ru; triphos=I; 2: M=Ru; triphos=II; 3: M=Ru; triphos=III; 4: M=Ru; triphos=IV; 5: M=Fe; triphos=I; 6: M=Fe; triphos=II; 7: M=Fe; triphos=III and 8: M=Fe; triphos=IV) have

Piotr Jaunky; Helmut W. Schmalle; Olivier Blacque; Thomas Fox; Heinz Berke

2005-01-01

198

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)

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

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

2014-06-01

199

Crystal structures of cytochrome P450 2B4 in complex with the inhibitor 1-biphenyl-4-methyl-1H–imidazole: ligand induced structural response through ?-helical repositioning†‡  

PubMed Central

Two different ligand occupancy structures of cytochrome P450 2B4 (CYP2B4) in complex with 1-biphenyl-4-methyl-1H–imidazole (1-PBI) have been solved by x-ray crystallography. 1-PBI belongs to a series of tight binding, imidazole-based CYP2B4 inhibitors. 1-PBI binding to CYP2B4 yields a type II spectrum with a Ks value of 0.23 µM and inhibits enzyme activity with an IC50 value of 0.035 µM. Previous CYP2B4 structures have shown a large degree of structural movement in response to ligand size. With two phenyl rings, 1-PBI is larger than 1-(4-chlorophenyl)imidazole (1-CPI) and 4-(4-chlorophenyl)imidazole (4-CPI) but smaller than bifonazole, which is branched and contains three phenyl rings. The CYP2B4:1-PBI complex is a structural intermediate to the closed CPI and the open bifonazole structures. The B/C loop reorganizes itself to include two short partial helices while closing one side of the active site. The F-G helix cassette pivots over the I-helix in direct response to the size of the ligand in the active site. A cluster of Phe residues at the fulcrum of this pivot point allows for dramatic repositioning of the cassette with only a relatively small amount of secondary structure rearrangement. Comparisons of ligand bound CYP2B4 structures reveal trends in plastic region mobility that could allow for predictions of their position in future structures based on ligand shape and size. PMID:19397311

Gay, Sean C.; Sun, Ling; Maekawa, Keiko; Halpert, James R.; Stout, C. David

2009-01-01

200

DNA Methylation and Cancer  

Microsoft Academic Search

DNA methylation is one of the most intensely studied epigenetic modifications in mammals. In normal cells, it assures the proper regulation of gene expression and stable gene silencing. DNA methylation is associated with histone modifications and the interplay of these epigenetic modifications is crucial to regulate the functioning of the genome by changing chromatin architecture. The covalent addition of a

Marta Kulis; Manel Esteller

2010-01-01

201

Gene Regulation by Methylation  

Microsoft Academic Search

Epigenetic gene regulation of specific genes strongly affects clinical outcome of malignant glioma. MGMT is the best studied gene for the connection of promoter methylation and clinical course in glioblastoma. While MGMT promoter methylation analysis currently does not alter treatment of glioblastoma patients, mainly because of a lack of convincing\\u000a therapy to radiotherapy and concomitant administration of alkylating drugs, there

Wolf C. Mueller; Andreas von Deimling

202

Guiding DNA methylation.  

PubMed

How DNA methyltransferases, with their limited target specificity, establish cell-type-specific epigenetic patterns is poorly understood. Schübeler and colleagues (Lienert et al., 2011) now show that methylation-determining regions (MDRs) within promoter regions are sufficient to recapitulate endogenous patterns and dynamics of DNA methylation. PMID:22056134

Meissner, Alexander

2011-11-01

203

DNA methylation-mediated epigenetic control.  

PubMed

During differentiation and development cells undergo dramatic morphological and functional changes without any change in the DNA sequence. The underlying changes of gene expression patterns are established and maintained by epigenetic processes. Early mechanistic insights came from the observation that gene activity and repression states correlate with the DNA methylation level of their promoter region. DNA methylation is a postreplicative modification that occurs exclusively at the C5 position of cytosine residues (5mC) and predominantly in the context of CpG dinucleotides in vertebrate cells. Here, three major DNA methyltransferases (Dnmt1, 3a, and 3b) establish specific DNA methylation patterns during differentiation and maintain them over many cell division cycles. CpG methylation is recognized by at least three protein families that in turn recruit histone modifying and chromatin remodeling enzymes and thus translate DNA methylation into repressive chromatin structures. By now a multitude of histone modifications have been linked in various ways with DNA methylation. We will discuss some of the basic connections and the emerging complexity of these regulatory networks. PMID:19565567

Rottach, Andrea; Leonhardt, Heinrich; Spada, Fabio

2009-09-01

204

DNA Methylation Biomarkers: Cancer and Beyond  

PubMed Central

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

Mikeska, Thomas; Craig, Jeffrey M.

2014-01-01

205

Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping  

Microsoft Academic Search

Genomic DNA methylation profiles exhibit substan- tial variation within the human population, with important functional implications for gene regula- tion. So far little is known about the characteristics and determinants of DNA methylation variation among healthy individuals. We performed bioinfor- matic analysis of high-resolution methylation pro- files from multiple individuals, uncovering complex patterns of inter-individual variation that are strongly correlated

Christoph Bock; Jörn Walter; Martina Paulsen; Thomas Lengauer

2008-01-01

206

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

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 ?(1):?(1):?(1):? mpko(-) ligands. The Ni(II) centre is octahedrally coordinated by the six nitrogen atoms of the mpko(-) ligands in a facial arrangement. The Ln(III) centre is bound to an (O(oximate))(3)N(6) set of donor atoms, the nitrogen atoms belonging to the three N,N'-bidentate chelating mpkoH ligands. The stereochemistry of the Ln(III) atoms has been evaluated by means of continuous shape measures (CShM). The two crystallographically independent Ce(III) atoms in 1 have tricapped trigonal prismatic and capped square antiprismatic coordination geometries, while the polyhedra of the Dy(III) atoms in 8 are both close to a tricapped trigonal prism. The octahedral Ni(II) atoms in 11 are both facially bound to a N(6) set of donor atoms from three N,N'-bidentate chelating mpkoH ligands, while the 12-coordinate La(III) centre in [La(NO(3))(6)](3-) is coordinated by six bidentate chelating nitrato groups. Variable-temperature, solid state dc magnetic susceptibility studies were carried out on complexes 2, 6, 7 and 8. The dc susceptibility data for 6 in the 2.0-300 K range have been fit to a model with one J value, revealing an antiferromagnetic Ni(II)···Gd(III) exchange interaction [J = -1.1 cm(-1) based on H = -J (?(Ni)·?(Gd))]. Antiferromagnetic Ni(II)···Pr(III), Ni(II)···Tb(III) and Ni(II)···Dy(III) exchange interactions have also been suggested for 2, 7 and 8, respectively. The combined work demonstrates the usefulness of mpko(-) in the preparation of interesting Ni(II)/Ln(III) compounds, without requiring the presence of external base and ancillary organic ligands. PMID:23069731

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

2012-11-28

207

Smyd2 controls cytoplasmic lysine methylation of Hsp90 and myofilament organization  

PubMed Central

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

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

2012-01-01

208

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...

209

Epigenomics: Methylation matters  

Microsoft Academic Search

Genome-wide maps of methylated cytosine bases at single-base-pair resolution in human cells reveal distinct differences between cell types. These maps provide a starting point to decode the function of this enigmatic mark.

Dirk Schübeler

2009-01-01

210

DNA methylation changes in inflammatory bowel disease.  

PubMed

The cause of inflammatory bowel disease, encompassing Crohn's disease and ulcerative colitis, remains a mystery but evidence is accumulating that complex interactions between the genetic background and the gut microbiota of the host and environmental factors associated with rapid industrialization and westernized life styles may underlie its pathogenesis. Recent epigenetic studies have suggested that interactions between environment and host DNA may play a leading role in the phenotypical expression of both diseases, explaining amongst others the differences in disease expression in monozygotic twins. DNA methylation is the most studied epigenetic modification and during the last decade its correlation to IBD pathogenesis has been well established. Genes from different molecular pathways have been studied but till now there is no standardized database of methylated genes in IBD. Thus, a thorough and in depth study of DNA methylation, its potential relation to IBD and its interaction with the available pharmaceutical armamentarium is of great interest. PMID:24733658

Karatzas, Pantelis S; Gazouli, Maria; Safioleas, Michael; Mantzaris, Gerasimos J

2014-01-01

211

DNA methylation changes in inflammatory bowel disease  

PubMed Central

The cause of inflammatory bowel disease, encompassing Crohn’s disease and ulcerative colitis, remains a mystery but evidence is accumulating that complex interactions between the genetic background and the gut microbiota of the host and environmental factors associated with rapid industrialization and westernized life styles may underlie its pathogenesis. Recent epigenetic studies have suggested that interactions between environment and host DNA may play a leading role in the phenotypical expression of both diseases, explaining amongst others the differences in disease expression in monozygotic twins. DNA methylation is the most studied epigenetic modification and during the last decade its correlation to IBD pathogenesis has been well established. Genes from different molecular pathways have been studied but till now there is no standardized database of methylated genes in IBD. Thus, a thorough and in depth study of DNA methylation, its potential relation to IBD and its interaction with the available pharmaceutical armamentarium is of great interest. PMID:24733658

Karatzas, Pantelis S.; Gazouli, Maria; Safioleas, Michael; Mantzaris, Gerasimos J.

2014-01-01

212

Kinetics and mechanism of the reaction of palladium(II) complexes of o-(diphenylphosphino)thioanisole and o-(diphenylphosphino)selenoanisole with nucleophiles thiocyanate and iodide. Carbon-13 NMR spectroscopy of the methyl-heteroatom complexes and x-ray structural characterization of diiodobis(o-(diphenylphosphino)benzenethiolato)dipalladium(II)  

SciTech Connect

The kinetics of the reaction of the nucleophiles thiocyanate and iodide with complexes PdX/sub 2/(o-MeSC/sub 6/H/sub 4/PPh/sub 2/) (X = SCN, I) show a rate law rate = k/sub 2/(PdX/sub 2/(o-MeSC/sub 6/H/sub 4/PPh/sub 2/))(X/sup -/). Second-order rate constants k/sub 2/ for the thiocyanate reaction have been measured, and the activation parameters ..delta..H/sup + +/ and ..delta..S/sup + +/ are 22.9 +- 1.0 kcal/mol and -9.2 +- 2.1 cal/mol. For the selenium analogue complex these respective values are 18.9 +- 1.3 kcal/mol and -12.9 +- 2.3 cal/mol. With iodide as nucleophile an equilibrium condition is established. Rates are calculated from the data both for the demethylation and for the reverse addition of methyl iodide. The alkylation reaction is approximately 50 times faster. The product from the iodide demethylation reaction is considered to be the anion (PdI/sub 2/(o-SC/sub 6/H/sub 4/PPh/sub 2/))/sup -/ on the basis of visible spectroscopy. The mechanism of the nucleophile-induced demethylation reaction resembles the Zeisel ether cleavage.

Roundhill, D.M.; Roundhill, S.G.N.; Beaulieu, W.B.; Bagchi, U.

1980-11-01

213

Histone Lysine Methylation Dynamics: Establishment, Regulation, and Biological Impact  

PubMed Central

Histone lysine methylation has emerged as a critical player in the regulation of gene expression, cell cycle, genome stability, and nuclear architecture. Over the past decade, a tremendous amount of progress has led to the characterization of methyl modifications and the lysine methyltransferases (KMTs) and lysine demethylases (KDMs) that regulate them. Here, we review the discovery and characterization of the KMTs and KDMs and the methyl modifications they regulate. We discuss the localization of the KMTs and KDMs as well as the distribution of lysine methylation throughout the genome. We highlight how these data have shaped our view of lysine methylation as a key determinant of complex chromatin states. Finally, we discuss the regulation of KMTs and KDMs by proteasomal degradation, posttranscriptional mechanisms, and metabolic status. We propose key questions for the field and highlight areas that we predict will yield exciting discoveries in the years to come. PMID:23200123

Black, Joshua C.; Van Rechem, Capucine; Whetstine, Johnathan R.

2013-01-01

214

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

PubMed Central

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

Roberts, Steven B.; Gavery, Mackenzie R.

2011-01-01

215

Abiotic Formation of Methyl Halides in the Terrestrial Environment  

NASA Astrophysics Data System (ADS)

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

Keppler, F.

2011-12-01

216

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

Code of Federal Regulations, 2014 CFR

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

2014-07-01

217

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

Code of Federal Regulations, 2013 CFR

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

2013-07-01

218

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

Code of Federal Regulations, 2010 CFR

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

2010-07-01

219

Metabolic production of methylated selenium species requires adequate methylation status  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

220

Epigenetic biomarkers of colorectal cancer: Focus on DNA methylation.  

PubMed

The original theory of the multi-step process of colorectal cancer (CRC), suggesting that the disease resulted from the accumulation of mutations in oncogenes and tumor suppressor genes in colonic mucosa cells, has been largely revised following the observation that epigenetic modifications of several genes occur in the average CRC genome. Therefore, the current opinion is that CRCs are the consequence of the accumulation of both mutations and epigenetic modifications of several genes. This mini-review article focuses on DNA methylation biomarkers in CRC. Recent large-scale DNA methylation studies suggest that CRCs can be divided into at least three-four subtypes according to the frequency of DNA methylation and those of mutations in key CRC genes. Despite hundreds of genes might be epigenetically modified in CRC cells, there is interest in the identification of DNA methylation biomarkers to be used for CRC diagnosis, progression, tendency to tissue invasion and metastasis, prognosis, and response to chemotherapeutic agents. Moreover, DNA methylation largely depends on one-carbon metabolism, the metabolic pathway required for the production of S-adenosylmethionine, the major intracellular methylating agent. Complex interactions are emerging among dietary one-carbon nutrients (folates, vitamin B6, vitamin B12, methionine, and others), their metabolic genes, CRC risk, and DNA methylation profiles in CRC. Moreover, active research is also focused on the possible contribution of folic acid dietary fortification during pregnancy and the possible methylation of CRC-related genes in the offspring. PMID:22202641

Coppedè, Fabio

2014-01-28

221

Cancer DNA Methylation: Molecular Mechanisms and Clinical Implications  

PubMed Central

DNA methylation plays a crucial role in the regulation of gene expression and chromatin organization within normal eukaryotic cells. In cancer, however, global patterns of DNA methylation are altered with global hypomethylation of repeat-rich intergenic regions and hypermethylation of a subset of CpG-dense gene-associated regions (CpG islands). Extensive research has revealed the cellular machinery that catalyzes DNA methylation, as well as several large protein complexes that mediate the transcriptional repression of hypermethylated genes. However, research is only just beginning to uncover the molecular mechanisms underlying the origins of cancer-specific DNA methylation. Herein, we present several recent advances regarding these mechanisms and discuss the relationship between histone modifications (i.e. H3K4me2/3, H4K16Ac, H3K9me2/3, H3K27me3, H4K20me3), chromatin-modifying enzymes (G9a, EZH2, hMOF, SUV4?20H), and aberrant DNA methylation. Additionally, the role played by inflammation, DNA damage, and miRNAs in the etiology of aberrant DNA methylation is considered. Finally, we discuss the clinical implications of aberrant DNA methylation and the utility of methylated biomarkers in cancer diagnosis and management. PMID:19509173

McCabe, Michael T.; Brandes, Johann C.; Vertino, Paula M.

2009-01-01

222

DNA Methylation and Cancer Diagnosis  

PubMed Central

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

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

2013-01-01

223

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 ...

224

Kapok oil methyl esters  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

225

Nutrients and DNA Methylation  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

226

DNA methylation profiling in nanochannels  

Microsoft Academic Search

We report the profiling of the 5-methyl cytosine distribution within single genomic-sized DNA molecules at a gene-relevant resolution. This method linearizes and stretches DNA molecules by confinement to channels with a dimension of about 250×200nm2. The methylation state is detected using fluorescently labeled methyl-CpG binding domain proteins (MBD), with high signal contrast and low background. DNA barcodes consisting of methylated

Shuang Fang Lim; Alena Karpusenko; John J. Sakon; Joseph A. Hook; Tyra A. Lamar; Robert Riehn

2011-01-01

227

DNA METHYLATION, CANCER SUSCEPTIBILITY, AND NUTRIENT INTERACTIONS  

Technology Transfer Automated Retrieval System (TEKTRAN)

DNA methylation is an important epigenetic mechanism of transcriptional control. DNA methylation plays an essential role in maintaining cellular function, and changes in methylation patterns may contribute to the development of cancer. Aberrant methylation of DNA (global hypomethylation accompanied ...

228

Understanding the relationship between DNA methylation and histone lysine methylation?  

PubMed Central

DNA methylation acts as an epigenetic modification in vertebrate DNA. Recently it has become clear that the DNA and histone lysine methylation systems are highly interrelated and rely mechanistically on each other for normal chromatin function in vivo. Here we examine some of the functional links between these systems, with a particular focus on several recent discoveries suggesting how lysine methylation may help to target DNA methylation during development, and vice versa. In addition, the emerging role of non-methylated DNA found in CpG islands in defining histone lysine methylation profiles at gene regulatory elements will be discussed in the context of gene regulation. This article is part of a Special Issue entitled: Methylation: A Multifaceted Modification — looking at transcription and beyond. PMID:24560929

Rose, Nathan R.; Klose, Robert J.

2014-01-01

229

Dynamic DNA methylation across diverse human cell lines and tissues  

PubMed Central

As studies of DNA methylation increase in scope, it has become evident that methylation has a complex relationship with gene expression, plays an important role in defining cell types, and is disrupted in many diseases. We describe large-scale single-base resolution DNA methylation profiling on a diverse collection of 82 human cell lines and tissues using reduced representation bisulfite sequencing (RRBS). Analysis integrating RNA-seq and ChIP-seq data illuminates the functional role of this dynamic mark. Loci that are hypermethylated across cancer types are enriched for sites bound by NANOG in embryonic stem cells, which supports and expands the model of a stem/progenitor cell signature in cancer. CpGs that are hypomethylated across cancer types are concentrated in megabase-scale domains that occur near the telomeres and centromeres of chromosomes, are depleted of genes, and are enriched for cancer-specific EZH2 binding and H3K27me3 (repressive chromatin). In noncancer samples, there are cell-type specific methylation signatures preserved in primary cell lines and tissues as well as methylation differences induced by cell culture. The relationship between methylation and expression is context-dependent, and we find that CpG-rich enhancers bound by EP300 in the bodies of expressed genes are unmethylated despite the dense gene-body methylation surrounding them. Non-CpG cytosine methylation occurs in human somatic tissue, is particularly prevalent in brain tissue, and is reproducible across many individuals. This study provides an atlas of DNA methylation across diverse and well-characterized samples and enables new discoveries about DNA methylation and its role in gene regulation and disease. PMID:23325432

Varley, Katherine E.; Gertz, Jason; Bowling, Kevin M.; Parker, Stephanie L.; Reddy, Timothy E.; Pauli-Behn, Florencia; Cross, Marie K.; Williams, Brian A.; Stamatoyannopoulos, John A.; Crawford, Gregory E.; Absher, Devin M.; Wold, Barbara J.; Myers, Richard M.

2013-01-01

230

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

The binuclear hydrazone, H2L, ligand derived from 4-amino-6-methyl-3-thioxo-3,4-dihydro-1,2,4-triazin-5(2H)-one and 4,6-diacetylresorcinol, in the molar ratio 2:1, and its copper(II), nickel(II), cobalt(II), zinc(II), cadmium(II), cerium(III), iron(III), oxovanadium(IV) and dioxouranium(VI) complexes have been synthesized. Structures of the ligand and its metal complexes were characterized by elemental analyses, spectral (infrared, electronic, mass, 1H NMR and ESR) data, magnetic susceptibility, molar conductivity measurements and thermal gravimetric analysis (TGA). The ligand acts as dibasic with two ONS tridentate sites. The bonding sites are the azomethine nitrogen, phenolate oxygen and sulfur atoms. The metal complexes exhibit different geometrical arrangements such as square planer, tetrahedral and octahedral. The Coats-Redfern equation was used to calculate the kinetic and thermodynamic parameters for the different thermal decomposition steps of some complexes. The ligand and its metal complexes showed antimicrobial activity towards Gram-positive bacteria (Staphylococcus aureus and Bacillus subtilis), Gram-negative bacteria (Salmonella typhimurium and Escherichia coli), yeast (Candida albicans) and fungus (Aspergillus fumigatus). Structural parameters of the ligand and its metal complexes were theoretically computed on the basis of semiempirical PM3 level, and the results were correlated with their experimental data. PMID:24858350

Adly, Omima M I; Emara, Adel A A

2014-11-11

231

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)

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.

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

2014-11-01

232

Molecular coupling of DNA methylation and histone methylation  

PubMed Central

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

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

2011-01-01

233

Histone Acetylation And Methylation  

Microsoft Academic Search

Post-synthetic modification of histone proteins in chromatin architecture plays a central role in the epigenetic regulation\\u000a of transcription. Histone acetylation and methylation are the two major modifications that function as a specific transcription\\u000a regulator in response to various cellular signals. Albeit the mechanism of action of these modifications in transcription\\u000a is not well understood, recent discovery of histone acetyltransferase (HAT)

Woojin An

234

Differential methylation of the TRPA1 promoter in pain sensitivity  

PubMed Central

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

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.; Ahmadi, Kourosh R.; Ainali, Chrysanthi; Barrett, Amy; Bataille, Veronique; Bell, Jordana T.; Buil, Alfonso; Deloukas, Panos; Dermitzakis, Emmanoil T.; Dimas, Antigone S.; Durbin, Richard; Glass, Daniel; Grundberg, Elin; Hassanali, Neelam; Hedman, Asa K.; Ingle, Catherine; Knowles, David; Krestyaninova, Maria; Lindgren, Cecilia M.; Lowe, Christopher E.; McCarthy, Mark I.; Meduri, Eshwar; di Meglio, Paola; Min, Josine L.; Montgomery, Stephen B.; Nestle, Frank O.; Nica, Alexandra C.; Nisbet, James; O’Rahilly, Stephen; Parts, Leopold; Potter, Simon; Sekowska, Magdalena; Shin, So-Youn; Small, Kerrin S.; Soranzo, Nicole; Spector, Tim D.; Surdulescu, Gabriela; Travers, Mary E.; Tsaprouni, Loukia; Tsoka, Sophia; Wilk, Alicja; Yang, Tsun-Po; Zondervan, Krina T.; Williams, F.M.K.; Li, N.; Deloukas, P.; Beck, S.; McMahon, S.B.; Wang, J.; John, S.L.; Spector, T.D.

2014-01-01

235

Different measures of “genome-wide” DNA methylation exhibit unique properties in placental and somatic tissues  

PubMed Central

DNA methylation of CpGs located in two types of repetitive elements—LINE1 (L1) and Alu—is used to assess “global” changes in DNA methylation in studies of human disease and environmental exposure. L1 and Alu contribute close to 30% of all base pairs in the human genome and transposition of repetitive elements is repressed through DNA methylation. Few studies have investigated whether repetitive element DNA methylation is associated with DNA methylation at other genomic regions, or the biological and technical factors that influence potential associations. Here, we assess L1 and Alu DNA methylation by Pyrosequencing of consensus sequences and using subsets of probes included in the Illumina Infinium HumanMethylation27 BeadChip array. We show that evolutionary age and assay method affect the assessment of repetitive element DNA methylation. Additionally, we compare Pyrosequencing results for repetitive elements to average DNA methylation of CpG islands, as assessed by array probes classified into strong, weak and non-islands. We demonstrate that each of these dispersed sequences exhibits different patterns of tissue-specific DNA methylation. Correlation of DNA methylation suggests an association between L1 and weak CpG island DNA methylation in some of the tissues examined. We caution, however, that L1, Alu and CpG island DNA methylation are distinct measures of dispersed DNA methylation and one should not be used in lieu of another. Analysis of DNA methylation data is complex and assays may be influenced by environment and pathology in different or complementary ways. PMID:22531475

Price, E. Magda; Cotton, Allison M.; Peñaherrera, Maria S.; McFadden, Deborah E.; Kobor, Michael S.; Robinson, Wendy

2012-01-01

236

40 CFR 721.1576 - 1,3-Benzenedicarboxylic acid, bis[[4-[(ethenyloxy)methyl] cyclohexyl] methyl] ester.  

Code of Federal Regulations, 2010 CFR

...ethenyloxy)methyl] cyclohexyl] methyl] ester. 721.1576 Section 721.1576 Protection...ethenyloxy)methyl] cyclohexyl] methyl] ester. (a) Chemical substance and significant...ethenyloxy)methyl] cyclohexyl] methyl] ester (PMN P-98-1162; CAS No....

2010-07-01

237

Atmospheric photoxidation of methyl sulfide  

NASA Astrophysics Data System (ADS)

Major gas phase products of the photooxidation of methyl sulfide (CH3SCH3) under atmospheric conditions are sulfur dioxide, formaldehyde, ozone and nitric acid, along with smaller amounts of methyl nitrate. Substantial formation of light-scattering aerosols was observed, with inorganic sulfate and methane sulfonic acid as major components of the aerosol. Experimental results are discussed in terms of reaction pathways initiated by reaction of methyl sulfide with the hydroxyl radical.

Grosjean, D.; Lewis, R.

1982-10-01

238

Electrochemical strategy for sensing DNA methylation and DNA methyltransferase activity.  

PubMed

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

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

2013-03-20

239

Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping.  

PubMed

Genomic DNA methylation profiles exhibit substantial variation within the human population, with important functional implications for gene regulation. So far little is known about the characteristics and determinants of DNA methylation variation among healthy individuals. We performed bioinformatic analysis of high-resolution methylation profiles from multiple individuals, uncovering complex patterns of inter-individual variation that are strongly correlated with the local DNA sequence. CpG-rich regions exhibit low and relatively similar levels of DNA methylation in all individuals, but the sequential order of the (few) methylated among the (many) unmethylated CpGs differs randomly across individuals. In contrast, CpG-poor regions exhibit substantially elevated levels of inter-individual variation, but also significant conservation of specific DNA methylation patterns between unrelated individuals. This observation has important implications for experimental analysis of DNA methylation, e.g. in the context of epigenome projects. First, DNA methylation mapping at single-CpG resolution is expected to uncover informative DNA methylation patterns for the CpG-poor bulk of the human genome. Second, for CpG-rich regions it will be sufficient to measure average methylation levels rather than assaying every single CpG. We substantiate these conclusions by an in silico benchmarking study of six widely used methods for DNA methylation mapping. Based on our findings, we propose a cost-optimized two-track strategy for mammalian methylome projects. PMID:18413340

Bock, Christoph; Walter, Jörn; Paulsen, Martina; Lengauer, Thomas

2008-06-01

240

Methylation and liver cancer.  

PubMed

Cancer evolution at all stages (including initiation, progression and invasion) is driven by both epigenetic abnormalities and genetic alterations. Epigenetics refer to any structural modification of genomic regions, which lead to modification in gene expression without alterations in DNA sequence. Progressive deregulation of epigenetic process is being increasingly recognized in liver carcinogenesis. This review will provide an overview of DNA methylation, one of the most commonly epigenetic events, which profoundly contributes to liver cancer initiation and progression. Furthermore, the recent advancements in the knowledge of epigenetic reprogramming underlying hepatic cancer stem cells will be highlighted. PMID:23806627

Raggi, Chiara; Invernizzi, Pietro

2013-12-01

241

Reaction of Grignard Compounds with 4-Chloro-2-methyl-3-butyn-2-ol in Diethyl Ether Equivalents  

Microsoft Academic Search

Reactions of RMgX·THF complexes with 4-chloro-2-methyl-3-butyn-2-ol in aromatic hydrocarbons were studied. The complexes formed by arylmagnesium halides require the presence of anisole for the reaction to occur. 4-Chloro-2-methyl-3-butyn-2-ol can be synthesized by reaction of 2-methyl-3-butyn-2-ol with sodium hypochloride in the two-phase system water-benzene.

S. A. Shchelkunov; O. A. Sivolobova; S. O. Mataeva; D. B. Minbaev; Z. M. Muldakhmetov

2001-01-01

242

Methyl Bromide and Methyl Chloride Degradation in the Southern Ocean  

NASA Astrophysics Data System (ADS)

The oceans are both a source and sink for atmospheric methyl bromide and methyl chloride and play a significant role in the atmospheric budgets of these ozone-active gases. We have carried out a series of shipboard studies designed to characterize the loss rate of methyl halides in the surface ocean, using a 13C stable isotope incubation technique. Here we present the first degradation measurements of methyl bromide and methyl chloride in the Southern Ocean. The cruise was conducted from October to December, 2001, aboard the Australian icebreaker "Aurora Australis". The cruise track extended from Hobart, Tasmania to Buchanan Bay (Mertz Glacier) at the coast of Antarctica (46-67°S, 138-145°E). For methyl bromide, loss rate constants measured over the course of the cruise in unfiltered seawater samples ranged from 0.00 to 0.17 d-1 with a mean of 0.04ñ0.04 d-1 (n=102). Chemical loss rates in these waters were extremely low, because of the low seawater temperatures, and the observed loss rate constants are largely (98%) attributable to biological processes. For methyl chloride, loss rate constants measured over the course of the cruise in unfiltered seawater samples ranged from 0.00 to 0.22 d-1, with a mean of 0.07+/-0.08 (n=43). Loss in filtered samples was undetectable, as expected from the known rate of hydrolysis. As in the case of methyl bromide, the loss mechanism for methyl chloride is presumed to be biological. These results demonstrate that biological degradation of methyl bromide and methyl chloride can occur at significant rates even in very cold, polar waters, and explain the tendency for high latitude waters to be undersaturated with respect to atmospheric methyl bromide. These are the first open ocean observations of biological methyl chloride uptake. The high rates observed confirm earlier coastal measurements, and support the idea that the oceans can be a major sink for atmospheric methyl chloride.

Tokarczyk, R.; Goodwin, K.; Saltzman, E. S.

2002-12-01

243

Synthesis and characterization of Ni(II) and Zn(II) complexes of (furan-2-yl)methyl(2-(thiophen-2-yl)ethyl)dithiocarbamate (ftpedtc): X-ray structures of [Zn(ftpedtc)2(py)] and [Zn(ftpedtc)Cl(1,10-phen)].  

PubMed

Seven complexes of a new dithiocarbamate ligand (ftpedtc = (furan-2-yl)methyl(2-(thiophen-2-yl)ethyl)dithiocarbamate) namely [Ni(ftpedtc)2] (1), [Ni(ftpedtc)(NCS)(PPh3)] (2), [Ni(ftpedtc)(PPh3)2]ClO4 (3), [Zn(ftpedtc)2] (4), [Zn(ftpedtc)2(py)] (5), [Zn(ftpedtc)2(1,10-phen)] (6) and [Zn(ftpedtc)2(2,2'-bipy] (7) have been prepared. The complexes were characterized by IR, UV-Vis and NMR ((1)H and (13)C) spectroscopy. Single crystal X-ray structural analysis was carried out for complexes 5 and [Zn(ftpedtc)Cl(1,10-phen)] (8). Electronic spectral studies suggest square planar geometry for nickel complexes. The (13)C NMR peaks of the group N(13)CS2 are found in all the cases, at around 205.0 ppm, which indicates the bidentate character of the dithiocarbamate ligand. X-ray structures of 5 and 8 show bidentate coordination by dithiocarbamate ligands and a distorted trigonal bipyramidal geometry for zinc, defined by NS4 and ClN2S2 donor sets, respectively. The packing in 8 involves ?-? stacking interactions involving the 1,10-phenanthroline ring systems with the distance between ring centroids being 3.587 Å. PMID:25305608

Jamuna Rani, Palanisamy; Thirumaran, Subbiah; Ciattini, Samuele

2015-02-25

244

Neural Tube Defects, Folic Acid and Methylation  

PubMed Central

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

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

2013-01-01

245

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

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

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

2015-03-15

246

DNA Methylation and Gene Function  

Microsoft Academic Search

In most higher organisms, DNA is modified after synthesis by the enzymatic conversion of many cytosine residues to 5-methylcytosine. For several years, control of gene activity by DNA methylation has been recognized as a logically attractive possibility, but experimental support has proved elusive. However, there is now reason to believe, from recent studies, that DNA methylation is a key element

Aharon Razin; Arthur D. Riggs

1980-01-01

247

Molecular Structure of Methyl benzoate  

NSDL National Science Digital Library

Methyl benzoate is used mainly as a perfume; it has a very pleasant smell and mixes well with scents of ylang ylang, musk, rose, and geranium. Methyl benzoate also acts as a solvent for cellulose esters, as a dying carrier, disinfectant additive, penetrating agent, and as a pesticide.

2002-10-11

248

Managing Nematodes without Methyl Bromide  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

249

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

PubMed Central

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

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

2008-01-01

250

Methods of DNA methylation detection  

NASA Technical Reports Server (NTRS)

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.

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

2010-01-01

251

The 'golden age' of DNA methylation in neurodegenerative diseases.  

PubMed

DNA methylation reactions are regulated, in the first instance, by enzymes and the intermediates that constitute the 'so called' one-carbon metabolism. This is a complex biochemical pathway, also known as the homocysteine cycle, regulated by the presence of B vitamins (folate, B6, B12) and choline, among other metabolites. One of the intermediates of this metabolism is S-adenosylmethionine, which represent the methyl donor in all the DNA methyltransferase reactions in eukaryotes. The one-carbon metabolism therefore produces the substrate necessary for the transferring of a methyl group on the cytosine residues of DNA; S-adenosylmethionine also regulates the activity of the enzymes that catalyze this reaction, namely the DNA methyltransferases (DNMTs). Alterations of this metabolic cycle can therefore be responsible for aberrant DNA methylation processes possibly leading to several human diseases. As a matter of fact, increasing evidences indicate that a number of human diseases with multifactorial origin may have an epigenetic basis. This is also due to the great technical advances in the field of epigenetic research. Among the human diseases associated with epigenetic factors, aging-related and neurodegenerative diseases are probably the object of most intense research. This review will present the main evidences linking several human diseases to DNA methylation, with particular focus on neurodegenerative diseases, together with a short description of the state-of-the-art of methylation assays. PMID:23183753

Fuso, Andrea

2013-03-01

252

Factors underlying variable DNA methylation in a human community cohort  

PubMed Central

Epigenetics is emerging as an attractive mechanism to explain the persistent genomic embedding of early-life experiences. Tightly linked to chromatin, which packages DNA into chromosomes, epigenetic marks primarily serve to regulate the activity of genes. DNA methylation is the most accessible and characterized component of the many chromatin marks that constitute the epigenome, making it an ideal target for epigenetic studies in human populations. Here, using peripheral blood mononuclear cells collected from a community-based cohort stratified for early-life socioeconomic status, we measured DNA methylation in the promoter regions of more than 14,000 human genes. Using this approach, we broadly assessed and characterized epigenetic variation, identified some of the factors that sculpt the epigenome, and determined its functional relation to gene expression. We found that the leukocyte composition of peripheral blood covaried with patterns of DNA methylation at many sites, as did demographic factors, such as sex, age, and ethnicity. Furthermore, psychosocial factors, such as perceived stress, and cortisol output were associated with DNA methylation, as was early-life socioeconomic status. Interestingly, we determined that DNA methylation was strongly correlated to the ex vivo inflammatory response of peripheral blood mononuclear cells to stimulation with microbial products that engage Toll-like receptors. In contrast, our work found limited effects of DNA methylation marks on the expression of associated genes across individuals, suggesting a more complex relationship than anticipated. PMID:23045638

Lam, Lucia L.; Emberly, Eldon; Fraser, Hunter B.; Neumann, Sarah M.; Chen, Edith; Miller, Gregory E.; Kobor, Michael S.

2012-01-01

253

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

PubMed Central

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

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

2013-01-01

254

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

PubMed

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

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

2013-10-01

255

Accounting for Population Stratification in DNA Methylation Studies  

PubMed Central

DNA methylation is an important epigenetic mechanism that has been linked to complex disease 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 (GWAS), 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 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 principal-components 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 SNP-based principal components, followed by methylation-based principal components, which out-perform both surrogate variable analysis and genomic control. Among our different approaches to computing methylation-based principal components, we find that principal components based on CpG sites chosen for their potential to proxy nearby SNPs can provide a powerful and computationally efficient approach to adjustment for population stratification in DNA methylation studies when genome-wide SNP data are unavailable. PMID:24478250

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.

2014-01-01

256

[Age-related DNA methylation changes in peripheral whole blood].  

PubMed

Aging is associated with many complex diseases such as cancer and neurodegenerative diseases. Recently, many age-related DNA methylation biomarkers in peripheral whole blood have been identified. These biomarkers may reflect DNA methylation changes derived from changes in the number of a specific leukocyte cell type during aging. To clarify the source of these age-related DNA methylation changes, we analysed DNA methylation profile of peripheral whole blood from three independent cohorts of healthy subjects and identified age-related DNA methylation CpG sites (arCpGs) using the Spearman's rank test with high reproducibility (Hypergeometric test, P=1.65 × 10?¹¹). Using a deconvolution algorithm, we found that the proportion of myeloid lineage cells was increased while that of lymphoid lineage cells was decreased in the peripheral whole blood with age (Spearman's rank correlation test, P<0.05, r ? 0.22). The CpG sites, whose methylation levels were significantly different in myeloid cells and lymphoid cells, were preferentially recognized as arCpGs in peripheral whole blood. Moreover, the arCpGs in CD4+ T cells significantly overlapped with that in peripheral whole blood (Hypergeometric test, P=6.14 × 10?¹²) and 99.1% of the overlapping arCpGs had consistent positive or negative correlations with age. Though the arCpGs in CD14+ monocytes did not significantly overlap with that in peripheral whole blood (Hypergeometric test, P=0.232), 90.1% of 51 overlapping arCpGs were correlated with age in CD14+ monocytes, peripheral whole blood, and CD4+ T cells consistently. In summary, most of the methylation changes in arCpGs identified in peripheral whole blood come from common or specific DNA methylation changes in leukocyte subtypes, while part of them reflect alterations in the number of specific cell types of leukocytes. PMID:25665643

Hongdong, Li; Guini, Hong; Zheng, Guo

2015-02-01

257

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

E-print Network

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

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

2012-07-27

258

Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc  

PubMed Central

Characterization of DNA methylation patterns in the Pacific oyster, Crassostrea gigas, indicates that this epigenetic mechanism plays an important functional role in gene regulation and may be involved in the regulation of developmental processes and environmental responses. However, previous studies have been limited to in silico analyses or characterization of DNA methylation at the single gene level. Here, we have employed a genome-wide approach to gain insight into how DNA methylation supports the regulation of the genome in C. gigas. Using a combination of methylation enrichment and high-throughput bisulfite sequencing, we have been able to map methylation at over 2.5 million individual CpG loci. This is the first high-resolution methylome generated for a molluscan species. Results indicate that methylation varies spatially across the genome with a majority of the methylated sites mapping to intra genic regions. The bisulfite sequencing data was combined with RNA-seq data to examine genome-wide relationships between gene body methylation and gene expression, where it was shown that methylated genes are associated with high transcript abundance and low variation in expression between tissue types. The combined data suggest DNA methylation plays a complex role in regulating genome activity in bivalves. PMID:24282674

Gavery, Mackenzie R.

2013-01-01

259

Hydridomethyl iridium complex  

DOEpatents

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.

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

1989-01-01

260

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

PubMed Central

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

Lauss, Martin; Aine, Mattias; Sjödahl, Gottfrid; Veerla, Srinivas; Patschan, Oliver; Gudjonsson, Sigurdur; Chebil, Gunilla; Lövgren, Kristina; Fernö, Mårten; Månsson, Wiking; Liedberg, Fredrik; Ringnér, Markus; Lindgren, David; Höglund, Mattias

2012-01-01

261

Molecular Structure of Methyl mercaptan  

NSDL National Science Digital Library

Methyl mercaptan is a colorless, flammable and volatile sulfur compound that is responsible for the rotten cabbage or burnt rubber aroma. This substance can be found in the blood, brain, and other tissues of humans and other animals, it is released from animal feces and occurs naturally in foods such as nuts and cheeses. The formation of methyl mercaptan is commonly noted as a problem in the process of the post-fermentation of wine. Despite the repulsive smell methyl mercaptan is used as a gas odorant, as an intermediate in the production of fungicides, as jet fuel additives, flavoring agents, plastics, as well as in the synthesis of methionines, and as catalysts.

2003-06-03

262

Regulation of histone methylation by noncoding RNAs.  

PubMed

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

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

2014-12-01

263

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)

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.

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

2014-01-01

264

Methylation: a regulator of HIV-1 replication?  

PubMed Central

Recent characterizations of methyl transferases as regulators of cellular processes have spurred investigations into how methylation events might influence the HIV-1 life cycle. Emerging evidence suggests that protein-methylation can positively and negatively regulate HIV-1 replication. How DNA- and RNA- methylation might impact HIV-1 is also discussed. PMID:17274823

Yedavalli, Venkat RK; Jeang, Kuan-Teh

2007-01-01

265

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

PubMed

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

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

2007-07-01

266

Vibrational absorption, vibrational circular dichroism, and theoretical studies of methyl lactate self-aggregation and methyl lactate-methanol intermolecular interactions  

NASA Astrophysics Data System (ADS)

The infrared vibrational absorption (VA) and vibrational circular dichroism (VCD) spectra of methyl lactate in carbon tetrachloride and methanol have been measured in the 1000-1800 cm-1 region. Noticeable changes due to the solute self-aggregation and solvent-solute intermolecular hydrogen-bonding interactions have been detected in the reported spectra of the 2M methyl lactate solution in CCl4 and in methanol, respectively. Molecular dynamics simulations and a series of density functional theory (DFT) B3LYP/6-311++G??) and single point MP2/6-311++G?? energy calculations have been performed to identify and to model the explicit hydrogen-bonding interactions between the methanol solvent and the methyl lactate solute and among the methyl lactate molecules. Geometry search and optimization have been performed for the most stable conformers of the methyl lactate dimer and the methyl lactate-(methanol)N clusters, with N =1, 2, and 3. The relative single point MP2 energies among conformers are noticeably different from those obtained with DFT for the larger methyl lactate-methanol complexes. The VA and VCD spectra of these complexes have been simulated and compared to the corresponding experimental spectra. From the combined experimental and theoretical VA and VCD studies, it has been identified that both the methyl lactate monomer and dimer are the main species in the 2M CCl4 solution with 65% and 35% relative abundances, respectively, while the binary (55%) and quaternary (30%) methyl lactate-methanol clusters dominate in the 2M methanol solution, together with a smaller amount (15%) of the methyl lactate monomer. The effects of solute self-aggregation and solute-solvent interactions have been investigated in detail.

Liu, Yang; Yang, Guochun; Losada, Martin; Xu, Yunjie

2010-06-01

267

Nickel-catalyzed reductive methylation of alkyl halides and acid chlorides with methyl p-tosylate.  

PubMed

Methylation of unactivated alkyl halides and acid chlorides under Ni-catalyzed reductive coupling conditions led to efficient formation of methylated alkanes and ketones using methyl p-methyl tosylate as the methylation reagent. Moderate to excellent coupling yields as well as excellent functional group tolerance were observed under the present mild and easy-to-operate reaction conditions. PMID:25333482

Liang, Zhuye; Xue, Weichao; Lin, Kunhua; Gong, Hegui

2014-11-01

268

ACID DISSOCIATION BEHAVIOR OF 2, 3- AND 2, 3, 9,lO-METHYL- OR CYCLOHEXYL-SUBSTITUTED CYCLAMS, THEIR COMPLEXATION BEHAVIOR WITH COPPER@) AND THE AXIAL SOLVENT SPECTRUM OF THEIR COMPLEXESINTERACTION EFFECT ON THE LIGAND-FIELD  

Microsoft Academic Search

Stability constants of Cu(Il)-complexes for 1, 4, 8, 11-tetra-azacyclotetradecane (cyclam) analogs with periphery substituted [14]aneN4-ring, 2, 3-tetramethyl-, 2, 3, 9, 10-octamethyl-, 2, 3-cyclohexyl, and 2, 3, 9, 10-dicyclohexyl-cyclams have been determined at 25°C in aqueous solution. The UV-Vis absorption spectra of their complexes, ([Cu(L)] (C1O4)2), were measured in water and some typical organic solvents (methanol, acetone, propylene carbonate, formamide, N,

Yoshiki Moriguch; Kazunori Sakata; Kazuya Kobiro; Yoshito Tobe

1997-01-01

269

Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism.  

PubMed

DNA methylation of CpG dinucleotides is an important epigenetic modification of mammalian genomes and is essential for the regulation of chromatin structure, of gene expression and of genome stability. Differences in DNA methylation patterns underlie a wide range of biological processes, such as genomic imprinting, inactivation of the X chromosome, embryogenesis, and carcinogenesis. Inheritance of the epigenetic methylation pattern is mediated by the enzyme DNA methyltransferase 1 (Dnmt1), which methylates newly synthesized CpG sequences during DNA replication, depending on the methylation status of the template strands. The protein UHRF1 (also known as Np95 and ICBP90) recognizes hemi-methylation sites via a SET and RING-associated (SRA) domain and directs Dnmt1 to these sites. Here we report the crystal structures of the SRA domain in free and hemi-methylated DNA-bound states. The SRA domain folds into a globular structure with a basic concave surface formed by highly conserved residues. Binding of DNA to the concave surface causes a loop and an amino-terminal tail of the SRA domain to fold into DNA interfaces at the major and minor grooves of the methylation site. In contrast to fully methylated CpG sites recognized by the methyl-CpG-binding domain, the methylcytosine base at the hemi-methylated site is flipped out of the DNA helix in the SRA-DNA complex and fits tightly into a protein pocket on the concave surface. The complex structure suggests that the successive flip out of the pre-existing methylated cytosine and the target cytosine to be methylated is associated with the coordinated transfer of the hemi-methylated CpG site from UHRF1 to Dnmt1. PMID:18772891

Arita, Kyohei; Ariyoshi, Mariko; Tochio, Hidehito; Nakamura, Yusuke; Shirakawa, Masahiro

2008-10-01

270

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)

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.

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

2015-01-01

271

Electron paramagnetic resonance spectroscopy with N-methyl-D-glucamine dithiocarbamate iron complexes distinguishes nitric oxide and nitroxyl anion in a redox-dependent manner: applications in identifying nitrogen monoxide products from nitric oxide synthase.  

PubMed

Though a large number of studies indicate that nitric oxide synthase (NOS) is responsible for NO&z.rad; production in biological systems, controversy still remains concerning whether NOS directly produces NO&z.rad;. Schmidt et al. (PNAS 93:144492, 1996) proposed that NOS first synthesizes nitroxyl anion (NO(-)), which is then converted to NO&z.rad; by superoxide dismutase (SOD). With electron paramagnetic resonance spectroscopy using N-methyl-D-glucamine dithiocarbamate iron (Fe-MGD), we directly detected NO&z.rad; from purified NOS in the absence of SOD (Xia et al., PNAS 94:12705, 1997). We also showed that the requirement for SOD in the previous NO&z.rad; measurements appeared to be due to the high levels of exogenous superoxide production in their reaction system because of the presence of free FAD. However, it was recently questioned whether Fe-MGD can discriminate NO&z.rad; from NO(-) (Komarov et al., FRBM 28:739-742, 2000). In this study we examined the trapping specificity of different redox forms of Fe-MGD. With Fe(2+)-MGD, NO&z.rad; generated characteristic triplet NO&z.rad;-Fe(2+)-MGD signals (g = 2. 04, a(N) = 12.7 G), whereas NO(-) from Angeli's salt was EPR silent. Both NO&z.rad; and NO(-) gave rise to NO&z.rad;-Fe(2+)-MGD signals when Fe(3+)-MGD was used. Strong NO&z.rad; signals were measured from purified nNOS using the NO&z.rad; selective Fe(2+)-MGD and this was not affected by SOD. Thus, spin trapping with Fe-MGD can distinguish NO&z.rad; and NO(-) and this depends on the redox status of the iron. The detection of NO&z.rad; from purified NOS by Fe(2+)-MGD unambiguously reconfirms our previous report that NOS directly synthesizes NO&z.rad; but not NO(-). PMID:11053782

Xia, Y; Cardounel, A J; Vanin, A F; Zweier, J L

2000-10-15

272

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)

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

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

2014-07-01

273

DNA Methylation Modifications Associated with Chronic Fatigue Syndrome  

PubMed Central

Chronic Fatigue Syndrome (CFS), also known as myalgic encephalomyelitis, is a complex multifactorial disease that is characterized by the persistent presence of fatigue and other particular symptoms for a minimum of 6 months. Symptoms fail to dissipate after sufficient rest and have major effects on the daily functioning of CFS sufferers. CFS is a multi-system disease with a heterogeneous patient population showing a wide variety of functional disabilities and its biological basis remains poorly understood. Stable alterations in gene function in the immune system have been reported in several studies of CFS. Epigenetic modifications have been implicated in long-term effects on gene function, however, to our knowledge, genome-wide epigenetic modifications associated with CFS have not been explored. We examined the DNA methylome in peripheral blood mononuclear cells isolated from CFS patients and healthy controls using the Illumina HumanMethylation450 BeadChip array, controlling for invariant probes and probes overlapping polymorphic sequences. Gene ontology (GO) and network analysis of differentially methylated genes was performed to determine potential biological pathways showing changes in DNA methylation in CFS. We found an increased abundance of differentially methylated genes related to the immune response, cellular metabolism, and kinase activity. Genes associated with immune cell regulation, the largest coordinated enrichment of differentially methylated pathways, showed hypomethylation within promoters and other gene regulatory elements in CFS. These data are consistent with evidence of multisystem dysregulation in CFS and implicate the involvement of DNA modifications in CFS pathology. PMID:25111603

de Vega, Wilfred C.; Vernon, Suzanne D.; McGowan, Patrick O.

2014-01-01

274

DNA methylation modifications associated with chronic fatigue syndrome.  

PubMed

Chronic Fatigue Syndrome (CFS), also known as myalgic encephalomyelitis, is a complex multifactorial disease that is characterized by the persistent presence of fatigue and other particular symptoms for a minimum of 6 months. Symptoms fail to dissipate after sufficient rest and have major effects on the daily functioning of CFS sufferers. CFS is a multi-system disease with a heterogeneous patient population showing a wide variety of functional disabilities and its biological basis remains poorly understood. Stable alterations in gene function in the immune system have been reported in several studies of CFS. Epigenetic modifications have been implicated in long-term effects on gene function, however, to our knowledge, genome-wide epigenetic modifications associated with CFS have not been explored. We examined the DNA methylome in peripheral blood mononuclear cells isolated from CFS patients and healthy controls using the Illumina HumanMethylation450 BeadChip array, controlling for invariant probes and probes overlapping polymorphic sequences. Gene ontology (GO) and network analysis of differentially methylated genes was performed to determine potential biological pathways showing changes in DNA methylation in CFS. We found an increased abundance of differentially methylated genes related to the immune response, cellular metabolism, and kinase activity. Genes associated with immune cell regulation, the largest coordinated enrichment of differentially methylated pathways, showed hypomethylation within promoters and other gene regulatory elements in CFS. These data are consistent with evidence of multisystem dysregulation in CFS and implicate the involvement of DNA modifications in CFS pathology. PMID:25111603

de Vega, Wilfred C; Vernon, Suzanne D; McGowan, Patrick O

2014-01-01

275

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

PubMed Central

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

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

2015-01-01

276

High methylation rates of mercury bound to cysteine by Geobacter sulfurreducens  

NASA Astrophysics Data System (ADS)

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.

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

2009-02-01

277

Alcohol, DNA Methylation, and Cancer  

PubMed Central

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

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

2013-01-01

278

PCMdb: Pancreatic Cancer Methylation Database  

NASA Astrophysics Data System (ADS)

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.

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

2014-02-01

279

Using high-density DNA methylation arrays to profile copy number alterations  

PubMed Central

The integration of genomic and epigenomic data is an increasingly popular approach for studying the complex mechanisms driving cancer development. We have developed a method for evaluating both methylation and copy number from high-density DNA methylation arrays. Comparing copy number data from Infinium HumanMethylation450 BeadChips and SNP arrays, we demonstrate that Infinium arrays detect copy number alterations with the sensitivity of SNP platforms. These results show that high-density methylation arrays provide a robust and economic platform for detecting copy number and methylation changes in a single experiment. Our method is available in the ChAMP Bioconductor package: http://www.bioconductor.org/packages/2.13/bioc/html/ChAMP.html. PMID:24490765

2014-01-01

280

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

PubMed

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

Fenyvesi, Éva; Szemán, Julianna; Csabai, Katalin; Malanga, Milo; Szente, Lajos

2014-05-01

281

Dna Systems for B-Z Transition and Their Significance as Epigenetic Model: The Fundamental Role of the Methyl Group  

Microsoft Academic Search

Epigenetic systems involved in the dynamics of gene expression, which are fundamental to cell determination and function without alteration in DNA sequences, are based on methylation of the N-terminal tails of lysine residues and DNA methylation. We demonstrate the vital importance for genetic transfer by different (hydrogen) networks, suggesting a complex interaction between the two epigenetic modifications. In other words,

Henk M. Buck

2011-01-01

282

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...

283

Regulation of the transcriptional program by DNA methylation during human ?? T-cell development  

PubMed Central

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

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

284

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

PubMed Central

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

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

2014-01-01

285

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

PubMed Central

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

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

2014-01-01

286

METHYLATION OF MERCURY IN AGRICULTURAL SOILS  

EPA Science Inventory

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

287

Synthesis of (+)-spirolaxine methyl ether.  

PubMed

A short and efficient synthesis of (+)-spirolaxine methyl ether, a metabolite of the fungus Sporotrichum laxum with inhibitory activity against Helicobacter pylori, is described. The synthesis has been carried out by a Prins cyclization, to obtain the [6,5]-spiroketal system, and a Wadsworth-Emmons condensation, applied for the installation of the polymethylene chain on the phthalide moiety. PMID:16872220

Nannei, Raffaella; Dallavalle, Sabrina; Merlini, Lucio; Bava, Adriana; Nasini, Gianluca

2006-08-01

288

Methods of DNA methylation analysis.  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

289

DNA Methylation of Cancer Genome  

PubMed Central

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

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

2010-01-01

290

Gene methylation in gastric cancer.  

PubMed

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

Qu, Yiping; Dang, Siwen; Hou, Peng

2013-09-23

291

d-(+)Glucose rescue against 1-methyl-4-phenylpyridinium toxicity through anaerobic glycolysis in neuroblastoma cells  

Microsoft Academic Search

The active neurotoxin of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), 1-methyl-4-phenylpyridinium (MPP+), exerts its lethal effect by inhibiting Complex I of the electron transport chain (ETC). MPP+ shuts down aerobic oxidative phosphorylation and ETC-mediated ATP synthesis. The present investigation examines anaerobic survival during MPP+ toxicity in murine neuroblastoma cells Neuro 2-A (N2-A). MPP+ addition to the cells resulted in a reduction in cell viability,

E Mazzio; K. F. A Soliman

2003-01-01

292

Interindividual Concordance of Methylation Profiles in Human Genes for Tumor Necrosis Factors alpha and beta  

Microsoft Academic Search

The DNA in mammalian genomes is characterized by complex patterns of DNA methylation that reflect the states of all genetic activities of that genome. The modified nucleotide 5-methyldeoxycytidine (^5mdC) can affect the interactions of specific proteins with DNA sequence motifs. The most extensively studied effect of sequence-specific methylations is that of the long-term silencing of eukaryotic (mammalian) promoters. We have

Stefan Kochanek; Miklos Toth; Albrecht Dehmel; Doris Renz; Walter Doerfler

1990-01-01

293

Detailed chemical kinetic reaction mechanism for biodiesel components methyl stearate and methyl oleate  

E-print Network

Detailed chemical kinetic reaction mechanism for biodiesel components methyl stearate and methyl are developed for two of the five major components of biodiesel fuel, methyl stearate and methyl oleate renewable sources, can reduce net emissions of greenhouse gases. An important class of biodiesel fuels

Paris-Sud XI, Université de

294

The Neutral Hydrolysis of the Methyl Halides  

Microsoft Academic Search

The rate of hydrolysis of methyl chloride, methyl bromide and methyl iodide have been measured in water over a wide range of temperature by a conductance method. The temperature dependence of the rate was shown to conform to an equation of the general form log10 k = A\\/T + B log10 T + C within experimental error. This implies that

R. L. Heppolette; R. E. Robertson

1959-01-01

295

Relationship between nucleosome positioning and DNA methylation  

E-print Network

LETTERS Relationship between nucleosome positioning and DNA methylation Ramakrishna K. Chodavarapu1- ing this data with profiles of DNA methylation at single base reso- lution, we identified 10-base periodicities in the DNA methylation status of nucleosome-bound DNA and found that nucleosomal DNA was more

Jacobsen, Steve

296

5, 13611378, 2008 Methyl arsenic and  

E-print Network

BGD 5, 1361­1378, 2008 Methyl arsenic and antimony species in suspended matter L. Duester et al of Biogeosciences Methylated arsenic and antimony species in suspended matter of the river Ruhr, Germany L. Duester1 of the European Geosciences Union. 1361 #12;BGD 5, 1361­1378, 2008 Methyl arsenic and antimony species

Paris-Sud XI, Université de

297

DNA methylation: Bisulphite modification and analysis  

Microsoft Academic Search

DNA methylation is an important epigenetic modification of DNA in mammalian genomes. DNA methylation patterns are established early in development, modulated during tissue-specific differentiation and disrupted in many disease states, including cancer. To understand further the biological functions of these changes, accurate and reproducible methods are required to fully analyze the DNA methylation sequence. Here, we describe the 'gold-standard' bisulphite

Aaron Statham; Clare Stirzaker; Peter L Molloy; Marianne Frommer; Susan J Clark

2006-01-01

298

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 ...

299

Synthesis and characterization of rhenium(V) oxo complexes with N-[N-(3-diphenylphosphinopropionyl)glycyl]cysteine methyl ester. X-ray crystal structure of (ReO[Ph(2)P(CH(2))(2)C(O)-Gly-Cys-OMe(P,N,N,S)]).  

PubMed

The PN(2)S chelate N-[N-(3-diphenylphosphinopropionyl)glycyl]-S-tritylcysteine methyl ester [PN(2)S(Trt)-OMe] was synthesized and reacted with ReOCl(3)(PPh(3))(2) and Ph(4)P[ReOCl(4)]. The reactions of both tritylated and detritylated ligands with Re(V)O precursors gave two diastereomers, 9a and 9b, of the ReO(PN(2)S-OMe) complex. The two isomers, produced in a 1:1 molar ratio, are stable and do not interconvert. They were separated by reverse-phase HPLC and characterized by NMR, FT-IR, and UV-visible spectroscopy and electrospray mass spectrometry. X-ray analysis established for 9a the presence in the solid of the syn isomer. Compound 9a, C(21)H(23)N(2)O(5)PSRe, crystallized from warm acetonitrile in the triclinic space group Ponemacr;, a = 9.828(2) A, b = 11.163(2) A, c = 11.641(2) A, alpha = 106.48(3) degrees, beta = 109.06(3) degrees, gamma = 102.81(3) degrees, V = 1085.7(4) A(3), Z = 2. The PN(2)S coordination set is in the equatorial plane, and the complex shows a distorted square pyramidal coordination. The anti configuration assigned to 9b is consistent with all the available physicochemical data. Follow-up of the reaction of the detritylated ligand with Ph(4)P[ReOCl(4)] in ethanol or acetonitrile indicated that the phosphorus atom of the chelate binds first to the metal and that this bond acts as the driving force for coordination. PMID:12588125

Visentin, Roberta; Rossin, Raffaella; Giron, Maria Cecilia; Dolmella, Alessandro; Bandoli, Giuliano; Mazzi, Ulderico

2003-02-24

300

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 Thermo dynamics of the Hydration Waters of Ligand-Thermolysin Complexes  

PubMed Central

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. PMID:22894131

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

2012-01-01

301

Identification of Differentially Methylated Sequences in Colorectal Cancer by Methylated CpG Island Amplification1  

Microsoft Academic Search

CpG island methylation has been linked to tumor suppressor gene inactivation in neoplasia and may serve as a useful marker to clone novel cancer-related genes. We have developed a novel PCR-based method, methylated CpG island amplification (MCA), which is useful for both methylation analysis and cloning differentially methylated genes. Using restriction enzymes that have differential sensitivity to 5-methyl-cytosine, followed by

Minoru Toyota; Coty Ho; Nita Ahuja; Kam-Wing Jair; Qing Li; Mutsumi Ohe-Toyota; Stephen B. Baylin; Jean-Pierre J. Issa

1999-01-01

302

How to interpret Methylation Sensitive Amplified Polymorphism (MSAP) profiles?  

PubMed Central

Background DNA methylation plays a key role in development, contributes to genome stability, and may also respond to external factors supporting adaptation and evolution. To connect different types of stimuli with particular biological processes, identifying genome regions with altered 5-methylcytosine distribution at a genome-wide scale is important. Many researchers are using the simple, reliable, and relatively inexpensive Methylation Sensitive Amplified Polymorphism (MSAP) method that is particularly useful in studies of epigenetic variation. However, electrophoretic patterns produced by the method are rather difficult to interpret, particularly when MspI and HpaII isoschizomers are used because these enzymes are methylation-sensitive, and any C within the CCGG recognition motif can be methylated in plant DNA. Results Here, we evaluate MSAP patterns with respect to current knowledge of the enzyme activities and the level and distribution of 5-methylcytosine in plant and vertebrate genomes. We discuss potential caveats related to complex MSAP patterns and provide clues regarding how to interpret them. We further show that addition of combined HpaII?+?MspI digestion would assist in the interpretation of the most controversial MSAP pattern represented by the signal in the HpaII but not in the MspI profile. Conclusions We recommend modification of the MSAP protocol that definitely discerns between putative hemimethylated mCCGG and internal CmCGG sites. We believe that our view and the simple improvement will assist in correct MSAP data interpretation. PMID:24393618

2014-01-01

303

The Reaction Mechanism of Methyl-Coenzyme M Reductase: HOW AN ENZYME ENFORCES STRICT BINDING ORDER.  

PubMed

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(Ni(I))·CH3SCoM) is highly favored (Kd = 79 ?m). 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(Ni(II))·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

Wongnate, Thanyaporn; Ragsdale, Stephen W

2015-04-10

304

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

Code of Federal Regulations, 2013 CFR

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

2013-07-01

305

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

Code of Federal Regulations, 2014 CFR

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

2014-07-01

306

Increased DNA methylation in the suicide brain  

PubMed Central

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

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

2014-01-01

307

The revival of DNA methylation  

PubMed

Current Topics in Microbiology and Immunology. Vol. 249: DNA Methylation and Cancer edited by P. A. Jones and P. K. Vogt Springer-Verlag (2000) pp. 170. ISBN 3-540-66608-7 75.50/$129.00 After a long period of relative confidentiality, the DNA methylation field has become a major research domain over the last few years. In this context, the importance of DNA methylation in human cancer has only become apparent over the last 5 to10 years. This small book (9 articles) provides a comprehensive overview of the main data and, more interestingly, presents the new concepts emerging from the recent extensive work, essentially performed over 2-3 years. The article written by B. Hendrich and A. Bird gives an overview of our current knowledge about the proteins implicated in DNA methylation, including DNA-methyltransferases and methylated-DNA-binding-proteins. It should be noted that the discovery of several of these proteins is a direct consequence of the human genome sequencing program, since they were first found 'in silico' by searching the databases. The specific properties of each of these partners of DNA methylation are beginning to be identified. Their implication in the regulation of histone acetylation suggests some possible mechanisms for regulation of gene expression. These models take into account, in particular, the remodeling of the chromatin structure. The value of mouse models in the understanding of the role of these proteins is discussed by P. W. Laird in another article. The present limitations of these approaches, essentially due to the non-viability of homozygous mutant mice for the main DNA-methyltransferase (Dnmt1) could be passed in the near future by the generation of conditional knockouts. Three articles by J. G. Herman and S. B. Baylin, M. F. Chan, G. Liang and P. A. Jones and J. P. Issa focus on the role of CpG island methylation in cancer and aging. These small stretches of DNA are frequently located around the transcription-start sites of approximately half of all human genes. For virtually all of these genes, with the exception of genes of the inactive X chromosome and some imprinted genes, these regions are maintained free of methylation in normal cells regardless of whether these genes are transcribed. It has been recognized that the CpG islands of a growing number of genes, either known to be involved in carcinogenesis (p16, E-cadherin, hMLH1,.) or candidate tumor supressor genes (p15, GST-&Pgr;,.) are methylated in many types of human cancer. The implication of the hypermethylation of CpG islands in tumor progression is discussed in its various aspects. In particular, the article by Chan et al. highlights the necessity to not oversimplify the relationships between methylation/inactivation and demethylation/activation. Moreover, extending his work on cancer, J. P. Issa shows that specific genes are affected by age-related methylation (EGFR, ER,.) and that such hypermethylation has disastrous consequences for the integrity of aged tissues. The article of A. P. Feinberg covers another area in this field and discusses the role of DNA methylation in imprinting and proposes a model for a role for the of loss of imprinting in cancer. Two articles investigate the action of tumor causing agents: the exogenous carcinogens and the Epstein-Barr virus (EBV). G. P. Pfeifer, M. S. Tang and M. F. Denissenko present the now well known effect of the deamination of methylcytosine on the formation of mutations. However, they insist on the finding that cytosine methylation can increase the rates of mutation by enhancing the binding of chemical carcinogens to DNA. This mechanisms is likely to have important implications for both chemical and ultra violet light induced carcinogenesis. K. D. Robertson summarize his work on the consequences of the inactivation of EBV genes on the virus' life cycle. The use of demethylating agents, like azacytidine, for reactivation of Cp-derived antigens, which could result in specific immune recognition of the tumor, is an interesting idea; however, as analyzed by M. (ABSTRACT TRUNCATED)

Malfoy

2000-11-01

308

Molecular Structure of Methyl Acrylate  

NSDL National Science Digital Library

Commercially available since 1944, methyl acrylate is a clear, colorless liquid with a sweet, fruity odor. This lachrymator often found in tobacco smoke, is used in the manufacturing of polymers, leather finishing, resins, textile, paper coatings, and plastic films. It is highly flammable and polymerizes explosively with exposure to light or heat. Inhibition by hydroquinone monomethyl ether, MEHQ, helps to prevent this problem. Because MEHQ functionality is reliant on oxygen, methyl acrylate must never be stored in an inert environment. Contact with skin will lead to severe deep burns, while ingestion or inhalation could lead to nausea, cough and abdominal pain. The liver, lungs, and kidneys are target organs for this compound, and medical attention should be sought immediately upon exposure.

2002-10-01

309

Reprogramming DNA methylation in the mammalian life cycle: building and breaking epigenetic barriers  

PubMed Central

In mammalian development, epigenetic modifications, including DNA methylation patterns, play a crucial role in defining cell fate but also represent epigenetic barriers that restrict developmental potential. At two points in the life cycle, DNA methylation marks are reprogrammed on a global scale, concomitant with restoration of developmental potency. DNA methylation patterns are subsequently re-established with the commitment towards a distinct cell fate. This reprogramming of DNA methylation takes place firstly on fertilization in the zygote, and secondly in primordial germ cells (PGCs), which are the direct progenitors of sperm or oocyte. In each reprogramming window, a unique set of mechanisms regulates DNA methylation erasure and re-establishment. Recent advances have uncovered roles for the TET3 hydroxylase and passive demethylation, together with base excision repair (BER) and the elongator complex, in methylation erasure from the zygote. Deamination by AID, BER and passive demethylation have been implicated in reprogramming in PGCs, but the process in its entirety is still poorly understood. In this review, we discuss the dynamics of DNA methylation reprogramming in PGCs and the zygote, the mechanisms involved and the biological significance of these events. Advances in our understanding of such natural epigenetic reprogramming are beginning to aid enhancement of experimental reprogramming in which the role of potential mechanisms can be investigated in vitro. Conversely, insights into in vitro reprogramming techniques may aid our understanding of epigenetic reprogramming in the germline and supply important clues in reprogramming for therapies in regenerative medicine. PMID:23166394

Seisenberger, Stefanie; Peat, Julian R.; Hore, Timothy A.; Santos, Fátima; Dean, Wendy; Reik, Wolf

2013-01-01

310

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

PubMed Central

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

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

2011-01-01

311

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

PubMed Central

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

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

2013-01-01

312

Active Repression of Methylated Genes by the Chromosomal Protein MBD1  

PubMed Central

MBD1 belongs to a family of mammalian proteins that share a methyl-CpG binding domain. Previous work has shown that MBD1 binds to methylated sites in vivo and in vitro and can repress transcription from methylated templates in transcription extracts and in cultured cells. In the present study we established by several experimental criteria that, contrary to a previous report, MBD1 is not a component of the MeCP1 repressor complex. We identified a powerful transcriptional repression domain (TRD) at the C terminus of MBD1 that can actively repress transcription at a distance. Methylation-dependent repression in vivo depends on the presence of both the TRD and the methyl-CpG binding domain. The mechanism is likely to involve deacetylation, since the deacetylase inhibitor trichostatin A can overcome MBD1-mediated repression. Accordingly, we found that endogenous MBD1 is particularly concentrated at sites of centromeric heterochromatin, where acetylated histone H4 is deficient. Unlike MBD2 and MeCP2, MBD1 is not depleted by antibodies to the histone deacetylase HDAC1. Thus, the deacetylase-dependent pathway by which MBD1 actively silences methylated genes is likely to be different from that utilized by the methylation-dependent repressors MeCP1 and MeCP2. PMID:10648624

Ng, Huck-Hui; Jeppesen, Peter; Bird, Adrian

2000-01-01

313

Space Complexity Algorithms & Complexity  

E-print Network

Space Complexity Algorithms & Complexity Space Complexity Nicolas Stroppa Patrik Lambert - plambert@computing.dcu.ie CA313@Dublin City University. 2008-2009. December 4, 2008 #12;Space Complexity Hierarchy of problems #12;Space Complexity NP-intermediate Languages If P = NP, then are there languages which neither in P

Way, Andy

314

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

PubMed Central

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

Marinus, Martin G.; Casadesus, Josep

2010-01-01

315

The Dynamics of DNA Methylation in Schizophrenia and Related Psychiatric Disorders  

PubMed Central

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

Grayson, Dennis R; Guidotti, Alessandro

2013-01-01

316

Interactions of methyl farnesoate and related compounds with a crustacean retinoid X receptor.  

PubMed

While a functional role for the sesquiterpenoid hormone methyl farnesoate in arthropods has been recognized for decades, the identification of a receptor that mediates the action of this hormone remains equivocal. Luciferase reporter assays were used in the present study to evaluate the ability of methyl farnesoate and other putative ligands to activate gene transcription associated with the retinoid X receptor (RXR) and RXR:EcR heterodimeric complexes from the crustacean (Daphnia magna). The daphnid RXR constructs, transfected into HepG2 cells along with the reporter construct, significantly activated luciferase gene expression in response to tributyltin indicating that the crustacean RXR is indeed ligand activated. However, RXR was not activated by methyl farnesoate or other putative RXR ligands. Cells co-transfected with the daphnid RXR and EcR produced luciferase in response to ecdysteroids and this activation was significantly enhanced when cells were also provided either methyl farnesoate or other putative RXR ligands. This synergy among RXR and EcR ligands was not dependent upon the co-activator SRC-1 and did not correlate to a physiological response of daphnids to juvenoid hormones (male sex determination). Results indicate that methyl farnesoate, along with compounds that are functionally similar to methyl farnesoate synergize with ecdysteroids to activate the RXR:EcR receptor complex. However, this effect appears to be unrelated to the ability of these compounds to stimulate male sex determination. PMID:19486925

Wang, Ying H; LeBlanc, Gerald A

2009-10-15

317

Epigenomics: genome-wide study of methylation phenomena.  

PubMed

Epigenetics is one of the key areas of future research that can elucidate how genomes work. It combines genetics and the environment to address complex biological systems such as the plasticity of our genome. While all nucleated human cells carry the same genome, they express different genes at different times. Much of this is governed by epigenetic changes resulting in differential methylation of our genome--or different epigenomes. Individual studies over the past decades have already established the involvement of DNA methylation in imprinting, gene regulation, chromatin structure, genome stability and disease, especially cancer. Now, in the wake of the Human Genome Project (HGP), epigenetic phenomena can be studied genome-wide and are giving rise to a new field, epigenomics. Here, we review the current and future potential of this field and introduce the pilot study towards the Human Epigenome Project (HEP). PMID:12432963

Novik, K L; Nimmrich, I; Genc, B; Maier, S; Piepenbrock, C; Olek, A; Beck, S

2002-10-01

318

N6-Adenosine Methylation in MiRNAs  

PubMed Central

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

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

2015-01-01

319

Molecular modeling of methyl-?-Neu5Ac analogues docked against cholera toxin - a molecular dynamics study.  

PubMed

Molecular modeling of synthetic methyl-?-Neu5Ac analogues modified in C-9 position was investigated by molecular docking and molecular dynamics (MD) simulation methods. Methyl-?-Neu5Ac analogues were docked against cholera toxin (CT) B subunit protein and MD simulations were carried out for three Methyl-?-Neu5Ac analogue-CT complexes (30, 10 and 10 ns) to estimate the binding activity of cholera toxin-Methyl-?-Neu5Ac analogues using OPLS_2005 force field. In this study, direct and water mediated hydrogen bonds play a vital role that exist between the methyl-?-9-N-benzoyl-amino-9-deoxy-Neu5Ac (BENZ)-cholera toxin active site residues. The Energy plot, RMSD and RMSF explain that the simulation was stable throughout the simulation run. Transition of phi, psi and omega angle for the complex was calculated. Molecular docking studies could be able to identify the binding mode of methyl-?-Neu5Ac analogues in the binding site of cholera toxin B subunit protein. MD simulation for Methyl-?-9-N-benzoyl-amino-9-deoxy-Neu5Ac (BENZ), Methyl-?-9-N-acetyl-9-deoxy-9-amino-Neu5Ac and Methyl-?-9-N-biphenyl-4-acetyl-deoxy-amino-Neu5Ac complex with CT B subunit protein was carried out, which explains the stable nature of interaction. These methyl-?-Neu5Ac analogues that have computationally acceptable pharmacological properties may be used as novel candidates for drug design for cholera disease. PMID:25676314

Blessy, J Jino; Sharmila, D Jeya Sundara

2015-02-01

320

Polycomb complexes and silencing mechanisms  

Microsoft Academic Search

Advances in the past couple of years have brought important new knowledge on the mechanisms by which Polycomb-group proteins regulate gene expression and on the consequences of their actions. The discovery of histone methylation imprints specific for Polycomb and Trithorax complexes has provided mechanistic insight on how this ancient epigenetic memory system acts to repress and indicates that it may

Anders H Lund; Maarten van Lohuizen

2004-01-01

321

DNA methylation: old dog, new tricks?  

PubMed

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

Spruijt, Cornelia G; Vermeulen, Michiel

2014-11-01

322

Wp specific methylation of highly proliferated LCLs  

SciTech Connect

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.

Park, Jung-Hoon [Functional Genomics Lab, Graduate School of Life Science and Biotechnology, CHA Research Institute, Bundang Campus, College of Medicine, Pochon CHA University, 222 Yatap-Dong, Bundang-Gu, Sungnam-Si, Kyunggi-Do 436-836, South Korea (Korea, Republic of); Jeon, Jae-Pil [Division of Genome Resources Bank and Reservation, National Genome Research Institute, National Institute of Health, 5 Nokbun-Dong, Eunpyung-Gu, Seoul 122-701, South Korea (Korea, Republic of); Shim, Sung-Mi [Division of Genome Resources Bank and Reservation, National Genome Research Institute, National Institute of Health, 5 Nokbun-Dong, Eunpyung-Gu, Seoul 122-701, South Korea (Korea, Republic of); Nam, Hye-Young [Division of Genome Resources Bank and Reservation, National Genome Research Institute, National Institute of Health, 5 Nokbun-Dong, Eunpyung-Gu, Seoul 122-701, South Korea (Korea, Republic of); Kim, Joon-Woo [Division of Genome Resources Bank and Reservation, National Genome Research Institute, National Institute of Health, 5 Nokbun-Dong, Eunpyung-Gu, Seoul 122-701, South Korea (Korea, Republic of); Han, Bok-Ghee [Division of Genome Resources Bank and Reservation, National Genome Research Institute, National Institute of Health, 5 Nokbun-Dong, Eunpyung-Gu, Seoul 122-701, South Korea (Korea, Republic of); Lee, Suman [Functional Genomics Lab, Graduate School of Life Science and Biotechnology, CHA Research Institute, Bundang Campus, College of Medicine, Pochon CHA University, 222 Yatap-Dong, Bundang-Gu, Sungnam-Si, Kyunggi-Do 436-836, South Korea (Korea, Republic of)]. E-mail: suman@cha.ac.kr

2007-06-29

323

Proton affinities of saturated aliphatic methyl esters  

Microsoft Academic Search

The kinetic method was used to determine the proton affinities of methyl esters of several saturated fatty acids. Decompositions\\u000a of the proton-bound dimers of the methyl esters, AHB+, were observed under different conditions with two instruments. The proton affinities (PAs) of the methyl esters increase\\u000a continually with increasing carbon number in the acid. Equilibrium and initial rate experiments were performed

Jason Evans; Gordon Nicol; Burnaby Munson

2000-01-01

324

Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions  

PubMed Central

Analysis of bisulfite sequencing data usually requires two tasks: to call methylated cytosines (mCs) in a sample, and to detect differentially methylated regions (DMRs) between paired samples. Although numerous tools have been proposed for mC calling, methods for DMR detection have been largely limited. Here, we present Bisulfighter, a new software package for detecting mCs and DMRs from bisulfite sequencing data. Bisulfighter combines the LAST alignment tool for mC calling, and a novel framework for DMR detection based on hidden Markov models (HMMs). Unlike previous attempts that depend on empirical parameters, Bisulfighter can use the expectation-maximization algorithm for HMMs to adjust parameters for each data set. We conduct extensive experiments in which accuracy of mC calling and DMR detection is evaluated on simulated data with various mC contexts, read qualities, sequencing depths and DMR lengths, as well as on real data from a wide range of biological processes. We demonstrate that Bisulfighter consistently achieves better accuracy than other published tools, providing greater sensitivity for mCs with fewer false positives, more precise estimates of mC levels, more exact locations of DMRs and better agreement of DMRs with gene expression and DNase I hypersensitivity. The source code is available at http://epigenome.cbrc.jp/bisulfighter. PMID:24423865

Saito, Yutaka; Tsuji, Junko; Mituyama, Toutai

2014-01-01

325

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

PubMed

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

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

2015-02-27

326

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

PubMed Central

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

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

2015-01-01

327

Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome  

PubMed Central

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

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

2014-01-01

328

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

PubMed Central

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

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

329

Plasticity of DNA methylation in mouse T cell activation and differentiation  

PubMed Central

Background Circulating CD4+ T helper cells are activated through interactions with antigen presenting cells and undergo differentiation into specific T helper cell subsets depending on the type of antigen encountered. In addition, the relative composition of the circulating CD4+ T cell population changes as animals mature with an increased percentage of the population being memory/effector type cells. Results Here, we report on the highly plastic nature of DNA methylation at the genome-wide level as T cells undergo activation, differentiation and aging. Of particular note were the findings that DNA demethylation occurred rapidly following T cell activation and that all differentiated T cell populations displayed lower levels of global methylation than the non-differentiated population. In addition, T cells from older mice had a reduced level of DNA methylation, most likely explained by the increase in the memory/effector cell fraction. Although significant genome-wide changes were observed, changes in DNA methylation at individual genes were restricted to specific cell types. Changes in the expression of enzymes involved in DNA methylation and demethylation reflect in most cases the changes observed in the genome-wide DNA methylation status. Conclusion We have demonstrated that DNA methylation is dynamic and flexible in CD4+ T cells and changes rapidly both in a genome-wide and in a targeted manner during T cell activation, differentiation. These changes are accompanied by parallel changes in the enzymatic complexes that have been implicated in DNA methylation and demethylation implying that the balance between these opposing activities may play a role in the maintaining the methylation profile of a given cell type but also allow flexibility in a cell population that needs to respond rapidly to environmental signals. PMID:22642378

2012-01-01

330

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

SciTech Connect

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.

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

2010-01-22

331

Molecular Structure of Methyl Cyanide  

NSDL National Science Digital Library

Methyl Cyanide is a toxic, colorless liquid with an aromatic (ether like) odor and forms explosive mixtures with air. It is a critical solvent for several important processes e.g., it is widely used as a mobile phase solvent in chromatography applications, as a wash solvent and in preparing reagent solutions for oligonucleotide synthesis. It is employed in the manufacturing of acrylic fibers, pharmaceuticals, perfumes, nitrile rubber, batteries, pesticides, and inorganic salts. It can be utilized to remove tars, phenols, and coloring matter from petroleum hydrocarbons, to extract fatty acids from fish liver, animal, and vegetable oils, and to recrystallize steroids.

2003-06-03

332

Aberrant DNA methylation patterns in diabetic nephropathy  

PubMed Central

Background The aim of this study was to evaluate whether global levels of DNA methylation status were associated with albuminuria and progression of diabetic nephropathy in a case-control study of 123 patients with type 2 diabetes- 53 patients with albuminuria and 70 patients without albuminuria. Methods The 5-methyl cytosine content was assessed by reverse phase high pressure liquid chromatography (RP-HPLC) of peripheral blood mononuclear cells to determine individual global DNA methylation status in two groups. Results Global DNA methylation levels were significantly higher in patients with albuminuria compared with those in normal range of albuminuria (p?=?0.01). There were significant differences in global levels of DNA methylation in relation to albuminuria (p?=?0.028) and an interesting pattern of increasing global levels of DNA methylation in terms of albuminuria severity. In patients with micro- and macro albuminuria, we found no significant correlations between global DNA methylation levels and duration of diabetes (p?>?0.05). In both sub groups, there were not significant differences between global DNA methylation levels with good and poor glycaemic control (p?>?0.05). In addition, in patients with albuminuria, no differences in DNA methylation levels were observed between patients with and without other risk factors including age, gender, hypertension, dyslipidaemia and obesity. Conclusions These data may be helpful in further studies to develop novel biomarkers and new strategies for clinical care of patients at risk of diabetic nephropathy. PMID:25028646

2014-01-01

333

Analysing and interpreting DNA methylation data.  

PubMed

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

Bock, Christoph

2012-10-01

334

Methylation – an uncommon modification of glycans*  

PubMed Central

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

Staudacher, Erika

2013-01-01

335

Emissions of Methyl Halides and Methane from Rice Paddies  

Microsoft Academic Search

Methyl halide gases are important sources of atmospheric inorganic halogen compounds, which in turn are central reactants in many stratospheric and tropospheric chemical processes. By observing emissions of methyl chloride, methyl bromide, and methyl iodide from flooded California rice fields, we estimate the impact of rice agriculture on the atmospheric budgets of these gases. Factors influencing methyl halide emissions are

K. R. Redeker; N.-Y. Wang; J. C. Low; A. McMillan; S. C. Tyler; R. J. Cicerone

2000-01-01

336

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

Microsoft Academic Search

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

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

2010-01-01

337

Detailed chemical kinetic reaction mechanism for biodiesel components methyl stearate and methyl oleate  

Microsoft Academic Search

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

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

2011-01-01

338

Detection of global DNA methylation and paternally imprinted H19 gene methylation in preeclamptic placentas  

Microsoft Academic Search

Preeclampsia (PE) is a severe hypertensive disorder associated with pregnancy; despite substantial research effort in the past several years, the etiology of PE is still unclear. The role of epigenetic factors in the etiology of PE, including DNA methylation, has been poorly characterized. In the present study, we investigated global DNA methylation as well as DNA methylation of the paternally

Wen-long Gao; Dong Li; Zhong-xin Xiao; Qin-ping Liao; Hui-xia Yang; Yu-xia Li; Lei Ji; Yan-ling Wang

2011-01-01

339

E?ect of Soil Physical Factors on Methyl Iodide and Methyl Bromide  

Microsoft Academic Search

Production and importation of methyl bromide is scheduled to be banned by 2001. Methyl iodide was evaluated as a possible replacement soil fumigant. The e†ects of soil moisture, temperature, soil texture and fumigation time on the efficacy of methyl iodide for the control of two common weeds, Abutilon theophrasti and L olium multiÑorum, were characterized and compared with those of

Wenming Zhang; J. Ole Becker; Howard D. Ohr; James J. Sims; Steven D. Campbell

1998-01-01

340

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

PubMed

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

Noda, Yoshihiro; Mamiya, Natsuki; Kashin, Hitoshi

2013-07-01

341

Interaction between N-vinylpyrrolidone and methyl methacrylate  

NASA Astrophysics Data System (ADS)

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

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

2014-04-01

342

Chicago area methyl parathion response.  

PubMed

The Illinois Department of Public Health participated in the Chicago, Illinois, area methyl parathion (MP) response with several other federal, state, and local government agencies beginning in April 1997. This response was initiated on evidence that hundreds of homes in the Chicago area were illegally treated for cockroaches with MP over a period of several years. Through applicator receipt books and information reported by property owners and tenants, 968 homes were identified as having been treated with MP. Upon implementation of a response plan developed by the Methyl Parathion Health Sciences Steering Committee, environmental sampling and urine monitoring were provided for eligible households. Environmental sampling was conducted in 903 homes, with MP detected above levels of concern in 596 residences. Residents of these homes were offered urine sampling to determine the extent of exposure to MP. Urine samples were collected and analyzed for p-nitrophenol in 1,913 individuals. Implementation of the protocol resulted in 550 residents being relocated during the remediation of 100 households. PMID:12634143

McCann, Kenneth G; Moomey, C Michael; Runkle, Kenny D; Hryhorczuk, Daniel O; Clark, J Milton; Barr, Dana B

2002-12-01

343

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

PubMed Central

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

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

344

EZH2 Methyltransferase and H3K27 Methylation in Breast Cancer  

PubMed Central

Histone modifications are thought to control the regulation of genetic programs in normal physiology and cancer. Methylation (mono-, di-, and tri-methylation) on histone H3 lysine (K) 27 induces transcriptional repression, and thereby participates in controlling gene expression patterns. Enhancer of zeste (EZH) 2, a methyltransferase and component of the polycomb repressive complex 2 (PRC2), plays an essential role in the epigenetic maintenance of the H3K27me3 repressive chromatin mark. Abnormal EZH2 expression has been associated with various cancers including breast cancer. Here, we discuss the contribution of EZH2 and the PRC2 complex in controlling the H3K27 methylation status and subsequent consequences on genomic instability and the cell cycle in breast cancer cells. We also discuss distinct molecular mechanisms used by EZH2 to suppress BRCA1 functions. PMID:22211105

Yoo, Kyung Hyun; Hennighausen, Lothar

2012-01-01

345

Chloride and ethyl ester morpholine thiourea derivatives and their Ni(II) complexes. Crystal and molecular structures of the thiourea derivative L-leucine methyl ester and its complexes with Cu(II) and Pt(II). Growth of the pathogenic fungus Botrytis cinerea  

Microsoft Academic Search

We have synthesized a series of ligands (1, 3, 4, 6 and 7) and some of their complexes with Ni (II), Cu (II) and Pt (II) (2, 5, 8 and 9). These compounds were studied and characterized by elemental analysis, IR and UV–Vis spectra, conductivity measurements in solution, FAB+\\/MS, 1H and 13C NMR, ESR, etc. Compound 7 crystallized in the

E. Rodr??guez-Fernández; Eva Garc??a; M. R. Hermosa; A. Jiménez-Sánchez; M. Mar Sánchez; Enrique Monte; Julio J. Criado

1999-01-01

346

DNA methylation in placentas of interspecies mouse hybrids.  

PubMed

Interspecific hybridization in the genus Mus results in several hybrid dysgenesis effects, such as male sterility and X-linked placental dysplasia (IHPD). The genetic or molecular basis for the placental phenotypes is at present not clear. However, an extremely complex genetic system that has been hypothesized to be caused by major epigenetic changes on the X chromosome has been shown to be active. We have investigated DNA methylation of several single genes, Atrx, Esx1, Mecp2, Pem, Psx1, Vbp1, Pou3f4, and Cdx2, and, in addition, of LINE-1 and IAP repeat sequences, in placentas and tissues of fetal day 18 mouse interspecific hybrids. Our results show some tendency toward hypomethylation in the late gestation mouse placenta. However, no differential methylation was observed in hyper- and hypoplastic hybrid placentas when compared with normal-sized littermate placentas or intraspecific Mus musculus placentas of the same developmental stage. Thus, our results strongly suggest that generalized changes in methylation patterns do not occur in trophoblast cells of such hybrids. PMID:14504229

Schütt, Sabine; Florl, Andrea R; Shi, Wei; Hemberger, Myriam; Orth, Annie; Otto, Sabine; Schulz, Wolfgang A; Fundele, Reinald H

2003-09-01

347

Preparation of ? -methyl- ? -butyrolactone: Mechanism of its formation and utilization in 2-methyl-1-tetralone synthesis  

Microsoft Academic Search

?-Methyl-?-butyrolactone (III) has been prepared directly from ?-butyrolactone (I) in 89 % yield by selective monomethylation conditions: K2CO3\\/DMC\\/210°C\\/7 h. The reaction mechanism was elucidated and described. An intermediate and two byproducts: methyl tetrahydro-3-methyl-2-oxofuran-3-carboxylate\\u000a (II), 3-(methoxycarbonyl)propyl methyl carbonate (IV) and 3-(methoxycarbonyl)butyl methyl carbonate (V) were identified. The high temperature disproportionation of K2CO3 in the presence of dimethyl carbonate to MeOK was

Vladislav Semak; Andrej Bohá?; Marta Sališová; Gabriela Addová; Peter Danko

2008-01-01

348

7 CFR 305.6 - Methyl bromide fumigation treatment schedules.  

Code of Federal Regulations, 2010 CFR

...2010-01-01false Methyl bromide fumigation treatment schedules....Treatments § 305.6Methyl bromide fumigation treatment schedules. ...quarantined area may be treated with methyl bromide fumigation in...

2010-01-01

349

21 CFR 173.385 - Sodium methyl sulfate.  

Code of Federal Regulations, 2013 CFR

...CONSUMPTION Specific Usage Additives § 173.385 Sodium methyl sulfate. Sodium methyl sulfate may be present in pectin in accordance...and methyl alcohol and subsequent treatment with sodium bicarbonate. (b) It does not exceed 0.1 percent...

2013-04-01

350

21 CFR 173.385 - Sodium methyl sulfate.  

Code of Federal Regulations, 2012 CFR

...CONSUMPTION Specific Usage Additives § 173.385 Sodium methyl sulfate. Sodium methyl sulfate may be present in pectin in accordance...and methyl alcohol and subsequent treatment with sodium bicarbonate. (b) It does not exceed 0.1 percent...

2012-04-01

351

21 CFR 173.385 - Sodium methyl sulfate.  

Code of Federal Regulations, 2014 CFR

...CONSUMPTION Specific Usage Additives § 173.385 Sodium methyl sulfate. Sodium methyl sulfate may be present in pectin in accordance...and methyl alcohol and subsequent treatment with sodium bicarbonate. (b) It does not exceed 0.1 percent...

2014-04-01

352

21 CFR 173.385 - Sodium methyl sulfate.  

Code of Federal Regulations, 2011 CFR

...CONSUMPTION Specific Usage Additives § 173.385 Sodium methyl sulfate. Sodium methyl sulfate may be present in pectin in accordance...and methyl alcohol and subsequent treatment with sodium bicarbonate. (b) It does not exceed 0.1 percent...

2011-04-01

353

21 CFR 173.385 - Sodium methyl sulfate.  

Code of Federal Regulations, 2010 CFR

...CONSUMPTION Specific Usage Additives § 173.385 Sodium methyl sulfate. Sodium methyl sulfate may be present in pectin in accordance...and methyl alcohol and subsequent treatment with sodium bicarbonate. (b) It does not exceed 0.1 percent...

2010-04-01

354

ABIOLOGICAL METHYLATION OF MERCURY IN SOIL  

EPA Science Inventory

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

355

Effects of DNA methylation on nucleosome stability  

PubMed Central

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

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

2013-01-01

356

DNA methylation landscapes: provocative insights from epigenomics  

Microsoft Academic Search

The genomes of many animals, plants and fungi are tagged by methylation of DNA cytosine. To understand the biological significance of this epigenetic mark it is essential to know where in the genome it is located. New techniques are making it easier to map DNA methylation patterns on a large scale and the results have already provided surprises. In particular,

Adrian Bird; Miho M. Suzuki

2008-01-01

357

DNA methylation contributes to natural human variation.  

PubMed

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

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

2013-09-01

358

Conservation and divergence in eukaryotic DNA methylation  

E-print Network

of Delaware, Newark, DE 19711 C ytosine methylation is a com- mon DNA modification found in most eukaryotic nucleotides in DNA does not change the primary DNA se- quence, but the covalent modification of DNAConservation and divergence in eukaryotic DNA methylation Tzuu-fen Lee, Jixian Zhai, and Blake C

359

Methylation of mouse ribosomal RNA genes.  

PubMed

Ribosomal DNA (rDNA) methylation was studied in various strains of mice. We used restriction enzymes that are sensitive to methylation and a cloned probe containing the transcribed spacer and part of the 18S and 28S gene. Strains C3H/He3, C57/B6-3, and AKR/J were found to have less than 9% of the rDNA methylated. In sharp contrast, Balb/c mice showed 30-50% of the Hpa II and Hha I sites to be methylated. Further study of the Balb/c DNA showed that there are three groups of rDNA sequences. In the first group, all the Hpa II and Hha I sites are almost completely unmethylated; in the second group these sites are all methylated (greater than 30 sites for each enzyme); in the third group most sites are methylated, but there are discrete hypomethylation sites. These hypomethylation positions are at similar sites for both Hpa II and Hha I and show a tissue-specific pattern. Comparison of AKR/J with Balb/c copy level showed that AKR/J had about 60% fewer rDNA genes. The rDNA methylation level might thus be correlated directly with the number of rDNA genes. Finally, analysis of F1 mice from a cross between Balb/c and AKR/J showed both low copy number and low methylation levels. PMID:6301785

Reilly, J G; Thomas, C A; Lundell, M J

1982-01-01

360

Conformation-Selective Methylation of Geminivirus DNA ?  

PubMed Central

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

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

2011-01-01

361

The Synthesis of Methyl Salicylate: Amine Diazotization.  

ERIC Educational Resources Information Center

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)

Zanger, Murray; McKee, James R.

1988-01-01

362

Methyl bromide alternatives for grape replant  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

363

ALTERNATIVES TO METHYL BROMIDE: A FLORIDA PERSPECTIVE  

Technology Transfer Automated Retrieval System (TEKTRAN)

The use of methyl bromide as a soil fumigant has been important to crop production in Florida for nearly found decades. Since its discovery and implementation, methyl bromide has been consistently effective for control of nematodes, fungi, insects and weeds and has been used on more than 100 crop...

364

Role of histone methylation and demethylation in adipogenesis and obesity  

PubMed Central

Adipocyte differentiation is a complex developmental process that involves the coordinated interplay of numerous transcription factors. PPAR? has emerged as a master regulator of adipogenesis and recent global target gene analysis demonstrated that PPAR? targets many genes encoding chromatin modification enzymes as well as genes of lipid metabolism and storage. Among such modification enzymes are histone lysine methyltransferases, which play important roles in transcriptional regulation. Histone methyltransferases are involved in PPAR? gene expression and subsequent adipogenesis. In addition, recent studies revealed that demethylation of histone H3 at lys9 is associated with resistance to obesity. We here review the role of histone methylation and demethylation in adipogenesis, metabolism and obesity. PMID:20592862

Okamura, Masashi; Inagaki, Takeshi; Tanaka, Toshiya

2010-01-01

365

Mercury methylation by fish intestinal contents.  

PubMed Central

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

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

1980-01-01

366

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

NASA Astrophysics Data System (ADS)

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

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

1986-03-01

367

Evolving insights on how cytosine methylation affects protein–DNA binding  

PubMed Central

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

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

2015-01-01

368

The aberrant methylation of TSP1 suppresses TGF-?1 activation in colorectal cancer  

PubMed Central

Colorectal cancer arises from the progressive accumulation of mutations and epigenetic alterations in colon epithelial cells. Such alterations often deregulate signaling pathways that affect the formation of colon cancer, such as the Wnt, RAS-MAPK and TGF-? pathways. The tumor promoting effects of mutations in genes, such as APC, have been demonstrated in cancer cell lines and in mouse models of intestinal cancer; however, the biological effects of most epigenetic events identified in colorectal cancer remain unknown. Consequently, we assessed whether the aberrant methylation of TSP1, the gene for thrombospondin 1, a regulator of TGF-? ligand activation, is an epigenetic mechanism for inhibiting the TGF-? signaling pathway. We found methylated TSP1 occurs in colon cancer cell lines (33%), colon adenomas (14%) and colon adenocarcinomas (21%). In primary colorectal cancers, loss of TSP1 expression correlated with impaired TGF-? signaling as indicated by decreased Smad2 phosphorylation and nuclear localization. Furthermore, methylation-induced silencing of TSP1 expression reduced the concentration of secreted active TGF-?1 and attenuated TGF-? signaling. Reversal of TSP1 methylation resulted in increased TSP1 mediated activation of the latent LAP:TGF-? complex and subsequent TGF-? receptor activation. Our results demonstrate that the aberrant methylation of TSP1 has biological consequences and provide evidence that the aberrant methylation of TSP1 is a novel epigenetic mechanism for suppressing TGF-? signaling in colorectal cancer. PMID:18425817

Rojas, Andres; Meherem, Shereen; Kim, Young-Ho; Washington, M. Kay; Willis, Joseph E.; Markowitz, Sanford D.; Grady, William M.

2009-01-01

369

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

USGS Publications Warehouse

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.

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

2002-01-01

370

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

PubMed Central

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

Murgatroyd, Chris; Spengler, Dietmar

2014-01-01

371

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

SciTech Connect

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.

Cole, Callie A.; Wehres, Nadine; Yang Zhibo; Thomsen, Ditte L.; Bierbaum, Veronica M. [Department of Chemistry and Biochemistry, 215 UCB, University of Colorado, Boulder, CO 80309-0215 (United States); Snow, Theodore P., E-mail: Callie.Cole@colorado.edu, E-mail: Nadine.Wehres@colorado.edu, E-mail: Zhibo.Yang@colorado.edu, E-mail: Veronica.Bierbaum@colorado.edu, E-mail: Theodore.Snow@colorado.edu, E-mail: dlt@chem.ku.dk [Center for Astrophysics and Space Astronomy, 389 UCB, University of Colorado, Boulder, CO 80309-0389 (United States)

2012-07-20

372

Reductive methylation of proteins with sodium cyanoborohydride. Identification, suppression and possible uses of N-cyanomethyl by-products.  

PubMed Central

Reductive methylation of protein amino groups with formaldehyde and sodium cyanoborohydride is shown to give up to 25% yield of N-cyanomethyl (-CH2CN) product; on work up of the reaction this is hydrolysed back to starting amine, lowering the methylation yield. Addition of metal ions such as Ni2+, which complex with free cyanide ion, improve reductive methylation yields by suppressing by-product formation. The N-cyanomethyl group itself, produced in good yield when cyanide ion replaces cyanoborohydride, may have some value as a reversible modifier of amino groups in proteins. PMID:7103947

Gidley, M J; Sanders, J K

1982-01-01

373

CARMA: CARM1 methylation of SWI/SNF in breast cancer  

PubMed Central

In this issue of Cancer Cell, Wang and colleagues report that CARM1, a protein arginine methyltransferase, specifically methylates BAF155/SMARCC1, a core subunit of the SWI/SNF chromatin remodeling/tumor suppressor complex. This modification facilitates the targeting of BAF155 to genes of the c-Myc pathway and enhances breast cancer progression and metastases. PMID:24434203

Wang, Xiaofeng; Roberts, Charles W. M.

2014-01-01

374

CARMA: CARM1 methylation of SWI/SNF in breast cancer.  

PubMed

In this issue of Cancer Cell, Wang and colleagues report that CARM1, a protein arginine methyltransferase, specifically methylates BAF155/SMARCC1, a core subunit of the SWI/SNF chromatin remodeling/tumor suppressor complex. This modification facilitates the targeting of BAF155 to genes of the c-Myc pathway and enhances breast cancer progression and metastasis. PMID:24434203

Wang, Xiaofeng; Roberts, Charles W M

2014-01-13

375

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...

376

Catalytic Transformation of C7-C9 Methyl Benzenes over USY-based FCC Zeolite Catalyst  

E-print Network

Catalytic Transformation of C7-C9 Methyl Benzenes over USY-based FCC Zeolite Catalyst S. Al (toluene, m-xylene, and 1,2,4-trimethyl benzene) has been investigated over USY based FCC zeolite catalyst investigated over the USY zeolite. This phenomenon can be explained by the complex inter-relationship between

Al-Khattaf, Sulaiman

377

Split -Lactamase Sensor for the Sequence-Specific Detection of DNA Methylation  

E-print Network

of epigenetic regulation of genetic information. Toward this end, we have recently reported the first design the recruitment of chromatin modification complexes.4-6 Though CpG methylation is distributed throughout the genome, this chemical modification is normally excluded from promoter-associated CpG-rich regions of a se

Ghosh, Indraneel

378

Investigation of Electronic Effects of Rh(II)-Mediated r-Methyl-Substituted  

E-print Network

Investigation of Electronic Effects of Rh(II)-Mediated r-Methyl-Substituted Carbenoid University, Beijing 100871, People's Republic of China Received June 30, 1998 The electronic effects of Rh-substituent on the carbenoid carbon is expected to exert a similar effect on the reactivity of carbene-Rh complex.2c,3

Wang, Jianbo

379

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

EPA Science Inventory

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

380

Is the fungus Magnaporthe losing DNA methylation?  

PubMed

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

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

2013-11-01

381

Aberrant methylation of Reprimo in human malignancies.  

PubMed

Reprimo is a new candidate mediator of p53-mediated cell cycle arrest at the G2 phase. Loss of Reprimo gene expression accompanied by its promoter methylation was identified in pancreatic and lung cancers. Our aim was to examine the methylation status of Reprimo in a broad range of cancers. We examined Reprimo expression by RT-PCR and the DNA methylation status of the Reprimo promoter by MSP in 39 tumor cell lines. Loss or downregulation of Reprimo expression was frequent (62%), and we confirmed that transcriptional repression of Reprimo was caused by hypermethylation (overall concordance 92%). Treatment of expression-negative cells with 5-aza-2'-deoxycytidine restored Reprimo expression. We then examined aberrant methylation of Reprimo in 645 tumors representing 16 tumor types. Promoter methylation of Reprimo was found in 79% of gastric cancers, 62% of gallbladder cancers, 57% of lymphomas, 56% of colorectal cancers, 40% of esophageal adenocarcinomas, 37% of breast cancers and 31% of leukemias. Methylation frequencies in ovarian cancers, bladder cancers, cervical cancers, brain tumors, malignant mesotheliomas and pediatric tumors were lower (0-20%). Reprimo methylation was rarely detected in nonmalignant tissues (0-11%) except for gastric epithelia. While colorectal polyps were also frequently methylated (27%), chronic cholecystitis samples were infrequently methylated (4%). Furthermore, we failed to identify Reprimo mutation in colorectal and gastric cancer cell lines and 50 primary colorectal cancers. Aberrant methylation of Reprimo with loss of expression is a common event and may contribute to the pathogenesis of some types of human malignancy. PMID:15700311

Takahashi, Takao; Suzuki, Makoto; Shigematsu, Hisayuki; Shivapurkar, Narayan; Echebiri, Chinyere; Nomura, Masaharu; Stastny, Victor; Augustus, Meena; Wu, Chew-Wun; Wistuba, Ignacio I; Meltzer, Stephen J; Gazdar, Adi F

2005-07-01

382

Is the Fungus Magnaporthe Losing DNA Methylation?  

PubMed Central

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

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

2013-01-01

383

Theoretical study of the regioselectivity of the interaction of 3-methyl-4-pyrimidone and 1-methyl-2-pyrimidone with Lewis acids.  

PubMed

A density functional theory (DFT) study is performed to determine the stability of the complexes formed between either the N or O site of 3-methyl-4-pyrimidone and 1-methyl-2-pyrimidone molecules and different ligands. The studied ligands are boron and alkali Lewis acids, namely, B(CH(3))(3), HB(CH(3))(2), H(2)B(CH(3)), BH(3), H(2)BF, HBF(2), BF(3), Li(+), Na(+), and K(+). The acids are divided into two groups according to their hardness. The reactivity predictions, according to the molecular electrostatic potential (MEP) map and the natural bond orbital (NBO) analysis, are in agreement with the calculated relative stabilities. Our findings reveal a strong regioselectivity with borane and its derivatives preferring the nitrogen site in both pyrimidone isomers, while a preference for oxygen is observed for the alkali acids in the 3-methyl-4-pyrimidone molecule. The complexation of 1-methyl-2-pyrimidone with these hard alkali acids does not show any discrimination between the two sites due to the presence of a continuous delocalized density region between the nitrogen and the oxygen atoms. The preference of boron Lewis acids toward the N site is due to the stronger B-N bond as compared to the B-O bond. The influence of fluorine or methyl substitution on the boron atom is discussed through natural orbital analysis (NBO) concentrating on the overlap of the boron empty p-orbital with the F lone pairs and methyl hyperconjugation, respectively. The electrophilicity of the boron acids gives a good overall picture of the interaction capabilities with the Lewis base. PMID:22853776

Kasende, Okuma Emile; Muya, Jules Tshishimbi; Broeckaert, Lies; Maes, Guido; Geerlings, Paul

2012-08-23

384

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

PubMed Central

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

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

2014-01-01

385

Frequent SOCS3 and 3OST2 promoter methylation and their epigenetic regulation in endometrial carcinoma  

PubMed Central

DNA methylation has been considered as an important means of early diagnosis of cancer, which cooperates with histone modifications, playing a crucial role in silencing tumor suppressor genes (TSGs). However, how TSGs are regulated by these epigenetic mechanisms in cancer remains unknown. In this study, we first evaluated 7 TSGs methylation in the early diagnosis of endometrial carcinoma (EC), and then explored the epigenetic mechanisms of their transcriptional regulation. The results showed that SOCS3 and 3OST2 were the most frequently methylated genes in EC (88.3% and 78.3%, respectively), and 3OST2 was correlated with younger patients (< 57 years, P = 0.030) and well-differentiated EC (P = 0.026). Unlike 3OST2, SOCS3 methylation occurred even in complex hyperplasia (53.3%) and atypical hyperplasia (54.2%). 5-aza-2’-deoxycytidine (5-Aza-CdR) or trichostatin A (TSA) alone could partially reverse SOCS3 and 3OST2 methylation, and their combination completely reversed the methylation of both genes. In addition, UHRF1 and methylated H3R8 were enriched on both hypermethylated SOCS3 and 3OST2 promoters, but after 5-Aza-CdR or TSA treatment, the UHRF1 and H3R8me2s enrichment was decreased while H3R8me2a enrichment was increased. In conclusion, we demonstrate for the first time that SOCS3 and 3OST2 methylation plays an important role in endometrial carcinogenesis, and could be directly regulated by UHRF1. Moreover, H3R8me2s acts as a repressive mark, while H3R8me2a was correlated with transcriptional activity in EC. PMID:25628929

Chen, Haiyan; Zhang, Cuijuan; Sheng, Yan; Yao, Shuzhe; Liu, Zhiyan; Zhang, Cheng; Zhang, Tingguo

2015-01-01

386

Prognostic Value of PLAGL1-Specific CpG Site Methylation in Soft-Tissue Sarcomas  

PubMed Central

Soft tissue sarcomas (STS) are rare, complex tumors with a poor prognosis. The identification of new prognostic biomarkers is needed to improve patient management. Our aim was to determine the methylation status of the 118 CpG sites in the PLAGL1 tumor-suppressor gene P1 CpG island promoter and study the potential prognostic impact of PLAGL1 promoter methylation CpG sites in STS. Training cohorts constituted of 28 undifferentiated sarcomas (US) and 35 leiomyosarcomas (LMS) were studied. PLAGL1 mRNA expression was investigated by microarray analysis and validated by RT-qPCR. Pyrosequencing was used to analyze quantitative methylation of the PLAGL1 promoter. Associations between global promoter or specific CpG site methylation and mRNA expression were evaluated using Pearson’s product moment correlation coefficient. Cox univariate and multivariate proportional hazard models were used to assess the predictive power of CpG site methylation status. Sixteen CpG sites associated with PLAGL1 mRNA expression were identified in US and 6 in LMS. Statistical analyses revealed an association between CpG107 methylation status and both overall and metastasis-free survival in US, which was confirmed in a validation cohort of 37 US. The exhaustive study of P1 PLAGL1 promoter methylation identified a specific CpG site methylation correlated with mRNA expression, which was predictive for both metastasis-free and overall survival and may constitute the first US-specific biomarker. Such a biomarker may be relevant for identifying patients likely to derive greater benefit from treatment. PMID:24260468

Peille, Anne-Lise; Brouste, Veronique; Kauffmann, Audrey; Lagarde, Pauline; Le Morvan, Valerie; Coindre, Jean-Michel; Chibon, Frederic; Bresson-Bepoldin, Laurence

2013-01-01

387

DNA methylation and methylation polymorphism in ecotypes of Jatropha curcas L. using methylation-sensitive AFLP markers.  

PubMed

We investigated DNA methylation and polymorphism in the methylated DNA using AFLP based methylation-sensitive amplification polymorphism (MS-AFLP) markers in ecotypes of Jatropha curcas L. growing in similar and different geo-ecological conditions. Three ecotypes growing in different geo-ecological conditions with environmental heterogeneity (Group-1) and five ecotypes growing in similar environmental conditions (Group-2) were assessed. In ecotypes growing in group-1, 44.32 % DNA was methylated and of which 93.59 % DNA was polymorphic. While in group-2, 32.27 % DNA was methylated, of which 51.64 % DNA was polymorphic. In site 1 and site 2 of group-1, overall methylation was 18.94 and 22.44 % respectively with difference of 3.5 %, while overall polymorphism was 41.14 and 39.23 % with a difference of 1.91 %. In site 1 and site 2 of group-2, overall methylation was 24.68 and 24.18 % respectively with difference of 0.5 %, while overall polymorphism was 12.19 and 12.65 % with a difference of 0.46 %. The difference of methylation percentage and percentage of methylation polymorphism throughout the genome of J. curcas at site 1 and 2 of group-1 is higher than that of J. curcas at site 1 and 2 of group-2. These results correlated the physico-chemical properties of soil at these sites. The variations of physico-chemical properties of soil at Chorwadla (site 1 in group-1 and site 2 in group-2) compared to the soil at Brahmapur (site 2 in group-1) is higher than that of soil at Neswad (site 1 in group-2). The study suggests that these homologous nucleotide sequences probably play important role in ecotype adaptation to environmental heterogeneity by creating epiallelic variations hence in evolution of ecotypes/clines or forms of species showing phenotypic/genotypic differences in different geographical areas. PMID:25227523

Mastan, Shaik G; Rathore, Mangal S; Bhatt, Vacha D; Chikara, J; Ghosh, A

2014-12-01

388

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

PubMed Central

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

2014-01-01

389

Methylation and expression analysis of 15 genes and three normally-methylated genes in 13 Ovarian cancer cell lines  

Microsoft Academic Search

Aberrant methylation of CpG islands (CGIs) in promoter regions of tumor-suppressor genes causes their silencing, and aberrant demethylation of normally methylated CGIs in promoter regions causes aberrant expression of cancer-testis antigens. Here, we comprehensively analyzed aberrant methylation of 15 genes and demethylation of three normally methylated genes in 13 ovarian cancer cell lines. RASSF1A was most frequently methylated (complete methylation

Masayoshi Imura; Satoshi Yamashita; Li-yi Cai; Jun-ichi Furuta; Mika Wakabayashi; Toshiharu Yasugi; Toshikazu Ushijima

2006-01-01

390

Interfield and intrafield variability of methyl halide emissions from rice paddies  

Microsoft Academic Search

Methyl halide gases are important sources of atmospheric inorganic halogen radicals. We measured methyl halide emissions from three rice fields over two full growing seasons. Rice paddy emissions of methyl chloride, methyl bromide and methyl iodide are insignificant until field flooding. Rice growth stage determines methyl bromide and methyl iodide emissions while methyl chloride emissions are comparable between planted and

K. R. Redeker; J. Andrews; F. Fisher; R. Sass; R. J. Cicerone

2002-01-01

391

INFLUENCE OF DISSOLVED ORGANIC MATTER ON THE COMPLEXATION OF MERCURY UNDER SULFIDIC CONDITIONS  

Microsoft Academic Search

The complexation of Hg under sulfidic conditions influences its bioavailability for microbial methylation. Neutral dissolved Hg-sulfide complexes are readily available to Hg-methylating bacteria in culture, and thermodynamic models predict that inorganic Hg-sulfide complexes dominate dissolved Hg speciation under natural sulfidic conditions. However, these models have not been validated in the field. To examine the complexation of Hg in natural sulfidic

Carrie L. Miller; Robert P. Mason; Cynthia C. Gilmour; Andrew Heyes

2007-01-01

392

On your histone mark, SET, methylate!  

PubMed Central

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

Binda, Olivier

2013-01-01

393

Neurological manifestation of methyl bromide intoxication.  

PubMed

Methyl bromide is a highly toxic gas with poor olfactory warning properties. It is widely used as insecticidal fumigant for dry foodstuffs and can be toxic to central and peripheral nervous systems. Most neurological manifestations of methyl bromide intoxication occur from inhalation. Acute toxicity characterized by headache, dizziness, abdominal pain, nausea, vomiting and visual disturbances. Tremor, convulsion, unconsciousness and permanent brain damage may occur in severe poisoning. Chronic exposure can cause neuropathy, pyramidal and cerebellar dysfunction, as well as neuropsychiatric disturbances. The first case of methyl bromide intoxication in Thailand has been described. The patient was a 24-year-old man who worked in a warehouse of imported vegetables fumigated with methyl bromide. He presented with unstable gait, vertigo and paresthesia of both feet, for two weeks. He had a history of chronic exposure to methyl bromide for three years. His fourteen co-workers also developed the same symptoms but less in severity. Neurological examination revealed ataxic gait, decreased pain and vibratory sense on both feet, impaired cerebellar signs and hyperactive reflex in all extremities. The serum concentration of methyl bromide was 8.18 mg/dl. Electrophysilogical study was normal. Magnetic resonance imaging of the brain (MRI) revealed bilateral symmetrical lesion of abnormal hypersignal intensity on T2 and fluid-attenuation inversion recovery (FLAIR) sequences at bilateral dentate nuclei of cerebellum and periventricular area of the fourth ventricle. This incident stresses the need for improvement of worker education and safety precautions during all stages of methyl bromide fumigation. PMID:18575299

Suwanlaong, Kanokrat; Phanthumchinda, Kammant

2008-03-01

394

DNA methylation analysis reveals distinct methylation signatures in pediatric germ cell tumors  

PubMed Central

Background Aberrant DNA methylation is a prominent feature of many cancers, and may be especially relevant in germ cell tumors (GCTs) due to the extensive epigenetic reprogramming that occurs in the germ line during normal development. Methods We used the Illumina GoldenGate Cancer Methylation Panel to compare DNA methylation in the three main histologic subtypes of pediatric GCTs (germinoma, teratoma and yolk sac tumor (YST); N?=?51) and used recursively partitioned mixture models (RPMM) to test associations between methylation pattern and tumor and demographic characteristics. We identified genes and pathways that were differentially methylated using generalized linear models and Ingenuity Pathway Analysis. We also measured global DNA methylation at LINE1 elements and evaluated methylation at selected imprinted loci using pyrosequencing. Results Methylation patterns differed by tumor histology, with 18/19 YSTs forming a distinct methylation class. Four pathways showed significant enrichment for YSTs, including a human embryonic stem cell pluripotency pathway. We identified 190 CpG loci with significant methylation differences in mature and immature teratomas (q?methylation at LINE1 elements compared with normal adjacent tissue while there was no difference between teratoma (mature and immature) and normal tissue. DNA methylation at imprinted loci differed significantly by tumor histology and location. Conclusion Understanding methylation patterns may identify the developmental stage at which the GCT arose and the at-risk period when environmental exposures could be most harmful. Further, identification of relevant genetic pathways could lead to the development of new targets for therapy. PMID:23806198

2013-01-01

395

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

NASA Astrophysics Data System (ADS)

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

Modica, P.; Palumbo, M. E.

2010-09-01

396

A genetic sensor for strong methylating compounds  

PubMed Central

Methylating chemicals are common in industry and agriculture and are often toxic, partly due to their propensity to methylate DNA. The Escherichia coli Ada protein detects methylating compounds by sensing aberrant methyl adducts on the phosphoester backbone of DNA. We characterize this system as a genetic sensor and engineer it to lower the detection threshold. By overexpressing Ada from a plasmid, we improve the sensor’s dynamic range to 350-fold induction and lower its detection threshold to 40 µM for methyl iodide. In eukaryotes, there is no known sensor of methyl adducts on the phosphoester backbone of DNA. By fusing the N-terminal domain of Ada to the Gal4 transcriptional activation domain, we built a functional sensor for methyl phosphotriester adducts in Saccharomyces cerevisiae. This sensor can be tuned to variable specifications by altering the expression level of the chimeric sensor and changing the number of Ada operators upstream of the Gal4-sensitive reporter promoter. These changes result in a detection threshold of 28 µM and 5.2-fold induction in response to methyl iodide. When the yeast sensor is exposed to different SN1 and SN2 alkylating compounds, its response profile is similar to that observed for the native Ada protein in E. coli, indicating that its native function is retained in yeast. Finally, we demonstrate that the specifications achieved for the yeast sensor are suitable for detecting methylating compounds at relevant concentrations in environmental samples. This work demonstrates the movement of a sensor from a prokaryotic to eukaryotic system and its rational tuning to achieve desired specifications. PMID:24032656

Moser, Felix; Horwitz, Andrew; Chen, Jacinto; Lim, Wendell A.; Voigt, Christopher A.

2013-01-01

397

Methyl chloride via oxhydrochlorination of methane  

SciTech Connect

Dow Corning is developing a route from methane to methyl chloride via oxyhydrochlorination (OHC) chemistry with joint support from the Gas Research Institute and the Department of Energy Federal Energy Technology Center. Dow Corning is the world`s largest producer of methyl chloride and uses it as an intermediate in the production of silicone materials. Other uses include production of higher hydrocarbons, methyl cellulose, quaternary ammonium salts and herbicides. The objective of this project is to demonstrate and develop a route to methyl chloride with reduced variable cost by using methane instead of methanol raw materials. Methyl chloride is currently produced from methanol, but U.S. demand is typically higher than available domestic supply, resulting in fluctuating prices. OHC technology utilizes domestic natural gas as a feedstock, which allows a lower-cost source of methyl chloride which is independent of methanol. In addition to other uses of methyl chloride, OHC could be a key step in a gas-to-liquid fuels process. These uses could divert significant methanol demand to methane. A stable and selective catalyst has been developed in the laboratory and evaluated in a purpose-built demonstration unit. Materials of construction issues have been resolved and the unit has been run under a range of conditions to evaluate catalyst performance and stability. Many technological advances have been made, especially in the areas of catalyst development, online FTIR analysis of the product stream, and recovery of methyl chloride product via an absorber/stripper system. Significant technological hurdles still remain including heat transfer, catalysts scaleup, orthogonality in modeling, and scaleable absorption data. Economics of the oxyhydrochlorination process have been evaluated an found to be unfavorable due to high capital and utility costs. Future efforts will focus on improved methane conversion at high methyl chloride selectivity.

Jarvis, R.F. Jr.

1997-12-31

398

Effects of sulforaphane and 3,3'-diindolylmethane on genome-wide promoter methylation in normal prostate epithelial cells and prostate cancer cells.  

PubMed

Epigenetic changes, including aberrant DNA methylation, result in altered gene expression and play an important role in carcinogenesis. Phytochemicals such as sulforaphane (SFN) and 3,3'-diindolylmethane (DIM) are promising chemopreventive agents for the treatment of prostate cancer. Both have been shown to induce re-expression of genes, including tumor suppressor genes silenced in cancer cells, via modulation of epigenetic marks including DNA methylation. However, it remained unclear the effects SFN and DIM on DNA methylation at a genomic scale. The goal of this study was to determine the genome-wide effects of SFN and DIM on promoter methylation in normal prostate epithelial cells and prostate cancer cells. Both SFN and DIM treatment decreased DNA methyltransferase expression in normal prostate epithelial cells (PrEC), and androgen-dependent (LnCAP) and androgen-independent (PC3) prostate cancer cells. The effects of SFN and DIM on promoter methylation profiles in normal PrEC, LnCAP and PC3 prostate cancer cells were determined using methyl-DNA immunoprecipitation followed by genome-wide DNA methylation array. We showed widespread changes in promoter methylation patterns, including both increased and decreased methylation, in all three prostate cell lines in response to SFN or DIM treatments. In particular, SFN and DIM altered promoter methylation in distinct sets of genes in PrEC, LnCAP, and PC3 cells, but shared similar gene targets within a single cell line. We further showed that SFN and DIM reversed many of the cancer-associated methylation alterations, including aberrantly methylated genes that are dysregulated or are highly involved in cancer progression. Overall, our data suggested that both SFN and DIM are epigenetic modulators that have broad and complex effects on DNA methylation profiles in both normal and cancerous prostate epithelial cells. Results from our study may provide new insights into the epigenetic mechanisms by which SFN and DIM exert their cancer chemopreventive effects. PMID:24466240

Wong, Carmen P; Hsu, Anna; Buchanan, Alex; Palomera-Sanchez, Zoraya; Beaver, Laura M; Houseman, E Andres; Williams, David E; Dashwood, Roderick H; Ho, Emily

2014-01-01

399

Infrared spectra and chemical abundance of methyl propionate in icy astrochemical conditions  

NASA Astrophysics Data System (ADS)

We carried out an experiment in order to obtain the infrared (IR) spectra of methyl propionate (CH3CH2COOCH3) in astrochemical conditions and present the IR spectra for future identification of this molecule in the interstellar medium (ISM). The experimental IR spectrum is compared with the theoretical spectrum, and an attempt was made to assign the observed peak positions to their corresponding molecular vibrations in condensed phase. Moreover, our calculations suggest that methyl propionate must be synthesized efficiently within the complex chemical network of the ISM and therefore be present in cold dust grains, awaiting identification.

Sivaraman, B.; Radhika, N.; Das, A.; Gopakumar, G.; Majumdar, L.; Chakrabarti, S. K.; Subramanian, K. P.; Raja Sekhar, B. N.; Hada, M.

2015-04-01

400

Controlled shift in the tautomeric equilibrium of 4-((phenylimino)methyl)naphthalen-1-ol  

NASA Astrophysics Data System (ADS)

4-((Phenylimino)methyl)naphthalen-1-ol and 4-((phenylimino)methyl)-2-(piperidin-1-ylmethyl)naphthalen-1-ol have been synthesized and their tautomeric properties were investigated using molecular spectroscopy (UV-Vis absorption/emission and NMR), X-ray crystallographic analysis and quantum-chemical calculations. The results show that with the implementation of a flexible piperidine ring a controlled shift in the tautomeric equilibrium will be achieved upon protonation/deprotonation in acetonitrile. The addition of a metal salt also shifts the tautomeric equilibrium, but at very high concentrations, which is caused not by a complex formation, but a special effect of the salt addition.

Deneva, V.; Manolova, Y.; Lubenov, L.; Kuteva, V.; Kamounah, F. S.; Nikolova, R.; Shivachev, B.; Antonov, L.

2013-03-01

401

Methyl-CpG island-associated genome signature tags  

DOEpatents

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.

Dunn, John J

2014-05-20

402

DNA methylation alterations exhibit intra-individual stability and inter-individual heterogeneity in prostate cancer metastases  

PubMed Central

Human cancers nearly ubiquitously harbor epigenetic alterations. While such alterations in epigenetic marks, including DNA methylation, are potentially heritable, they can also be dynamically altered. Given this potential for plasticity, the degree to which epigenetic changes can be subject to selection and act as drivers of neoplasia has been questioned. Here, we carried out genome-scale analyses of DNA methylation alterations in lethal metastatic prostate cancer and created DNA methylation “cityscape” plots to visualize these complex data. We show that somatic DNA methylation alterations, despite showing marked inter-individual heterogeneity among men with lethal metastatic prostate cancer, were maintained across all metastases within the same individual. The overall extent of maintenance in DNA methylation changes was comparable to that of genetic copy number alterations. Regions that were frequently hypermethylated across individuals were markedly enriched for cancer and development/differentiation related genes. Additionally, regions exhibiting high consistency of hypermethylation across metastases within individuals, even if variably hypermethylated across individuals, showed enrichment of cancer-related genes. Interestingly, whereas some regions showed intra-individual metastatic tumor heterogeneity in promoter methylation, such methylation alterations were generally not correlated with gene expression. This was despite a general tendency for promoter methylation patterns to be strongly correlated with gene expression, particularly at regions that were variably methylated across individuals. These findings suggest that DNA methylation alterations have the potential for producing selectable driver events in carcinogenesis and disease progression and highlight the possibility of targeting such epigenome alterations for development of longitudinal markers and therapeutic strategies. PMID:23345608

Aryee, Martin J; Liu, Wennuan; Engelmann, Julia C; Nuhn, Philipp; Gurel, Meltem; Haffner, Michael C; Esopi, David; Irizarry, Rafael A; Getzenberg, Robert H; Nelson, William G; Luo, Jun; Xu, Jianfeng; Isaacs, William B; Bova, G Steven; Yegnasubramanian, Srinivasan

2013-01-01

403

A new statistical approach to detecting differentially methylated loci for case control Illumina array methylation data  

PubMed Central

Motivation: As an epigenetic alteration, DNA methylation plays an important role in epigenetic controls of gene transcription. Recent advances in genome-wide scan of DNA methylation provide great opportunities in studying the impact of DNA methylation on many human diseases including various types of cancer. Due to the unique feature of this type of data, applicable statistical methods are limited and new sophisticated approaches are desirable. Results: In this article, we propose a new statistical test to detect differentially methylated loci for case control methylation data generated by Illumina arrays. This new method utilizes the important finding that DNA methylation is highly correlated with age. The proposed method estimates the overall P-value by combining the P-values from independent individual tests each for one age group. Through real data application and simulation study, we show that the proposed test is robust and usually more powerful than other methods. Contact: Zhongxue.Chen@uth.tmc.edu PMID:22368244

Chen, Zhongxue; Liu, Qingzhong; Nadarajah, Saralees

2012-01-01

404

Aberrant Methylation in Gastric Cancer Associated with the CpG Island Methylator Phenotype1  

Microsoft Academic Search

Aberrant methylation of 5* CpG islands is thought to play an important role in the inactivation of tumor suppressor genes in cancer. In colorectal cancer, a group of tumors is characterized by a hypermethylator pheno- type termed CpG island methylator phenotype (CIMP), which includes methylation of such genes as p16 and hMLH1. To study whether CIMP is present in gastric

Minoru Toyota; Nita Ahuja; Hiromu Suzuki; Fumio Itoh; Mutsumi Ohe-Toyota; Kohzoh Imai; Stephen B. Baylin; Jean-Pierre J. Issa

1999-01-01

405

MGMT promoter methylation in gliomas-assessment by pyrosequencing and quantitative methylation-specific PCR  

PubMed Central

Background Methylation of the O6-methylguanine-DNA methyltransferase (MGMT) gene promoter is a favorable prognostic factor in glioblastoma patients. However, reported methylation frequencies vary significantly partly due to lack of consensus in the choice of analytical method. Method We examined 35 low- and 99 high-grade gliomas using quantitative methylation specific PCR (qMSP) and pyrosequencing. Gene expression level of MGMT was analyzed by RT-PCR. Results When examined by qMSP, 26% of low-grade and 37% of high-grade gliomas were found to be methylated, whereas 97% of low-grade and 55% of high-grade gliomas were found methylated by pyrosequencing. The average MGMT gene expression level was significantly lower in the group of patients with a methylated promoter independent of method used for methylation detection. Primary glioblastoma patients with a methylated MGMT promoter (as evaluated by both methylation detection methods) had approximately 5 months longer median survival compared to patients with an unmethylated promoter (log-rank test; pyrosequencing P = .02, qMSP P = .06). One third of the analyzed samples had conflicting methylation results when comparing the data from the qMSP and pyrosequencing. The overall survival analysis shows that these patients have an intermediate prognosis between the groups with concordant MGMT promoter methylation results when comparing the two methods. Conclusion In our opinion, MGMT promoter methylation analysis gives sufficient prognostic information to merit its inclusion in the standard management of patients with high-grade gliomas, and in this study pyrosequencing came across as the better analytical method. PMID:22390413

2012-01-01

406

Methyl-combing: single-molecule analysis of DNA methylation on stretched DNA fibers.  

PubMed

The methyl-combing technique combines the dynamic molecular combing method with the detection of DNA modifications. The assay allows the single-molecule analysis of epigenetic marks on regularly stretched DNA fibers, at the megabase scale with kilobase resolution. The protocol presented in this chapter is based on proof-of-principle experiments where the single-molecule detection of DNA methylation has been performed on unmethylated and in vitro methylated ? phage DNA. PMID:24162992

Németh, Attila

2014-01-01

407

Prognostic Significance of DNA and Histone Methylation  

Cancer.gov

Nutritional Science Research Group Recently Funded Projects Prognostic Significance of DNA and Histone Methylation Principal Investigator: Piyathilake, Chandrika J Institution: University of Alabama at Birmingham   NCI/DCP Program Director: Ross, Sharon

408

75 FR 19272 - Thifensulfuron methyl; Pesticide Tolerances  

Federal Register 2010, 2011, 2012, 2013, 2014

...thifensulfuron methyl on safflower seed at 0.05ppm. EPA's assessment...deficiency. FQPA SF = Food Quality Protection Act Safety Factor...2-thiophenecarboxylate), in or on safflower, seed at 0.05 ppm. VI. Statutory...Safflower,...

2010-04-14

409

Experimental Pathology Laboratories, Inc. Methyl Alcohol  

E-print Network

................................................................................................................4 Audit of Pathology Specimens........................................................................................... A-1 ­ A-58 APPENDIX B Audit of Pathology Specimens Experimental Pathology Laboratories, Inc. Methyl Alcohol C00117E/00117-68 AMENDED PATHOLOGY

Baker, Chris I.

410

Targeting DNA Methylation for Epigenetic Therapy  

PubMed Central

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

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

2010-01-01

411

Incorporating DNA Methylation Dynamics Into Epigenetic Codes  

PubMed Central

Summary Genomic function is dictated by a combination of DNA sequence and the molecular mechanisms controlling access to genetic information. Access to DNA can be determined by the interpretation of covalent modifications that influence the packaging of DNA into chromatin, including DNA methylation and histone modifications. These modifications are believed to be forms of “epigenetic codes” that exist in discernable combinations that reflect cellular phenotype. Although DNA methylation is known to play important roles in gene regulation and genomic function, its contribution to the encoding of epigenetic information is just beginning to emerge. Here we discuss paradigms associated with the various components of DNA methylation/demethylation and recent advances in the understanding of its dynamic regulation in the genome, integrating these mechanisms into a framework to explain how DNA methylation could contribute to epigenetic codes. PMID:24242211

Szulwach, Keith E.; Jin, Peng

2014-01-01

412

Aberrant DNA methylation in malignant melanoma  

PubMed Central

Malignant Melanoma remains one of the most deadly human cancers with no effective cures for metastatic disease. The poor efficacy of current therapy in advanced melanoma highlights the need for better understanding of molecular mechanisms contributing to the disease. Recent work has shown that epigenetic changes, including aberrant DNA methylation, lead to alterations in gene expression and are as important in the development of malignant melanoma as the specific and well characterized genetic events. Reversion of these methylation patterns could thus lead to a more targeted therapy and are currently under clinical investigation. The purpose of this review is to compile recent information on aberrant DNA methylation of melanoma, to highlight key genes and molecular pathways in melanoma development that have found to be epigenetically altered and to provide insight as of how DNA methylation might serve as targeted treatment option as well as a molecular and prognostic marker in malignant melanoma. PMID:20418788

Schinke, Carolina; Mo, Yongkai; Yu, Yiting; Amiri, Kathy; Sosman, Jeff; Greally, John; Verma, Amit

2010-01-01

413

Aberrant DNA Methylation in ES Cells  

PubMed Central

Both mouse and human embryonic stem cells can be differentiated in vitro to produce a variety of somatic cell types. Using a new developmental tracing approach, we show that these cells are subject to massive aberrant CpG island de novo methylation that is exacerbated by differentiation in vitro. Bioinformatics analysis indicates that there are two distinct forms of abnormal de novo methylation, global as opposed to targeted, and in each case the resulting pattern is determined by molecular rules correlated with local pre-existing histone modification profiles. Since much of the abnormal methylation generated in vitro appears to be stably maintained, this modification may inhibit normal differentiation and could predispose to cancer if cells are used for replacement therapy. Excess CpG island methylation is also observed in normal placenta, suggesting that this process may be governed by an inherent program. PMID:24852222

Hecht, Merav; Orlanski, Shari; Abu-Remaileh, Monther; Yanuka, Ofra; Sandler, Oded; Marx, Amichai; Roberts, Douglas; Benvenisty, Nissim; Bergman, Yehudit; Mendelsohn, Monica; Cedar, Howard

2014-01-01

414

METHYL TERTIARY-BUTYL ETHER (MTBE): Gasoline  

NSDL National Science Digital Library

This site gives an explanation of Methyl tertiary butyl ether (MTBE), also known as an oxygenate, a chemical compound used as a gasoline additive to enhance the octane and subsequently burn the fuel more completely.

415

Emission of methyl bromide from biomass burning  

SciTech Connect

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.

Manoe, S.; Andreae, M.O. (Max Planck Institute for Chemistry, Mainz (Germany))

1994-03-04

416

METHYLATED TRIVALENT ARSENIC SPECIES ARE GENOTOXIC  

EPA Science Inventory

ABSTRACT The genotoxic effects of arsenic compounds are generally believed to result from other than direct interacton with DNA. The reactivties of methyloxarsine (MAsIII) and iododimethylarsine (DMAsIII), two methylated trivalent arsenicals, toward supercoiled X174 RFI ...

417

Computational prediction of methylation status in human genomic sequences  

E-print Network

G islands Although progress recently has been made toward whole- genome DNA methylation profiling by using of human brain DNA. This method can be applied both to CpG islands and to non-CpG island regions methylation patterns for all 22 human autosomes. DNA methylation epigenomics methylation prediction Cp

418

DNA Methylation and Epigenetic Inheritance in Plants and Filamentous Fungi  

NSDL National Science Digital Library

Plants and filamentous fungi share with mammals enzymes responsible for DNA methylation. In these organisms, DNA methylation is associated with gene silencing and transposon control. However, plants and fungi differ from mammals in the genomic distribution, sequence specificity, and heritability of methylation. We consider the role that transposons play in establishing methylation patterns and the epigenetic consequences of their perturbation.

Robert A. Martienssen (Cold Spring Harbor Laboratory; )

2001-08-10

419

Detecting differentially methylated loci for multiple treatments based on high-throughput methylation data  

PubMed Central

Background Because of its important effects, as an epigenetic factor, on gene expression and disease development, DNA methylation has drawn much attention from researchers. Detecting differentially methylated loci is an important but challenging step in studying the regulatory roles of DNA methylation in a broad range of biological processes and diseases. Several statistical approaches have been proposed to detect significant methylated loci; however, most of them were designed specifically for case-control studies. Results Noticing that the age is associated with methylation level and the methylation data are not normally distributed, in this paper, we propose a nonparametric method to detect differentially methylated loci under multiple conditions with trend for Illumina Array Methylation data. The nonparametric method, Cuzick test is used to detect the differences among treatment groups with trend for each age group; then an overall p-value is calculated based on the method of combining those independent p-values each from one age group. Conclusions We compare the new approach with other methods using simulated and real data. Our study shows that the proposed method outperforms other methods considered in this paper in term of power: it detected more biological meaningful differentially methylated loci than others. PMID:24884464

2014-01-01

420

Heterochromatin dynamics during the differentiation process revealed by the DNA methylation reporter mouse, MethylRO.  

PubMed

In mammals, DNA is methylated at CpG sites, which play pivotal roles in gene silencing and chromatin organization. Furthermore, DNA methylation undergoes dynamic changes during development, differentiation, and in pathological processes. The conventional methods represent snapshots; therefore, the dynamics of this marker within living organisms remains unclear. To track this dynamics, we made a knockin mouse that expresses a red fluorescent protein (RFP)-fused methyl-CpG-binding domain (MBD) protein from the ROSA26 locus ubiquitously; we named it MethylRO (methylation probe in ROSA26 locus). Using this mouse, we performed RFP-mediated methylated DNA immunoprecipitation sequencing (MeDIP-seq), whole-body section analysis, and live-cell imaging. We discovered that mobility and pattern of heterochromatin as well as DNA methylation signal intensity inside the nuclei can be markers for cellular differentiation status. Thus, the MethylRO mouse represents a powerful bioresource and technique for DNA methylation dynamics studies in developmental biology, stem cell biology, as well as in disease states. PMID:24936475