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1

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

Microsoft Academic Search

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)\\u000a complex with cysteine methyl ester (2) was partially saponified. Both complexes were characterised by common analytical techniques in their solid state. Thus,\\u000a an octahedral complex structure with 2(NH2,S) co-ordination in the equatorial

Sylvia Kirsch; Ruediger Jankowsky; Peter Leibnitz; Hartmut Spies; Bernd Johannsen

1999-01-01

2

The platinum hydrido-methyl complex: A frozen reaction intermediate?  

SciTech Connect

Methane activation by transition metals has been a topic of growing interest during the past decade, due to economic interest in methane conversion and chemistry. Reactions of platinum-argon complexes Pt{sup +}Ar{sub m}, m = 1--6, with methane (CH{sub 4}) and methane-d{sub 4} (CD{sub 4}) were investigated by means of FT-ICR mass spectrometry and DFT calculations. Ligand exchange reactions are observed for Pt{sup +}Ar{sub m}, m = 2--6, in which up to four argon ligands are replaced by methane. In contrast, the bare platinum ion and platinum solvated with one argon ligand lead to the formation of a platinum-carbene complex. Gibbs free enthalpies from ligand exchange reactions of Pt{sup +}CH{sub 4} with CD{sub 4} and H{sub 2}O provide evidence for the inserted hydrido-methyl complex HPt{sup +}CH{sub 4} with CD{sub 4} (and the reverse reaction). This is attributed to the inability of the platinum cation to form more than three covalent bonds.

Achatz, U.; Beyer, M.; Joos, S.; Fox, B.S.; Niedner-Schatteburg, G.; Bondybey, V.E.

1999-10-14

3

Histone H3 Lysine 36 Methylation Targets the Isw1b Remodeling Complex to Chromatin  

PubMed Central

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.

2012-01-01

4

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

5

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

6

Histone H3 Lysine 36 Methylation Antagonizes Silencing in Saccharomyces cerevisiae Independently of the Rpd3S Histone Deacetylase Complex  

Microsoft Academic Search

In yeast, methylation of histone H3 on lysine 36 (H3-K36) is catalyzed by the NSD1 leukemia on- coprotein homolog Set2. The histone deacetylase complex Rpd3S is recruited to chromatin via binding of the chromodomain protein Eaf3 to methylated H3-K36 to prevent erroneous transcription initiation. Here we identify a distinct function for H3-K36 methylation. We used random mutagenesis of histones H3

Rachel Tompa; Hiten D. Madhani

2007-01-01

7

Efficient Oxidative Methyl Esterification of Aldehydes By Silica-supported Manganese Complex: Clean and Recyclable Catalyst  

Microsoft Academic Search

An oxidative methyl esterification of aldehydes was carried out using hydrogen peroxide as oxidant and silica supported manganese complex as catalyst. The catalyst was prepared by grafting method and characterized by surface area analysis by the BET method, elemental and thermogravimetric analyses, FT-IR, C-CPMAS spectral studies and atomic absorption spectrometry technique (AAS). The work-up procedure is very simple and products

R. K. Sharma; Chetna Sharma

2010-01-01

8

N-terminal methylation of the core light-harvesting complex in purple photosynthetic bacteria  

Microsoft Academic Search

Several core light-harvesting complexes from both sulfur and non-sulfur purple photosynthetic bacteria have been identified to be methylated at the N-terminal ?-amino group of ?-polypeptides by using matrix-assisted laser desorption\\/ionization time-of-flight mass spectrometry and nuclear magnetic resonance. Monomethylation has been confirmed for the N-terminal alanine residues of the ?-polypeptides from Rhodospirillum rubrum, Thermochromatium tepidum and Chromatium vinosum, but not for

Zheng-Yu Wang; Masahiro Shimonaga; Masayuki Kobayashi; Tsunenori Nozawa

2002-01-01

9

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

10

Directional DNA Methylation Changes and Complex Intermediate States Accompany Lineage Specificity in the Adult Hematopoietic Compartment  

PubMed Central

SUMMARY DNA methylation has been implicated as an epigenetic component of mechanisms that stabilize cell-fate decisions. Here, we have characterized the methylomes of human female hematopoietic stem/progenitor cells (HSPCs) and mature cells from the myeloid and lymphoid lineages. Hypomethylated regions (HMRs) associated with lineage-specific genes were often methylated in the opposing lineage. In HSPCs, these sites tended to show intermediate, complex patterns that resolve to uniformity upon differentiation, by increased or decreased methylation. Promoter HMRs shared across diverse cell types typically display a constitutive core that expands and contracts in a lineage-specific manner to fine-tune the expression of associated genes. Many newly identified intergenic HMRs, both constitutive and lineage specific, were enriched for factor binding sites with an implied role in genome organization and regulation of gene expression, respectively. Overall, our studies represent an important reference data set and provide insights into directional changes in DNA methylation as cells adopt terminal fates. PMID:21924933

Hodges, Emily; Molaro, Antoine; Dos Santos, Camila O.; Thekkat, Pramod; Song, Qiang; Uren, Philip J.; Park, Jin; Butler, Jason; Rafii, Shahin; McCombie, W. Richard; Smith, Andrew D.; Hannon, Gregory J.

2012-01-01

11

Synthesis and characterization of a novel high luminescent gold-2-mercapto-1-methyl-imidazole complex.  

PubMed

Synthesis and characterization of a new gold-2-mercapto-1-methyl imidazole are reported. This new organic material shows an extraordinary fluorescence activity (superfluorescence) up to 220°C with an unusual quantum yield of 0.2. Both fluorescence and NMR spectroscopy were applied to understand the behavior of the gold-2-mercapto-1-methylimidazole complex. Results suggest that the superfluorescence activity can be attributed to the shrinking of the HOMO-LUMO band gap energy following complexation of the organic imidazole system with gold. PMID:22162452

Cardone, Giorgio; Carotenuto, Gianfranco; Conte, Pellegrino; Alonzo, Giuseppe

2011-01-01

12

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

13

Synthesis and phosphorescent properties of the copolymers of N-vinylcarbazole, methyl methacrylate and iridium complex  

NASA Astrophysics Data System (ADS)

The copolymers containing carbazole unit and iridium complexes, such as (Ir(bpy)2Cl, Ir(mbpy)2Cl and Ir(Brbpy)2Cl, were synthesized via radical copolymerization of N-vinylcarbazole, methyl methacrylate and iridium complex. The synthesized copolymers were characterized by FT-IR, UV-Vis absorption spectroscopy and photoluminescence (PL) spectroscopy, respectively. According to the results, the copolymers (Ir(Brbpy)2Cl/PVK and Ir(mbpy)2Cl/PVK) exhibit yellow phosphorescence with an emission peak at around 553 nm under UV-visible light in the solid state. The results also reveal almost complete energy transfer from the host carbazole segments to the guest Ir complex in the copolymer film when the Ir content reaches 1.0 wt.%. The synthesized copolymers are good candidates as blue or yellow phosphorescent materials for PLED applications.

Wang, Wen; Zhou, Minglu; Liang, Luying; Lin, Meijuan; Ling, Qidan

2014-06-01

14

Synthesis and antimicrobial studies of silver N-heterocyclic carbene complexes bearing a methyl benzoate substituent  

PubMed Central

Due to the properties of silver as an antimicrobial, our research group has synthesized many different silver carbene complexes. Two new silver N-heterocyclic carbene complexes derived from 4,5-dichloroimidazole and theobromine bearing methyl benzoate substituents were synthesized by in situ carbene formation using silver acetate as the base in the reaction. The new compounds were fully characterized by several methods including NMR spectroscopy and X-ray crystallography. Preliminary antimicrobial efficacy studies against Pseudomonas aeruginosa, Staphylococcus aureus, and Escherichia coli were conducted. The results of this study demonstrated antimicrobial efficacy of the two complexes comparable to silver nitrate, showing their potential for use in the treatment of bacterial infections. PMID:21218156

Knapp, Amanda R.; Panzner, Matthew J.; Medvetz, Doug A.; Wright, Brian D.; Tessier, Claire A.; Youngs, Wiley J.

2010-01-01

15

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

16

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

PubMed Central

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

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

2014-01-01

17

Poly(acrylic acid-co-methyl methacrylate)/metronidazole systems: synthesis and complexation.  

PubMed

We report on preparation of poly(acrylic acid-co-methyl methacrylate) (PAM) micro- and nanoparticles and, in the subsequent stage, complexation reaction with the active substance - metronidazole (MET). The drug release behavior of MET - loaded PAM micro- and nanoparticles was evaluated in water and phosphate buffered saline (PBS, 0.9% NaCl) at 37ºC. It has been found that introduction of MET into PAM micro- and nanoparticles enabled gradual and controlled release of the active substance. Structural analysis using FT-IR (ATR) and (1)H NMR, as well as surface morphology assessment by SEM, were performed. PMID:24432342

Bialik-W?s, Katarzyna; Pielichowski, Krzysztof

2013-01-01

18

Isomerization of methyl linoleate on ruthenium(III) alkoxide complex; Mathematical modeling  

SciTech Connect

The isomerization of methyl linoleate using ruthenium alkoxide complexes is described. With alcohols, such as isopropyl alcohol (IPA), 1-butanol, 1-hexanol, and 1-octanol, isomerization of double bonds to produce a conjugated system is the main reaction, with hydrogenation being the side reaction. The latter is formed via the conjugated product. Based on kinetic and infrared spectroscopic data, it is concluded that the active catalytic species is a ruthenium hydride complex formed by the decomposition of the unstable alkoxide. The reaction is mathematically modeled, and the rate parameters are obtained by fitting the simulation to experimental data. These values are compared with data obtained from reactions carried out with supported ruthenium-nickel heterogeneous catalyst.

Mukesh, D.; Narasimhan, C.S.; Ramnarayan, K.; Deshpande, V.M

1989-08-01

19

Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex.  

PubMed

The yeast histone deacetylase Rpd3 can be recruited to promoters to repress transcription initiation. Biochemical, genetic, and gene-expression analyses show that Rpd3 exists in two distinct complexes. The smaller complex, Rpd3C(S), shares Sin3 and Ume1 with Rpd3C(L) but contains the unique subunits Rco1 and Eaf3. Rpd3C(S) mutants exhibit phenotypes remarkably similar to those of Set2, a histone methyltransferase associated with elongating RNA polymerase II. Chromatin immunoprecipitation and biochemical experiments indicate that the chromodomain of Eaf3 recruits Rpd3C(S) to nucleosomes methylated by Set2 on histone H3 lysine 36, leading to deacetylation of transcribed regions. This pathway apparently acts to negatively regulate transcription because deleting the genes for Set2 or Rpd3C(S) bypasses the requirement for the positive elongation factor Bur1/Bur2. PMID:16286008

Keogh, Michael-Christopher; Kurdistani, Siavash K; Morris, Stephanie A; Ahn, Seong Hoon; Podolny, Vladimir; Collins, Sean R; Schuldiner, Maya; Chin, Kayu; Punna, Thanuja; Thompson, Natalie J; Boone, Charles; Emili, Andrew; Weissman, Jonathan S; Hughes, Timothy R; Strahl, Brian D; Grunstein, Michael; Greenblatt, Jack F; Buratowski, Stephen; Krogan, Nevan J

2005-11-18

20

Synthesis, spectra and crystal structure of 2-(?[3-(methyl?3-[(2-hydroxybenzylidene)amino]propyl? amino)propyl]imino?methyl)phenol copper(II) complex  

NASA Astrophysics Data System (ADS)

A copper(II) complex, [Cu(salenN3], [salenN3H2=2-({[3-(methyl{3-[(2-hydroxybenzylidene)amino]propyl}amino)propyl]imino}methyl)phenol] was synthesized and characterized by elemental analyses, FTIR spectra and single crystal X-ray diffraction. The complex crystallizes in the monoclinic space group P21/ c with a=6.877(3), b=14.109(6), c=20.106(8) Å, ?=92.231(14)°, V=1949.5(14) Å 3. The salen ligand loses two phenolic hydrogens being a dianion and coordinates to the copper(II) ion as a pentadentate ligand through its two O and three N atoms. The copper(II) complex is five-coordinate, lying between perfect square pyramidal and trigonal-bipyramidal extremes. Use of the structural index parameter ( ?) for five coordinate metal complexes indicated that the copper(II) complex exhibits a grater tendency toward trigonal-based-pyramidal geometry ( ?>0.5). The individual molecules in the crystal are held together by C-H⋯? and H⋯H interactions. The IR and electronic spectra of the complex were discussed in detail.

Yilmaz, Veysel T.; Degirmencioglu, Ismail; Andac, Omer; Karabocek, Serdar; Slawin, Alexandra M. Z.

2003-06-01

21

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

PubMed

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

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

2013-01-14

22

Mechanistic Study of the Oxidation of a Methyl Platinum(II) Complex with O2 in Water: PtII  

E-print Network

Mechanistic Study of the Oxidation of a Methyl Platinum(II) Complex with O2 in Water: PtII Me substrates with platinum(II) complexes. Previously, we reported a number of reactions, allowing for a highly. At pH 8, the reaction leads to a C1-symmetric monomethyl PtIV complex (dpms)PtIV Me(OH)2 (5) with high

Goddard III, William A.

23

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

24

N-terminal methylation of the core light-harvesting complex in purple photosynthetic bacteria.  

PubMed

Several core light-harvesting complexes from both sulfur and non-sulfur purple photosynthetic bacteria have been identified to be methylated at the N-terminal alpha-amino group of beta-polypeptides by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and nuclear magnetic resonance. Monomethylation has been confirmed for the N-terminal alanine residues of the beta-polypeptides from Rhodospirillum rubrum, Thermochromatium tepidum and Chromatium vinosum, but not for the beta-polypeptide from Rhodobacter sphaeroides. The modification appears to be related with the amino acid sequence and charge distribution in the N-terminal end. Some common features and possible functions are discussed. PMID:12023037

Wang, Zheng Yu; Shimonaga, Masahiro; Kobayashi, Masayuki; Nozawa, Tsunenori

2002-05-22

25

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

26

NDUFAF7 methylates arginine 85 in the NDUFS2 subunit of human complex I.  

PubMed

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 ?-N(G),N(G') 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

2013-11-15

27

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

28

Five friends of methylated chromatin target of protein-arginine-methyltransferase[prmt]-1 (chtop), a complex linking arginine methylation to desumoylation.  

PubMed

Chromatin target of Prmt1 (Chtop) is a vertebrate-specific chromatin-bound protein that plays an important role in transcriptional regulation. As its mechanism of action remains unclear, we identified Chtop-interacting proteins using a biotinylation-proteomics approach. Here we describe the identification and initial characterization of Five Friends of Methylated Chtop (5FMC). 5FMC is a nuclear complex that can only be recruited by Chtop when the latter is arginine-methylated by Prmt1. It consists of the co-activator Pelp1, the Sumo-specific protease Senp3, Wdr18, Tex10, and Las1L. Pelp1 functions as the core of 5FMC, as the other components become unstable in the absence of Pelp1. We show that recruitment of 5FMC to Zbp-89, a zinc-finger transcription factor, affects its sumoylation status and transactivation potential. Collectively, our data provide a mechanistic link between arginine methylation and (de)sumoylation in the control of transcriptional activity. PMID:22872859

Fanis, Pavlos; Gillemans, Nynke; Aghajanirefah, Ali; Pourfarzad, Farzin; Demmers, Jeroen; Esteghamat, Fatemehsadat; Vadlamudi, Ratna K; Grosveld, Frank; Philipsen, Sjaak; van Dijk, Thamar B

2012-11-01

29

Study of the complexation behaviour of gliclazide with partially methylated beta-cyclodextrin in solution and solid state.  

PubMed

The complexation of Gliclazide (GL) with a partially methylated beta-cyclodextrin was studied. Phase-solubility and (1)H NMR spectroscopy were employed to investigate the complexation behaviour in solution and to demonstrate the complexation in liquid medium with the participation of both azabicyclooctyl and tolyl moieties of GL in the inclusion process. Solid systems prepared by kneading, co-grinding and spray drying have also been checked, using DSC and HSM, for assessing the formation of the inclusion compound. Experimental evidence of the complexation between drug and cyclodextrin was reported for the co-ground and spray-dried systems. PMID:10477821

Moyano; Arias-Blanco; Ginés; Giordano

1997-11-28

30

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

31

DNA methylation reprogramming in cancer: Does it act by re-configuring the binding landscape of Polycomb repressive complexes?  

PubMed Central

DNA methylation is a repressive epigenetic mark vital for normal development. Recent studies have uncovered an unexpected role for the DNA methylome in ensuring the correct targeting of the Polycomb repressive complexes throughout the genome. Here, we discuss the implications of these findings for cancer, where DNA methylation patterns are widely reprogrammed. We speculate that cancer-associated reprogramming of the DNA methylome leads to an altered Polycomb binding landscape, influencing gene expression by multiple modes. As the Polycomb system is responsible for the regulation of genes with key roles in cell fate decisions and cell cycle regulation, DNA methylation induced Polycomb mis-targeting could directly drive carcinogenesis and disease progression. PMID:24277643

Reddington, James P; Sproul, Duncan; Meehan, Richard R

2014-01-01

32

Platinum complexes with 5-methyl-5(4-pyridyl)hydantoin and its 3-methyl derivatives: synthesis and cytotoxic activity - quantitative structure-activity relationships.  

PubMed

3,5-Dimethyl-5-(4-pyridyl)hydantoin (L) and its platinum(II) and platinum(IV) complexes with the general formula cis-[PtL(2) X(2) ]?·?n H(2) O and [PtL(2) Cl(4) ], where X?Cl, I and n?=?2-4 were synthesized. A new Pt(IV) complex with 5-methyl-5-(4-pyridyl)hydantoin (L') with the formula cis-[Pt(L')(2) Cl(2) (OH)(2) ]?·?5 H(2) O was also synthesized. The novel compounds were characterized by elemental analysis, IR, (1) H-, (13) C-, (195) Pt-NMR spectra and molar conductivity. The cytotoxic effects of these complexes were examined on three human tumor cell lines by MTT-dye reduction assay. These four new Pt(II) and Pt(IV) complexes and a set of another twelve Pt(II), Pt(IV), and Pd(II) complexes previously synthesized and tested were compiled and a QSAR model was derived in order to direct the further rational synthesis. PMID:21469169

Bakalova, Adriana; Varbanov, Hristo; Buyukliev, Rossen; Momekov, Georgi; Ivanov, Darvin; Doytchinova, Irini

2011-04-01

33

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

NASA Astrophysics Data System (ADS)

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

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

2003-01-01

34

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

PubMed

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

Sampath, Krishnan; Sathiyaraj, Subbaiyan; Jayabalakrishnan, Chinnasamy

2013-03-15

35

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

36

?-[11C]-Methyl-l-tryptophan–PET in 191 patients with tuberous sclerosis complex  

PubMed Central

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

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

2013-01-01

37

Histone H3 lysine 36 methylation antagonizes silencing in Saccharomyces cerevisiae independently of the Rpd3S histone deacetylase complex.  

PubMed

In yeast, methylation of histone H3 on lysine 36 (H3-K36) is catalyzed by the NSD1 leukemia oncoprotein homolog Set2. The histone deacetylase complex Rpd3S is recruited to chromatin via binding of the chromodomain protein Eaf3 to methylated H3-K36 to prevent erroneous transcription initiation. Here we identify a distinct function for H3-K36 methylation. We used random mutagenesis of histones H3 and H4 followed by a reporter-based screen to identify residues necessary to prevent the ectopic spread of silencing from the silent mating-type locus HMRa into flanking euchromatin. Mutations in H3-K36 or deletion of SET2 caused ectopic silencing of a heterochromatin-adjacent reporter. Transcriptional profiling revealed that telomere-proximal genes are enriched for those that display decreased expression in a set2Delta strain. Deletion of SIR4 rescued the expression defect of 26 of 37 telomere-proximal genes with reduced expression in set2Delta cells, implying that H3-K36 methylation prevents the spread of telomeric silencing. Indeed, Sir3 spreads from heterochromatin into neighboring euchromatin in set2Delta cells. Furthermore, genetic experiments demonstrated that cells lacking the Rpd3S-specific subunits Eaf3 or Rco1 did not display the anti-silencing phenotype of mutations in SET2 or H3-K36. Thus, antagonism of silencing is independent of the only known effector of this conserved histone modification. PMID:17179083

Tompa, Rachel; Madhani, Hiten D

2007-02-01

38

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.

39

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

40

Stable uranium(VI) methyl and acetylide complexes and the elucidation of an inverse trans influence ligand series.  

PubMed

Thermally stable uranium(VI)-methyl and -acetylide complexes: U(VI)OR[N(SiMe3)2]3 R = -CH3, -C?CPh were prepared in which coordination of the hydrocarbyl group is directed trans to the uranium-oxo multiple bond. The stability of the uranium-carbon bond is attributed to an inverse trans influence. The hydrocarbyl complexes show greater ITI stabilization than that of structurally related U(VI)OX[N(SiMe3)2]3 (X = F(-), Cl(-), Br(-)) complexes, demonstrated both experimentally and computationally. An inverse trans influence ligand series is presented, developed from a union of theoretical and experimental results and based on correlations between the extent of cis-destabilization, the complexes stabilities toward electrochemical reduction, the thermodynamic driving forces for U?O bond formation, and the calculated destabilization of axial ?* and ?* antibonding interactions. PMID:23924364

Lewis, Andrew J; Carroll, Patrick J; Schelter, Eric J

2013-09-01

41

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

42

Iridium(i) PNP complexes in the sp(3) 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

2014-12-23

43

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

NASA Astrophysics Data System (ADS)

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

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

2008-04-01

44

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

PubMed

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

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

2012-05-01

45

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

PubMed

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

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

2014-06-14

46

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

NASA Astrophysics Data System (ADS)

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

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

2012-02-01

47

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

EPA Science Inventory

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

48

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

49

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

PubMed

N(6)A 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 N(6)-methylated adenosine reader domain and report its solution structure in complex with a N(6)-methylated RNA. The structure reveals a binding preference for NGANNN RNA hexamer and a deep hydrophobic cleft for m(6)A recognition. These findings establish a molecular function for YTH domains as m(6)A reader domains and should guide further studies into the biological functions of YTH-containing proteins in m(6)A recognition. PMID:25389274

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

2014-12-16

50

Preparation of silver\\/poly(methyl methacrylate) nanocomposites by in-situ radical polymerization using silver carbamate complex  

Microsoft Academic Search

Silver\\/poly(methyl methacrylate) (PMMA) nanocomposites were synthesized in situ by thermally heating a solution of a silver n-propylcarbamate (Ag-PCB) complex and PMMA\\/MMA (1\\/9) in the presence of a radical initiator. Polymerization of the MMA monomers\\u000a and reduction of the silver ions occurred simultaneously, leading to the formation of Ag\\/PMMA nanocomposites. The resulting\\u000a Ag\\/PMMA nanocomposites were characterized by infrared spectroscopy (IR), X-ray

Heon-Su Park; Hyung-Seok Park; Myoung-Seon Gong

2010-01-01

51

Platinum(IV) complexes with some derivatives of 5-methyl-5-(4-pyridyl) hydantoin. Synthesis, study and comparative pharmacological investigation.  

PubMed

3 Pt(IV) complexes with 3-ethyl-5-methyl-5-(4-pyridyl)hydantoin (4), 3-propyl-5-methyl-5-(4-pyridyl)hydantoin (5) and 3-benzyl-5-methyl-5-(4-pyridyl)hydantoin (6) with general formulae cis-[Pt(L)2Cl4] were synthesized. The novel compounds were characterized by elemental analysis, IR, 1H, 13C, NMR spectra in solid state and in solution. The studies showed that the ligands coordinate to the platinum ions in a monodentate manner through the nitrogen atom from the pyridine ring. The cytotoxic activity in vitro of newly synthesized complexes as well as their previously prepared analogous of Pt(IV) with other derivatives like 3-amino-5-methyl-5-(4-pyridyl)hydantoin (1), 5-methyl-5-(4-pyridyl)hydantoin (2), 3,5-dimethyl-5-(4-pyridyl)hydantoin (3) was screened against a panel of human tumor cell lines. The tested compounds displayed cytotoxic activity which was invariably superior with the Pt(IV) complex with 3-benzyl-5-methyl-5-(4-pyridyl)hydantoin (6) causing 50% inhibition of cellular viability at micromolar concentration, though the activity of the other studied Pt(IV) complexes proved to greatly decrease in the order 5-4-3-2-1. PMID:23677699

Bakalova, A; Buyukliev, R; Ivanova, Z; Momekov, G; Ivanov, D

2013-08-01

52

Structure and tunneling splitting spectra of methyl groups of tetramethylpyrazine in complexes with chloranilic and bromanilic acids.  

PubMed

The crystal and molecular structure of the 2,3,5,6-tetramethylpyrazine (TMP) complex with 2,5-dibromo-3,6-dihydroxy-p-quinone (bromanilic acid, BRA) has been studied and the results are compared with TMP CLA (2,5-dichloro-3,6-dihydroxy-p-quinone (chloranilic acid, CLA) complex. The X-ray structure of TMP BRA complex indicates the formation of dimeric units, in which two BRA(-) anions are connected by two O-H···O (2.646(2) Å) hydrogen bonds, whereas the cations and anions are joined together by strong N(+)-H···O(-) (2.657(2) Å) hydrogen bonds. The results are analyzed in terms of both the methyl group surroundings and the C-H···O and N(+)-H···O(-) (or N···H-O) bridge formations. Both effects, the strength of the N(+)-H···O(-) hydrogen bonds and steric hindrance for the rotations, are responsible for the CH3 group dynamics. For the TMP CLA and TMP BRA complexes, the inelastic neutron backscattering spectra were also investigated. In the case of TMP CLA, four tunneling signals have been observed in the energy range ±30 ?eV, which indicates four inequivalent methyl groups in the crystal structure at the lowest temperature. No tunneling splitting is observed in the case of the TMP BRA complex, most probably due to the overlapping with the elastic peak. The tunneling results are consistent with the (1)H NMR spin-lattice relaxation time investigations in a wide temperature range, which also point to the CH3 group tunneling effect in the case of TMP CLA. PMID:25099129

Piecha-Bisiorek, A; Bator, G; Sawka-Dobrowolska, W; Sobczyk, L; Rok, M; Medycki, W; Schneider, G J

2014-08-28

53

Stable dispersions of poly(ethylene glycol) methyl ether-magnetite complexes in water  

Microsoft Academic Search

We herein describe a facile synthesis of superparamagnetic magnetite ferrofluids having long-term stability in aqueous dispersions. A single-step thermal decomposition reaction of iron (III) acetylacetonate (Fe(acac)3) was carried out in the presence of poly(ethylene glycol) methyl ether (mPEG) to serve both as a reducing agent and reaction solvent. The role of number average molecular weight () of mPEG (350 and

Thapanapong Theppaleak; Uthai Wichai; Boonjira Boontha; Gamolwan Tumcharern; Metha Rutnakornpituk

2011-01-01

54

Differential back-invasion of a single complex dendrite of an abducens motoneuron by N-methyl- d-aspartate-induced oscillations: a simulation study  

Microsoft Academic Search

Intracellular recording of abducens motoneurons in vivo has shown that ionophoretic applications of N-methyl-d-aspartate produced long-lasting membrane potential oscillations including slow depolarization plateau with a burst of fast action potentials. This complex N-methyl-d-aspartate pattern was reproduced in the model of abducens motoneuron in vivo identified, intracellularly stained with horseradish peroxidase and reconstructed at high spatial resolution. The excitable soma of

S. M Korogod; I. L Kopysova; H Bras; P Gogan; S Tyc-Dumont

1996-01-01

55

Proteomic Analysis of ?-Amino-3-hydroxy-5-methyl-4-isoxazole Propionate Receptor Complexes*  

PubMed Central

The AMPA receptor (AMPA-R) is a major excitatory neurotransmitter receptor in the brain. Identifying and characterizing the neuronal proteins interacting with AMPA-Rs have provided important information about the molecular mechanisms underlying synaptic transmission and plasticity. In this study, to identify more AMPA-R interactors in vivo, we performed proteomic analyses of AMPA-R complexes from the brain. AMPA-R complexes were isolated from the brain through various combinations of biochemical techniques for solubilization, enrichment, and immunoprecipitation. Mass spectrometry analyses of these isolated complexes identified several novel components of the AMPA-R complexes as well as some previously identified components. The identification of these novel components helps to further define the complex mechanisms involved in the regulation of AMPA receptor function and synaptic plasticity. PMID:22753414

Kang, Myoung-Goo; Nuriya, Mutsuo; Guo, Yurong; Martindale, Kevin D.; Lee, Daniel Z.; Huganir, Richard L.

2012-01-01

56

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

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

57

Nickel(II) complexes with methyl(2-pyridyl)ketone oxime: Synthesis, crystal structures and DFT calculations  

NASA Astrophysics Data System (ADS)

The synthesis and structural characterization of the three novel nickel(II) complexes [Ni(OOCPh)2(mpkoH)2] (1), [Ni(NO3)2(mpkoH)2] (2) and [Ni(mpkoH)3](NO3)2?½H2O (3?½H2O), with mpkoH = methyl(2-pyridyl)ketone oxime is reported. Geometry optimization and population analyses were performed by means of DFT calculations for the previously mentioned compounds as well as for [NiCl2(mpkoH)2] (4). Electronic UV-vis spectra were also simulated in the TD-DFT framework to assign the origin of the absorption bands and in doing so, to have a clear picture of the absorptive features of the coordination compounds under investigation.

Martínez, Lorena; Gancheff, Jorge S.; Hahn, F. Ekkehardt; Burrow, Robert A.; González, Ricardo; Kremer, Carlos; Chiozzone, Raúl

2013-03-01

58

Nickel(II) complexes with methyl(2-pyridyl)ketone oxime: synthesis, crystal structures and DFT calculations.  

PubMed

The synthesis and structural characterization of the three novel nickel(II) complexes [Ni(OOCPh)(2)(mpkoH)(2)] (1), [Ni(NO(3))(2)(mpkoH)(2)] (2) and [Ni(mpkoH)(3)](NO(3))(2)·½H(2)O (3·½H(2)O), with mpkoH=methyl(2-pyridyl)ketone oxime is reported. Geometry optimization and population analyses were performed by means of DFT calculations for the previously mentioned compounds as well as for [NiCl(2)(mpkoH)(2)] (4). Electronic UV-vis spectra were also simulated in the TD-DFT framework to assign the origin of the absorption bands and in doing so, to have a clear picture of the absorptive features of the coordination compounds under investigation. PMID:23337748

Martínez, Lorena; Gancheff, Jorge S; Hahn, F Ekkehardt; Burrow, Robert A; González, Ricardo; Kremer, Carlos; Chiozzone, Raúl

2013-03-15

59

Lanthanide complexes of 3-acetyl-4-hydroxy-6-methyl-2H-pyran-2-one  

SciTech Connect

The title ligand (H(Dh), dehydroacetic acid) reacts with lanthanide(III) acetates in anhydrous methanol to form complexes of formula (M(Dh){sub 3}(MeOH)). When hydrated lanthanide acetates are used, hydrated compounds such as (Ce(Dh){sub 3}(H{sub 2}O)) or (Eu(Dh){sub 3}(H{sub 2}O)).H{sub 2}O are obtained. The reaction of lanthanum triacetate with H(Dh) yields the mixed complex (La(Dh){sub 2}(O{sub 2}CMe)), formation of the 1:3 complex also being unfavored in the presence of a large ligand excess. The complexes have been characterized by infrared and NMR ({sup 1}H and {sup 13}C) spectroscopy and by thermogravimetric measurements.

Sitran, S; Fregona, D. (Istituto di Chimica e Tecnologia dei Radioelementi del C.N.R., Padova (Italy)); Faraglia, G. (Dipartimento di Chimica Inorganica, Metallorganica ed Analitica dell'Universita, Padova (Italy))

1990-01-01

60

Spectroscopic characterization of copper(II) complexes of indoxyl N(4)-methyl thiosemicarbazone  

NASA Astrophysics Data System (ADS)

New copper(II) complexes of indoxyl thiosemicarbazone (ITSC) of general composition CuL 2X 2 (where L: ITSC; X: Cl -, NO 3-, ClO 4-, NCS -) have been synthesized and characterized by elemental analysis, molar conductance, magnetic susceptibility measurements and spectral (electronic, IR, EPR, 1H NMR , Mass) studies. Cyclic voltammetry measurements show quasi-reversible Cu 2+/Cu 1+ couple. Various physico-chemical techniques suggest a tetragonal structure for these copper(II) complexes.

Chandra, Sulekh; Kumar, Umendra

2004-10-01

61

(Eta2-alkyne)methyl(dioxo)rhenium complexes as aldehyde-olefination catalysts.  

PubMed

Complexes CH3ReO2L (L = 2-butyne, 3-hexyne, diphenylacetylene) are catalysts for the olefination of aldehydes, using 4-nitrobenzaldehyde (4-nba) as the standard aldehyde and ethyldiazoacetate (eda) as the diazo compound. Spectroscopic studies including in situ 31P, 17O, 13C, and 1H NMR spectroscopy are used to elucidate the mechanism and the nature of the active species. One of the key steps of the mechanism is the rapid formation of phosphazine at the beginning of the cycle and its subsequent reaction with the metal dioxide complex to form the catalytically active carbene species. PMID:12603128

Santos, Ana M; Romão, Carlos C; Kühn, Fritz E

2003-03-01

62

Structural basis for the recognition of methylated histone H3K36 by the Eaf3 subunit of histone deacetylase complex Rpd3S.  

PubMed

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

2008-11-12

63

Critical role of a methyl group on the ?-lactone ring of annonaceous acetogenins in the potent inhibition of mitochondrial complex I.  

PubMed

C34-epi and C34-epi-C35-trifluoro analogues of solamin, a mono-THF annonaceous acetogenin, were synthesized. Their inhibitory activity, along with previously synthesized analogues (C35-fluoro, C35-difluoro, and C35-trifluorosolamins), against bovine mitochondrial NADH-ubiquinone oxidoreductase (complex I) was determined. The present study revealed that the methyl group on the ?-lactone moiety is critical to the potent inhibition of complex I by natural acetogenins. PMID:23375227

Kojima, Naoto; Abe, Masato; Suga, Yuki; Ohtsuki, Kazufumi; Tanaka, Tetsuaki; Iwasaki, Hiroki; Yamashita, Masayuki; Miyoshi, Hideto

2013-03-01

64

Methyl Groups as Probes for Proteins and Complexes in In-Cell NMR Experiments  

E-print Network

also minimizing signals of the cellular environment. Experimental Section Suspensions of bacteria-mail: vdoetsch@em.uni-frankfurt.de Abstract: Studying protein components of large intracellular complexes by in for observing proteins in the bacterial cytoplasm, and we demonstrated that bacteria grown in uniformly 15N

Craik, Charles S.

65

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

66

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

67

1-Methyl-4-phenylpyridinium-induced cell death via autophagy through a Bcl-2/Beclin 1 complex-dependent pathway.  

PubMed

Several lines of evidence suggest that the mechanism underlying drug-induced neuronal apoptosis is initiated by the increased production of reactive oxygen species (ROS). 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), a neurotoxin, has been shown to initiate an apoptotic cascade by increasing ROS in the dopaminergic neurons of the substantia nigra, leading to the morphological and physiological features associated with Parkinson's disease. Recently, it has been reported that autophagy, a type of programmed cell death independent of the apoptotic cascade, also plays a role in neuronal damage. Although autophagy is negatively regulated by the mammalian target of rapamycin receptor (mTOR), there is some evidence showing a novel function for the anti-apoptotic protein Bcl-2. Bcl-2 is proposed to play a role in negatively regulating autophagy by blocking an essential protein in the signaling pathway, Beclin 1. Nevertheless, it is unclear whether autophagy is also correlated with apoptotic signaling in 1-methyl-4-phenylpyridinium (MPP(+)) toxicity. Therefore, we hypothesized that the MPP(+) toxicity generally associated with initiating the apoptotic signaling cascade also increases an autophagic phenotype in neuronal cells. Using the SK-N-SH dopaminergic cell lines, we demonstrate that MPP(+) increases the expression of microtubule-associated protein light chain 3 (LC3-II), an autophagosome membrane marker and the mTOR signaling pathway, and Beclin 1 while decreasing the Bcl-2 levels. Moreover, these expressions correlate with a decreased binding ratio between Bcl-2 and Beclin 1, in effect limiting the regulation of the downstream autophagic markers, such as LC3-II. Our results indicate that MPP(+) can induce autophagy in SK-N-SH cells by decreasing the Bcl-2/Beclin 1 complex. PMID:24326530

Nopparat, Chutikorn; Porter, James E; Ebadi, Manuchair; Govitrapong, Piyarat

2014-02-01

68

Hydroxynaphthoquinone Metal Complexes as Antitumor Agents X: Synthesis, Structure, Spectroscopy and In Vitro Antitumor Activity of 3-Methyl-Phenylazo Lawsone Derivatives and Their Metal Complexes Against Human Breast Cancer Cell Line MCF-7  

PubMed Central

The C-3 substituted phenylazo derivatives of lawsone (2-hydroxy-l,4 p-naphthoquinone, III) were synthesized and characterized. The X-ray crystal structure was determined for the ligand 3-(3?-methyl phenylazo) lawsone. The copper complexes of these derivatives were found to possess 1:2 metal stoichiometry and square planar geometries with intermolecular stackings, resulting in antiferromagnetic exchange interactions. The in vitro activity of all the synthesized compounds was examined against human breast cancer cell-line, MCF-7, which revealed enhanced activities for the metal complexes, the highest activity being observed for the copper compound of 3-(3?-methyl phenylazo) lawsone. PMID:18475934

Gokhale, Nikhil; Newton, Chris; Pritchard, Robin

2000-01-01

69

Methylation analysis of complex carbohydrates in small amounts: capillary gas chromatography-mass fragmentography of methylalditol acetates obtained from N-glycosidically linked glycoprotein oligosaccharides.  

PubMed

A version of the methylation analysis of complex carbohydrates by gas chromatography-mass spectrometry of the methylalditol acetates (H. Björndal, C. G. Hellerquist, B. Lindberg, and S. Svensson (1970) Angew. Chem. 82, 643-674) is described. With this version 100- to 500-pmol samples of N-glycosidically linked glycoprotein oligosaccharides may be analyzed. The method is based on the use of capillary columns which allow the separation of all partially methylated alditol acetates potentially obtained from this group of oligosaccharides and on their selective and sensitive detection by mass fragmentography after chemical ionization with ammonia. PMID:6638480

Geyer, R; Geyer, H; Kühnhardt, S; Mink, W; Stirm, S

1983-08-01

70

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

71

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

PubMed

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

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

2012-11-20

72

The USP7/Dnmt1 complex stimulates the DNA methylation activity of Dnmt1 and regulates the stability of UHRF1  

PubMed Central

Aberrant DNA methylation is often associated with cancer and the formation of tumors; however, the underlying mechanisms, in particular the recruitment and regulation of DNA methyltransferases remain largely unknown. In this study, we identified USP7 as an interaction partner of Dnmt1 and UHRF1 in vivo. Dnmt1 and USP7 formed a soluble dimer complex that associated with UHRF1 as a trimeric complex on chromatin. Complex interactions were mediated by the C-terminal domain of USP7 with the TS-domain of Dnmt1, whereas the TRAF-domain of USP7 bound to the SRA-domain of UHRF1. USP7 was capable of targeting UHRF1 for deubiquitination and affects UHRF1 protein stability in vivo. Furthermore, Dnmt1, UHRF1 and USP7 co-localized on silenced, methylated genes in vivo. Strikingly, when analyzing the impact of UHRF1 and USP7 on Dnmt1-dependent DNA methylation, we found that USP7 stimulated both the maintenance and de novo DNA methylation activity of Dnmt1 in vitro. Therefore, we propose a dual role of USP7, regulating the protein turnover of UHRF1 and stimulating the enzymatic activity of Dnmt1 in vitro and in vivo. PMID:21745816

Felle, Max; Joppien, Saskia; Németh, Attila; Diermeier, Sarah; Thalhammer, Verena; Dobner, Thomas; Kremmer, Elisabeth; Kappler, Roland; Längst, Gernot

2011-01-01

73

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

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

74

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

NASA Astrophysics Data System (ADS)

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

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

1994-09-01

75

(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

76

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

77

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

PubMed

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

Botsi, A; Yannakopoulou, K; Hadjoudis, E

1993-03-17

78

Neonatal DNA methylation profile in human twins is specified by a complex interplay between intrauterine environmental and genetic factors, subject to tissue-specific influence  

PubMed Central

Comparison between groups of monozygotic (MZ) and dizygotic (DZ) twins enables an estimation of the relative contribution of genetic and shared and nonshared environmental factors to phenotypic variability. Using DNA methylation profiling of ?20,000 CpG sites as a phenotype, we have examined discordance levels in three neonatal tissues from 22 MZ and 12 DZ twin pairs. MZ twins exhibit a wide range of within-pair differences at birth, but show discordance levels generally lower than DZ pairs. Within-pair methylation discordance was lowest in CpG islands in all twins and increased as a function of distance from islands. Variance component decomposition analysis of DNA methylation in MZ and DZ pairs revealed a low mean heritability across all tissues, although a wide range of heritabilities was detected for specific genomic CpG sites. The largest component of variation was attributed to the combined effects of nonshared intrauterine environment and stochastic factors. Regression analysis of methylation on birth weight revealed a general association between methylation of genes involved in metabolism and biosynthesis, providing further support for epigenetic change in the previously described link between low birth weight and increasing risk for cardiovascular, metabolic, and other complex diseases. Finally, comparison of our data with that of several older twins revealed little evidence for genome-wide epigenetic drift with increasing age. This is the first study to analyze DNA methylation on a genome scale in twins at birth, further highlighting the importance of the intrauterine environment on shaping the neonatal epigenome. PMID:22800725

Gordon, Lavinia; Joo, Jihoon E.; Powell, Joseph E.; Ollikainen, Miina; Novakovic, Boris; Li, Xin; Andronikos, Roberta; Cruickshank, Mark N.; Conneely, Karen N.; Smith, Alicia K.; Alisch, Reid S.; Morley, Ruth; Visscher, Peter M.; Craig, Jeffrey M.; Saffery, Richard

2012-01-01

79

Neonatal DNA methylation profile in human twins is specified by a complex interplay between intrauterine environmental and genetic factors, subject to tissue-specific influence.  

PubMed

Comparison between groups of monozygotic (MZ) and dizygotic (DZ) twins enables an estimation of the relative contribution of genetic and shared and nonshared environmental factors to phenotypic variability. Using DNA methylation profiling of ?20,000 CpG sites as a phenotype, we have examined discordance levels in three neonatal tissues from 22 MZ and 12 DZ twin pairs. MZ twins exhibit a wide range of within-pair differences at birth, but show discordance levels generally lower than DZ pairs. Within-pair methylation discordance was lowest in CpG islands in all twins and increased as a function of distance from islands. Variance component decomposition analysis of DNA methylation in MZ and DZ pairs revealed a low mean heritability across all tissues, although a wide range of heritabilities was detected for specific genomic CpG sites. The largest component of variation was attributed to the combined effects of nonshared intrauterine environment and stochastic factors. Regression analysis of methylation on birth weight revealed a general association between methylation of genes involved in metabolism and biosynthesis, providing further support for epigenetic change in the previously described link between low birth weight and increasing risk for cardiovascular, metabolic, and other complex diseases. Finally, comparison of our data with that of several older twins revealed little evidence for genome-wide epigenetic drift with increasing age. This is the first study to analyze DNA methylation on a genome scale in twins at birth, further highlighting the importance of the intrauterine environment on shaping the neonatal epigenome. PMID:22800725

Gordon, Lavinia; Joo, Jihoon E; Powell, Joseph E; Ollikainen, Miina; Novakovic, Boris; Li, Xin; Andronikos, Roberta; Cruickshank, Mark N; Conneely, Karen N; Smith, Alicia K; Alisch, Reid S; Morley, Ruth; Visscher, Peter M; Craig, Jeffrey M; Saffery, Richard

2012-08-01

80

Modelling neurotransmitter functions: a laser spectroscopic study of (1S,2S)-N-methyl pseudoephedrine and its complexes with achiral and chiral molecules.  

PubMed

Wavelength and mass resolved resonance-enhanced two photon ionization (R2PI) excitation spectra of (1S,2S)-N-methyl pseudoephedrine (MPE) and its complexes with several achiral and chiral solvent molecules, including water (W), methyl (R)-lactate (L(R)), methyl (S)-lactate (L(S)), (R)-2-butanol (B(R)), and (S)-2-butanol (B(S)), have been recorded after a supersonic molecular beam expansion and examined in the light of ab initio calculations. The spectral patterns of the selected complexes have been interpreted in terms of the specific hydrogen-bond interactions operating in the diastereomeric complexes, whose nature in turn depends on the structure and the configuration of the solvent molecule. The obtained results confirm the view that a representative neurotransmitter molecule, like MPE, "communicates" with the enantiomers of a chiral substrate through different, specific interactions. These findings can be regarded as a further contribution to modelling neurotransmitter functions in biological systems. PMID:16688345

Giardini Guidoni, A; Paladini, A; Piccirillo, S; Rondino, F; Satta, M; Speranza, M

2006-05-21

81

Synthesis, crystal structure, DNA binding and photo-induced DNA cleavage activity of ( S-methyl- l-cysteine)copper(II) complexes of heterocyclic bases  

Microsoft Academic Search

Ternary S-methyl-l-cysteine (SMe-l-cys) copper(II) complexes [Cu(SMe-l-cys)(B)(H2O)](X) (1–4), where the heterocyclic base B is 2,2?-bipyridine (bpy, 1), 1,10-phenanthroline (phen, 2), dipyridoquinoxaline (dpq, 3) and dipyridophenazine (dppz, 4), and X is ClO4- (1–3) or NO3- (4), are prepared and their DNA binding and cleavage properties studied. Complexes 2 and 4 are structurally characterized by X-ray crystallography. Both the crystal structures show distorted

Ashis K. Patra; Munirathinam Nethaji; Akhil R. Chakravarty

2007-01-01

82

Synthesis and Crystal Structure of a Dibridged Dinuclear Cadmium(II) Complex with Schiff Base 2-[(2-Dimethylaminoethylimino)methyl]-6-methoxyphenol  

Microsoft Academic Search

A tetradentate Schiff base compound 2-[(2-dimethylaminoethylimino)methyl]-6-methoxyphenol (HL) reacts with cadmium nitrate and ammonium thiocyanate in a methanol solution to give a dinuclear complex [Cd2L2(?1,1-NCS)(NCS)(OH2)]. The complex was characterized by physico-chemical and spectroscopic methods. X-ray crystallography indicates that each Cd(II) atom is in a distorted octahedral coordination. The two metal atoms are bridged by one phenolate O and one end-on thiocyanate

San-Jun Peng; Hai-Yun Hou; Qiong Wang; Tao Yang; Cong-Shan Zhou

2008-01-01

83

The Drosophila methyl-DNA binding protein MBD2/3 interacts with the NuRD complex via p55 and MI-2  

PubMed Central

Background Methyl-DNA binding proteins help to translate epigenetic information encoded by DNA methylation into covalent histone modifications. MBD2/3 is the only candidate gene in the Drosophila genome with extended homologies to mammalian MBD2 and MBD3 proteins, which represent a co-repressor and an integral component of the Nucleosome Remodelling and Deacetylase (NuRD) complex, respectively. An association of Drosophila MBD2/3 with the Drosophila NuRD complex has been suggested previously. We have now analyzed the molecular interactions between MBD2/3 and the NuRD complex in greater detail. Results The two MBD2/3 isoforms precisely cofractionated with NuRD proteins during gel filtration of extracts derived from early and late embryos. In addition, we demonstrate that MBD2/3 forms multimers, and engages in specific interactions with the p55 and MI-2 subunits of the Drosophila NuRD complex. Conclusion Our data provide novel insights into the association between Drosophila MBD2/3 and NuRD proteins. Additionally, this work provides a first analysis of the architecture of the Drosophila NuRD complex. PMID:15516265

Marhold, Joachim; Brehm, Alexander; Kramer, Katja

2004-01-01

84

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

NASA Astrophysics Data System (ADS)

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

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

2013-10-01

85

Synthesis and characterization of 3-methyl-5-oxo-N,1-diphenyl-4,5-dihydro-1-H-pyrazole-4-carbothioamide and its metal complexes.  

PubMed

The molecular parameters have been calculated to confirm the geometry of 3-methyl-5-oxo-N,1-diphenyl-4,5-dihydro-1-H-pyrazole-4-carbothioamide, HL. The compound is introduced as a new chelating agent for complexation with Cr(III), Fe(III), Co(II), Ni(II) and Cu(II) ions. The isolated chelates were characterized by partial elemental analyses, magnetic moments, spectra (IR, UV-vis, ESR; (1)H NMR) and thermal studies. The protonation constant of HL (5.04) and the stepwise stability constants of its Co(II), Cu(II), Cr(III) and Fe(III) complexes were calculated. The ligand coordinates as a monobasic bidentate through hydroxo and thiol groups in all complexes except Cr(III) which acts as a monobasic monodentate through the enolized carbonyl oxygen. Cr(III) and Fe(III) complexes measured normal magnetic moments; Cu(II) and Co(II) measured subnormal while Ni(II) complex is diamagnetic. The data confirm a high spin and low spin octahedral structures for the Fe(III) and Co(II) complexes. The ESR spectrum of the Cu(II) complex support the binuclear structure. The molecular parameters have also been calculated for the Cu(II) and Fe(III) complexes. The thermal decomposition stages of the complexes confirm the MS to be the residual part. Also, the thermodynamic and kinetic parameters were calculated for some decomposition steps. PMID:19647478

El-Shazly, R M

2009-09-15

86

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

87

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

88

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

PubMed

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

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

2014-03-21

89

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

PubMed

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; Decottignies, Anabelle

2014-10-01

90

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

91

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

NASA Astrophysics Data System (ADS)

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

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

2012-04-01

92

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

93

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

PubMed

[structure: see text] The whole set (five compounds) of partially O-methylated products of p-tert-butyl[3.1.3.1]homooxacalixarene, currently named p-tert-butyltetrahomodioxacalix[4]arene, have been prepared. Their structure has been investigated in solution through NMR techniques and in the solid state by single-crystal X-ray diffraction. A systematic investigation, extended to the parent tetraphenol and to the tetramethyl ether derivative, has been carried out on the complexation of tetramethylammonium, acetylcholine, N-methylpyridinium, and tetraethylammonium picrate in CDCl3. The observed trends in the binding and in the selectivity of the strictly related hosts could be analyzed on the basis of the varying importance of intramolecular hydrogen bonding and its effects on the conformation of the free and of the complexed ligands. On increasing the number of methyl ether functions, the cone conformation appears to be relatively less stable but deeper, so small organic cations can be more effectively encircled. PMID:16408957

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

2006-01-20

94

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

NASA Astrophysics Data System (ADS)

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

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

2010-06-01

95

Conductivity, Mechanical and Thermal Studies on Poly(methyl methacrylate)-Based Polymer Electrolytes Complexed with Lithium Tetraborate and Propylene Carbonate  

NASA Astrophysics Data System (ADS)

A series of different composition ratio of polymer electrolytes based on poly(methyl methacrylate) (PMMA) as host polymer, lithium tetraborate (Li2B4O7) as salt, and propylene carbonate (PC) as plasticizer is produced by solution casting method. Fourier transform infrared (FTIR) spectroscopy studies are used to confirm the formation of polymer electrolyte complex. PMMA: Li2B4O7: PC (52.5:22.5:25.0 wt.%) is obtained as the highest conducting polymer electrolyte with a conductivity of 5.14 × 10-6 S/cm at room temperature (23 °C). The temperature-dependent conductivity of the polymer films shows Arrhenius-like behavior which reveals that the charge carriers move in a liquid-like environment. The addition of PC decreases the Young's modulus and stress at peak values of the complexes. Thermogravimetric analysis (TGA) is employed to study the thermal stability of the electrolytes.

Ramesh, S.; Bing, Khoo Ne

2012-01-01

96

Preparation of a nitrate-coordinated copper(II) complex of 2-(pyrazol-3-yl)-6-(pyrazolate)pyridine as an efficient catalyst for methyl methacrylate polymerization.  

PubMed

Treatment of [CuCl(2)(bppyH(2))] (1, bppyH(2) = 2,6-di(1H-pyrazol-3-yl)pyridine) with 2 equiv. of AgNO(3) in DMF gave rise to a binuclear Cu(II) complex [Cu(2)(bppyH)(2)(NO(3))(2)] (bppyH = 2-(pyrazol-3-yl)-6-(pyrazolate)pyridine) (2). Complex 2 was characterized by elemental analysis, IR and single crystal X-ray diffraction. Complex 2 has a dimeric structure in which the two Cu(ii) centers are bridged by a couple of the in situ-generated bppyH(-) anions. Each Cu(II) center is further coordinated by one O atom of a NO(3)(-) anion and three N atoms of one bppyH(-) anion. Complex 2 exhibited a higher catalytic activity in the polymerization of methyl methacrylate (MMA) than the precursor complex 1. Even though the ratio of catalyst to MMA was raised up to 1 : 1500, the PDI for 2 (reaction time was fixed at 4 h) is 1.63 and the conversion is up to 72%. The effects of solvent, reaction temperature and the ratio of MMA to catalyst were also investigated. PMID:22301825

Miao, Li-Li; Li, Hong-Xi; Yu, Miao; Zhao, Wei; Gong, Wei-Jie; Gao, Jun; Ren, Zhi-Gang; Wang, Hui-Fang; Lang, Jian-Ping

2012-03-28

97

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

98

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

99

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

100

Synthesis, characterization and biological activity of Pt(II) and Pt(IV) complexes with 5-methyl-5(4-pyridyl)-2,4-imidazolidenedione.  

PubMed

New platinum(II) and platinum(IV) complexes with 5-methyl-5(4-pyridyl)-2,4-imidazolidenedione and various halogen ions with general formula [PtL(2)X(2)] and [PtL(2)Cl(4)], where L is the organic ligand and X is Cl(-), Br(-), J(-), were synthesized. The molecular formulae of all the complexes were confirmed by elemental analysis, IR, (1)H, (13)C NMR spectral analyses and molar conductivity. The cytotoxic effects of these complexes were examined on some human tumor cell lines. The newly synthesized cis-[PtL(2)Cl(2)] exerted cytotoxic activity against SKW-3, MCF-7, EJ, U-266 tumor cell lines, while cis-[PtL(2)Br(2)], trans-[PtL(2)I(2)] were less active. The higher oxidation state complex cis-[PtL(2)Cl(4)] was inactive in all cell lines but in SKW-3 some augmentation of the cytotoxicity was seen after co-administration of ascorbic acid but not when treated in combination with reduced glutathione or N-acetylcysteine. A DNA-fragmentation analysis revealed that the cytotoxicity of the dichloro analogue, characterized with superior activity compared to the other complexes, is mediated by induction of apoptotic cell death. PMID:17707952

Bakalova, Adriana; Varbanov, Hristo; Buyukliev, Rossen; Momekov, Georgi; Ferdinandov, Dilyan; Konstantinov, Spiro; Ivanov, Darvin

2008-05-01

101

Noncoding RNAs and DNA Methylation in Plants  

PubMed Central

Cytosine DNA methylation is an epigenetic modification in eukaryotes that maintains genome integrity and regulates gene expression. The DNA methylation patterns in plants are more complex than those in animals, and plants and animals have common as well as distinct pathways in regulating DNA methylation. Recent studies involving genetic, molecular, biochemical and genomic approaches have greatly expanded our knowledge of DNA methylation in plants. The roles of many proteins as well as non-coding RNAs in DNA methylation have been uncovered.

Zhao, Yuanyuan; Chen, Xuemei

2015-01-01

102

Synthesis, spectral characterisation of 2-(5-methyl-1H-benzimidazol-2-yl)-4-bromo/nitro-phenols and their complexes with zinc(II) ion, and solvent effect on complexation.  

PubMed

2-(5-Methyl-1H-benzimidazol-2-yl)-4-bromo/nitro-phenols (HLBr and HLNO2) and their Zn(II) complexes with ZnX2 (X = Cl, I, NO3) were synthesized and characterized by elemental analysis, molar conductivity, IR, 1H and 13C NMR spectra. The OH proton appears near the NH protons in the 1H NMR spectra of the ligands because of the strong intramolecular hydrogen bonding between the OH hydrogen and the C=N nitrogen atoms. The complexation is investigated in ethanol and isopropanol and it is observed that isopropanol is a better solvent than ethanol for the complex forming. HLBr gives harder complexation reaction with Zn(II) according to HLNO2 because of the stronger intramolecular hydrogen bonding in HLBr, and the both ligands react easier with Zn(NO3)2 than ZnCl2 and ZnI2. The Zn(II) complexes of HLBr have 1:1 M:L ratio and ionic character, however, HLNO2 give a non-ionic complex that has 1:2 M:L ratio. In the complexes the phenolic hydrogen is eliminated and a chelate structure is formed. PMID:15978864

Tavman, Aydin

2006-02-01

103

Zinc complexes supported by methyl salicylato ligands: synthesis, structure, and application in ring-opening polymerization of L-lactide.  

PubMed

Two novel zinc alkoxides supported by chelating methyl salicylato (MesalO; MesalOH = methyl salicylate) ligands were successfully synthesized and characterized. Reaction of MesalOH with ZnEt2 (2:1) gives a tetranuclear cluster [Zn(MesalO)2]4 (1), which by addition of pyridine is transformed to the mononuclear compound [Zn(MesalO)2(py)2] (2). Compounds 1 and 2 were characterized by elemental analysis, NMR, IR, and single crystal X-ray diffraction. The catalytic activity of both compounds was tested for the ring-opening polymerization (ROP) of L-lactide (L-LA). It was found that compounds 1 and 2 are efficient initiators of the ROP of L-LA, yielding cyclic PLLA with weight average molecular weights up to 100 kDa for 2. The treatment of 2 with 1 equiv. of BnOH in toluene afforded a dimeric compound [Zn(OBn)(MesalO)(py)]2 (3). The addition of L-LA to a combination of 1 and 4 equiv. of BnOH in THF or 2 and 1 equiv. of BnOH in toluene led to the rapid and efficient generation of PLLA with end-capped BnO groups. PMID:23811782

Petrus, Rafa?; Sobota, Piotr

2013-10-14

104

Biochemical and Structural Insights into the Mechanisms of SARS Coronavirus RNA Ribose 2?-O-Methylation by nsp16/nsp10 Protein Complex  

PubMed Central

The 5?-cap structure is a distinct feature of eukaryotic mRNAs, and eukaryotic viruses generally modify the 5?-end of viral RNAs to mimic cellular mRNA structure, which is important for RNA stability, protein translation and viral immune escape. SARS coronavirus (SARS-CoV) encodes two S-adenosyl-L-methionine (SAM)-dependent methyltransferases (MTase) which sequentially methylate the RNA cap at guanosine-N7 and ribose 2?-O positions, catalyzed by nsp14 N7-MTase and nsp16 2?-O-MTase, respectively. A unique feature for SARS-CoV is that nsp16 requires non-structural protein nsp10 as a stimulatory factor to execute its MTase activity. Here we report the biochemical characterization of SARS-CoV 2?-O-MTase and the crystal structure of nsp16/nsp10 complex bound with methyl donor SAM. We found that SARS-CoV nsp16 MTase methylated m7GpppA-RNA but not m7GpppG-RNA, which is in contrast with nsp14 MTase that functions in a sequence-independent manner. We demonstrated that nsp10 is required for nsp16 to bind both m7GpppA-RNA substrate and SAM cofactor. Structural analysis revealed that nsp16 possesses the canonical scaffold of MTase and associates with nsp10 at 1?1 ratio. The structure of the nsp16/nsp10 interaction interface shows that nsp10 may stabilize the SAM-binding pocket and extend the substrate RNA-binding groove of nsp16, consistent with the findings in biochemical assays. These results suggest that nsp16/nsp10 interface may represent a better drug target than the viral MTase active site for developing highly specific anti-coronavirus drugs. PMID:22022266

Ke, Min; Jin, Xu; Xu, Lirong; Zhang, Zhou; Wu, Andong; Sun, Ying; Yang, Zhouning; Tien, Po; Ahola, Tero; Liang, Yi; Liu, Xinqi; Guo, Deyin

2011-01-01

105

Synthesis, spectral characterisation of 2-(5-methyl-1 H-benzimidazol-2-yl)-4-bromo\\/nitro-phenols and their complexes with zinc(II) ion, and solvent effect on complexation  

Microsoft Academic Search

2-(5-Methyl-1H-benzimidazol-2-yl)-4-bromo\\/nitro-phenols (HLBr and HLNO2) and their Zn(II) complexes with ZnX2 (X=Cl, I, NO3) were synthesized and characterized by elemental analysis, molar conductivity, IR, 1H and 13C NMR spectra. The OH proton appears near the NH protons in the 1H NMR spectra of the ligands because of the strong intramolecular hydrogen bonding between the OH hydrogen and the CN nitrogen atoms.

Ayd?n Tavman

2006-01-01

106

Mercury(II) complexes with 5-methyl-5-(4-pyridyl)-2,4-imidazolidenedione: Synthesis, structural characterization, and theoretical studies  

NASA Astrophysics Data System (ADS)

New Hg(II) complexes with 5-methyl-5-(4-pyridyl)-2,4-imidazolidenedione (L) and various halogen ions were synthesized. Based on elemental analysis and flame atomic absorption spectroscopy, complexes have general formula HgL2X2 (X = Cl- (1), Br- (2), and I- (3)). These compounds have been studied by IR, 1H and 13C NMR spectroscopy at room temperature. According to X-ray diffraction analysis, complex 2 crystallizes in monoclinic system. Hg(II) ion has been surrounded by a distorted tetrahedral arrangement of two monodentate ligands (each one coordinating by a Npyridine ring atom) and two bromine atoms. Based on crystal packing findings, intermolecular classical H-bonds of the type Nsbnd H⋯O and non-classical H-bonds of the type Csbnd H⋯O and Csbnd H⋯Br, as an important member of noncovalent interaction family, are driving forces for the formation of a very distorted structure. Theoretical studies showed that neither the size of the halide anion nor the intramolecular interactions between two ligands are the reason for the very small Nsbnd Hgsbnd N bond angle, observed in complex 2.

Sabounchei, Seyyed Javad; Shahriary, Parisa; Salehzadeh, Sadegh; Gholiee, Yasin; Khavasi, Hamid Reza

2013-11-01

107

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

PubMed Central

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

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

2013-01-01

108

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

PubMed

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, (1)H NMR, (1)H-(1)H NOESY, (13)C 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 × 10(4)M(-1). PMID:25022499

Louiz, S; Labiadh, H; Abderrahim, R

2015-01-01

109

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

110

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.

111

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

112

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

113

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

PubMed

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

114

Influence of 2-methyl substitution on the geometry and complexing ability of sparteine: Packing of chiral vs. racemic building blocks  

NASA Astrophysics Data System (ADS)

2-Methylsparteine ( 1) and its complexes with ZnL 2 of the general formula [(C 16H 28N 2)ZnL 2] [L = CN - ( 2), Br - ( 3), CH 3COO - ( 4), CHO2- ( 5)] have been prepared and the 1:1 (metal:alkaloid) stoichiometry was confirmed by elemental analysis. The complexes have been characterised by IR and NMR spectroscopy. Crystal structures are reported for racemic compounds 1, 2 and 3, and compared with the structures of chiral (-)-sparteine analogues. For the sake of comparison, synthesis and crystal structure of 1:1 (-)-sparteine complex with Zn(CN) 2 ( 6) is also reported. The crystal structures of 2, 3 and 6 reveal the zinc center four coordinated by two nitrogen atoms from the alkaloid and two halides or cyanide groups in the form of distorted tetrahedral. Comparison with the crystal structure of 1 reveals that coordination to metal center in 2 and 3 brings about an inversion at the N16 nitrogen and consequent change in configuration at the ring junction from trans to cis, accompanied by a change in the C-ring conformation from boat to chair. The racemic crystals of 2 and 3 display only moderate packing similarity, but 3 exhibits very similar supramolecular architecture to that of the previously reported chiral C 16H 28N 2ZnCl 2, albeit in space groups P1¯ and P2 1, respectively. Packing of 2-methylsparteine ZnL 2 metal complexes in racemic crystals is more efficient and diverse than in chiral crystals of the analogous (-)-sparteine and ?-sparteine complexes which, in turn, tend to form an isomorphic series.

Jasiewicz, Beata; War?ajtis, Beata; Rychlewska, Urszula

2008-11-01

115

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

PubMed

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, (1)H and (13)CNMR, 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. PMID:25171052

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

2015-01-25

116

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

117

An H3K36 methylation engaging Tudor motif of polycomb-like proteins mediates PRC2 complex targeting  

PubMed Central

SUMMARY Polycomb repressive complex 2 (PRC2) regulates pluripotency, differentiation and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. However, the mechanisms that underlie PRC2 recruitment and spreading on chromatin remain unclear. Here we report that histone H3 lysine 36 trimethylation (H3K36me3)-binding activity is harbored in the Tudor motifs of PRC2-associated polycomblike (PCL) proteins PHF1/PCL1 and PHF19/PCL3. Ectopically expressed PHF1 induced Tudor-dependent stabilization of PRC2 complexes on bulk chromatin and mediated spreading of PRC2 and H3K27me3 into H3K36me3-containing chromatin regions. In murine pluripotent stem cells, we identified coexistence of H3K36me3, H3K27me3, and PHF19/PCL3 at a subset of ‘poised’ developmental genes, and demonstrated that PHF19/PCL3 Tudor function is required for optimal H3K27me3 and repression of these loci. Collectively, our data suggest that PCL recognition of H3K36me3 promotes intrusion of PRC2 complexes into active chromatin regions to promote gene silencing and modulate the chromatin landscape during development. PMID:23273982

Cai, Ling; Rothbart, Scott B.; Lu, Rui; Xu, Bowen; Chen, Wei-Yi; Tripathy, Ashutosh; Rockowitz, Shira; Zheng, Deyou; Patel, Dinshaw J; Allis, C. David; Strahl, Brian D.; Song, Jikui; Wang, Gang Greg

2012-01-01

118

In vitro biochemical and pharmacological evaluation of a novel cytotoxic dinuclear platinum(II) complex with 3-amino-5-methyl-5-phenylhydantoin.  

PubMed

An in vitro pharmacological evaluation of a novel dinuclear platinum complex ([KL(2)](2)[Pt(2)I(6)], where L is 3-amino-5-methyl-5-phenylhydantoin; Ad-1) was carried out. The cytotoxicity of [KL(2)](2)[Pt(2)I(6)] against human tumor cell lines was assessed using the MTT [-3-(4,5-dimethylthiazol-2-Yl)-2,5-diphenyltetrazolium bromide] assay. The complex exerted concentration-dependent cytotoxic effects that were comparable or even superior to that of cisplatin. Moreover, the novel complex retained significant activity against CaCo-2 and Neuro-2A cells, which showed primary resistance to cisplatin. As evidenced by the rising level of genomic DNA fragmentation following treatment with [KL(2)](2)[Pt(2)I(6)], the cytotoxic effects are at least partly mediated by induction of apoptosis. The DNA binding of [KL(2)](2)[Pt(2)I(6)] and cisplatin were assessed using a 40-base fragment, whereby the present GG-motif is the recognition sequence of the nuclease BamH1. The DNA platination was determined after BamH1 treatment, 5% PAGE, and ethidium bromide staining. Cisplatin completely inhibited the BamH1-mediated fragmentation of the target DNA molecule. [KL(2)](2)[Pt(2)I(6)] also significantly inhibited the fragmentation of the target DNA sequence. The platination induced by [KL(2)](2)[Pt(2)I(6)] was better repaired by the nucleotide excision repair than the cisplatin lesions. As evidenced by electrophoresis mobility shift assay, the Ad-1-modified DNA was efficiently recognized and bound by the high mobility group box (HMGB)-1 protein, a member of the HMG domain proteins, which implies that the latter are most probably important for the cytotoxicity mode of action of this agent. PMID:19723116

Momekov, Georgi Ts; Ugrinova, Iva; Pasheva, Evdokia A; Bakalova, Adriana G; Varbanov, Hristo Pl; Ferdinandov, Dilyan V; Ivanov, Darvin Sl; Konstantinov, Spiro M

2009-08-01

119

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

120

Multivalent di-nucleosome recognition enables the Rpd3S histone deacetylase complex to tolerate decreased H3K36 methylation levels  

PubMed Central

The Rpd3S histone deacetylase complex represses cryptic transcription initiation within coding regions by maintaining the hypo-acetylated state of transcribed chromatin. Rpd3S recognizes methylation of histone H3 at lysine 36 (H3K36me), which is required for its deacetylation activity. Rpd3S is able to function over a wide range of H3K36me levels, making this a unique system to examine how chromatin regulators tolerate the reduction of their recognition signal. Here, we demonstrated that Rpd3S makes histone modification-independent contacts with nucleosomes, and that Rpd3S prefers di-nucleosome templates since two binding surfaces can be readily accessed simultaneously. Importantly, this multivalent mode of interaction across two linked nucleosomes allows Rpd3S to tolerate a two-fold intramolecular reduction of H3K36me. Our data suggest that chromatin regulators utilize an intrinsic di-nucleosome-recognition mechanism to prevent compromised function when their primary recognition modifications are diluted. PMID:22863776

Huh, Jae-Wan; Wu, Jun; Lee, Chul-Hwan; Yun, Miyong; Gilada, Daniel; Brautigam, Chad A; Li, Bing

2012-01-01

121

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

122

Photodissociation of methyl iodide embedded in a host-guest complex: A full dimensional (189D) quantum dynamics study of CH3I@resorc[4]arene  

NASA Astrophysics Data System (ADS)

Accurate full dimensional quantum dynamics calculations studying the photodissociation of CH3I@resorc[4]arene on an ab initio based potential energy surface (PES) model are reported. The converged 189D quantum dynamics calculations are facilitated by the multilayer multi-configurational time-dependent Hartree (ML-MCTDH) approach combined with the correlation discrete variable representation (CDVR) for the evaluation of potential energy matrix elements. The potential employed combines an established ab initio PES describing the photodissociation of methyl iodide in the A band with a harmonic description of the resorc[4]arene host and a bilinear modeling of the host-guest interaction. All potential parameters required in the description of the vibrations of the host molecule and the host-guest interaction are derived from ab initio calculations on the host-guest complex. Absorption spectra at 0 K and 300 K are calculated and the electronic population dynamics during the bond breaking process occurring in the first 20-30 fs after the photoexcitation is investigated. Weak but significant effects resulting from the host-guest interaction on this time scale are found and interpreted. The present study demonstrates that accurate fully quantum mechanical dynamics calculations can be preformed for systems consisting of more than 50 atoms using the ML-MCTDH/CDVR approach. Utilizing an efficient statistical approach for the construction of the ensemble of initial wavepackets, these calculations are not restricted to zero temperature but can also study the dynamics at 300 K.

Westermann, Till; Brodbeck, Ralf; Rozhenko, Alexander B.; Schoeller, Wolfgang; Manthe, Uwe

2011-11-01

123

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

124

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

125

In Vitro and Murine Efficacy and Toxicity Studies of Nebulized SCC1, a Methylated Caffeine-Silver(I) Complex, for Treatment of Pulmonary Infections ?  

PubMed Central

The expanding clinical challenge of respiratory tract infections due to resistant bacteria necessitates the development of new forms of therapy. The development of a compound composed of silver coupled to a methylated caffeine carrier (silver carbene complex 1 [SCC1]) that demonstrated in vitro efficacy against bacteria, including drug-resistant organisms, isolated from patients with respiratory tract infections was described previously. The findings of current in vitro studies now suggest that bactericidal concentrations of SCC1 are not toxic to airway epithelial cells in primary culture. Thus, it was hypothesized that SCC1 could be administered by the aerosolized route to concentrate delivery to the lung while minimizing systemic toxicity. In vivo, aerosolized SCC1 delivered to mice resulted in mild aversion behavior, but it was otherwise well tolerated and did not cause lung inflammation following administration over a 5-day period. The therapeutic efficacy of SCC1 compared to that of water was shown in a 3-day prophylaxis protocol, in which mice infected with a clinical strain of Pseudomonas aeruginosa had increased survival, decreased amounts of bacteria in the lung, and a lower prevalence of bacteremia. Similarly, by using an airway infection model in which bacteria were impacted in the airways by agarose beads, the administration of SCC1 was significantly superior to water in decreasing the lung bacterial burden and the levels of bacteremia and markers of airway inflammation. These observations indicate that aerosolized SCC1, a novel antimicrobial agent, warrants further study as a potential therapy for bacterial respiratory tract infections. PMID:19451294

Cannon, Carolyn L.; Hogue, Lisa A.; Vajravelu, Ravy K.; Capps, George H.; Ibricevic, Aida; Hindi, Khadijah M.; Kascatan-Nebioglu, Aysegul; Walter, Michael J.; Brody, Steven L.; Youngs, Wiley J.

2009-01-01

126

Phencyclidine-induced discriminative stimulus is mediated via phencyclidine binding sites on the N-methyl-D-aspartate receptor-ion channel complex, not via sigma(1) receptors.  

PubMed

The effects of several N-methyl-D-aspartate (NMDA) receptor- and sigma receptor-related compounds on the discriminative stimulus effects of phencyclidine (PCP) were examined in rats trained to discriminate PCP (1.5 mg/kg, i.p.) from saline under a two-lever fixed ratio 20 schedule of food reinforcement. PCP produced a dose-dependent increase in PCP-appropriate responding. A non-competitive NMDA receptor antagonist, dizocilpine (0.2 mg/kg, i.p.) and a putative sigma(1) receptor agonist, (+)-SKF-10047 (10 mg/kg, i.p.) fully substituted for PCP in every rat tested. Neither a competitive NMDA receptor antagonist, CGS-19755 (0.1-3 mg/kg, i.p.), sigma(1) receptor agonist, (+)-pentazocine (10-30 mg/kg, i.p.) nor dextromethorphan (10-20 mg/kg, i.p.) produced PCP-like discriminative stimulus effects. The discriminative stimulus effects of PCP (1.5 mg/kg, i.p.), dizocilpine (0.2 mg/kg, i.p.) and (+)-SKF-10047 (10 mg/kg, i.p.) were significantly attenuated by CGS-19755 (1 mg/kg, i.p.), but not by sigma(1) receptor antagonist BMY-14802 (10 mg/kg, i.p.) and NE-100 (5 mg/kg, i.p.). These results suggest that the discriminative stimulus effects of PCP are predominantly mediated via PCP binding sites on the NMDA receptor-ion channel complex, not via sigma(1) receptors. In addition, the PCP-like discriminative stimulus effects of (+)-SKF-10047 were demonstrated to be mediated via PCP binding sites. PMID:11164523

Mori, A; Noda, Y; Mamiya, T; Miyamoto, Y; Nakajima, A; Furukawa, H; Nabeshima, T

2001-02-15

127

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

NASA Astrophysics Data System (ADS)

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

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

2014-11-01

128

Methyl eucomate  

PubMed Central

The crystal structure of the title compound [systematic name: methyl 3-carboxy-3-hydr­oxy-3-(4-hydroxy­benz­yl)propanoate], C12H14O6, is stabilized by inter­molecular O—H?O and C—H?O hydrogen bonds. The mol­ecules are arranged in layers, parallel to (001), which are inter­connected by the O—H?O hydrogen bonds. PMID:21202973

Li, Linglin; Zhou, Guang-Xiong; Jiang, Ren-Wang

2008-01-01

129

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

130

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

131

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

132

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

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 (HL(1)), 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 HL(1) 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; Ozmen, Ali; Biyik, Halil

2014-01-01

133

Biological activity of palladium(II) and platinum(II) complexes of the acetone Schiff bases of S-methyl- and S-benzyldithiocarbazate and the X-ray crystal structure of the [Pd(asme) 2] (asme=anionic form of the acetone Schiff base of S-methyldithiocarbazate) complex  

Microsoft Academic Search

Palladium(II) and platinum(II) complexes of general empirical formula, [M(NS)2] (NS=uninegatively charged acetone Schiff bases of S-methyl- and S-benzyldithiocarbazate; M=PtII and PdII) have been prepared and characterized by a variety of physicochemical techniques. Based on conductance, IR and electronic spectral evidence, a square-planar structure is assigned to these complexes. The crystal and molecular structure of the [Pd(asme)2] complex (asme=anionic form of

Mohammad Akbar Ali; Aminul Huq Mirza; Raymond J Butcher; M. T. H Tarafder; Tan Boon Keat; A. Manaf Ali

2002-01-01

134

Grafting of methyl methacrylate to cellulose and polypropylene with UV and ionising radiation in the presence of additives including CT complexes  

Microsoft Academic Search

Detailed studies of the grafting of polar methyl methacrylate (MMA) to two representative backbone polymers, cellulose and polypropylene (PPE) in the presence of additives, using ionising radiation and UV as initiating sources, are reported. The results are compared with analogous grafting work with non polar styrene previously studied. The additives chosen for examination were predominantly components used in radiation curing

John L. Garnett; Loo-Teck Ng; Visay Viengkhou

1999-01-01

135

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

136

Complex methyl groups dynamics in [(CH3)4P]3Sb2Br9 (PBA) from low to high temperatures by proton spin-lattice relaxation and narrowing of proton NMR spectrum.  

PubMed

Molecular dynamics of a polycrystalline sample of [(CH(3))(4)P](3)Sb(2)Br(9) (PBA) has been studied on the basis of the T(1) (24.7 MHz) relaxation time measurement, the proton second moment of NMR and the earlier published T(1) (90 MHz) relaxation times. The study was performed in a wide range of temperatures (30-337 K). The tunnel splitting omega(T) of the methyl groups was estimated as of low frequency (from kHz to few MHz). The proton spin pairs of the methyl group are known to perform a complex internal motion being a resultant of four components. Three of them involve mass transportation over and through the potential barrier and are characterized by the correlation times tau(3) and tau(T)of the jumps over the barrier and tunnel jumps in the threefold potential of the methyl group and tau(iso) the correlation time of isotropic rotation of the whole TMP cation. For tau(3) and tau(iso) the Arrhenius temperature dependence was assumed, while for tau(T)--the Schrödinger one. The fourth motion causes fluctuations of the tunnel splitting frequency, omega(T), and it is related to the lifetime of the methyl spin at the energy level. The correlation function for this fourth motion (tau(omega) correlation time) has been proposed by Müller-Warmuth et al. In this paper a formula for the correlation function and spectral density of the complex motion made of the above-mentioned four components was derived and used in interpretation of the T(1) relaxation time. The second moment of proton NMR line at temperatures below 50K is four times lower than its value for the rigid structure. The three components of the internal motion characterized by tau(T), tau(H), and tau(iso) were proved to reduce the second moment of the NMR line. The tunnel jumps of the methyl group reduce M(2) at almost 0K, the classical jumps over the barrier reduce M(2) in the vicinity of 50K, while the isotropic motion near 150K. Results of the study on the dynamics of CH(3) groups of TMP cation based on the second moment measurements were correlated with those based on T(1) time measurements. PMID:19853419

Latanowicz, L; Medycki, W; Jakubas, R

2009-11-01

137

The solution structure of the first PHD finger of autoimmune regulator in complex with non-modified histone H3 tail reveals the antagonistic role of H3R2 methylation  

PubMed Central

Plant homeodomain (PHD) fingers are often present in chromatin-binding proteins and have been shown to bind histone H3 N-terminal tails. Mutations in the autoimmune regulator (AIRE) protein, which harbours two PHD fingers, cause a rare monogenic disease, autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED). AIRE activates the expression of tissue-specific antigens by directly binding through its first PHD finger (AIRE-PHD1) to histone H3 tails non-methylated at K4 (H3K4me0). Here, we present the solution structure of AIRE-PHD1 in complex with H3K4me0 peptide and show that AIRE-PHD1 is a highly specialized non-modified histone H3 tail reader, as post-translational modifications of the first 10 histone H3 residues reduce binding affinity. In particular, H3R2 dimethylation abrogates AIRE-PHD1 binding in vitro and reduces the in vivo activation of AIRE target genes in HEK293 cells. The observed antagonism by R2 methylation on AIRE-PHD1 binding is unique among the H3K4me0 histone readers and represents the first case of epigenetic negative cross-talk between non-methylated H3K4 and methylated H3R2. Collectively, our results point to a very specific histone code responsible for non-modified H3 tail recognition by AIRE-PHD1 and describe at atomic level one crucial step in the molecular mechanism responsible for antigen expression in the thymus. PMID:19293276

Chignola, Francesca; Gaetani, Massimiliano; Rebane, Ana; Org, Tõnis; Mollica, Luca; Zucchelli, Chiara; Spitaleri, Andrea; Mannella, Valeria; Peterson, Pärt; Musco, Giovanna

2009-01-01

138

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

139

New rhodium(III) and ruthenium(II) water-soluble complexes with 3,5-diaza-1-methyl-1-azonia-7-phosphatricyclo[3.3.1.1(3,7)]decane.  

PubMed

The new water-soluble phosphine complexes of rhodium(III), [RhI(4)(mtpa)(2)]I (1), and ruthenium(II), [RuI(4)(mtpa)(2)].2H(2)O (2) and [RuI(2)(mtpa)(3)(H(2)O)]I(3).2H(2)O (3) (mtpa = 3,5-diaza-1-methyl-1-azonia-7-phosphatricyclo[3.3.1.1(3,7)]decane cation), have been prepared in the reactions of RhCl(3).3H(2)O and RuCl(3).3H(2)O in water in the presence of phosphine and potassium iodide. Properties and reactivity of the complexes have been investigated using (1)H and (31)P NMR and IR spectroscopies. The complexes have also been structurally characterized by single crystal X-ray diffraction studies. The compounds [RhI(4)(mtpa)(2)]I and [RuI(4)(mtpa)(2)].2H(2)O are zwitterionic octahedral complexes. The compounds were tested as catalysts for two-phase hydroformylation of 1-hexene and hydrogenation of cinnamaldehyde. Complex 1 is a selective catalyst for reduction of the C=C bond while complexes 2 and 3 selectively hydrogenate the C=O bond. PMID:12739973

Smole?ski, Piotr; Pruchnik, Florian P; Ciunik, Zbigniew; Lis, Tadeusz

2003-05-19

140

Self-assembly of three Cd(II) complexes: From 0-D to 1-D and 2-D structures based on 1-((benzotriazol-1-yl)methyl)-1- H-1,3-imidazole ligand and different anions  

NASA Astrophysics Data System (ADS)

Three new complexes with the formulas [Cd(bmi) 2I 2] ( 1), [Cd(bmi) 2(Cl) 2] n ( 2) and [Cd(bmi) 2(SCN) 2] n ( 3) have been obtained through the self-assembly of an unsymmetrical ligand 1-((benzotriazol-1-yl)methyl)-1- H-1,3-imidazole (bmi) with Cd(II) salts at room temperature. Single crystal X-ray diffraction determination shows that complex 1 possesses mononuclear structure, complex 2 displays 1-D chain structure constructed by chloride bridging Cd(II) ions, and complex 3 exhibits 2-D grid network structure. In complexes 1 and 2, the unsymmetrical bmi ligands coordinate to metal ions as monodentate mode with the N atom from imidazole ring in preference to the N atom from benzotriazol ring. While in complex 3, bmi ligands coordinate to metal ions as ? 2-bridging mode with N atoms from imidazole and benzotriazol rings simultaneously. Additionally, their fluorescent properties also have been determined.

Duan, Likun; Ding, Yanan; Meng, Xiangru; Li, Weiqiang; Hou, Hongwei; Fan, Yaoting

2010-06-01

141

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

142

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

PubMed Central

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

Inomata, Masataka; Suenaga, Yusaku

2014-01-01

143

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

144

Poly(diallyldimethylammonium chlorides) and their N-methyl-N-vinylacetamide copolymer-based DNA-polyplexes: role of molecular weight and charge density in complex formation, stability, and in vitro activity.  

PubMed

Poly(diallyldimethylammonium chlorides) (pDADMAC) of different molecular weights (5-244 kDa) and DADMAC/N-methyl-N-vinylacetamide (NMVA) copolymers (coDADMAC) with different composition (24-75 mol%) and therefore varying cationic charge densities were used to investigate the relationship between polymer structure, polyplex formation and stability, as well as their biological activity. All polymers interacted electrostatically with DNA to form polyplexes as detected by electrophoresis. Complexation and condensation of DNA by the polycations as well as protection of DNA against mechanical and enzymatic degradation were found to increase with higher molecular weights and charge densities of the polymers as well as increasing charge ratios of the complexes. Static and dynamic light scattering revealed for all DNA/polymer complexes sphere-like structures of about 100-150 nm forming more compact structures with increasing charge ratios which were stable over 24 h. The in vitro cytotoxicity of the free polymers determined by MTT-assay was directly correlated to molecular weight and charge density of the polycations which was also confirmed for polymer/DNA complexes quantifying the membrane toxic effects by LDH-release. The transfection efficiency of the complexes was low independent from different charge ratios, presence or absence of serum and lysosomotropic agents. In conclusion, the DADMACs are an interesting tool to study structure-function-relationships due to the specific adjustment of molecular weight as well as number and density of charges. PMID:15265564

Fischer, Dagmar; Dautzenberg, Herbert; Kunath, Klaus; Kissel, Thomas

2004-08-01

145

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

146

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

147

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

NASA Astrophysics Data System (ADS)

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

Ferreira, Ivania R.; Ando, Rômulo A.

2012-01-01

148

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

PubMed Central

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

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

2014-01-01

149

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

150

Methyl salicylate overdose  

MedlinePLUS

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

151

Cancer mistunes methylation  

PubMed Central

Metabolic aberrations affecting protein and DNA methylation are a potential source of cancer. A new study shows that the metabolic enzyme nicotinamide N-methyl-transferase, which is overexpressed in several types of tumors, can enhance cancer aggressiveness by draining methyl groups from S-adenosyl-methionine. PMID:23594782

Shlomi, Tomer; Rabinowitz, Joshua D

2013-01-01

152

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

153

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

154

Evaluating genome-wide DNA methylation changes in mice by Methylation Specific Digital Karyotyping  

PubMed Central

Background The study of genome-wide DNA methylation changes has become more accessible with the development of various array-based technologies though when studying species other than human the choice of applications are limited and not always within reach. In this study, we adapted and tested the applicability of Methylation Specific Digital Karyotyping (MSDK), a non-array based method, for the prospective analysis of epigenetic changes after perinatal nutritional modifications in a mouse model of allergic airway disease. MSDK is a sequenced based method that allows a comprehensive and unbiased methylation profiling. The method generates 21 base pairs long sequence tags derived from specific locations in the genome. The resulting tag frequencies determine in a quantitative manner the methylation level of the corresponding loci. Results Genomic DNA from whole lung was isolated and subjected to MSDK analysis using the methylation-sensitive enzyme Not I as the mapping enzyme and Nla III as the fragmenting enzyme. In a pair wise comparison of the generated mouse MSDK libraries we identified 158 loci that are significantly differentially methylated (P-value = 0.05) after perinatal dietary changes in our mouse model. Quantitative methylation specific PCR and sequence analysis of bisulfate modified genomic DNA confirmed changes in methylation at specific loci. Differences in genomic MSDK tag counts for a selected set of genes, correlated well with changes in transcription levels as measured by real-time PCR. Furthermore serial analysis of gene expression profiling demonstrated a dramatic difference in expressed transcripts in mice exposed to perinatal nutritional changes. Conclusion The genome-wide methylation survey applied in this study allowed for an unbiased methylation profiling revealing subtle changes in DNA methylation in mice maternally exposed to dietary changes in methyl-donor content. The MSDK method is applicable for mouse models of complex human diseases in a mixed cell population and might be a valuable technology to determine whether environmental exposures can lead to epigenetic changes. PMID:19077247

Boon, Kathy; Tomfohr, John K; Bailey, Nathaniel W; Garantziotis, Stavros; Li, Zhuowei; Brass, David M; Maruoka, Shuichiro; Hollingsworth, John W; Schwartz, David A

2008-01-01

155

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  

NASA Astrophysics Data System (ADS)

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, 1H, 13C 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) Å and 12.1667(4) Å, b = 8.0121(3) Å and 10.4792(3) Å, c = 13.9625(4) Å and 129.6616(3)Å, V = 1155.22(6) Å 3 and 1155.22(6) Å 3, Dx = 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.

Ünver, Hüseyin; Hayvali, Zeliha

2010-02-01

156

Highly luminescent poly(methyl methacrylate)-incorporated europium complex supported by a carbazole-based fluorinated ?-diketonate ligand and a 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene oxide co-ligand.  

PubMed

A novel efficient antenna complex of Eu(3+) [Eu(CPFHP)(3)(DDXPO)] supported by a highly fluorinated carbazole-substituted ?-diketonate ligand, namely, 1-(9H-carbazol-2-yl)-4,4,5,5,5-pentafluoro-3-hydroxypent-2-en-1-one (CPFHP) and the 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene oxide (DDXPO) ancillary ligand, has been synthesized, structurally characterized, and its photoluminescent behavior examined. The single-crystal X-ray diffraction analysis of Eu(CPFHP)(3)(DDXPO) revealed that this complex is mononuclear, and that the central Eu(3+) ion is surrounded by eight oxygen atoms, six of which are provided by the three bidentate ?-diketonate ligands. The remaining two oxygen atoms are furnished by the chelating phosphine oxide ligand. The coordination polyhedron is best described as that of a distorted square antiprism. The photophysical properties of Eu(CPFHP)(3)(DDXPO) benefit from adequate protection of the metal by the ligands with respect to non-radiative deactivation as well as an efficient ligand-to-metal energy transfer process which exceeds 66% in chloroform solution with a quantum yield of 47%. As an integral part of this work, the synthesis, characterization, and luminescent properties of poly(methyl methacrylate) (PMMA) polymer films doped with Eu(CPFHP)(3)(DDXPO) are also reported. The luminescent efficiencies of the doped films (photoluminescence quantum yields 79-84%) are dramatically enhanced in comparison with that of the precursor complex. The new luminescent PMMA-doped Eu(CPFHP)(3)(DDXPO) complex therefore shows considerable promise for polymer light-emitting diode and active polymer optical fiber applications. PMID:20831258

Raj, D B Ambili; Francis, Biju; Reddy, M L P; Butorac, Rachel R; Lynch, Vincent M; Cowley, Alan H

2010-10-01

157

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

PubMed

In this study, two types of nanoparticles have been used as additives for the encapsulation of Candida rugosa lipase via the sol-gel method. In one case, the nanoparticles were covalently linked with a new synthesized calix[8]arene octa valeric acid derivative (C[8]-C4-COOH) to produce new calix[8]arene-adorned magnetite nanoparticles (NP-C[8]-C4-COOH), and then NP-C[8]-C4-COOH was used as an additive in the sol-gel encapsulation process. In the other case, iron oxide nanoparticles were directly added into the sol-gel encapsulation process in order to interact electrostatically with both C[8]-C4-COOH and Candida rugosa lipase. The catalytic activities and enantioselectivities of two novel encapsulated lipases (Enc-NP-C[8]-C4-COOH and Enc-C[8]-C4-COOH@Fe3O4) in the hydrolysis reaction of racemic naproxen methyl ester were evaluated. The results showed that the activity and enantioselectivity of the lipase were improved when the lipase was encapsulated in the presence of calixarene-based additives. Indeed, the encapsulated lipases have an excellent rate of enantioselectivity, with E = 371 and 265, respectively, as compared to the free enzyme (E = 137). The lipases encapsulated with C[8]-C4-COOH and iron oxide nanoparticles (Enc-C[8]-C4-COOH@Fe3O4) retained more than 86% of their initial activities after 5 repeated uses and 92% with NP-C[8]-C4-COOH. PMID:25012138

Sayin, Serkan; Akoz, Enise; Yilmaz, Mustafa

2014-09-14

158

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

159

Methylation of Sm proteins by a complex containing PRMT5 and the putative U snRNP assembly factor pICln  

Microsoft Academic Search

Seven Sm proteins, termed B\\/B?, D1, D2, D3, E, F, and G, assemble in an ordered manner onto U snRNAs to form the Sm core of the spliceosomal snRNPs U1, U2, U4\\/U6, and U5 [1–4]. The survival of motor neuron (SMN) protein binds to Sm proteins and mediates in the context of a macromolecular (SMN-) complex the assembly of the

Gunter Meister; Christian Eggert; Dirk Bühler; Hero Brahms; Christian Kambach; Utz Fischer

2001-01-01

160

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

161

Donor-dictated interlocking co-complexation reactions of LiNHDipp with dimethylzinc: synthesis and structures of new methyl(amido)zincates.  

PubMed

A systematic study of the interlocking co-complexation reactions between the primary lithium amide LiNHDipp (Dipp = 2,6-diisopropylphenyl) and dimethylzinc in the presence of different donor ligands is presented which concludes that the final outcome of these reactions is largely dictated by the type of structure that is formed when the donor is coordinated to the lithium amide. When chelating diamine TMEDA (N,N,N',N'-tetramethylethylenediamine) is employed [{Li(2)(NHDipp)(2)(TMEDA)}(infinity)] (1) is obtained, where Li(2)N(2) rings are connected by TMEDA bridges generating a polymeric chain arrangement which does not form a co-complex with Me(2)Zn even in the presence of an excess of TMEDA. The tridentate ligand PMDETA (N,N,N',N'',N''-pentamethyldiethylenetriamine) when reacted with LiNHDipp forms monomeric [(PMDETA)Li(NHDipp)](4) which successfully forms a mixed-metal co-complex with Me(2)Zn affording dialkyl(amido)zincate [(PMDETA)LiZn(NHDipp)(Me)(2)] (2). When the co-complexation reaction is carried out in the presence of monodentate tetrahydrofuran (THF), zincate [(THF)(3)LiZn(NHDipp)(Me)(2)] (3) is obtained which was found to partially decompose in hexane solution after long periods of time at room temperature (2 weeks) to afford the unprecedented "zinc-rich" zincate [(THF)(3)LiZn(2)(Me)(3)(NHDipp)(2)] (5). This compound presents a unique structure in the solid state previously unknown in organozincate chemistry with a trinuclear Li...Zn...Zn chain arrangement where the metals are connected by only two amido bridges and therefore both zinc centers exhibit trigonal planar geometries. 5 can be prepared in good yields by the rational reaction of LiNHDipp with a 2:1:3 mixture of Me(2)Zn, NH(2)Dipp and THF. The different solid-state structural motifs of compounds 1, 2, 4, and 5 have been revealed by X-ray crystallographic studies. Multinuclear NMR ((1)H, (13)C and (7)Li) spectroscopic data recorded in C(6)D(6) solution are also reported for compounds 1-6. Mixed-metal compounds 2 and 5 constitute the first examples of crystallographically characterized alkyl(amido)zincates containing a primary amide. PMID:19408922

Clegg, William; Graham, David V; Herd, Emma; Hevia, Eva; Kennedy, Alan R; McCall, Matthew D; Russo, Luca

2009-06-15

162

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

163

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

164

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

PubMed

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

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

2013-05-21

165

Methyl rotors in flavoproteins.  

PubMed

In this contribution we present the study of the thermal dependence of the ENDOR spectra of flavodoxin at low temperatures which reveals the dynamics of the methyl groups bound to the flavin moiety in flavoproteins. The methyl groups behave as quantum rotors locked by a deep rotational well and undergoing a tunneling process. At room temperature, methyl rotors are locked and the hopping motion is slow. This picture of the dynamics of the methyl groups of the flavin ring is quite different from the one usually accepted and has relevant consequences on the understanding of the mechanisms of flavoproteins. PMID:25363087

Martínez, Jesús I; Alonso, Pablo J; García-Rubio, Inés; Medina, Milagros

2014-12-21

166

Molecular Structure, Acidic Properties, and Kinetic Behavior of the Cationic Complex (Methyl)(dimethyl sulfoxide)(bis-2-pyridylamine)platinum(II) Ion.  

PubMed

The complex [PtMe(dpa)(Me(2)SO)](+)(CF(3)SO(3))(-) (dpa = bis(2-pyridyl)amine) crystallizes in the monoclinic space group P2(1)/c with a = 11.010(2) Å, b = 18.366(2) Å, c = 10.333(5) Å, beta = 111.62(2) degrees, and Z = 4. Least-squares refinement of the structure led to an R factor of 2.41%. To avoid steric repulsions, the chelate six-membered ring assumes a boat configuration in which the two pyridyl rings are folded with a dihedral angle of 46.4(1) degrees. There is a strong hydrogen-bonding interaction involving the amine hydrogen (N3) and a triflate anion oxygen O3, 2.898(5) Å. The tendency by the NH group of the ligand moiety to attract anions is maintained in a solution of nonpolar solvents. Tight ion-pairs of structure similar to that in the solid state are formed with PF(6)(-), BF(4)(-), CF(3)SO(3)(-), and Cl(-) in chloroform, as shown by the strong dependence of the chemical shifts of the NH, H(3), and H(3') protons of the dpa ligand on the nature of the counterion. (19)F{(1)H} HOESY experiments on [PtMe(dpa)(Me(2)SO)](+)(PF(6))(-) in CD(2)Cl(2) confirmed that the preferential position of the counterion is close to the NH proton. The absorption spectra are also strongly affected by the nature of the counterion. This allowed for a stopped-flow measure of the PF(6)(-) for Cl(-) exchange rate at the NH site, which is a bimolecular process with k(2) = 96.4 +/- 4 M(-)(1) s(-)(1). The cation [PtMe(dpa)(Me(2)SO)](+) shows acidic properties in water (pK(a) = 12.1 +/- 0.2, at 25 degrees C, &mgr; = 0.1 M, NaNO(3)), and the corresponding amido species [PtMe(dpa-H)(Me(2)SO)] can be isolated on basification. Ion-pairing and full deprotonation of the amine ligand have remarkably little effect on the reactivity, as shown by the comparison of the rates of isotopic exchange of dimethyl sulfoxide of these species followed by (1)H NMR in chloroform. The rates of substitution of dimethyl sulfoxide from [PtMe(dpa)(Me(2)SO)](+) by various charged nucleophiles were measured in methanol, where ion-pairing effects are absent, and compared with those of the parent [PtMe(phen)(Me(2)SO)](+) (phen = 1,10-phenanthroline) complex. Because of the reduced capacity of electron withdrawal from the metal of the ancillary ligand, the dpa complex is less reactive and possesses a minor nucleophilic discrimination ability compared with the phen complex. PMID:11670688

Romeo, Raffaello; Nastasi, Nicola; Scolaro, Luigi Monsù; Plutino, Maria Rosaria; Albinati, Alberto; Macchioni, Alceo

1998-10-19

167

Upper critical solution temperature phase behavior, composition fluctuations, and complex formation in poly (vinyl methyl ether)/D2O solutions: small-angle neutron-scattering experiments and wertheim lattice thermodynamic perturbation theory predictions.  

PubMed

Small-angle neutron-scattering measurements are presented for homogeneous mixtures of poly (methyl vinyl ether) (PVME) and deuterium oxide (D(2)O) at high polymer concentrations and for temperatures lower than the equilibrium melting point of the solvent. The experimental data are analyzed to give values for the second-order compositional derivative of the Gibbs energy and the Ornstein-Zernike correlation length. The experimental data together with earlier SANS data determined at higher temperatures cannot be represented with an extended Flory-Huggins (F-H) interaction function depending on composition and temperatures. The experimental data confirm the existence of a narrow upper critical solution temperature (UCST) miscibility gap at high concentrations in agreement with theoretical predictions of the Wertheim lattice thermodynamic perturbation theory (LTPT). The Wertheim LTPT incorporates the influence of hydrogen bonding and predicts not only the existence of bimodal lower critical solution temperature (LCST) phase behavior but also the occurrence of highly unconventional two narrow adjacent UCST miscibility gaps. Finally, the experimental data do not support the existence of a stable molecular complex at the investigated temperatures and compositions. Even at the lowest investigated temperature, the energy required to induce typical Ornstein-Zernike-like concentration fluctuations is smaller than the thermal energy. Also, in this case, the Wertheim LTPT provides a theoretical basis to understand the formation of polymer solvent associations in PVME/water. PMID:16539464

Nies, Erik; Li, Ting; Berghmans, Hugo; Heenan, Richard K; King, Stephen M

2006-03-23

168

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

NASA Astrophysics Data System (ADS)

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

Diwaker

2015-02-01

169

Microwave Spectroscopic Measurements of the Rotational Spectrum of Methyl Cyclopentadienyl Iron Dicarbonyl  

NASA Astrophysics Data System (ADS)

The rotational spectra of the methyl cyclopentadienyl iron dicarbonyl complex (namely methyl-Fip) were measured using a pulsed molecular beam Fourier transform microwave spectrometer. Methyl-Fip is an asymmetric top complex with a single methyl rotor bound to iron. The complex is challenging to study experimentally in the gas phase because it is unstable and exhibits methyl internal rotation. We report here the first measurements of the a-type rotational spectrum and determination of a methyl torsional barrier height. Analysis of the observed doublet splittings of low J and K lines yielded a barrier height of 8.7(8) kJ. The observed rotational constants for the parent (^5^6Fe) complex are A = 1431.74(13), B = 1062.263(84), and C = 828.016(15) MHz. Assignment of the measured rotational spectrum, quantum chemical calculations, and the molecular structure of methyl-Fip will be discussed.

Tanjaroon, Chakree; Kukolich, Stephen G.

2009-06-01

170

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

171

Palladium(II) complexes with R(2)edda derived ligands. Part IV. O,O'-dialkyl esters of (S,S)-ethylenediamine-N,N'-di-2-(4-methyl)-pentanoic acid dihydrochloride and their palladium(II) complexes: synthesis, characterization and in vitro antitumoral activity against chronic lymphocytic leukemia (CLL) cells.  

PubMed

Four novel bidentate N,N'-ligand precursors, including O,O'-dialkyl esters (alkyl = ethyl, n-propyl, n-butyl and n-pentyl), L1 x 2 HCl-L4 x 2 HCl, of (S,S)-ethylenediamine-N,N'-di-2-(4-methyl)-pentanoic acid dihydrochloride [(S,S)-H(4)eddl]Cl(2) and the corresponding palladium(II) complexes 1-4, were prepared and characterized by IR, (1)H NMR and (13)C NMR spectroscopy and elemental analysis. In vitro cytotoxicity of all compounds was determined against chronic lymphocytic leukemia cells (CLL). The compounds were found to exhibit higher antitumoral activity than cisplatin. The most active compound 2, [PdCl(2){(S,S)-nPr(2)eddl}], was found to be 13.6 times more active than cisplatin on CLL cells. PMID:20570025

Vuji?, Jelena M; Cvijovi?, Milica; Kaluderovi?, Goran N; Milovanovi?, Marija; Zmejkovski, Bojana B; Volarevi?, Vladislav; Arsenijevi?, Nebojsa; Sabo, Tibor J; Trifunovi?, Sre?ko R

2010-09-01

172

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

Microsoft Academic Search

BACKGROUND: The computational prediction of DNA methylation has become an important topic in the recent years due to its role in the epigenetic control of normal and cancer-related processes. While previous prediction approaches focused merely on differences between methylated and unmethylated DNA sequences, recent experimental results have shown the presence of much more complex patterns of methylation across tissues and

Christopher Previti; Oscar Harari; Igor Zwir; Coral Del Val

2009-01-01

173

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

174

Biological activity of palladium(II) and platinum(II) complexes of the acetone Schiff bases of S-methyl- and S-benzyldithiocarbazate and the X-ray crystal structure of the [Pd(asme)2] (asme=anionic form of the acetone Schiff base of S-methyldithiocarbazate) complex.  

PubMed

Palladium(II) and platinum(II) complexes of general empirical formula, [M(NS)(2)] (NS=uninegatively charged acetone Schiff bases of S-methyl- and S-benzyldithiocarbazate; M=Pt(II) and Pd(II)) have been prepared and characterized by a variety of physicochemical techniques. Based on conductance, IR and electronic spectral evidence, a square-planar structure is assigned to these complexes. The crystal and molecular structure of the [Pd(asme)(2)] complex (asme=anionic form of the acetone Schiff base of S-methyldithiocarbazate) has been determined by X-ray diffraction. The complex has a distorted cis-square planar structure with the ligands coordinated to the palladium(II) ions as uninegatively charged bidentate NS chelating agents via the azomethine nitrogen and the mercaptide sulfur atoms. The distortion from a regular square-planar geometry is attributed to the restricted bite angles of the ligands. Antimicrobial tests indicate that the Schiff bases exhibit strong activities against the pathogenic bacteria, Bacillus subtilis (mutant defective DNA repair), methicillin-resistant Staphylococcus aureus, B. subtilis (wild type) and Pseudomonas aeruginosa and the fungi, Candida albicans (CA), Candida lypotica (2075), Saccharomyces cerevisiae (20341) and Aspergillus ochraceous (398)-the activities exhibited by these compounds being greater than that of the standard antibacterial and antifungal drugs, streptomycin and nystatin, respectively. The palladium(II) and platinum(II) complexes are inactive against most of these organisms but, the microbe, Pseudomonas aeruginosa shows strong sensitivity to the platinum(II) complexes. Screening of the compounds for their cytotoxicities against T-lymphoblastic leukemia cancer cells has shown that the acetone Schiff base of S-methyldithiocarbazate (Hasme) exhibits a very weak activity, whereas the S-benzyl derivative (Hasbz) is inactive. However, the palladium(II) complexes exhibit strong cytotoxicities against this cancer; their activities being more than that of the standard anticancer drug, tamoxifen. The [Pt(asme)(2)] complex exhibits a very weak cytotoxicity, whereas [Pt(asbz)(2)] is inactive against leukemic cells. PMID:12433421

Akbar Ali, Mohammad; Mirza, Aminul Huq; Butcher, Raymond J; Tarafder, M T H; Keat, Tan Boon; Ali, A Manaf

2002-11-25

175

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...

176

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

177

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

178

miRNA and Methylation: A Multifaceted Liaison.  

PubMed

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

Chhabra, Ravindresh

2014-12-01

179

Array-based DNA methylation profiling in follicular lymphoma  

PubMed Central

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

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

2009-01-01

180

On the presence and role of human gene-body DNA methylation  

PubMed Central

DNA methylation of promoter sequences is a repressive epigenetic mark that down-regulates gene expression. However, DNA methylation is more prevalent within gene-bodies than seen for promoters, and gene-body methylation has been observed to be positively correlated with gene expression levels. This paradox remains unexplained, and accordingly the role of DNA methylation in gene-bodies is poorly understood. We addressed the presence and role of human gene-body DNA methylation using a meta-analysis of human genome-wide methylation, expression and chromatin data sets. Methylation is associated with transcribed regions as genic sequences have higher levels of methylation than intergenic or promoter sequences. We also find that the relationship between gene-body DNA methylation and expression levels is non-monotonic and bell-shaped. Mid-level expressed genes have the highest levels of gene-body methylation, whereas the most lowly and highly expressed sets of genes both have low levels of methylation. While gene-body methylation can be seen to efficiently repress the initiation of intragenic transcription, the vast majority of methylated sites within genes are not associated with intragenic promoters. In fact, highly expressed genes initiate the most intragenic transcription, which is inconsistent with the previously held notion that gene-body methylation serves to repress spurious intragenic transcription to allow for efficient transcriptional elongation. These observations lead us to propose a model to explain the presence of human gene-body methylation. This model holds that the repression of intragenic transcription by gene-body methylation is largely epiphenomenal, and suggests that gene-body methylation levels are predominantly shaped via the accessibility of the DNA to methylating enzyme complexes. PMID:22577155

Jjingo, Daudi; Conley, Andrew B.; Yi, Soojin V.; Lunyak, Victoria V.; Jordan, I. King

2012-01-01

181

Evolution of DNA methylation is linked to genetic aberrations in chronic lymphocytic leukemia.  

PubMed

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

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

2014-03-01

182

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

PubMed Central

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

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

2014-01-01

183

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

184

[DNA methylation in obesity].  

PubMed

The number of overweight and obese people is increasing at an alarming rate, especially in the developed and developing countries. Obesity is a major risk factor for diabetes, cardiovascular disease, and cancer, and in consequence for premature death. The development of obesity results from the interplay of both genetic and environmental factors, which include sedentary life style and abnormal eating habits. In the past few years a number of events accompanying obesity, affecting expression of genes which are not directly connected with the DNA base sequence (e.g. epigenetic changes), have been described. Epigenetic processes include DNA methylation, histone modifications such as acetylation, methylation, phosphorylation, ubiquitination, and sumoylation, as well as non-coding micro-RNA (miRNA) synthesis. In this review, the known changes in the profile of DNA methylation as a factor affecting obesity and its complications are described. PMID:25531701

Pokrywka, Ma?gorzata; Kie?-Wilk, Beata; Polus, Anna; Wybra?ska, Iwona

2014-01-01

185

Versatile synthetic approach to new bifunctional chelating agents tailor made for labeling with the fac-[M(CO)(3)](+) core (M = Tc, (99m)Tc, Re): synthesis, in vitro, and in vivo behavior of the model complex [M(APPA)(CO)(3)] (APPA = [(5-amino-pentyl)-pyridin-2-yl-methyl-amino]-acetic acid).  

PubMed

A general synthetic approach for potent tridentate, bifunctional chelating agent (BFCA) for the [M(CO)(3)](+) fragment (M = (99g)Tc, (99m)Tc, and Re) has been elaborated. The strategy allows the facile preparation of BFCA with a pendent amino or carboxylic acid functionality for coupling to peptides and proteins via formation of an amide bond. [(5-amino-pentyl)-pyridin-2-yl-methyl-amino]-acetic acid (APPA) and [pyridin-2-yl-methyl-amino]-diacetic acid (PADA) were synthesized according to this protocol. The BFCA were labeled with the [M(CO)(3)](+) fragment, which resulted in formation of uniform products with a ligand to metal ratio of 1:1. The complexes have been fully characterized by means of mass spectrometry, IR, and NMR ((1)H, (13)C, (99)Tc) spectroscopy. Coordination of the tricarbonyl core with APPA and PADA was exclusively tridentate (via the acid function, the ternary amine, and the pyridine nitrogen). On the n.c.a. level the complexes were almost quantitatively formed (yield >90%) at ligand concentrations of 10+/-2 microM (PADA) or 50+/-4 microM (APPA) after 30 min at 70 degrees C. Chromatographic behavior of the (99m)Tc complexes is similar to that of the corresponding (99)Tc/Re complexes suggesting the identical chemical structure. Pharmacokinetic experiments with the (99m)Tc-APPA complex were performed in BALB/c mice and compared with previously published results of the (99m)Tc-PADA complex. The (99m)Tc-APPA complex revealed good clearance from the blood pool (0.29 +/- 0.03% ID after 24h p.i.) and a low uptake in the liver (2.41 +/- 0.14% ID/g), in the kidneys (2.81 +/- 0.12% ID/g) and other tissue and organs. PMID:12831983

Stichelberger, Albert; Waibel, Robert; Dumas, Cécile; Schubiger, P A; Schibli, Roger

2003-07-01

186

In vitro methylation assay to study protein arginine methylation.  

PubMed

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

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

2014-01-01

187

What difference does a methyl group make: pentamethylbenzene?  

PubMed

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

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

2014-12-01

188

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

PubMed Central

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

2009-01-01

189

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 ...

190

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

191

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 ...

192

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...

193

Trans-chromosomal methylation.  

PubMed

The epigenome plays a vital role in helping to maintain and regulate cell functions in all organisms. Alleles with differing epigenetic marks in the same nucleus do not function in isolation but can interact in trans to modify the epigenetic state of one or both alleles. This is particularly evident when two divergent epigenomes come together in a hybrid resulting in thousands of alterations to the methylome. These changes mainly involve the methylation patterns at one allele being changed to resemble the methylation patterns of the other allele, in processes we have termed trans-chromosomal methylation (TCM) and trans-chromosomal demethylation (TCdM). These processes are primarily modulated by siRNAs and the RNA directed DNA methylation pathway. Drawing from other examples of trans-allelic interactions, we describe the process of TCM and TCdM and the effect such changes can have on genome activity. Trans-allelic epigenetic interactions may be a common occurrence in many biological systems. PMID:22705969

Greaves, Ian; Groszmann, Michael; Dennis, Elizabeth S; Peacock, W James

2012-08-01

194

Repression of genes by DNA methylation depends on CpG density and promoter strength: evidence for involvement of a methyl-CpG binding protein.  

PubMed Central

Repression of transcription from densely methylated genes can be mediated by the methyl-CpG binding protein MeCP-1 (Boyes and Bird, 1991). Here we have investigated the effect of methylation on genes with a low density of methyl-CpG. We found that sparse methylation could repress transfected genes completely, but the inhibition was fully overcome by the presence in cis of an SV40 enhancer. Densely methylated genes, however, could not be reactivated by the enhancer. In vitro studies showed that the sparsely methylated genes bound weakly to MeCP-1 and that binding interfered with transcription. In the absence of available MeCP-1, methylation had minimal effects on transcription. From these and other results we propose that sparsely methylated genes form an unstable complex with MeCP-1 which prevents transcription when the promoter is weak. This complex can be disrupted by a strong promoter, thereby allowing the methylated gene to be transcribed. Images PMID:1310933

Boyes, J; Bird, A

1992-01-01

195

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

196

Mercury Methylation by Desulfovibrio desulfuricans ND132 in the Presence of Polysulfides  

PubMed Central

The extracellular speciation of mercury may control bacterial uptake and methylation. Mercury-polysulfide complexes have recently been shown to be prevalent in sulfidic waters containing zero-valent sulfur. Despite substantial increases in total dissolved mercury concentration, methylation rates in cultures of Desulfovibrio desulfuricans ND132 equilibrated with cinnabar did not increase in the presence of polysulfides, as expected due to the large size and charged nature of most of the complexes. In natural waters not at saturation with cinnabar, mercury-polysulfide complexes would be expected to shift the speciation of mercury from HgS0(aq) toward charged complexes, thereby decreasing methylation rates. PMID:12406773

Jay, Jenny Ayla; Murray, Karen J.; Gilmour, Cynthia C.; Mason, Robert P.; Morel, François M. M.; Roberts, A. Lynn; Hemond, Harold F.

2002-01-01

197

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

SciTech Connect

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

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

1984-08-01

198

Altered DNA Methylation in Leukocytes with Trisomy 21  

PubMed Central

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

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

2010-01-01

199

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

Microsoft Academic Search

Targeted liquid chromatography–mass spectrometry (LC–MS) technology using size exclusion chromatography and metabolite profiling based on gas chromatography–mass spectrometry (GC–MS) were used to study the nickel-rich latex of the hyperaccumulating tree Sebertia acuminata. More than 120 compounds were detected, 57 of these were subsequently identified. A methylated aldaric acid (2,4,5-trihydroxy-3-methoxy-1,6-hexan-dioic acid) was identified for the first time in biological extracts and

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

2008-01-01

200

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

PubMed

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

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

2011-01-01

201

DNA methylation and the regulation of gene transcription.  

PubMed

The regulation of gene transcription is not simply dependent on the presence or absence of DNA-binding transcription factors that turn genes on or off, but also involves processes determining the ability of transcription factors to gain access to and bind their target DNA. Methylation of DNA cytosine bases leads to the inaccessibility of DNA regulatory elements to their transcription factors by a number of mechanisms. Our understanding of DNA methylation has advanced rapidly in recent years with the identification of an increasingly large number of novel proteins involved in this process. These include methylcytosine-binding proteins as well as additional members of the DNA methyltransferase family. The creation of mice with targeted deletions in a number of genes involved in DNA methylation has further elucidated the functions of many of these proteins. The characterization of complexes that contain proteins known to be involved in DNA methylation has led to the identification of additional proteins, especially those involved in histone deacetylation, indicating that DNA methylation and histone deacetylation very likely act in a synergistic fashion to regulate gene transcription. Finally, the implication of DNA methylation in tumorigenesis and the realization that some congenital diseases are caused by deficiency of proteins involved in DNA methylation has confirmed the importance of this process in regulating gene expression. PMID:11915942

Attwood, J T; Yung, R L; Richardson, B C

2002-02-01

202

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing  

PubMed Central

DNA methylation stabilizes developmentally programmed gene expression states. Aberrant methylation is associated with disease progression and is a common feature of cancer genomes. Presently, few methods enable quantitative, large-scale, single-base resolution mapping of DNA methylation states in desired regions of a complex mammalian genome. Here, we present an approach that combines array-based hybrid selection and massively parallel bisulfite sequencing to profile DNA methylation in genomic regions spanning hundreds of thousands of bases. This single molecule strategy enables methylation variable positions to be quantitatively examined with high sampling precision. Using bisulfite capture, we assessed methylation patterns across 324 randomly selected CpG islands (CGI) representing more than 25,000 CpG sites. A single lane of Illumina sequencing permitted methylation states to be definitively called for >90% of target sties. The accuracy of the hybrid-selection approach was verified using conventional bisulfite capillary sequencing of cloned PCR products amplified from a subset of the selected regions. This confirmed that even partially methylated states could be successfully called. A comparison of human primary and cancer cells revealed multiple differentially methylated regions. More than 25% of islands showed complex methylation patterns either with partial methylation states defining the entire CGI or with contrasting methylation states appearing in specific regional blocks within the island. We observed that transitions in methylation state often correlate with genomic landmarks, including transcriptional start sites and intron-exon junctions. Methylation, along with specific histone marks, was enriched in exonic regions, suggesting that chromatin states can foreshadow the content of mature mRNAs. PMID:19581485

Hodges, Emily; Smith, Andrew D.; Kendall, Jude; Xuan, Zhenyu; Ravi, Kandasamy; Rooks, Michelle; Zhang, Michael Q.; Ye, Kenny; Bhattacharjee, Arindam; Brizuela, Leonardo; McCombie, W. Richard; Wigler, Michael; Hannon, Gregory J.; Hicks, James B.

2009-01-01

203

Methyl group tunnelling studies in calixarenes  

NASA Astrophysics Data System (ADS)

Inelastic neutron scattering has been used to study the tunnelling of methyl groups belonging to several guest molecules (toluene, p-xylene, ?-picoline) incarcerated in a host calixarene matrix. In all the cases investigated, the low temperature neutron spectra show a number of bands which may be interpreted as being due to transitions between tunnel-split librational states of the guest methyl groups. The main line occurs near 0.63meV, very close to the CH 3 quantum free rotor limit. In the toluence complex, the quantum regime persists at least up to 60 K. Effects of coupling between rotational and vibrational modes are discussed. Very subtle structural changes not revealed by diffraction measurements are suggested by the neutron spectroscopy results.

Caciuffo, R.; Amoretti, G.; Carlile, C. J.; Fillaux, F.; Francescangeli, O.; Prager, M.; Ugozzoli, F.

1994-10-01

204

Genomics of CpG methylation in developing and developed zebrafish.  

PubMed

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

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

2014-05-01

205

Genomics of CpG Methylation in Developing and Developed Zebrafish  

PubMed Central

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

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

2014-01-01

206

DNA methylation regulated nucleosome dynamics.  

PubMed

A strong correlation between nucleosome positioning and DNA methylation patterns has been reported in literature. However, the mechanistic model accounting for the correlation remains elusive. In this study, we evaluated the effects of specific DNA methylation patterns on modulating nucleosome conformation and stability using FRET and SAXS. CpG dinucleotide repeats at 10?bp intervals were found to play different roles in nucleosome stability dependent on their methylation states and their relative nucleosomal locations. An additional (CpG)5 stretch located in the nucleosomal central dyad does not alter the nucleosome conformation, but significant conformational differences were observed between the unmethylated and methylated nucleosomes. These findings suggest that the correlation between nucleosome positioning and DNA methylation patterns can arise from the variations in nucleosome stability dependent on their sequence and epigenetic content. This knowledge will help to reveal the detailed role of DNA methylation in regulating chromatin packaging and gene transcription. PMID:23817195

Jimenez-Useche, Isabel; Ke, Jiaying; Tian, Yuqing; Shim, Daphne; Howell, Steven C; Qiu, Xiangyun; Yuan, Chongli

2013-01-01

207

Antagonism between DNA and H3K27 Methylation at the Imprinted Rasgrf1 Locus  

PubMed Central

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

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

2008-01-01

208

Methylation signature of lymph node metastases in breast cancer patients  

PubMed Central

Background Invasion and metastasis are two important hallmarks of malignant tumors caused by complex genetic and epigenetic alterations. The present study investigated the contribution of aberrant methylation profiles of cancer related genes, APC, BIN1, BMP6, BRCA1, CST6, ESR-b, GSTP1, P14 (ARF), P16 (CDKN2A), P21 (CDKN1A), PTEN, and TIMP3, in the matched axillary lymph node metastasis in comparison to the primary tumor tissue and the adjacent normal tissue from the same breast cancer patients to identify the potential of candidate genes methylation as metastatic markers. Methods The quantitative methylation analysis was performed using the SEQUENOM’s EpiTYPER™ assay which relies on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Results The quantitative DNA methylation analysis of the candidate genes showed higher methylation proportion in the primary tumor tissue than that of the matched normal tissue and the differences were significant for the APC, BIN1, BMP6, BRCA1, CST6, ESR-b, P16, PTEN and TIMP3 promoter regions (P<0.05). Among those candidate methylated genes, APC, BMP6, BRCA1 and P16 displayed higher methylation proportion in the matched lymph node metastasis than that found in the normal tissue (P<0.05). The pathway analysis revealed that BMP6, BRCA1 and P16 have a role in prevention of neoplasm metastasis. Conclusions The results of the present study showed methylation heterogeneity between primary tumors and metastatic lesion. The contribution of aberrant methylation alterations of BMP6, BRCA1 and P16 genes in lymph node metastasis might provide a further clue to establish useful biomarkers for screening metastasis. PMID:22695536

2012-01-01

209

Phencyclidine-induced discriminative stimulus is mediated via phencyclidine binding sites on the N-methyl- d-aspartate receptor-ion channel complex, not via sigma 1 receptors  

Microsoft Academic Search

The effects of several N-methyl-d-aspartate (NMDA) receptor- and sigma receptor-related compounds on the discriminative stimulus effects of phencyclidine (PCP) were examined in rats trained to discriminate PCP (1.5 mg\\/kg, i.p.) from saline under a two-lever fixed ratio 20 schedule of food reinforcement. PCP produced a dose-dependent increase in PCP-appropriate responding. A non-competitive NMDA receptor antagonist, dizocilpine (0.2 mg\\/kg, i.p.) and

Akitomo Mori; Yukihiro Noda; Takayoshi Mamiya; Yoshiaki Miyamoto; Akira Nakajima; Hiroshi Furukawa; Toshitaka Nabeshima

2001-01-01

210

Research report Phencyclidine-induced discriminative stimulus is mediated via phencyclidine binding sites on the N-methyl-D-aspartate receptor-ion channel complex, not via sigma1 receptors  

Microsoft Academic Search

The effects of several N-methyl-D-aspartate (NMDA) receptor- and sigma receptor-related compounds on the discriminative stimulus effects of phencyclidine (PCP) were examined in rats trained to discriminate PCP (1.5 mg:kg, i.p.) from saline under a two-lever fixed ratio 20 schedule of food reinforcement. PCP produced a dose-dependent increase in PCP-appropriate responding. A non-competitive NMDA receptor antagonist, dizocilpine (0.2 mg:kg, i.p.) and

Akitomo Mori; Yukihiro Nod; Takayoshi Mamiya; Yoshiaki Miyamoto; Akira Nakajima; Hiroshi Furukawa; Toshitaka Nabeshima

211

Response of Sunflower (Helianthus annuus L.) Leaf Surface Defenses to Exogenous Methyl Jasmonate  

E-print Network

Response of Sunflower (Helianthus annuus L.) Leaf Surface Defenses to Exogenous Methyl Jasmonate of America Abstract Helianthus annuus, the common sunflower, produces a complex array of secondary compounds (Helianthus annuus L.) Leaf Surface Defenses to Exogenous Methyl Jasmonate. PLoS ONE 7(5): e37191. doi:10

Rieseberg, Loren

212

HISTONE METHYLATION REGULATES MEMORY FORMATION  

PubMed Central

It has been established that regulation of chromatin structure through post-translational modification of histone proteins, primarily histone H3 phosphorylation and acetylation, is an important early step in the induction of synaptic plasticity and formation of long-term memory. In this study, we investigated the contribution of another histone modification, histone methylation, to memory formation in the adult hippocampus. We found that tri-methylation of histone H3 at lysine 4 (H3K4), an active mark for transcription, is upregulated in hippocampus one hour following contextual fear conditioning. In addition, we found that di-methylation of histone H3 at lysine 9 (H3K9), a molecular mark associated with transcriptional silencing, is increased one hour after fear conditioning and decreased twenty-four hours after context exposure alone and contextual fear conditioning. Tri-methylated H3K4 levels returned to baseline levels at twenty-four hours. We also found that mice deficient in the H3K4-specific histone methyltransferase, Mll, displayed deficits in contextual fear conditioning relative to wildtype animals. This suggests that histone methylation is required for proper long-term consolidation of contextual fear memories. Interestingly, inhibition of histone deacetylases (HDACs) with sodium butyrate (NaB) resulted in increased H3K4 tri-methylation and decreased H3K9 di-methylation in hippocampus following contextual fear conditioning. Correspondingly, we found that fear learning triggered increases in H3K4 tri-methylation at specific gene promoter regions (Zif268 and bdnf) with altered DNA methylation and MeCP2 DNA binding. Zif268 DNA methylation levels returned to baseline at twenty-four hours. Together, these data demonstrate that histone methylation is actively regulated in the hippocampus and facilitates long-term memory formation. PMID:20219993

Gupta, Swati; Kim, Se Y.; Artis, Sonja; Molfese, David L.; Schumacher, Armin; Sweatt, J. David; Paylor, Richard E.; Lubin, Farah D.

2010-01-01

213

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)  

NASA Astrophysics Data System (ADS)

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 (1H and 13C) 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 13C NMR peaks of the group N13CS2 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.

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

2015-02-01

214

Neural tube defects, folic acid and methylation.  

PubMed

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

2013-09-01

215

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

216

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

217

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

218

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...

219

DNA Methylation: Hemodialysis Versus Hemodiafiltration.  

PubMed

Aberrant DNA methylation is an emerging characteristic of chronic kidney disease including dialysis patients. It appears to be associated to inflammation. We compared the global DNA methylation status in 10 control subjects compared to 80 dialysis patients (N?=?40 on-line hemodiafiltration, N?=?40 high-flux hemodialysis) in relation to the dialysis technique and inflammation. Whole blood DNA methylation was assessed with a 5-mc DNA enzyme linked immunosorbent assay Kit. Global DNA methylation was higher in hemodialysis (HD) compared to on-line hemodiafiltration (HDF) patients (0.045 vs. 0.039; P?methylation we divided dialysis patients according to the median value of 5-mC. DNA methylation was highest in inflamed patients on hemodialysis. The dialysis technique was the only independent predictor of global DNA methylation in dialysis patients. On-line HDF could be associated with a favorable DNA methylation profile. PMID:25404498

Ghigolea, Adrian-Bogdan; Moldovan, Raluca Argentina; Gherman-Caprioara, Mirela

2014-11-18

220

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

221

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

PubMed

Reaction of each of the known starting complexes [PtR(C^N)(SMe2)], 1, in which R = Me or p-MeC6H4 and C^N is either ppy (deprotonated 2-phenylpyridine) or bhq (deprotonated benzo[h]quinoline), with one equivalent of CF3CO2H, gave the complexes [Pt(C^N)(CF3CO2)(SMe2)], 3 (C^N = ppy, 3a; bhq, 3b). The bis-chelate complexes [Pt(C^N)(P^P)](CF3CO2), 4, were obtained by reaction of complexes 3 with one equivalent of either of the P^P bisphosphine reagents, dppf = 1,1'-bis(diphenylphosphino)ferrocene or dppe = bis(diphenylphosphino)ethane. Complexes 4 were alternatively made by reaction of the complexes [PtMe(?(1)C-C^N)(P^P)], 2, with one equivalent of CF3CO2H. When the complex 3b was reacted with 0.5 equivalents of dppe, 0.5 equivalents of the related bis-chelate product, 4d, formed along with 0.5 equivalents of the unreacted starting complex 3b. In contrast, when the complex 3b was reacted with 0.5 equivalents of dppf, then the dimeric complex [Pt2(bhq)2(CF3CO2)2(?-dppf)], 5, formed in pure form. In all the above-mentioned acid reactions, the M-R bond rather than the M-C bond of the cycloplatinated complex is cleaved. When the PPh3 analogues of complexes 1, i.e. the complexes [PtR(C^N)(PPh3)], 6, in which C^N is ppy or tpy = deprotonated 2-p-tolylpyridine, were reacted with one equivalent of CF3CO2H, the course of the reaction reversed and the M-C bonds of the cycloplatinated complexes are cleaved rather than the M-R bonds. The latter reaction gave [PtR(?(1)N-HC^N)(PPh3)(CF3CO2)], as an equilibrium mixture of two isomers 7 and 8. Crystal structures of the typical complexes show a variety of extensive intermolecular hydrogen bonding involving C-H bonds from the different ligands and electronegative atoms (O or F) from the CF3CO2 moiety. On the basis of data obtained from kinetic studies (using (1)H NMR spectroscopy), a dissociative mechanism is proposed for the case of the 7c/8c isomerization process, involving dissociation of the ?(1)N-Htpy neutral ligand, rather than the alternative route of PPh3 or CF3CO2 ligand dissociation. PMID:23887622

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

2013-10-01

222

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

223

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

224

Histone methylation in myelodysplastic syndromes  

PubMed Central

Histone methylation is a type of epigenetic modification that is critical for the regulation of gene expression. Numerous studies have demonstrated that abnormalities of this newly characterized epigenetic modification are involved in the development of multiple diseases, including cancer. There is also emerging evidence for a link between histone methylation and the pathogenesis of myeloid neoplasms, including myelodysplastic syndromes (MDS). This article provides an overview of recent progress in the studies of histone methylation in myeloid malignancies, with an emphasis on MDS. We cover each type of histone methylation modification and their regulatory mechanisms, as well as their abnormalities in MDS or potential connections to MDS. We also summarize the recent progress in the development of inhibitors targeting histone methylation and their applications as potential therapeutic agents. PMID:22122281

Wei, Yue; Gañán-Gómez, Irene; Salazar-Dimicoli, Sophie; McCay, Sara L.; Garcia-Manero, Guillermo

2013-01-01

225

COMPARATIVE IN VITRO METHYLATION OF TRIVALENT AND PENTAVALENT ARSENIC SPECIES  

EPA Science Inventory

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

226

Methyl Halide Production by Fungi  

NASA Astrophysics Data System (ADS)

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

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

2005-12-01

227

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

228

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

PubMed Central

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

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

2014-01-01

229

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

230

Is there an attractive interaction between two methyl groups?  

NASA Astrophysics Data System (ADS)

A weak interaction was found between the two methyl groups in the complexes of XCH3-CH3BH2 (X = F, CN, NO2, HCO, and SOCH3), where the former methyl group acts as a Lewis acid and the latter one as a Lewis base. This directional interaction has small interaction energy, accompanied with some small changes in geometry and spectroscopy. Stronger Lewis acids FYH3 (Y = Si, Ge, and Sn) as well as Lewis bases CH3BeH and CH3MgH were compared. Dispersion energy is the major source of attraction and electrostatic contribution grows up to exceed dispersion energy for stronger interactions.

Zhuo, Hong-Ying; Jiang, Li-Xia; Li, Qing-Zhong; Li, Wen-Zuo; Cheng, Jian-Bo

2014-07-01

231

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  

E-print Network

An extensive search has been conducted to confirm transitions of \\textit{trans}-ethyl methyl ether (tEME, C$_2$H$_5$OCH$_3$), toward the high mass star forming region W51 e1/e2 using the 12 m Telescope of the Arizona Radio Observatory (ARO) 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 \\citet{FuchsSpace}. Additionally, reevaluation 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 - 30 mK, yielding an upper limit of the tEME column density of $\\leq$ 1.5 $\\times$ 10$^{15}$ cm$^{-2}$. This would make tEME at least a factor 2 times less abundant than dimethyl ether (CH$_3$OCH$_3$) toward W51 e1/e2. We also performed an extensive search for this species toward the high mass star forming region Sgr...

Carroll, P Brandon; Blake, Geoffrey A; Apponi, A J; Ziuyrs, L M; Remijan, Anthony

2014-01-01

232

AGAGE Observations of Methyl Bromide and Methyl Chloride at Mace Head, Ireland, and Cape Grim, Tasmania, 1998–2001  

Microsoft Academic Search

In situ AGAGE GC-MS measurements of methyl bromide (CH3Br) and methyl chloride (CH3Cl) at Mace Head, Ireland and Cape Grim, Tasmania (1998–2001) reveal a complex pattern of sources. At Mace Head both gases\\u000a have well-defined seasonal cycles with similar average annual decreases of 3.0% yr?1 (CH3Br) and 2.6% yr?1 (CH3Cl), and mean northern hemisphere baseline mole fractions of 10.37 0.05

P. G. Simmonds; R. G. Derwent; A. J. Manning; P. J. Fraser; P. B. Krummel; S. O'Doherty; R. G. Prinn; D. M. Cunnold; B. R. Miller; H. J. Wang; D. B. Ryall; L. W. Porter; R. F. Weiss; P. K. Salameh

2004-01-01

233

DNA methylation analysis in human cancer  

PubMed Central

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

O'Sullivan, Eileen; Goggins, Michael

2014-01-01

234

DNA methylation in inflammatory bowel disease and beyond  

PubMed Central

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

Low, Daren; Mizoguchi, Atsushi; Mizoguchi, Emiko

2013-01-01

235

Functional analysis of CpG methylation in the BRCA1 promoter region.  

PubMed

Understanding the role for DNA methylation in tumorigenesis has evolved from defining the location and extent of methylation in a variety of cancer-related genes to clarifying the functional and site-specific effects of aberrant methylation on gene expression. Our objectives were to characterize the functional effects of DNA methylation in the BRCA1 promoter and to clarify the functional status of the BRCA1 CRE (cAMP response element) motif. Luciferase reporter assays confirm that an intact CRE is important for BRCA1 expression in transient transfections. Luciferase activities were decreased in constructs where the CRE recognition sequence was altered and when constructs were methylated in vitro. Gel mobility shift and competition assays identified a DNA-protein complex recognizing the CRE motif that we were able to supershift using CREB-specific antibody. Furthermore this CRE is methylation sensitive, and we localized this methylation effect to a CpG dinucleotide within the BRCA1 CRE motif. The consequences of aberrant DNA methylation at specific transcription factor motifs, along with the multiple mutational events that can occur in a variety of essential genes such as BRCA1, paint a complex picture where both genetic and epigenetic changes contribute to tumour formation. PMID:11536045

DiNardo, D N; Butcher, D T; Robinson, D P; Archer, T K; Rodenhiser, D I

2001-08-30

236

Methylation of ribosomal proteins in bacteria: evidence of conserved modification of the eubacterial 50S subunit.  

PubMed Central

Methylation of the 50S ribosomal proteins from Bacillus stearothermophilus, Bacillus subtilis, Alteromonas espejiana, and Halobacterium cutirubrum was measured after the cells were grown in the presence of [1-14C]methionine or [methyl-3H]methionine or both. Two-dimensional polyacrylamide gel electrophoretic analysis revealed, in general, similar relative electrophoretic mobilities of the methylated proteins from each eubacterium studied. Proteins known to be structurally and functionally homologous in several microorganisms were all methylated. Thus, the following group of proteins, which appear to be involved in peptidyltransferase or in polyphenylalanine-synthesizing activity in B. stearothermophilus (P.E. Auron and S. R. Fahnestock, J. Biol. Chem. 256:10105-10110, 1981), were methylated (possible Escherichia coli methylated homologs are indicated in parentheses): BTL5(EL5), BTL6(EL3), BTL8(EL10), BTL11(EL11), BTL13(EL7L12) and BTL20b(EL16). In addition, the pentameric ribosomal complex BTL13 X BTL8, analogous to the complex EL7L12 X EL10 of E. coli, contained methylated proteins. Analysis of the methylated amino acids in the most heavily methylated proteins, BSL11 from B. subtilis and BTL11 from B. stearothermophilus, showed the presence of epsilon-N-trimethyllysine as the major methylated amino acid in both proteins, in agreement with known data for E. coli. In addition, BSL11 appeared to contain trimethylalanine, a characteristic, modified amino acid previously described only in EL11 from E. coli. These results and those previously obtained from other bacteria indicate a high degree of conservation for ribosomal protein methylation and suggest an important, albeit unknown, role for the modification of these components in eubacterial ribosomes. Images PMID:6425271

Amaro, A M; Jerez, C A

1984-01-01

237

4,4'-, 5,5'-, and 6,6'-dimethyl-2,2'-bipyridyls: The structures, phase transitions, vibrations, and methyl group tunneling of their complexes with chloranilic acid  

NASA Astrophysics Data System (ADS)

The crystal and molecular structures of 4,4'- and 6,6'-dimethyl-2,2'-bipyridyl complexes with 2,5-dichloro-3,6-dihydroxy-p-benzoquinone (chloranilic acid, CLA) have been determined and compared with those of the complex with the 5,5'-derivative, which is known to possess interesting antiferroelectric properties. In the crystalline state, all three compounds form hydrogen bonded chains with N+-H...O- and O-H...N bridges on both sides of the bipyridyl constituent. The comparison of three derivatives indicates that the N+-H...O- hydrogen bonds are shortest for the 5,5'-dimethyl complex. The 4,4'- and 6,6'-derivatives do not show any ferroelectric feature. The 6,6'-one is, however, characterized by a continuous phase transition, revealed in the differential scanning calorimetry, dilatometric, and dielectric characteristics. The tunneling splitting measured by neutron backscattering in the energy range ±30 ?eV for the neat dimethyl bipyridyls and their complexes with CLA indicates that the different splittings are primarily due to the crystal packing effect and that charge transfer between interacting compounds plays only a minor role.

Bator, G.; Sawka-Dobrowolska, W.; Sobczyk, L.; Grech, E.; Nowicka-Scheibe, J.; Pawlukoj?, A.; Wuttke, J.; Baran, J.; Owczarek, M.

2011-07-01

238

4,4'-, 5,5'-, and 6,6'-dimethyl-2,2'-bipyridyls: the structures, phase transitions, vibrations, and methyl group tunneling of their complexes with chloranilic acid.  

PubMed

The crystal and molecular structures of 4,4(')- and 6,6(')-dimethyl-2,2(')-bipyridyl complexes with 2,5-dichloro-3,6-dihydroxy-p-benzoquinone (chloranilic acid, CLA) have been determined and compared with those of the complex with the 5,5(')-derivative, which is known to possess interesting antiferroelectric properties. In the crystalline state, all three compounds form hydrogen bonded chains with N(+)-H···O(-) and O-H···N bridges on both sides of the bipyridyl constituent. The comparison of three derivatives indicates that the N(+)-H···O(-) hydrogen bonds are shortest for the 5,5(')-dimethyl complex. The 4,4(')- and 6,6(')-derivatives do not show any ferroelectric feature. The 6,6(')-one is, however, characterized by a continuous phase transition, revealed in the differential scanning calorimetry, dilatometric, and dielectric characteristics. The tunneling splitting measured by neutron backscattering in the energy range ±30 ?eV for the neat dimethyl bipyridyls and their complexes with CLA indicates that the different splittings are primarily due to the crystal packing effect and that charge transfer between interacting compounds plays only a minor role. PMID:21806140

Bator, G; Sawka-Dobrowolska, W; Sobczyk, L; Grech, E; Nowicka-Scheibe, J; Pawlukoj?, A; Wuttke, J; Baran, J; Owczarek, M

2011-07-28

239

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

PubMed Central

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

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

2013-01-01

240

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

PubMed

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

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

2015-01-27

241

In utero supplementation with methyl donors enhances allergic airway disease in mice  

PubMed Central

Asthma is a complex heritable disease that is increasing in prevalence and severity, particularly in developed countries such as the United States, where 11% of the population is affected. The contribution of environmental and genetic factors to this growing epidemic is currently not well understood. We developed the hypothesis, based on previous literature, that changes in DNA methylation resulting in aberrant gene transcription may enhance the risk of developing allergic airway disease. Our findings indicate that in mice, a maternal diet supplemented with methyl donors enhanced the severity of allergic airway disease that was inherited transgenerationally. Using a genomic approach, we discovered 82 gene-associated loci that were differentially methylated after in utero supplementation with a methyl-rich diet. These methylation changes were associated with decreased transcriptional activity and increased disease severity. Runt-related transcription factor 3 (Runx3), a gene known to negatively regulate allergic airway disease, was found to be excessively methylated, and Runx3 mRNA and protein levels were suppressed in progeny exposed in utero to a high-methylation diet. Moreover, treatment with a demethylating agent increased Runx3 gene transcription, further supporting our claim that a methyl-rich diet can affect methylation status and consequent transcriptional regulation. Our findings indicate that dietary factors can modify the heritable risk of allergic airway disease through epigenetic mechanisms during a vulnerable period of fetal development in mice. PMID:18802477

Hollingsworth, John W.; Maruoka, Shuichiro; Boon, Kathy; Garantziotis, Stavros; Li, Zhuowei; Tomfohr, John; Bailey, Nathaniel; Potts, Erin N.; Whitehead, Gregory; Brass, David M.; Schwartz, David A.

2008-01-01

242

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

243

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

244

Cytosine methylation alters DNA mechanical properties  

PubMed Central

DNA methylation plays an essential role in transcriptional control of organismal development in epigenetics, from turning off a specific gene to inactivation of entire chromosomes. While the biological function of DNA methylation is becoming increasingly clear, the mechanism of methylation-induced gene regulation is still poorly understood. Through single-molecule force experiments and simulation we investigated the effects of methylation on strand separation of DNA, a crucial step in gene expression. Molecular force assay and single-molecule force spectroscopy revealed a strong methylation dependence of strand separation. Methylation is observed to either inhibit or facilitate strand separation, depending on methylation level and sequence context. Molecular dynamics simulations provided a detailed view of methylation effects on strand separation, suggesting the underlying physical mechanism. According to our study, methylation in epigenetics may regulate gene expression not only through mechanisms already known but also through changing mechanical properties of DNA. PMID:21775342

Severin, Philip M. D.; Zou, Xueqing; Gaub, Hermann E.; Schulten, Klaus

2011-01-01

245

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

Code of Federal Regulations, 2014 CFR

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

2014-07-01

246

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

Code of Federal Regulations, 2012 CFR

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

2012-07-01

247

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

Code of Federal Regulations, 2010 CFR

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

2010-07-01

248

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

Code of Federal Regulations, 2011 CFR

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

2011-07-01

249

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

Code of Federal Regulations, 2013 CFR

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

2013-07-01

250

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

251

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

PubMed Central

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

Doherty, Rachael; Couldrey, Christine

2014-01-01

252

Comparisons of Non-Gaussian Statistical Models in DNA Methylation Analysis  

PubMed Central

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

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

2014-01-01

253

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...

254

Comprehensive DNA methylation and hydroxymethylation analysis in the human brain and its implication in mental disorders.  

PubMed

Covalent modifications of nucleotides, such as methylation or hydroxymethylation of cytosine, regulate gene expression. Early environmental risk factors play a role in mental disorders in adulthood. This may be in part mediated by epigenetic DNA modifications. Methods for comprehensive analysis of DNA methylation and hydroxymethylation include DNA modification methods such as bisulfite sequencing, or collection of methylated, hydroxymethylated, or unmethylated DNA by specific binding proteins, antibodies, or restriction enzymes, followed by sequencing or microarray analysis. Results from these experiments should be interpreted with caution because each method gives different result. Cytosine hydroxymethylation has different effects on gene expression than cytosine methylation; methylation of CpG islands is associated with lower gene expression, whereas hydroxymethylation in intragenic regions is associated with higher gene expression. The role of hydroxymethylcytosine is of particular interest in mental disorders because the modification is enriched in the brain and synapse related genes, and it exhibits dynamic regulation during development. Many DNA methylation patterns are conserved across species, but there are also human specific signatures. Comprehensive analysis of DNA methylation shows characteristic changes associated with tissues, brain regions, cell types, and developmental states. Thus, differences in DNA methylation status between tissues, brain regions, cell types, and developmental stages should be considered when the role of DNA methylation in mental disorders is studied. Several disease-associated changes in methylation have been reported: hypermethylation of SOX10 in schizophrenia, hypomethylation of HCG9 (HLA complex group 9) in bipolar disorder, hypermethylation of PRIMA1, hypermethylation of SLC6A4 (serotonin transporter) in bipolar disorder, and hypomethylation of ST6GALNAC1 in bipolar disorder. These findings need to be replicated in different patient populations to be generalized. Further studies including animal experiments are necessary to understand the roles of DNA methylation in mental disorders. PMID:24389572

Kato, Tadafumi; Iwamoto, Kazuya

2014-05-01

255

Surprising enhancing effect of methyl group on the strength of O⋯XF and S⋯XF (X=Cl and Br) halogen bonds  

NASA Astrophysics Data System (ADS)

The role of methyl group in H2O⋯XF and H2S⋯XF (X=Cl and Br) halogen-bonded complexes has been investigated with quantum chemical calculations. The halogen bond in the H2O⋯XF complexes is stronger than that in the H2S⋯XF complexes. However, the S⋯X halogen bond is stronger than the O⋯X one with the increase of methyl number. The result shows that the methyl group in the halogen acceptor has a positive contribution to the formation of halogen bond and there is a positive nonadditivity of methyl groups. Surprisingly, the methyl groups in dimethyl sulfide causes an increase of 150% for the interaction energy of S⋯Cl halogen bond. The natural bond orbital analyses have been performed to unveil the mechanism of the methyl group in the halogen bonding formation.

Li, Qingzhong; Jing, Bo; Liu, Zhenbo; Li, Wenzuo; Cheng, Jianbo; Gong, Baoan; Sun, Jiazhong

2010-09-01

256

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

257

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

258

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

PubMed

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

2015-01-30

259

Photo-sensitized oxidation of unsaturated fatty acid methyl esters. The identification of different pathways  

Microsoft Academic Search

and Summary  The photo-sensitized oxidation of methyl linolenate and methyl oleate was studied using erythrosine and riboflavin as sensitizers.\\u000a The complex mixtures of hydroperoxides obtained were analyzed for the proportion of conjugated products and, after reduction\\u000a to the corresponding mixtures of hydroxystearates, for the distribution of positional isomers. By comparing the mixtures with\\u000a that obtained from autoxidation, it was shown that

Henry W.-S. Chan

1977-01-01

260

Biosynthesis of isoprenoids: Crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritol kinase  

Microsoft Academic Search

4-Diphosphocytidyl-2C-methyl-D-erythritol kinase, an essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis, catalyzes the single ATP-dependent phosphorylation stage affording 4-diphosphocytidyl-2C-methyl-D-erythritol-2-phosphate. The 2-Å resolution crystal structure of the Escherichia coli enzyme in a ternary complex with substrate and a nonhydrolyzable ATP analogue reveals the molecular determinants of specificity and catalysis. The enzyme subunit displays the \\/ fold

Linda Miallau; Magnus S. Alphey; Lauris E. Kemp; Gordon A. Leonard; Sean M. McSweeney; Stefan Hecht; Adelbert Bacher; Wolfgang Eisenreich; Felix Rohdich; William N. Hunter

2003-01-01

261

Synthesis, crystal structure, magnetic properties, and theoretical studies of [(Cu(mepirizole)Br)2(mu-OH)(mu-pz)] (mepirizole=4-methoxy-2-(5-methoxy-3-methyl-1H-pyrazol-1-yl)-6-methylpyrimidine; pz=pyrazolate), a novel mu-pyrazolato-mu-hydroxo-dibridged copper(II) complex.  

PubMed

A novel mu-pyrazolato-mu-hydroxo-dibridged copper(II) complex has been synthesized and structurally characterized: [(Cu(mepirizole)Br)2(mu-OH)(mu-pz)] (mepirizole=4-methoxy-2-(5-methoxy-3-methyl-1H-pyrazol-1-yl)-6-methylpyrimidine; pz=pyrazolate). The title compound crystallizes in the monoclinic system, space group P2(1)/c, with a=15.618(2) A, b=15.369(3) A, c=16.071(3) A, and beta=112.250(1) degrees. The structure is built up of dinuclear [(Cu(mepirizole)Br)2(mu-OH)(mu-pz)] units with five-coordinated copper(II) ions (CuBrN3O chromophores) linked by mu2-OH and mu2-pyrazolato bridges that are well separated from each others. The intramolecular copper-copper distance is 3.378(3) A. Magnetic susceptibility data show that the copper atoms are strongly antiferromagnetically coupled with J=-770 cm(-1). The obtained triplet-singlet energy gap is compared with those reported for a series of related dimers. The strong antiferromagnetic coupling arising from the complementarity of the hydroxo and pyrazolato bridges has been discussed on the basis of DFT calculations. PMID:14658885

Escrivà, Emilio; García-Lozano, Julia; Martínez-Lillo, José; Nuñez, Hugo; Server-Carrió, Juan; Soto, Lucía; Carrasco, Rosa; Cano, Joan

2003-12-15

262

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

E-print Network

hydrocarbon fossil fuels to biofuels (particularly bioethanol and biodiesel [1] and [2]). Since the principal rate analysis showed that reactions pathways for the oxidation of methyl esters in the low components of plant matter, cellulose and starch, have the molecular formula (C6H10O5)n, these new fuels

Paris-Sud XI, Université de

263

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...

264

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

265

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

266

Radical SAM-Mediated Methylation Reactions  

PubMed Central

A subset of enzymes that belong to the radical S-adenosylmethionine (SAM) superfamily are able to catalyze methylation reactions. Substrates of these enzymes are distinct from the nucleophilic substrates that undergo methylation by a polar mechanism. Recently, activities of several radical SAM methylating enzymes have been reconstituted in vitro and their mechanisms of catalysis investigated. The RNA modifying enzymes RlmN and Cfr catalyze methylation via a methyl synthase mechanism. These enzymes use SAM in two distinct roles: as a source of a methyl group transferred to a conserved cysteine and as a source of 5?-deoxyadenosyl radical (5?-dA•). Hydrogen atom abstraction by this species generates a thiomethylene radical which adds into the RNA substrate, forming an enzyme-substrate covalent adduct. In another recent study, methylation of the indole moiety of tryptophan by the radical SAM and cobalamin-binding domain enzyme TsrM has been reconstituted. Methylcobalamin serves as an intermediate methyl donor in TsrM, and is proposed to transfer the methyl group as a methyl radical. Interestingly, despite the presence of the radical SAM motif, no reductive cleavage of SAM has been observed in this methylation. These important reconstitutions set the stage for further studies on mechanisms of radical methylation. PMID:23835516

Fujimori, Danica Galoni?

2013-01-01

267

Conservation and divergence in eukaryotic DNA methylation  

E-print Network

restriction enzymes sensitive to methylated CG sites (11, 12); the level of DNA methylation is determined of resolu- tion, restriction enzyme bias, difficulty in characterizing genome regions rich in repeats, and enzymes mediating the process (3). In humans, aberrant DNA methylation has been associated with diseases

268

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 ...

269

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

270

Alternansucrase acceptor reactions with methyl hexopyranosides.  

PubMed

Alternansucrase (EC 2.4.1.140, sucrose: (1-->6), (1-->3)-alpha-D-glucan 6(3)-alpha-D-glucosyltransferase) is a D-glucansucrase that synthesizes an alternating alpha-(1-->3), (1-->6)-linked D-glucan from sucrose. It also synthesizes oligosaccharides via D-glucopyranosyl transfer to various acceptor sugars. We have studied the acceptor products arising from methyl glycosides as model compounds in order to better understand the specificity of alternansucrase acceptor reactions. The initial product arising from methyl beta-D-glucopyranoside was methyl beta-isomaltoside, which was subsequently glucosylated to yield methyl beta-isomaltotrioside and methyl alpha-D-glucopyranosyl-(1-->3)-alpha-D-glucopyranosyl-(1-->6)-beta-D-glucopyranoside. These products are analogous to those previously described from methyl alpha-D-glucopyranoside. The major initial acceptor product from methyl alpha-D-mannopyranoside was methyl alpha-D-glucopyranosyl-(1-->6)-alpha-D-mannopyranoside, but several minor products were also isolated and characterized, including a 3,6-di-O-substituted mannopyranoside. Methyl alpha-D-galactopyranoside yielded two initial products, methyl alpha-D-glucopyranosyl-(1-->3)-alpha-D-galactopyranoside and methyl alpha-D-glucopyranosyl-(1-->4)-alpha-D-galactopyranoside, in a 2.5:1 molar ratio. Methyl D-allopyranosides were glucosylated primarily at position 6, yielding methyl alpha-D-glucopyranosyl-(1-->6)-D-allopyranosides. The latter subsequently gave rise to methyl alpha-D-glucopyranosyl-(1-->6)-alpha-D-glucopyranosyl-(1-->6)-D-allopyranosides. In general, the methyl alpha-D-hexopyranosides were better acceptors than the corresponding beta-glycosides. PMID:14499572

Côté, Gregory L; Dunlap, Christopher A

2003-09-10

271

The superiority of asymmetric alkyl methyl carbonates  

SciTech Connect

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

Ein-Eli, Y.; McDevitt, S.F.; Laura, R. [Covalent Associates, Inc., Woburn, MA (United States)

1998-01-01

272

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

SciTech Connect

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

Lawson, C.L.

1995-12-01

273

Increased DNA methylation in the suicide brain.  

PubMed

Clinical studies find that childhood adversity and stressful life events in adulthood increase the risk for major depression and for suicide. The predispositions to either major depression or suicide are thought to depend on genetic risk factors or epigenetic effects. We investigated DNA methylation signatures postmortem in brains of suicides with diagnosis of major depressive disorder. DNA methylation levels were determined at single C-phosphate-G (CpG) resolution sites within ventral prefrontal cortex of 53 suicides and nonpsychiatric controls, aged 16 to 89 years. We found that DNA methylation increases throughout the lifespan. Suicides showed an 8-fold greater number of methylated CpG sites relative to controls (P < 2.2 x 10(-16)), with greater DNA methylation changes over and above the increased methylation observed in normal aging. This increased DNA methylation may be a significant contributor to the neuropathology and psychopathology underlying the risk of suicide in depression. PMID:25364291

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

2014-09-01

274

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

275

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

276

Methylated Flavones from Teucrium polium.  

PubMed

The following four methylated flavones were obtained from the leaves of TEUCRIUM POLIUM L. (Labiatae). 4', 5-dihydroxy-6,7-dimethoxyflavone (cirsimaritin); 3', 5 dihydroxy-4',6,7-trimethoxyflavone (eupatorin); 5-hydroxy-4',7-dimethoxyflavone (apigenin-4', 7-dimethylether); 4', 5, 3'-trihydroxy-6,7-dimethoxyflavone (cirsiliol). One of these (4', 5-dihydroxy- 6,7-dimethoxyflavone) has been already reported in the same plant by Brieskorn and Biechele (1). PMID:17345353

Verykokidou-Vitsaropoulou, E; Vajias, C

1986-10-01

277

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

278

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

279

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

PubMed

The DNA adenine methyltransferase (Dam methylase) of Gammaproteobacteria and the cell cycle-regulated methyltransferase (CcrM) methylase of Alphaproteobacteria catalyze an identical reaction (methylation of adenosine moieties using S-adenosyl-methionine as a 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. The formation of 6-methyladenine reduces 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 have only partially been understood. Especially intriguing is the evidence that Dam methylation regulates virulence genes in Escherichia coli, Salmonella, and Yersinia at the posttranscriptional level. PMID:19175412

Marinus, Martin G; Casadesus, Josep

2009-05-01

280

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

PubMed Central

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

2013-01-01

281

Dynamics of Histone Lysine Methylation: Structures of Methyl Writers and Eraser  

PubMed Central

In Eukarya, the packaging of DNA into chromatin provides a barrier that allows for regulation of access to the genome. Chromatin is refractory to processes acting on DNA. ATP-dependent chromatin remodeling machines and histone-modifying complexes can overcome this barrier (or strengthen it in silencing processes). Both components of chromatin (DNA and histones) are subject to postsynthetic covalent modifications, including methylation of lysines (the focus of this chapter). These lysine marks are generated by a host of histone lysine methyltransferases (writers) and can be removed by histone lysine demethylases (erasers). Importantly, epigenetic modifications impact chromatin structure directly or can be read by effector regulatory modules. Here, we summarize current knowledge on structural and functional properties of various histone lysine methyltransfereases and demethylases, with emphasis on their importance as druggable targets. PMID:21141727

Upadhyay, Anup K.; Cheng, Xiaodong

2011-01-01

282

In vitro Assays of Inorganic Arsenic Methylation  

PubMed Central

Inorganic arsenic is extensively metabolized to produce mono-, di-, and trimethylated products. The formation of these metabolites produces a variety of intermediates that differ from inorganic arsenic in terms of patterns of distribution and retention and in toxic effects. In order to elucidate the pathway for arsenic methylation, it was necessary to develop a reliable in vitro assay system in which the formation of methylated metabolites could be monitored. Here, in vitro assay system that uses the postmicrosomal supernate from rat liver is used as the source of the enzymatic activity that catalyzes methylation reactions. This system can be used to study the requirements for methylation reactions (e.g., identifying the donor of methyl groups) and for screening of compounds as potential activators or inhibitors of arsenic methylation. PMID:20440380

Drobna, Zuzana; Styblo, Miroslav; Thomas, David J.

2009-01-01

283

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

284

Function and information content of DNA methylation.  

PubMed

Cytosine methylation is a DNA modification generally associated with transcriptional silencing. Factors that regulate methylation have been linked to human disease, yet how they contribute to malignances remains largely unknown. Genomic maps of DNA methylation have revealed unexpected dynamics at gene regulatory regions, including active demethylation by TET proteins at binding sites for transcription factors. These observations indicate that the underlying DNA sequence largely accounts for local patterns of methylation. As a result, this mark is highly informative when studying gene regulation in normal and diseased cells, and it can potentially function as a biomarker. Although these findings challenge the view that methylation is generally instructive for gene silencing, several open questions remain, including how methylation is targeted and recognized and in what context it affects genome readout. PMID:25592537

Schübeler, Dirk

2015-01-15

285

Electrogenerated chemiluminescence. 59. Rhenium complexes  

Microsoft Academic Search

Re(L)(CO)âCl complexes (where L is 1,10-phenanthroline, 2,2`-bipyridine, or a phenanthroline or bipyridine derivative containing methyl groups) are photoluminescent in fluid solution at room temperature. In acetonitrile solutions, these complexes display one chemically reversible one-electron reduction process and one chemically irreversible oxidation process. λ{sub max} for the luminescence is dependent on the nature of L, and a linear relationship between λ{sub

Mark M. Richter; Jeff D. Debad; A. J. Bard; D. R. Striplin; G. A. Crosby

1996-01-01

286

Effect of Body Mass Index on Global DNA Methylation in Healthy Korean Women  

PubMed Central

Obesity is known to be strongly associated with cardiovascular disease and cancer, the leading causes of mortality worldwide, and develops owing to interactions between genes and the environment. DNA methylation can act as a downstream effector of environmental signals, and analysis of this process therefore holds substantial promise for identifying mechanisms through which genetic and environmental factors jointly contribute to disease risk. Global DNA methylation of peripheral blood cells has recently been proposed as a potential biomarker for disease risk. Repetitive element DNA methylation has been shown to be associated with prominent obesity-related chronic diseases, but little is known about its relationship with weight status. In this study, we quantified the methylation of Alu elements in the peripheral blood DNA of 244 healthy women with a range of body mass indexes (BMIs) using pyrosequencing technology. Among the study participants, certain clinical laboratory parameters, including hemoglobin, serum glutamic oxaloacetic transaminase, serum glutamic-pyruvic transaminase, total cholesterol, and triglyceride levels were found to be strongly associated with BMI. Moreover, a U-shaped association between BMI and Alu methylation was observed, with the lowest methylation levels occurring at BMIs of between 23 and 30 kg/m2. However, there was no significant association between Alu methylation and age, smoking status, or alcohol consumption. Overall, we identified a differential influence of BMI on global DNA methylation in healthy Korean women, indicating that BMI-related changes in Alu methylation might play a complex role in the etiology and pathogenesis of obesity. Further studies are required to elucidate the mechanisms underlying this relationship. PMID:24938226

Na, Yeon Kyung; Hong, Hae Sook; Lee, Duk Hee; Lee, Won Kee; Kim, Dong Sun

2014-01-01

287

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

288

Transfer RNA methylating activity of yeast mitochondria  

PubMed Central

Mitochondria isolated from Saccharomyces cerevisiae and purified in Urografin or sucrose gradient contain tRNA methylating activity with specificities different from those of the cytoplasm. The main reaction product, using E.coli tRNA as methyl group acceptor, is N2,-N2-dimethylguanine. The corresponding mitochondrial methylase is coded by nuclear DNA. A DNA methylating activity is also associated with yeast mitochondria. PMID:10793751

Smolar, Nina; Svensson, Ingvar

1974-01-01

289

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

290

Characterization of DNA methylation in the rat.  

PubMed

In the rat, differentiation and cell proliferation both affect DNA methylation. We studied 5-methylcytosine at the inner cytosine of the sequence C-C-G-G, a common methylation site, using endonuclease MspI (which cleaves C-C-G-G- and C-mC-G-G), and its isoschizomer HpaII (which cleaves only C-C-G-G). DNA from all tissues and cell lines studied was methylated at C-C-G-G, at levels ranging from 45 to 80%, but the methylation sites were not distributed uniformly. Our analysis suggests a model in which cells contain variable amounts of three DNA methylation states, averaging 30-40, 70-80 and 95-100% methylation, respectively. One biological parameter that alters methylation is the proliferative state of the cell. We observed that NRK, a non-transformed cell line, increased its DNA methylation from 45 to 67% when monolayer cultures became confluent and non-dividing. We also observed that a class of repetitive DNA was completely methylated in DNA from all sources except a transformed cell line. PMID:6297564

Kunnath, L; Locker, J

1982-12-31

291

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

292

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

PubMed

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

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

2010-01-01

293

Review study on CG islands and CpG methylation  

E-print Network

is it important to study DNA methylation? · Methylation is one of the epigenetic marker. · Examples: · Experiments do motivate us to study more about the methylation and epigenetics. · Some mechanisms by which. · The impact of CpG methylation on structure of DNA · Role of different enzymes involved in DNA methylation

Rohs, Remo

294

Mapping the Epigenetic Basis of Complex Traits  

E-print Network

Mapping the Epigenetic Basis of Complex Traits Sandra Cortijo,1 * René Wardenaar,2 * Maria Colomé Johannes2 Quantifying the impact of heritable epigenetic variation on complex traits is an emerging that several of these differentially methylated regions (DMRs) act as bona fide epigenetic quantitative trait

Napp, Nils

295

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

SciTech Connect

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

Supakar, P.C.; Weist, D.; Zhang, D.; Inamdar, N.; Zhang, Xianyang; Khan, R.; Ehrlich, M. (Tulane Medical School, New Orleans, LA (USA)); Ehrlich, K.C. (Department of Agriculture, New Orleans, LA (USA))

1988-08-25

296

Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin  

Microsoft Academic Search

In mammals and plants, formation of heterochromatin is associated with hypermethylation of DNA at CpG sites and histone H3 methylation at lysine 9. Previous studies have revealed that maintenance of DNA methylation in Neurospora and Arabidopsis requires histone H3 methylation. A feedback loop from DNA methylation to histone methylation, however, is less understood. Its recent examination in Arabidopsis with a

Muhammad Tariq; Hidetoshi Saze; Aline V. Probst; Jacek Lichota; Yoshiki Habu; Jerzy Paszkowski

2003-01-01

297

Pathodiagnostic parameters and evaluation of O?- methyl guanine methyl transferase gene promoter methylation in meningiomas.  

PubMed

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

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

2014-04-01

298

40 CFR 180.445 - Bensulfuron methyl; tolerances for residues.  

Code of Federal Regulations, 2010 CFR

...bensulfuron methyl (methyl-2[[[[[(4,6-dimethoxy-pyrimidin-2-yl) amino] carbonyl] amino] sulfonyl] methyl] benzoate) in or on the following raw agricultural commodities: Commodity Parts per million Crayfish 0.05 Rice,...

2010-07-01

299

21 CFR 173.385 - Sodium methyl sulfate.  

Code of Federal Regulations, 2014 CFR

...Sodium methyl sulfate may be present in pectin in accordance with the following conditions...present as the result of methylation of pectin by sulfuric acid and methyl alcohol...exceed 0.1 percent by weight of the...

2014-04-01

300

21 CFR 173.385 - Sodium methyl sulfate.  

Code of Federal Regulations, 2013 CFR

...Sodium methyl sulfate may be present in pectin in accordance with the following conditions...present as the result of methylation of pectin by sulfuric acid and methyl alcohol...exceed 0.1 percent by weight of the...

2013-04-01

301

21 CFR 173.385 - Sodium methyl sulfate.  

Code of Federal Regulations, 2012 CFR

...Sodium methyl sulfate may be present in pectin in accordance with the following conditions...present as the result of methylation of pectin by sulfuric acid and methyl alcohol...exceed 0.1 percent by weight of the...

2012-04-01

302

21 CFR 173.385 - Sodium methyl sulfate.  

Code of Federal Regulations, 2011 CFR

...Sodium methyl sulfate may be present in pectin in accordance with the following conditions...present as the result of methylation of pectin by sulfuric acid and methyl alcohol...exceed 0.1 percent by weight of the...

2011-04-01

303

21 CFR 173.385 - Sodium methyl sulfate.  

Code of Federal Regulations, 2010 CFR

...Sodium methyl sulfate may be present in pectin in accordance with the following conditions...present as the result of methylation of pectin by sulfuric acid and methyl alcohol...exceed 0.1 percent by weight of the...

2010-04-01

304

Neurological Manifestation of Methyl Bromide Intoxication  

Microsoft Academic Search

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, un- consciousness

Kammant Phanthumchinda

305

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 ...

306

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

307

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

308

Adsorption kinetics of methyl violet onto perlite  

Microsoft Academic Search

This study examines adsorption kinetics and activation parameters of methyl violet on perlite. The effect of process parameters like contact time, concentration of dye, temperature and pH on the extent of methyl violet adsorption from solution has been investigated. Results of the kinetic studies show that the adsorption reaction is first order with respect to dye solution concentration with activation

Mehmet Do?an; Mahir Alkan

2003-01-01

309

Reaction of Lactobacillus histidine decarboxylase with L-histidine methyl ester.  

PubMed

L-Histidine methyl ester inactivates histidine decarboxylase in a time-dependent manner. The possibility was considered that an irreversible reaction between enzyme and inhibitor occurs [Recsei, P. A., & Snell, E. E. (1970) Biochemistry 9, 1492-1497]. We have confirmed time-dependent inactivation by histidine methyl ester and have investigated the structure of the enzyme-inhibitor complex. Upon exposure to either 8 M guanidinium chloride or 6% trichloroacetic acid, unchanged histidine methyl ester is recovered. Formation of the complex involves Schiff base formation, most likely with the active site pyruvyl residue [Huynh, Q. K., & Snell, E. E. (1986) J. Biol. Chem. 261, 4389-4394], but does not involve additional irreversible covalent interaction between inhibitor and enzyme. Complex formation is a two-step process involving rapidly reversible formation of a loose complex and essentially irreversible formation of a tight complex. For the formation of the tight complex, Ki = 80 nM and koff = 2.5 X 10(-4) min-1. Time-dependent inhibition was also observed with L-histidine ethyl ester, L-histidinamide, and DL-3-amino-4-(4-imidazolyl)-2-butanone. No inactivation was observed with glycine methyl ester or histamine. We propose that in the catalytic reaction the carboxyl group of the substrate is in a hydrophobic region. The unfavorable interaction between the carboxylate group and the hydrophobic region facilitates decarboxylation [Crosby, J., Stone, R., & Liehard, G. E. (1970) J. Am. Chem. Soc. 92, 2891-2900]. With histidine methyl ester this unfavorable interaction is no longer present; hence, there is tight binding.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:3651438

Alston, T A; Abeles, R H

1987-06-30

310

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

PubMed Central

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

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

2002-01-01

311

DNA Sequence Explains Seemingly Disordered Methylation Levels in Partially Methylated Domains of Mammalian Genomes  

PubMed Central

For the most part metazoan genomes are highly methylated and harbor only small regions with low or absent methylation. In contrast, partially methylated domains (PMDs), recently discovered in a variety of cell lines and tissues, do not fit this paradigm as they show partial methylation for large portions (20%–40%) of the genome. While in PMDs methylation levels are reduced on average, we found that at single CpG resolution, they show extensive variability along the genome outside of CpG islands and DNase I hypersensitive sites (DHS). Methylation levels range from 0% to 100% in a roughly uniform fashion with only little similarity between neighboring CpGs. A comparison of various PMD-containing methylomes showed that these seemingly disordered states of methylation are strongly conserved across cell types for virtually every PMD. Comparative sequence analysis suggests that DNA sequence is a major determinant of these methylation states. This is further substantiated by a purely sequence based model which can predict 31% (R2) of the variation in methylation. The model revealed CpG density as the main driving feature promoting methylation, opposite to what has been shown for CpG islands, followed by various dinucleotides immediately flanking the CpG and a minor contribution from sequence preferences reflecting nucleosome positioning. Taken together we provide a reinterpretation for the nucleotide-specific methylation levels observed in PMDs, demonstrate their conservation across tissues and suggest that they are mainly determined by specific DNA sequence features. PMID:24550741

Gaidatzis, Dimos; Burger, Lukas; Murr, Rabih; Lerch, Anita; Dessus-Babus, Sophie; Schübeler, Dirk; Stadler, Michael B.

2014-01-01

312

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

NASA Astrophysics Data System (ADS)

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

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

2012-07-01

313

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

314

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

315

An alternative mechanism for the methylation of phosphoethanolamine catalyzed by Plasmodium falciparum phosphoethanolamine methyltransferase.  

PubMed

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

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

2014-12-01

316

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

317

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

PubMed

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

318

DNA methylation: roles in rheumatoid arthritis.  

PubMed

Rheumatoid arthritis (RA) is an immune-mediated disease of unknown cause that primarily affects the joints and ultimately leads to joint destruction. In recent years, the potential role of DNA methylation in the development of RA is raising great expectations among clinicians and researchers. DNA methylation influences diverse aspects of the disease and regulates epigenetic silencing of genes and behavior of several cell types, especially fibroblast-like synoviocytes (FLS), the most resident cells in joints. The activation of FLS is generally regarded as a key process in the development of RA that actively results in the promotion of ongoing inflammation and joint damage. It has also been shown that aberrant DNA methylation occurs in the pathogenesis of RA and contributes to the development of the disease. Recently, there has been an impressive increase in studies involving DNA methylation in RA. In this paper, we consider the role of DNA methylation in the development of RA. PMID:24652004

Yuan, Feng-Lai; Li, Xia; Xu, Rui-Sheng; Jiang, Dong-Lin; Zhou, Xiao-Gang

2014-09-01

319

Prebiotic Methylation and the Evolution of Methyl Transfer Reactions in Living Cells  

NASA Astrophysics Data System (ADS)

An hypothesis is presented for the prebiotic origin of methyl groups and the evolution of methyl transfer reactions in living cells. This hypothesis, described in terms of prebiotic and early biotic chemical evolution, is based on experimental observations in our lab and in those of others, and on the mechanisms of enzymatic methyl transfer reactions that occur in living cells. Of particular interest is our demonstration of the reductive methylation of ethanolamine and glycine in aqueous solution by excess formaldehyde. These reactions, involving prebiotic compounds and conditions, are mechanistically analogous to the de novo origin of methyl groups in modern cells by reduction of methylene tetrahydrofolate. Furthermore, modern cellular methyl transfers from S-adenosylmethionine to amine nitrogen may involve formaldehyde as an intermediate and subsequent reductive methylation, analogous to the prebiotic chemistry observed herein.

Waddell, Thomas G.; Eilders, Lon L.; Patel, Bipin P.; Sims, Michael

2000-12-01

320

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...

321

Monozygotic twins affected with major depressive disorder have greater variance in methylation than  

E-print Network

Monozygotic twins affected with major depressive disorder have greater variance in methylation than their unaffected co-twin EM Byrne1,4 , T Carrillo-Roa2,4 , AK Henders2 , L Bowdler2 , AF McRae1,2 , AC Heath3 , NG suggests the additional role of epigenetic mechanisms influencing susceptibility for complex traits. DNA

Cai, Long

322

Dissolved organic matter enhances microbial mercury methylation under sulfidic conditions.  

PubMed

Dissolved organic matter (DOM) is generally thought to lower metal bioavailability in aquatic systems due to the formation of metal-DOM complexes that reduce free metal ion concentrations. However, this model may not be pertinent for metal nanoparticles, which are now understood to be ubiquitous, sometimes dominant, metal species in the environment. The influence of DOM on Hg bioavailability to microorganisms was examined under conditions (0.5-5.0 nM Hg and 2-10 ?M sulfide) that favor the formation of ?-HgS(s) (metacinnabar) nanoparticles. We used the methylation of stable-isotope enriched (201)HgCl(2) by Desulfovibrio desulfuricans ND132 in short-term washed cell assays as a sensitive, environmentally significant proxy for Hg uptake. Suwannee River humic acid (SRHA) and Williams Lake hydrophobic acid (WLHPoA) substantially enhanced (2- to 38-fold) the bioavailability of Hg to ND132 over a wide range of Hg/DOM ratios (9.4 pmol/mg DOM to 9.4 nmol/mg DOM), including environmentally relevant ratios. Methylmercury (MeHg) production by ND132 increased linearly with either SRHA or WLHPoA concentration, but SRHA, a terrestrially derived DOM, was far more effective at enhancing Hg-methylation than WLHPoA, an aquatic DOM dominated by autochthonous sources. No DOM-dependent enhancement in Hg methylation was observed in Hg-DOM-sulfide solutions amended with sufficient l-cysteine to prevent ?-HgS(s) formation. We hypothesize that small HgS particles, stabilized against aggregation by DOM, are bioavailable to Hg-methylating bacteria. Our laboratory experiments provide a mechanism for the positive correlations between DOC and MeHg production observed in many aquatic sediments and wetland soils. PMID:22309093

Graham, Andrew M; Aiken, George R; Gilmour, Cynthia C

2012-03-01

323

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

324

Structural Basis for Specific Binding of Human MPP8 Chromodomain to Histone H3 Methylated at Lysine 9  

Microsoft Academic Search

BackgroundM-phase phosphoprotein 8 (MPP8) was initially identified to be a component of the RanBPM-containing large protein complex, and has recently been shown to bind to methylated H3K9 both in vivo and in vitro. MPP8 binding to methylated H3K9 is suggested to recruit the H3K9 methyltransferases GLP and ESET, and DNA methyltransferase 3A to the promoter of the E-cadherin gene, mediating

Jing Li; Zhihong Li; Jianbin Ruan; Chao Xu; Yufeng Tong; Patricia W. Pan; Wolfram Tempel; Lissete Crombet; Jinrong Min; Jianye Zang; Nick Gay

2011-01-01

325

DNA Methylation: An Introduction to the Biology and the Disease-Associated Changes of a Promising Biomarker  

Microsoft Academic Search

DNA methylation occurring on the 5 position of the pyrimidine ring of cytosines in the context of the dinucleotide sequence\\u000a CpG forms one of the multiple layers of epigenetic mechanisms controlling and modulating gene expression through chromatin\\u000a structure. It closely interacts with histone modifications and chromatin remodeling complexes to form the genomic chromatin\\u000a landscape. DNA methylation is essential for proper

Jörg Tost

2010-01-01

326

DNA Methylation and Gene Expression Changes in Monozygotic Twins Discordant for Psoriasis: Identification of Epigenetically Dysregulated Genes  

Microsoft Academic Search

Monozygotic (MZ) twins do not show complete concordance for many complex diseases; for example, discordance rates for autoimmune diseases are 20%–80%. MZ discordance indicates a role for epigenetic or environmental factors in disease. We used MZ twins discordant for psoriasis to search for genome-wide differences in DNA methylation and gene expression in CD4+ and CD8+ cells using Illumina's HumanMethylation27 and

Kristina Gervin; Magnus D. Vigeland; Morten Mattingsdal; Martin Hammerø; Heidi Nygård; Anne O. Olsen; Ingunn Brandt; Jennifer R. Harris; Dag E. Undlien; Robert Lyle

2012-01-01

327

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

328

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

329

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.

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

2015-01-01

330

Kinetics and Thermodynamics of H Transfer from -C5R5)Cr(CO)3H (R ) Ph, Me, H) to Methyl Methacrylate and  

E-print Network

gives the corresponding metalloradical 1a as termination depletes the concentration of the methyl the original (and most effective) chain transfer catalysts have been cobalt(II) complexes,2 we have found

Baik, Mu-Hyun

331

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

332

The Rise and Fall of Mercury Methylation in an Experimental Reservoir  

Microsoft Academic Search

For the past 9 years, we experimentally flooded a wetland complex (peatland surrounding an open water pond) at the Experimental Lakes Area (ELA), northwestern Ontario, Canada, to examine the biogeochemical cycling of methyl mercury (MeHg) in reservoirs. Using input-output budgets, we found that prior to flooding, the wetland complex was a net source of approximately 1.7 mg MeHg ha -1

VINCENT L. S T. LOUIS; JOHN W. M. R UDD; CAROL A. K ELLY; KENNETH G. B EATY; RAYMOND H. H ESSLEIN; ANDREW H EYES; ANDREW R. M AJEWSKI

2004-01-01

333

Mercury methylation by the methanogen Methanospirillum hungatei.  

PubMed

Methylmercury (MeHg), a neurotoxic substance that accumulates in aquatic food chains and poses a risk to human health, is synthesized by anaerobic microorganisms in the environment. To date, mercury (Hg) methylation has been attributed to sulfate- and iron-reducing bacteria (SRB and IRB, respectively). Here we report that a methanogen, Methanospirillum hungatei JF-1, methylated Hg in a sulfide-free medium at comparable rates, but with higher yields, than those observed for some SRB and IRB. Phylogenetic analyses showed that the concatenated orthologs of the Hg methylation proteins HgcA and HgcB from M. hungatei are closely related to those from known SRB and IRB methylators and that they cluster together with proteins from eight other methanogens, suggesting that these methanogens may also methylate Hg. Because all nine methanogens with HgcA and HgcB orthologs belong to the class Methanomicrobia, constituting the late-evolving methanogenic lineage, methanogenic Hg methylation could not be considered an ancient metabolic trait. Our results identify methanogens as a new guild of Hg-methylating microbes with a potentially important role in mineral-poor (sulfate- and iron-limited) anoxic freshwater environments. PMID:23934484

Yu, Ri-Qing; Reinfelder, John R; Hines, Mark E; Barkay, Tamar

2013-10-01

334

Mercury Methylation by the Methanogen Methanospirillum hungatei  

PubMed Central

Methylmercury (MeHg), a neurotoxic substance that accumulates in aquatic food chains and poses a risk to human health, is synthesized by anaerobic microorganisms in the environment. To date, mercury (Hg) methylation has been attributed to sulfate- and iron-reducing bacteria (SRB and IRB, respectively). Here we report that a methanogen, Methanospirillum hungatei JF-1, methylated Hg in a sulfide-free medium at comparable rates, but with higher yields, than those observed for some SRB and IRB. Phylogenetic analyses showed that the concatenated orthologs of the Hg methylation proteins HgcA and HgcB from M. hungatei are closely related to those from known SRB and IRB methylators and that they cluster together with proteins from eight other methanogens, suggesting that these methanogens may also methylate Hg. Because all nine methanogens with HgcA and HgcB orthologs belong to the class Methanomicrobia, constituting the late-evolving methanogenic lineage, methanogenic Hg methylation could not be considered an ancient metabolic trait. Our results identify methanogens as a new guild of Hg-methylating microbes with a potentially important role in mineral-poor (sulfate- and iron-limited) anoxic freshwater environments. PMID:23934484

Reinfelder, John R.; Hines, Mark E.

2013-01-01

335

Methylation kinetics and CpG-island methylator phenotyope status in colorectal cancer cell lines  

PubMed Central

Background Hypermethylation of CpG islands is thought to contribute to carcinogenesis through the inactivation of tumor suppressor genes. Tumor cells with relatively high levels of CpG island methylation are considered CpG island methylator phenotypes (CIMP). The mechanisms that are responsible for regulating the activity of de novo methylation are not well understood. Results We quantify and compare de novo methylation kinetics in CIMP and non-CIMP colon cancer cell lines in the context of different loci, following 5-aza-2’deoxycytidine (5-AZA)-mediated de-methylation of cells. In non-CIMP cells, a relatively fast rate of re-methylation is observed that starts with a certain time delay after cessation of 5-AZA treatment. CIMP cells, on the other hand, start re-methylation without a time delay but at a significantly slower rate. A mathematical model can account for these counter-intuitive results by assuming negative feedback regulation of de novo methylation activity and by further assuming that this regulation is corrupted in CIMP cells. This model further suggests that when methylation levels have grown back to physiological levels, de novo methylation activity ceases in non-CIMP cells, while it continues at a constant low level in CIMP cells. Conclusions We propose that the faster rate of re-methylation observed in non-CIMP compared to CIMP cells in our study could be a consequence of feedback-mediated regulation of DNA methyl transferase activity. Testing this hypothesis will involve the search for specific feedback regulatory mechanisms involved in the activation of de novo methylation. Reviewers’ report This article was reviewed by Georg Luebeck, Tomasz Lipniacki, and Anna Marciniak-Czochra PMID:23758948

2013-01-01

336

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

337

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

338

Dietary and lifestyle factors of DNA methylation.  

PubMed

Lifestyle factors, such as diet, smoking, physical activity, and body weight management, are known to constitute the majority of cancer causes. Epigenetics has been widely proposed as a main mechanism that mediates the reversible effects of dietary and lifestyle factors on carcinogenesis. This chapter reviews human studies on potential dietary and lifestyle determinants of DNA methylation. Apart from a few prospective investigations and interventions of limited size and duration, evidence mostly comes from cross-sectional observational studies and supports some associations. Studies to date suggest that certain dietary components may alter genomic and gene-specific DNA methylation levels in systemic and target tissues, affecting genomic stability and transcription of tumor suppressors and oncogenes. Most data and supportive evidence exist for folate, a key nutritional factor in one-carbon metabolism that supplies the methyl units for DNA methylation. Other candidate bioactive food components include alcohol and other key nutritional factors of one-carbon metabolism, polyphenols and flavonoids in green tea, phytoestrogen, and lycopene. Some data also support a link of DNA methylation with physical activity and energy balance. Effects of dietary and lifestyle exposures on DNA methylation may be additionally modified by common genetic variants, environmental carcinogens, and infectious agents, an aspect that remains largely unexplored. In addition, growing literature supports that the environmental conditions during critical developmental stages may influence later risk of metabolic disorders in part through persistent programming of DNA methylation. Further research of these modifiable determinants of DNA methylation will improve our understanding of cancer etiology and may present certain DNA methylation markers as attractive surrogate endpoints for prevention research. Considering the plasticity of epigenetic marks and correlated nature of lifestyle factors, more longitudinal studies of healthy individuals of varying age, sex, and ethnic groups are warranted, ideally with comprehensive data collection on various lifestyle factors. PMID:22359306

Lim, Unhee; Song, Min-Ae

2012-01-01

339

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

PubMed Central

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

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

2010-01-01

340

Integrated genetic and epigenetic analysis identifies haplotype-specific methylation in the FTO type 2 diabetes and obesity susceptibility locus.  

PubMed

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

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

2010-01-01

341

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

342

Biological and biochemical modulation of DNA methylation.  

PubMed

Epigenetic regulation is facilitated by a battery of proteins that act as 'writers' or 'erasers' to add or remove biochemical modifications to DNA and histone proteins. DNA modifications, histone modifications and long noncoding RNAs function interdependently through reciprocal crosstalk. This review will focus on DNA methylation and DNA methyltransferases with emphasis on how biological and biochemical factors such as histone modifications and noncoding RNAs might play a role in modulating DNA methylation. Other physiological and biochemical factors that can modify DNA methylation marks will also be discussed including chemical exposures and inflammation. PMID:25531254

Lo, Raymond; Weksberg, Rosanna

2014-12-01

343

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

344

Prenatal Exposure to Polycyclic Aromatic Hydrocarbons, Benzo[a]pyrene–DNA Adducts, and Genomic DNA Methylation in Cord Blood  

PubMed Central

Background: Polycyclic aromatic hydrocarbons (PAHs) are carcinogenic environmental pollutants generated during incomplete combustion. After exposure and during metabolism, PAHs can form reactive epoxides that can covalently bind to DNA. These PAH–DNA adducts are established markers of cancer risk. PAH exposure has been associated with epigenetic alterations, including genomic cytosine methylation. Both global hypomethylation and hypermethylation of specific genes have been associated with cancer and other diseases in humans. Experimental evidence suggests that PAH–DNA adduct formation may preferentially target methylated genomic regions. Early embryonic development may be a particularly susceptible period for PAH exposure, resulting in both increased PAH–DNA adducts and altered DNA methylation. Objective: We explored whether prenatal exposure to PAHs is associated with genomic DNA methylation in cord blood and whether methylation levels are associated with the presence of detectable PAH–DNA adducts. Methods: In a longitudinal cohort study of nonsmoking women in New York City, we measured PAH exposure during pregnancy using personal air monitors, assessed PAH internal dose using prenatal urinary metabolites (in a subset), and quantified benzo[a]pyrene–DNA adducts and genomic DNA methylation in cord blood DNA among 164 participants. Results: Prenatal PAH exposure was associated with lower global methylation in umbilical cord white blood cells (p = 0.05), but global methylation levels were positively associated with the presence of detectable adducts in cord blood (p = 0.01). Conclusions: These observations suggest that PAH exposure was adequate to alter global methylation in our study population. Additional epidemiologic studies that can measure site-specific cytosine methylation and adduct formation will improve our ability to understand this complex molecular pathway in vivo. PMID:22256332

Tang, Deliang; Zhu, Deguang; Qu, Lirong; Sjödin, Andreas; Li, Zheng; Camann, David; Perera, Frederica P.

2012-01-01

345

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

346

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

347

Preparation and Characterization of Pioglitazone Cyclodextrin Inclusion Complexes  

PubMed Central

Pioglitazone, a class II Biopharmaceutical Classification System drug having poor water solubility and slow dissolution rate may have a negative impact on its subtherapeutic plasma drug levels leading to therapeutic failure. In order to improve its water solubility and thus dissolution, cyclodextrin complexation technique was followed. The phase solubility studies were carried using three different types of cyclodextrins viz., ?, methyl-? and ?-cyclodextrins. The Gibbs free energy was calculated in order to determine ease of the complexation. Binary systems of pioglitazone with cyclodextrins were prepared by kneading method and spray drying method. The phase solubility profiles with all the three cyclodextrins were classified as AL-type, indicating the formation of 1:1 stoichiometric inclusion complexes. The complexation capability of cyclodextrins with pioglitazone increased in the order of methyl-? > ? > ?-cyclodextrin. The Gibbs free energy was found to be in the order ? > methyl-? > ? cyclodextrin. Characterization of inclusion complexes was done by solubility studies, in vitro dissolution studies, Fourier transformation-infrared spectroscopy, scanning electron microscopy, differential scanning calorimetry and X-ray powder diffractometry studies. Inclusion complexes exhibited higher rates of dissolution than the corresponding physical mixtures and pure drug. Greater solubility was observed with spray-dried methyl-? cyclodextrin complexes (2.29 ± 0.001 mg/ml) in comparison to the kneaded methyl-? cyclodextrin complexes (1.584 ± 0.053 mg/ml) and pure drug (0.0714 ± 0.0018 mg/ml). PMID:22224032

Pandit, V; Gorantla, R; Devi, K; Pai, RS; Sarasija, S

2011-01-01

348

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

349

Seasonality, Sinks and Sources of Methyl Chloride and Methyl Bromide From the Tallgrass Prairie  

Microsoft Academic Search

Net and gross fluxes of methyl chloride (CH3Cl) and methyl bromide (CH3Br) were measured between 2006 and 2008 from a variety of vegetation types and climatic conditions at a tallgrass prairie (Konza Prairie, Manhattan, KS). Gross consumption and production rates were calculated using a stable isotope tracer technique that entailed a small addition of 13C labeled methyl halides, and an

T. Abel; R. C. Rhew

2008-01-01

350

Function and Evolution of DNA Methylation in Nasonia vitripennis  

PubMed Central

The parasitoid wasp Nasonia vitripennis is an emerging genetic model for functional analysis of DNA methylation. Here, we characterize genome-wide methylation at a base-pair resolution, and compare these results to gene expression across five developmental stages and to methylation patterns reported in other insects. An accurate assessment of DNA methylation across the genome is accomplished using bisulfite sequencing of adult females from a highly inbred line. One-third of genes show extensive methylation over the gene body, yet methylated DNA is not found in non-coding regions and rarely in transposons. Methylated genes occur in small clusters across the genome. Methylation demarcates exon-intron boundaries, with elevated levels over exons, primarily in the 5? regions of genes. It is also elevated near the sites of translational initiation and termination, with reduced levels in 5? and 3? UTRs. Methylated genes have higher median expression levels and lower expression variation across development stages than non-methylated genes. There is no difference in frequency of differential splicing between methylated and non-methylated genes, and as yet no established role for methylation in regulating alternative splicing in Nasonia. Phylogenetic comparisons indicate that many genes maintain methylation status across long evolutionary time scales. Nasonia methylated genes are more likely to be conserved in insects, but even those that are not conserved show broader expression across development than comparable non-methylated genes. Finally, examination of duplicated genes shows that those paralogs that have lost methylation in the Nasonia lineage following gene duplication evolve more rapidly, show decreased median expression levels, and increased specialization in expression across development. Methylation of Nasonia genes signals constitutive transcription across developmental stages, whereas non-methylated genes show more dynamic developmental expression patterns. We speculate that loss of methylation may result in increased developmental specialization in evolution and acquisition of methylation may lead to broader constitutive expression. PMID:24130511

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

2013-01-01

351

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;); Vincent Colot (Cold Spring Harbor Laboratory;)

2001-08-10

352

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

353

75 FR 19272 - Thifensulfuron methyl; Pesticide Tolerances  

Federal Register 2010, 2011, 2012, 2013, 2014

...risk posed by human exposure to the pesticide. For hazards...no adverse effects are observed...the adverse effect expected in...epa.gov/pesticides/factsheets...methyl used for human risk assessment...Assessment...

2010-04-14

354

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

355

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

356

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

357

Structural Dynamics of Protein Lysine Methylation and De-Methylation - 2006  

PubMed Central

Lysine methylation plays a central role in the “histone code” that regulates chromatin structure, impacts transcription, and responds to DNA damage. A single lysine can be mono-, di-, trimethylated, or unmethylated, with different functional consequences for each of the four forms. This review describes structural aspects of methylation of histone lysine residues by two enzyme families with entirely different structural scaffolding (the SET proteins and Dot1p), and the protein motifs that recognize (decode) these methyl-lysine signals. We also discuss the recently discovered protein lysine de-methylating enzymes (LSD1 and JmjC domains). PMID:17374386

Cheng, Xiaodong; Zhang, Xing

2007-01-01

358

Investigation of metal-polyelectrolyte complex toxicity.  

PubMed

Water-soluble binary and ternary copper complexes of polyelectrolytes were synthesized, and the toxicity of these complexes was tested in mouse fibroblast cell line (L929) in vitro. Both the binary and ternary complexes were prepared at the ratio of 0.4 mole copper(II) ions per monomer of acrylic acid and 0.5 mole copper(II) ions per monomer of methyl vinyl ether maleic anhydride, furthermore at the ratio of 1 and 2 mole bovine serum albumin per mole of polyacrylic acid and poly(methyl vinyl ether-co-maleic anhydride), respectively. Compared to binary copper(II)-polyelectrolyte complexes, these ternary complexes have been determined to be of least toxicity. PMID:22914259

Karahan, Mesut; Mustafaeva, Zeynep; Koç, Rabia Çak?r; Ba??rova, Melahat; Allahverdiyev, Adil M

2014-05-01

359

DNA methylation profiling reveals a predominant immune component in breast cancers  

PubMed Central

Breast cancer is a molecularly, biologically and clinically heterogeneous group of disorders. Understanding this diversity is essential to improving diagnosis and optimizing treatment. Both genetic and acquired epigenetic abnormalities participate in cancer, but the involvement of the epigenome in breast cancer and its contribution to the complexity of the disease are still poorly understood. By means of DNA methylation profiling of 248 breast tissues, we have highlighted the existence of previously unrecognized breast cancer groups that go beyond the currently known ‘expression subtypes’. Interestingly, we showed that DNA methylation profiling can reflect the cell type composition of the tumour microenvironment, and in particular a T lymphocyte infiltration of the tumours. Further, we highlighted a set of immune genes having high prognostic value in specific tumour categories. The immune component uncovered here by DNA methylation profiles provides a new perspective for the importance of the microenvironment in breast cancer, holding implications for better management of breast cancer patients. PMID:21910250

Dedeurwaerder, Sarah; Desmedt, Christine; Calonne, Emilie; Singhal, Sandeep K; Haibe-Kains, Benjamin; Defrance, Matthieu; Michiels, Stefan; Volkmar, Michael; Deplus, Rachel; Luciani, Judith; Lallemand, Françoise; Larsimont, Denis; Toussaint, Jérôme; Haussy, Sandy; Rothé, Françoise; Rouas, Ghizlane; Metzger, Otto; Majjaj, Samira; Saini, Kamal; Putmans, Pascale; Hames, Gérald; van Baren, Nicolas; Coulie, Pierre G; Piccart, Martine; Sotiriou, Christos; Fuks, François

2011-01-01

360

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

PubMed Central

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

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

2013-01-01

361

RNA cytosine methylation analysis by bisulfite sequencing  

PubMed Central

Covalent modifications of nucleic acids play an important role in regulating their functions. Among these modifications, (cytosine-5) DNA methylation is best known for its role in the epigenetic regulation of gene expression. Post-transcriptional RNA modification is a characteristic feature of noncoding RNAs, and has been described for rRNAs, tRNAs and miRNAs. (Cytosine-5) RNA methylation has been detected in stable and long-lived RNA molecules, but its function is still unclear, mainly due to technical limitations. In order to facilitate the analysis of RNA methylation patterns we have established a protocol for the chemical deamination of cytosines in RNA, followed by PCR-based amplification of cDNA and DNA sequencing. Using tRNAs and rRNAs as examples we show that cytosine methylation can be reproducibly and quantitatively detected by bisulfite sequencing. The combination of this method with deep sequencing allowed the analysis of a large number of RNA molecules. These results establish a versatile method for the identification and characterization of RNA methylation patterns, which will be useful for defining the biological function of RNA methylation. PMID:19059995

Schaefer, Matthias; Pollex, Tim; Hanna, Katharina; Lyko, Frank

2009-01-01

362

Exercise training and DNA methylation in humans.  

PubMed

The response to exercise training (trainability) has been shown to have a strong heritable component. There is growing evidence suggesting that traits such as trainability do not only depend on the genetic code, but also on epigenetic signals. Epigenetic signals play an important role in the modulation of gene expression, through mechanisms such as DNA methylation and histone modifications. There is an emerging evidence to show that physical activity influences DNA methylation in humans. The present review aims to summarize current knowledge on the link between DNA methylation and physical activity in humans. We have critically reviewed the literature and only papers focused on physical activity and its influence on DNA methylation status were included; a total of 25 papers were selected. We concluded that both acute and chronic exercises significantly impact DNA methylation, in a highly tissue- and gene-specific manner. This review also provides insights into the molecular mechanisms of exercise-induced DNA methylation changes, and recommendations for future research. PMID:25345837

Voisin, S; Eynon, N; Yan, X; Bishop, D J

2015-01-01

363

Type 2 diabetes mellitus in relation to global LINE-1 DNA methylation in peripheral blood: a cohort study.  

PubMed

In the last years, epigenetic processes have emerged as a promising area of complex diseases research. DNA methylation measured in Long Interspersed Nucleotide Element 1 (LINE-1) sequences has been considered a surrogate marker for global genome methylation. New findings have suggested the potential involvement of epigenetic mechanisms in Type 2 diabetes (T2DM) as a crucial interface between the effects of genetic predisposition and environmental influences. Our study evaluated whether global DNA methylation predicted increased risk from T2DM or other carbohydrate metabolism disorders in a cohort study. We used a prospective cohort intervention study and a control group. We collected phenotypic, anthropometric, biochemical, and nutritional information from all subjects. Global LINE-1 DNA methylation was quantified by pyrosequencing technology. Subjects that did not improve their carbohydrate metabolism status showed lower levels of global LINE-1 DNA methylation (63.9 ± 1.7 vs. 64.7 ± 2.4) and they practiced less intense physical activity (5.8% vs. 21.5%). Logistic regression analyses showed a significant association between LINE-1 DNA methylation and metabolic status after adjustment for sex, age, BMI, and physical activity. Our study showed that lower LINE-1 DNA methylation levels were associated with a higher risk metabolic status worsening, independent of other classic risk factors. This finding highlights the potential role for epigenetic biomarkers as predictors of T2DM risk or other related metabolic disorders. PMID:25437047

Martín-Núñez, Gracia María; Rubio-Martín, Elehazara; Cabrera-Mulero, Rebeca; Rojo-Martínez, Gemma; Olveira, Gabriel; Valdés, Sergio; Soriguer, Federico; Castaño, Luis; Morcillo, Sonsoles

2014-01-01

364

A study of the autoxidation of some unsaturated fatty acid methyl esters using Fourier transform Raman spectroscopy  

NASA Astrophysics Data System (ADS)

Near-infrared Fourier transform Raman and Fourier transform infrared spectroscopy have been used to investigate the chemical changes taking place during the curing reaction of several fatty acid methyl esters, which are used for modelling processes in the autoxidation of alkyd resin coatings. We have studied methyl oleate, methyl linoleate, and methyl linolenate in an attempt to monitor the degree of unsaturation within the fatty acid methyl esters (FAMES) during the complex autoxidation/polymerisation reaction that takes place once the paint system is coated onto a substrate and exposed to the atmosphere. The peaks around 1655 cm -1 have been assigned as follows: to the trans isomer at 1670 cm -1, the cis isomer at 1655 cm -1 and the conjugated structure at 1640 cm -1 [B. Schrader, Raman/Infrared Atlas of Organic Compounds (2nd Edn), VCH, Weinheim (1989); J. K. Abenyega, M. Claybourn and G. Ellis, in preparations]. Raman spectra for the cure of methyl linoleate after 24 h show several interesting features, suggesting the formation of a highly conjugated cyclic structure. Current theories about the mechanism for the autoxidation of methyl linoleate make no mention of this aromatic product.

Agbenyega, J. K.; Claybourn, M.; Ellis, G.

365

A Genome-Wide Screen for Promoter Methylation in Lung Cancer Identifies Novel Methylation Markers for Multiple Malignancies  

Microsoft Academic Search

BackgroundPromoter hypermethylation coupled with loss of heterozygosity at the same locus results in loss of gene function in many tumor cells. The “rules” governing which genes are methylated during the pathogenesis of individual cancers, how specific methylation profiles are initially established, or what determines tumor type-specific methylation are unknown. However, DNA methylation markers that are highly specific and sensitive for

David S Shames; Luc Girard; Boning Gao; Mitsuo Sato; Cheryl M Lewis; Narayan Shivapurkar; Aixiang Jiang; Charles M Perou; Young H Kim; Jonathan R Pollack; Kwun M Fong; Chi-Leung Lam; Maria Wong; Yu Shyr; Rita Nanda; Olufunmilayo I Olopade; William Gerald; David M Euhus; Jerry W Shay; Adi F Gazdar; John D Minna

2006-01-01

366

CpG Island Methylator Phenotype in Colorectal Cancer  

Microsoft Academic Search

Aberrant methylation of promoter region CpG islands is associated with transcriptional inactivation of tumor-suppressor genes in neoplasia. To understand global patterns of CpG island methylation in colorectal cancer, we have used a recently developed technique called methylated CpG island amplication to examine 30 newly cloned differentially methylated DNA sequences. Of these 30 clones, 19 (63%) were progressively methylated in an

Minoru Toyota; Nita Ahuja; Mutsumi Ohe-Toyota; James G. Herman; Stephen B. Baylin; Jean-Pierre J. Issa

1999-01-01

367

Methyl halide emissions from savanna fires in southern Africa  

Microsoft Academic Search

The methyl halides, methyl chloride (CH3Cl), methyl bromide (CH3Br), and methyl iodide (CH3I), were measured in regional air samples and smoke from savanna fires in southern Africa during the Southern Africa Fire-Atmosphere Research Initiative-92 (SAFARI-92) experiment (August-October 1992). All three species were significantly enhanced in the smoke plumes relative to the regional background. Good correlations were found between the methyl

M. O. Andreae; E. Atlas; G. W. Harris; G. Helas; A. de Kock; R. Koppmann; W. Maenhaut; S. Manø; W. H. Pollock; J. Rudolph; D. Scharffe; G. Schebeske; M. Welling

1996-01-01

368

Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas  

PubMed Central

Background High-grade soft tissue sarcomas are a heterogeneous, complex group of aggressive malignant tumors showing mesenchymal differentiation. Recently, soft tissue sarcomas have increasingly been classified on the basis of underlying genetic alterations; however, the role of aberrant DNA methylation in these tumors is not well understood and, consequently, the usefulness of methylation-based classification is unclear. Results We used the Infinium HumanMethylation27 platform to profile DNA methylation in 80 primary, untreated high-grade soft tissue sarcomas, representing eight relevant subtypes, two non-neoplastic fat samples and 14 representative sarcoma cell lines. The primary samples were partitioned into seven stable clusters. A classification algorithm identified 216 CpG sites, mapping to 246 genes, showing different degrees of DNA methylation between these seven groups. The differences between the clusters were best represented by a set of eight CpG sites located in the genes SPEG, NNAT, FBLN2, PYROXD2, ZNF217, COL14A1, DMRT2 and CDKN2A. By integrating DNA methylation and mRNA expression data, we identified 27 genes showing negative and three genes showing positive correlation. Compared with non-neoplastic fat, NNAT showed DNA hypomethylation and inverse gene expression in myxoid liposarcomas, and DNA hypermethylation and inverse gene expression in dedifferentiated and pleomorphic liposarcomas. Recovery of NNAT in a hypermethylated myxoid liposarcoma cell line decreased cell migration and viability. Conclusions Our analysis represents the first comprehensive integration of DNA methylation and transcriptional data in primary high-grade soft tissue sarcomas. We propose novel biomarkers and genes relevant for pathogenesis, including NNAT as a potential tumor suppressor in myxoid liposarcomas. PMID:24345474

2013-01-01

369

Laser capture microdissection–reduced representation bisulfite sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse  

PubMed Central

DNA methylation is a mechanism for long-term transcriptional regulation and is required for normal cellular differentiation. Failure to properly establish or maintain DNA methylation patterns leads to cell dysfunction and diseases such as cancer. Identifying DNA methylation signatures in complex tissues can be challenging owing to inaccurate cell enrichment methods and low DNA yields. We have developed a technique called laser capture microdissection-reduced representation bisulfite sequencing (LCM-RRBS) for the multiplexed interrogation of the DNA methylation status of cytosine–guanine dinucleotide islands and promoters. LCM-RRBS accurately and reproducibly profiles genome-wide methylation of DNA extracted from microdissected fresh frozen or formalin-fixed paraffin-embedded tissue samples. To demonstrate the utility of LCM-RRBS, we characterized changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse. Compared with adjacent normal tissue, the adrenocortical tumors showed reproducible gains and losses of DNA methylation at genes involved in cell differentiation and organ development. LCM-RRBS is a rapid, cost-effective, and sensitive technique for analyzing DNA methylation in heterogeneous tissues and will facilitate the investigation of DNA methylation in cancer and organ development. PMID:23589626

Schillebeeckx, Maximiliaan; Schrade, Anja; Löbs, Ann-Kathrin; Pihlajoki, Marjut; Wilson, David B.; Mitra, Robi D.

2013-01-01

370

Genome-wide analysis of DNA methylation in bovine placentas  

PubMed Central

Background DNA methylation is an important epigenetic modification that is essential for epigenetic gene regulation in development and disease. To date, the genome-wide DNA methylation maps of many organisms have been reported, but the methylation pattern of cattle remains unknown. Results We showed the genome-wide DNA methylation map in placental tissues using methylated DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq). In cattle, the methylation levels in the gene body are relatively high, whereas the promoter remains hypomethylated. We obtained thousands of highly methylated regions (HMRs), methylated CpG islands, and methylated genes from bovine placenta. DNA methylation levels around the transcription start sites of genes are negatively correlated with the gene expression level. However, the relationship between gene-body DNA methylation and gene expression is non-monotonic. Moderately expressed genes generally have the highest levels of gene-body DNA methylation, whereas the highly, and lowly expressed genes, as well as silent genes, show moderate DNA methylation levels. Genes with the highest expression show the lowest DNA methylation levels. Conclusions We have generated the genome-wide mapping of DNA methylation in cattle for the first time, and our results can be used for future studies on epigenetic gene regulation in cattle. This study contributes to the knowledge on epigenetics in cattle. PMID:24397284

2014-01-01

371

Methyl esterification of pectin plays a role during plant-pathogen interactions and affects plant resistance to diseases.  

PubMed

The cell wall is a complex structure mainly composed by a cellulose-hemicellulose network embedded in a cohesive pectin matrix. Pectin is synthesized in a highly methyl esterified form and is de-esterified in muro by pectin methyl esterases (PMEs). The degree and pattern of methyl esterification affect the cell wall structure and properties with consequences on both the physiological processes of the plants and their resistance to pathogens. PME activity displays a crucial role in the outcome of the plant-pathogen interactions by making pectin more susceptible to the action of the enzymes produced by the pathogens. This review focuses on the impact of pectin methyl esterification in plant-pathogen interactions and on the dynamic role of its alteration during pathogenesis. PMID:22717136

Lionetti, Vincenzo; Cervone, Felice; Bellincampi, Daniela

2012-11-01

372

PRMT1 mediated methylation of TAF15 is required for its positive gene regulatory function  

SciTech Connect

TAF15 (formerly TAF{sub II}68) is a nuclear RNA-binding protein that is associated with a distinct population of TFIID and RNA polymerase II complexes. TAF15 harbours an N-terminal activation domain, an RNA recognition motif (RRM) and many Arg-Gly-Gly (RGG) repeats at its C-terminal end. The N-terminus of TAF15 serves as an essential transforming domain in the fusion oncoprotein created by chromosomal translocation in certain human chondrosarcomas. Post-transcriptional modifications (PTMs) of proteins are known to regulate their activity, however, nothing is known on how PTMs affect TAF15 function. Here we demonstrate that endogenous human TAF15 is methylated in vivo at its numerous RGG repeats. Furthermore, we identify protein arginine N-methyltransferase 1 (PRMT1) as a TAF15 interactor and the major PRMT responsible for its methylation. In addition, the RGG repeat-containing C-terminus of TAF15 is responsible for the shuttling between the nucleus and the cytoplasm and the methylation of RGG repeats affects the subcellular localization of TAF15. The methylation of TAF15 by PRMT1 is required for the ability of TAF15 to positively regulate the expression of the studied endogenous TAF15-target genes. Our findings demonstrate that arginine methylation of TAF15 by PRMT1 is a crucial event determining its proper localization and gene regulatory function.

Jobert, Laure; Argentini, Manuela [Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 596, Universite Louis Pasteur de Strasbourg, BP 10142 - 67404 Illkirch Cedex, CU de Strasbourg (France)] [Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 596, Universite Louis Pasteur de Strasbourg, BP 10142 - 67404 Illkirch Cedex, CU de Strasbourg (France); Tora, Laszlo, E-mail: laszlo@igbmc.u-strasbg.fr [Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 596, Universite Louis Pasteur de Strasbourg, BP 10142 - 67404 Illkirch Cedex, CU de Strasbourg (France)] [Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 596, Universite Louis Pasteur de Strasbourg, BP 10142 - 67404 Illkirch Cedex, CU de Strasbourg (France)

2009-04-15

373

Dynamics of DNA methylation and Histone H4 acetylation during floral bud differentiation in azalea  

PubMed Central

Background The ability to control the timing of flowering is a key strategy for planning production in ornamental species such as azalea, however it requires a thorough understanding of floral transition. Floral transition is achieved through a complex genetic network and regulated by multiple environmental and endogenous cues. Dynamic changes between chromatin states facilitating or inhibiting DNA transcription regulate the expression of floral induction pathways in response to environmental and developmental signals. DNA methylation and histone modifications are involved in controlling the functional state of chromatin and gene expression. Results The results of this work indicate that epigenetic mechanisms such as DNA methylation and histone H4 acetylation have opposite and particular dynamics during the transition from vegetative to reproductive development in the apical shoots of azalea. Global levels of DNA methylation and histone H4 acetylation as well as immunodetection of 5-mdC and acetylated H4, in addition to a morphological study have permitted the delimitation of four basic phases in the development of the azalea bud and allowed the identification of a stage of epigenetic reprogramming which showed a sharp decrease of whole DNA methylation similar to that is defined in other developmental processes in plants and in mammals. Conclusion The epigenetic control and reorganization of chromatin seem to be decisive for coordinating floral development in azalea. DNA methylation and H4 deacetylation act simultaneously and co-ordinately, restructuring the chromatin and regulating the gene expression during soot apical meristem development and floral differentiation. PMID:20067625

2010-01-01

374

Mercury methylation coupled to iron reduction by dissimilatory iron-reducing bacteria.  

PubMed

Iron reduction and mercury methylation by dissimilatory iron-reducing bacteria (DIRB), Geobacter sulfurreducens and Shewanella oneidensis, were studied, and the relationship of mercury methylation coupled to iron reduction was determined. The ability of both bacteria for reducing iron was tested, and Fe(III) reduction occurred with the highest rate when ferric oxyhydroxide was used as a terminal electron acceptor. G. sulfurreducens had proven to mediate the production of methylmercury (MeHg), and a notable increase of MeHg following the addition of inorganic Hg was observed. When the initial concentration of HgCl2 was 500nM, about 177.03nM of MeHg was determined at 8d after G. sulfurreducens inoculation. S. oneidensis was tested negligible for Hg methylation and only 12.06nM of MeHg was determined. Iron reduction could potentially influence Hg methylation rates. The increase in MeHg was consistent with high rate of iron reduction, indicating that Fe(III) reduction stimulated the formation of MeHg. Furthermore, the net MeHg concentration increased at low Fe(III) additions from 1.78 to 3.57mM, and then decreased when the added Fe(III) was high from 7.14 to 17.85mM. The mercury methylation rate was suppressed with high Fe(III) additions, which might have been attributable to mercury complexation and low availability. PMID:25496739

Si, Youbin; Zou, Yan; Liu, Xiaohong; Si, Xiongyuan; Mao, Jingdong

2015-03-01

375

Mercury Methylation by HgcA: Theory Supports Carbanion Transfer to Hg(II)  

SciTech Connect

Many proteins use corrinoid cofactors to facilitate methyl transfer reactions. Recently, a corrinoid protein, HgcA, has been shown to be required for the production of the neurotoxin methylmercury by anaerobic bacteria. A strictly conserved Cys residue in HgcA was predicted to be a lower-axial ligand to Co(III), which has never been observed in a corrinoid protein. Here, we use density functional theory to study homolytic and heterolytic Co-C bond dissociation and methyl transfer to Hg(II) substrates with model methylcobalamin complexes containing a lower-axial Cys or His ligand to cobalt, the latter of which is commonly found in other corrinoid proteins. We find that Cys thiolate coordination to Co facilitates both methyl radical and methyl carbanion transfer to Hg(II) substrates, but carbanion transfer is more favorable overall in the condensed phase. Thus, our findings are consistent with HgcA representing a new class of corrinoid protein capable of transferring methyl groups to electrophilic substrates.

Zhou, Jing [University of Tennessee (UT)] [University of Tennessee (UT); Riccardi, Demian M [ORNL] [ORNL; Beste, Ariana [ORNL] [ORNL; Smith, Jeremy C [ORNL] [ORNL; Parks, Jerry M [ORNL] [ORNL

2014-01-01

376

Role of Morphological Growth State and Gene Expression in Desulfovibrio africanus strain Walvis Bay Mercury Methylation  

SciTech Connect

The biogeochemical transformations of mercury are a complex process, with the production of methylmercury, a potent human neurotoxin, repeatedly demonstrated in sulfate- and Fe(III)- reducing as well as methanogenic bacteria. However, little is known regarding the morphology, genes or proteins involved in methylmercury generation. Desulfovibrio africanus strain Walvis Bay is a Hg-methylating -proteobacterium with a sequenced genome and has unusual pleomorphic forms. In this study, a relationship between the pleomorphism and Hg methylation was investigated. Proportional increases in the sigmoidal (regular) cell form corresponded with increased net MeHg production, but decreased when the pinched cocci (persister) form became the major morphotype. D. africanus microarrays indicated that the ferrous iron transport genes (feoAB), as well as ribosomal genes and several genes whose products are predicted to have metal binding domains (CxxC), were up-regulated during exposure to Hg in the exponential phase. While no specific methylation pathways were identified, the finding that Hg may interfere with iron transport and the correlation of growth-phase dependent morphology with MeHg production are notable. The identification of these relationships between differential gene expression, morphology, and the growth phase dependence of Hg transformations suggests that actively growing cells are primarily responsible for methylation, and so areas with ample carbon and electron-acceptor concentrations may also generate a higher proportion of methylmercury than more oligotrophic environments. The observation of increased iron transporter expression also suggests that Hg methylation may interfere with iron biogeochemical cycles.

Moberly, James G [ORNL; Miller, Carrie L [ORNL; Brown, Steven D [ORNL; Biswas, Abir [ORNL; Brandt, Craig C [ORNL; Palumbo, Anthony Vito [ORNL; Elias, Dwayne A [ORNL

2012-01-01

377

Abnormalities of the DNA methylation mark and its machinery: an emerging cause of neurologic dysfunction.  

PubMed

Recently, Mendelian disorders of the DNA methylation machinery have been described which demonstrate the complex roles of epigenetics in neurodevelopment and disease. For example, defects of DNMT1, the maintenance methyltransferase, lead to adult-onset progressive neurologic disorders, whereas defects of the de novo methyltransferases DNMT3A and DNMT3B lead to nonprogressive neurodevelopmental conditions. Furthermore, patients with DNMT3A deficiency demonstrate overgrowth, a feature common to disorders of histone machinery and imprinting disorders, highlighting the interconnectedness of the many epigenetic layers. Disorders of the DNA methylation machinery include both the aforementioned "writers" and also the "readers" of the methyl mark, such as MeCP2, the cause of Rett syndrome. Any dosage disruption, either haploinsufficiency or overexpression of DNA methylation machinery leads to widespread gene expression changes in trans, disrupting expression of a subset of target genes that contribute to individual disease phenotypes. In contrast, classical imprinting disorders such as Angelman syndrome have been thought generally to cause epigenetic dysregulation in cis. However, the recent description of multilocus methylation disorders challenges this generalization. Here, in addition to summarizing recent developments in identifying the pathogenesis of these diseases, we highlight clinical considerations and some unexpected therapeutic opportunities, such as topoisomerase inhibitors for classical imprinting disorders. PMID:25192503

Weissman, Jacqueline; Naidu, Sakkubai; Bjornsson, Hans T

2014-07-01

378

Role of morphological growth state and gene expression in Desulfovibrio africanus strain Walvis Bay mercury methylation.  

PubMed

The biogeochemical transformations of mercury are a complex process, with the production of methylmercury, a potent human neurotoxin, repeatedly demonstrated in sulfate- and Fe(III)-reducing as well as methanogenic bacteria. However, little is known regarding the morphology, genes, or proteins involved in methylmercury generation. Desulfovibrio africanus strain Walvis Bay is a Hg-methylating ?-proteobacterium with a sequenced genome and has unusual pleomorphic forms. In this study, a relationship between the pleomorphism and Hg methylation was investigated. Proportional increases in the sigmoidal (regular) cell form corresponded with increased net MeHg production but decreased when the pinched cocci (persister) form became the major morphotype. D. africanus microarrays indicated that the ferrous iron transport genes (feoAB), as well as ribosomal genes and several genes whose products are predicted to have metal binding domains (CxxC), were up-regulated during exposure to Hg in the exponential phase. Whereas no specific methylation pathways were identified, the finding that Hg may interfere with iron transport and the correlation of growth-phase-dependent morphology with MeHg production are notable. The identification of these relationships between differential gene expression, morphology, and the growth-phase dependence of Hg transformations suggests that actively growing cells are primarily responsible for methylation, and so areas with ample carbon and electron-acceptor concentrations may also generate a higher proportion of methylmercury than more oligotrophic environments. The observation of increased iron transporter expression also suggests that Hg methylation may interfere with iron biogeochemical cycles. PMID:22500779

Moberly, James G; Miller, Carrie L; Brown, Steven D; Biswas, Abir; Brandt, Craig C; Palumbo, Anthony V; Elias, Dwayne A

2012-05-01

379

Methylation of the Protein Phosphatase 2A Catalytic Subunit Is Essential for Association of B? Regulatory Subunit But Not SG2NA, Striatin, or Polyomavirus Middle Tumor Antigen  

PubMed Central

Binding of different regulatory subunits and methylation of the catalytic (C) subunit carboxy-terminal leucine 309 are two important mechanisms by which protein phosphatase 2A (PP2A) can be regulated. In this study, both genetic and biochemical approaches were used to investigate regulation of regulatory subunit binding by C subunit methylation. Monoclonal antibodies selectively recognizing unmethylated C subunit were used to quantitate the methylation status of wild-type and mutant C subunits. Analysis of 13 C subunit mutants showed that both carboxy-terminal and active site residues are important for maintaining methylation in vivo. Severe impairment of methylation invariably led to a dramatic decrease in B? subunit binding but not of striatin, SG2NA, or polyomavirus middle tumor antigen (MT) binding. In fact, most unmethylated C subunit mutants showed enhanced binding to striatin and SG2NA. Certain carboxy-terminal mutations decreased B? subunit binding without greatly affecting methylation, indicating that B? subunit binding is not required for a high steady-state level of C subunit methylation. Demethylation of PP2A in cell lysates with recombinant PP2A methylesterase greatly decreased the amount of C subunit that could be coimmunoprecipitated via the B? subunit but not the amount that could be coimmunoprecipitated with A? subunit or MT. When C subunit methylation levels were greatly reduced in vivo, B? subunits were found complexed exclusively to methylated C subunits, whereas striatin and SG2NA in the same cells bound both methylated and unmethylated C subunits. Thus, C subunit methylation is critical for assembly of PP2A heterotrimers containing B? subunit but not for formation of heterotrimers containing MT, striatin, or SG2NA. These findings suggest that methylation may be able to selectively regulate the association of certain regulatory subunits with the A/C heterodimer. PMID:11160832

Yu, Xing Xian; Du, Xianxing; Moreno, Carlos S.; Green, Richard E.; Ogris, Egon; Feng, Qi; Chou, Lisa; McQuoid, Monica J.; Pallas, David C.

2001-01-01

380

Selenophene transition metal complexes  

SciTech Connect

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

White, C.J.

1994-07-27

381

DNA methylation and methyl-CpG binding proteins: developmental requirements and function.  

PubMed

DNA methylation is a major epigenetic modification in the genomes of higher eukaryotes. In vertebrates, DNA methylation occurs predominantly on the CpG dinucleotide, and approximately 60% to 90% of these dinucleotides are modified. Distinct DNA methylation patterns, which can vary between different tissues and developmental stages, exist on specific loci. Sites of DNA methylation are occupied by various proteins, including methyl-CpG binding domain (MBD) proteins which recruit the enzymatic machinery to establish silent chromatin. Mutations in the MBD family member MeCP2 are the cause of Rett syndrome, a severe neurodevelopmental disorder, whereas other MBDs are known to bind sites of hypermethylation in human cancer cell lines. Here, we review the advances in our understanding of the function of DNA methylation, DNA methyltransferases, and methyl-CpG binding proteins in vertebrate embryonic development. MBDs function in transcriptional repression and long-range interactions in chromatin and also appear to play a role in genomic stability, neural signaling, and transcriptional activation. DNA methylation makes an essential and versatile epigenetic contribution to genome integrity and function. PMID:19506892

Bogdanovi?, Ozren; Veenstra, Gert Jan C

2009-10-01

382

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

E-print Network

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

Hu, Lei

2012-10-19

383

Methylal and Methylal-Diesel Blended Fuels from Use In Compression-Ignition Engines  

SciTech Connect

Gas-to-liquids catalytic conversion technologies show promise for liberating stranded natural gas reserves and for achieving energy diversity worldwide. Some gas-to-liquids products are used as transportation fuels and as blendstocks for upgrading crude derived fuels. Methylal (CH{sub 3}-O-CH{sub 2}-O-CH{sub 3}) also known as dimethoxymethane or DMM, is a gas-to-liquid chemical that has been evaluated for use as a diesel fuel component. Methylal contains 42% oxygen by weight and is soluble in diesel fuel. The physical and chemical properties of neat methylal and for blends of methylal in conventional diesel fuel are presented. Methylal was found to be more volatile than diesel fuel, and special precautions for distribution and fuel tank storage are discussed. Steady state engine tests were also performed using an unmodified Cummins 85.9 turbocharged diesel engine to examine the effect of methylal blend concentration on performance and emissions. Substantial reductions of particulate matter emissions h ave been demonstrated 3r IO to 30% blends of methylal in diesel fuel. This research indicates that methylal may be an effective blendstock for diesel fuel provided design changes are made to vehicle fuel handling systems.

Keith D. Vertin; James M. Ohi; David W. Naegeli; Kenneth H. Childress; Gary P. Hagen; Chris I. McCarthy; Adelbert S. Cheng; Robert W. Dibble

1999-05-05

384

Methyl esters from vegetable oils with hydroxy fatty acids: Comparison of lesquerella and castor methyl esters  

Technology Transfer Automated Retrieval System (TEKTRAN)

The search for alternative feedstocks for biodiesel as partial replacement for petrodiesel has recently extended to castor oil. In this work, the castor oil methyl esters were prepared and their properties determined in comparison to the methyl esters of lesquerella oil, which in turn is seen as alt...

385

Detection of DNA methylation changes in micropropagated banana plants using methylation-sensitive amplification polymorphism (MSAP)  

Microsoft Academic Search

The extent of DNA methylation polymorphisms was evaluated in micropropagated banana (Musa AAA cv. ‘Grand Naine’) derived from either the vegetative apex of the sucker or the floral apex of the male inflorescence using the methylation-sensitive amplification polymorphism (MSAP) technique. In all, 465 fragments, each representing a recognition site cleaved by either or both of the isoschizomers were amplified using

Santy Peraza-Echeverria; Virginia Aurora Herrera-Valencia; Andrew-James Kay

2001-01-01

386

Growing season methyl bromide and methyl chloride fluxes at a sub-arctic wetland in Sweden   

E-print Network

Methyl bromide and methyl chloride fluxes were measured at several sites in a sub-arctic wetland near Abisko, Sweden (68°28?N 18°49?E) throughout the 2008 growing season. Averaged over 92 flux measurements the sub-arctic wetland was found to be a...

Hardacre, Catherine J.; Blei, Emanuel; Heal, Mathew R

2009-01-01

387

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

PubMed

Methyl N-phenyl carbamate was synthesized from aniline by using methyl formate as a green and efficient carbonylating agent. High yields were obtained at milder reaction conditions compared to the conventional CO/CH3 OH route. Studies on the reaction sequence led to suggest an alternative and more efficient route to the carbamate via formanilide as intermediate. PMID:25504838

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

2015-02-01

388

Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1.  

SciTech Connect

Epigenetic inheritance in mammals is characterized by high-fidelity replication of CpG methylation patterns during development. UHRF1 (also known as ICBP90 in humans and Np95 in mouse) is an E3 ligase important for the maintenance of global and local DNA methylation in vivo. The preferential affinity of UHRF1 for hemi-methylated DNA over symmetrically methylated DNA by means of its SET and RING-associated (SRA) domain and its association with the maintenance DNA methyltransferase 1 (DNMT1) suggests a role in replication of the epigenetic code. Here we report the 1.7 {angstrom} crystal structure of the apo SRA domain of human UHRF1 and a 2.2 {angstrom} structure of its complex with hemi-methylated DNA, revealing a previously unknown reading mechanism for methylated CpG sites (mCpG). The SRA-DNA complex has several notable structural features including a binding pocket that accommodates the 5-methylcytosine that is flipped out of the duplex DNA. Two specialized loops reach through the resulting gap in the DNA from both the major and the minor grooves to read the other three bases of the CpG duplex. The major groove loop confers both specificity for the CpG dinucleotide and discrimination against methylation of deoxycytidine of the complementary strand. The structure, along with mutagenesis data, suggests how UHRF1 acts as a key factor for DNMT1 maintenance methylation through recognition of a fundamental unit of epigenetic inheritance, mCpG.

Avvakumov, George V.; Walker, John R.; Xue, Sheng; Li, Yanjun; Duan, Shili; Bronner, Christian; Arrowsmith, Cheryl H.; Dhe-Paganon, Sirano (CNRS-UMR); (Toronto)

2008-11-17

389

DNA Methylation in the Neuropeptide S Receptor 1 (NPSR1) Promoter in Relation to Asthma and Environmental Factors  

PubMed Central

Asthma and allergy are complex disorders influenced by both inheritance and environment, a relationship that might be further clarified by epigenetics. Neuropeptide S Receptor 1 (NPSR1) has been associated with asthma and allergy and a study suggested modulation of the genetic risk by environmental factors. We aimed to study DNA methylation in the promoter region of NPSR1 in relation to asthma and environmental exposures. Electrophoretic Mobility Shift Assay (EMSA) was used to investigate potential functional roles of both genotypes and methylation status in the NPSR1 promoter. DNA methylation was analysed using EpiTYPER in blood samples from two well-characterized cohorts; the BIOAIR study of severe asthma in adults and the Swedish birth cohort BAMSE. We observed that DNA methylation and genetic variants in the promoter influenced the binding of nuclear proteins to DNA, suggesting functional relevance. Significant, although small, differences in methylation were related to both adult severe asthma (p?=?0.0001) and childhood allergic asthma (p?=?0.01). Furthermore, DNA methylation was associated with exposures such as current smoking in adults for two CpG sites (p?=?0.005 and 0.04), parental smoking during infancy in the children (p?=?0.02) and in which month the sample was taken (p?=?0.01). In summary, DNA methylation levels in the promoter of NPSR1 showed small but significant associations with asthma, both in adults and in children, and to related traits such as allergy and certain environmental exposures. Both genetic variation and the methylated state of CpG sites seem to have an effect on the binding of nuclear proteins in the regulatory region of NPSR1 suggesting complex regulation of this gene in asthma and allergy. PMID:23372674

Reinius, Lovisa E.; Gref, Anna; Sääf, Annika; Acevedo, Nathalie; Joerink, Maaike; Kupczyk, Maciej; D'Amato, Mauro; Bergström, Anna; Melén, Erik; Scheynius, Annika; Dahlén, Sven-Erik; Pershagen, Göran; Söderhäll, Cilla; Kere, Juha

2013-01-01

390

Suppression of Methylation-Mediated Transcriptional Gene Silencing by ?C1-SAHH Protein Interaction during Geminivirus-Betasatellite Infection  

PubMed Central

DNA methylation is a fundamental epigenetic modification that regulates gene expression and represses endogenous transposons and invading DNA viruses. As a counter-defense, the geminiviruses encode proteins that inhibit methylation and transcriptional gene silencing (TGS). Some geminiviruses have acquired a betasatellite called DNA ?. This study presents evidence that suppression of methylation-mediated TGS by the sole betasatellite-encoded protein, ?C1, is crucial to the association of Tomato yellow leaf curl China virus (TYLCCNV) with its betasatellite (TYLCCNB). We show that TYLCCNB complements Beet curly top virus (BCTV) L2- mutants deficient for methylation inhibition and TGS suppression, and that cytosine methylation levels in BCTV and TYLCCNV genomes, as well as the host genome, are substantially reduced by TYLCCNB or ?C1 expression. We also demonstrate that while TYLCCNB or ?C1 expression can reverse TGS, TYLCCNV by itself is ineffective. Thus its AC2/AL2 protein, known to have suppression activity in other geminiviruses, is likely a natural mutant in this respect. A yeast two-hybrid screen of candidate proteins, followed by bimolecular fluorescence complementation analysis, revealed that ?C1 interacts with S-adenosyl homocysteine hydrolase (SAHH), a methyl cycle enzyme required for TGS. We further demonstrate that ?C1 protein inhibits SAHH activity in vitro. That ?C1 and other geminivirus proteins target the methyl cycle suggests that limiting its product, S-adenosyl methionine, may be a common viral strategy for methylation interference. We propose that inhibition of methylation and TGS by ?C1 stabilizes geminivirus/betasatellite complexes. PMID:22028660

Raja, Priya; Li, Sizhun; Wolf, Jamie N.; Shen, Qingtang; Bisaro, David M.; Zhou, Xueping

2011-01-01

391

shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R  

PubMed Central

We present shinyMethyl, a Bioconductor package for interactive quality control of DNA methylation data from Illumina 450k arrays. The package summarizes 450k experiments into small exportable R objects from which an interactive interface is launched. Reactive plots allow fast and intuitive quality control assessment of the samples. In addition, exploration of the phenotypic associations is possible through coloring and principal component analysis. Altogether, the package makes it easy to perform quality assessment of large-scale methylation datasets, such as epigenome-wide association studies or the datasets available through The Cancer Genome Atlas portal. The shinyMethyl package is implemented in R and available via Bioconductor. Its development repository is at https://github.com/jfortin1/shinyMethyl. PMID:25285208

Fortin, Jean-Philippe; Fertig, Elana; Hansen, Kasper

2014-01-01

392

Chromatin and DNA methylation dynamics during retinoic acid-induced RET gene transcriptional activation in neuroblastoma cells  

PubMed Central

Although it is well known that RET gene is strongly activated by retinoic acid (RA) in neuroblastoma cells, the mechanisms underlying such activation are still poorly understood. Here we show that a complex series of molecular events, that include modifications of both chromatin and DNA methylation state, accompany RA-mediated RET activation. Our results indicate that the primary epigenetic determinants of RA-induced RET activation differ between enhancer and promoter regions. At promoter region, the main mark of RET activation was the increase of H3K4me3 levels while no significant changes of the methylation state of H3K27 and H3K9 were observed. At RET enhancer region a bipartite chromatin domain was detected in unstimulated cells and a prompt demethylation of H3K27me3 marked RET gene activation upon RA exposure. Moreover, ChIP experiments demonstrated that EZH2 and MeCP2 repressor complexes were associated to the heavily methylated enhancer region in the absence of RA while both complexes were displaced during RA stimulation. Finally, our data show that a demethylation of a specific CpG site at the enhancer region could favor the displacement of MeCP2 from the heavily methylated RET enhancer region providing a novel potential mechanism for transcriptional regulation of methylated RA-regulated loci. PMID:20952403

Angrisano, T.; Sacchetti, S.; Natale, F.; Cerrato, A.; Pero, R.; Keller, S.; Peluso, S.; Perillo, B.; Avvedimento, V. E.; Fusco, A.; Bruni, C. B.; Lembo, F.; Santoro, M.; Chiariotti, L.

2011-01-01

393

Glutamine methylation in Histone H2A is an RNA Polymerase I dedicated modification  

PubMed Central

Nucleosomes are decorated with numerous post-translational modifications capable of influencing many DNA processes1. Here, we describe a new class of histone modification, methylation of glutamine, occurring on yeast histone H2A at position 105 (Q105) and human H2A at Q104. We identify Nop1 as the methyltransferase in yeast and demonstrate that Fibrillarin is the ortholog enzyme in human cells. Glutamine methylation of H2A is restricted to the nucleolus. Global analysis in yeast, using an H2AQ105me specific antibody, show that this modification is exclusively enriched over the 35S rDNA transcriptional unit. We show that the Q105 residue is part of the binding site for the histone chaperone FACT (Facilitator of Transcription) complex2. Methylation of Q105 or its substitution to alanine disrupts binding to FACT in vitro. A yeast strain mutated at Q105 exhibits reduced histone incorporation and increased transcription at the rDNA locus. These features are phenocopied by mutations in FACT complex components. Together these data identify glutamine methylation of H2A as the first histone epigenetic mark dedicated to a specific RNA polymerase and define its function as a regulator of FACT interaction with nucleosomes. PMID:24352239

Tessarz, Peter; Santos-Rosa, Helena; Robson, Sam C.; Sylvestersen, Kathrine B.; Nelson, Christopher J; Nielsen, Michael L.; Kouzarides, Tony

2013-01-01

394

Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2.  

PubMed

The MBT repeat has been recently identified as a key domain capable of methyl-lysine histone recognition. Functional work has pointed to a role for MBT domain-containing proteins in transcriptional repression of developmental control genes such as Hox genes. In this study, L3MBTL2, a human homolog of Drosophila Sfmbt critical for Hox gene silencing, is demonstrated to preferentially recognize lower methylation states of several histone-derived peptides through its fourth MBT repeat. High-resolution crystallographic analysis of the four MBT repeats of this protein reveals its unique asymmetric rhomboid architecture, as well as binding mechanism, which preclude the interaction of the first three MBT repeats with methylated peptides. Structural elucidation of an L3MBTL2-H4K20me1 complex and comparison with other MBT-histone peptide complexes also suggests that an absence of distinct surface contours surrounding the methyl-lysine-binding pocket may underlie the lack of sequence specificity observed for members of this protein family. PMID:19233876

Guo, Yahong; Nady, Nataliya; Qi, Chao; Allali-Hassani, Abdellah; Zhu, Haizhong; Pan, Patricia; Adams-Cioaba, Melanie A; Amaya, Maria F; Dong, Aiping; Vedadi, Masoud; Schapira, Matthieu; Read, Randy J; Arrowsmith, Cheryl H; Min, Jinrong

2009-04-01

395

The Chirped-Pulse and Cavity Based Ftmw Spectroscopy of the Methyl Lactate-Water and Methyl Lactate-Deuterium Oxide Dimers  

NASA Astrophysics Data System (ADS)

The delicate competition between the inter- and intramolecular hydrogen-bonding in the complex consisting of a chiral alpha-hydroxy ester, methyl lactate, and water, has been studied using rotational spectroscopy and high level ab initio calculations. Extensive ab initio calculations have been performed to locate all possible low energy conformers of the methyl lactate-water contact pair and five lowest energy conformers have been identified. The most stable conformer forms a seven membered ring with two intermolecular hydrogen bonds: one between the alcoholic hydroxy group of methyl lactate and the oxygen of the water molecule and the other between the hydrogen of water and the oxygen of the carbonyl group. Broadband scans for the rotational spectra of these conformers have been carried out using a newly built chirped-pulse FTMW instrument and the final frequency measurements with a cavity based FTMW instrument. Spectral assignments have been made for the lowest energy conformer of methyl lactate-H2O and D2O. The hyperfine splitting and the source of the splitting will be discussed.

Thomas, Javix; Sukhorukov, Oleksandr; Jäger, Wolfgang; Xu, Yunjie

2011-06-01

396

Dynamic Alu Methylation during Normal Development, Aging, and Tumorigenesis  

PubMed Central

DNA methylation primarily occurs on CpG dinucleotides and plays an important role in transcriptional regulations during tissue development and cell differentiation. Over 25% of CpG dinucleotides in the human genome reside within Alu elements, the most abundant human repeats. The methylation of Alu elements is an important mechanism to suppress Alu transcription and subsequent retrotransposition. Decades of studies revealed that Alu methylation is highly dynamic during early development and aging. Recently, many environmental factors were shown to have a great impact on Alu methylation. In addition, aberrant Alu methylation has been documented to be an early event in many tumors and Alu methylation levels have been associated with tumor aggressiveness. The assessment of the Alu methylation has become an important approach for early diagnosis and/or prognosis of cancer. This review focuses on the dynamic Alu methylation during development, aging, and tumor genesis. The cause and consequence of Alu methylation changes will be discussed. PMID:25243180

Lu, Xuemei

2014-01-01

397

DNA methylation array analyses identified breast cancer-associated HYAL2 methylation in peripheral blood.  

PubMed

Breast cancer (BC) is the leading cause of cancer-related mortality in women worldwide. Changes in DNA methylation in peripheral blood could be associated with malignancy at early stage. However, the BC-associated DNA methylation signatures in peripheral blood were largely unknown. Here, we performed a genome-wide methylation screening and identified a BC-associated differentially methylated CpG site cg27091787 in the hyaluronoglucosaminidase 2 gene (HYAL2) (discovery round with 72 BC case and 24 controls: p = 2.61 × 10(-9) adjusted for cell-type proportions). The substantially decreased methylation of cg27091787 in BC cases was confirmed in two validation rounds (first validation round with 338 BC case and 507 controls: p < 0.0001; second validation round with 189 BC case and 189 controls: p < 0.0001). In addition to cg27091787, the decreased methylation of a 650-bp CpG island shore of HYAL2 was also associated with increased risk of BC. Moreover, the expression and methylation of HYAL2 were inversely correlated with a p-value of 0.006. To note, the BC-associated decreased HYAL2 methylation was replicated in the T-cell fraction (p = 0.034). The cg27091787 methylation level enabled a powerful discrimination of early-stage BC cases (stages 0 and I) from healthy controls [area under curve (AUC) = 0.89], and was robust for the detection of BC in younger women as well (age < 50, AUC = 0.87). Our study reveals a strong association between decreased HYAL2 methylation in peripheral blood and BC, and provides a promising blood-based marker for the detection of early BC. PMID:25213452

Yang, Rongxi; Pfütze, Katrin; Zucknick, Manuela; Sutter, Christian; Wappenschmidt, Barbara; Marme, Frederik; Qu, Bin; Cuk, Katarina; Engel, Christoph; Schott, Sarah; Schneeweiss, Andreas; Brenner, Hermann; Claus, Rainer; Plass, Christoph; Bugert, Peter; Hoth, Markus; Sohn, Christof; Schmutzler, Rita; Bartram, Claus R; Burwinkel, Barbara

2015-04-15

398

Methylation plotter: a web tool for dynamic visualization of DNA methylation data  

PubMed Central

Methylation plotter is a Web tool that allows the visualization of methylation data in a user-friendly manner and with publication-ready quality. The user is asked to introduce a file containing the methylation status of a genomic region. This file can contain up to 100 samples and 100 CpGs. Optionally, the user can assign a group for each sample (i.e. whether a sample is a tumoral or normal tissue). After the data upload, the tool produces different graphical representations of the results following the most commonly used styles to display this type of data. They include an interactive plot that summarizes the status of every CpG site and for every sample in lollipop or grid styles. Methylation values ranging from 0 (unmethylated) to 1 (fully methylated) are represented using a gray color gradient. A practical feature of the tool allows the user to choose from different types of arrangement of the samples in the display: for instance, sorting by overall methylation level, by group, by unsupervised clustering or just following the order in which data were entered. In addition to the detailed plot, Methylation plotter produces a methylation profile plot that summarizes the status of the scrutinized region, a boxplot that sums up the differences between groups (if any) and a dendrogram that classifies the data by unsupervised clustering. Coupled with this analysis, descriptive statistics and testing for differences at both CpG and group levels are provided. The implementation is based in R/shiny, providing a highly dynamic user interface that generates quality graphics without the need of writing R code. Methylation plotter is freely available at http://gattaca.imppc.org:3838/methylation_plotter/. PMID:25260021

2014-01-01

399

Methylation plotter: a web tool for dynamic visualization of DNA methylation data.  

PubMed

Methylation plotter is a Web tool that allows the visualization of methylation data in a user-friendly manner and with publication-ready quality. The user is asked to introduce a file containing the methylation status of a genomic region. This file can contain up to 100 samples and 100 CpGs. Optionally, the user can assign a group for each sample (i.e. whether a sample is a tumoral or normal tissue). After the data upload, the tool produces different graphical representations of the results following the most commonly used styles to display this type of data. They include an interactive plot that summarizes the status of every CpG site and for every sample in lollipop or grid styles. Methylation values ranging from 0 (unmethylated) to 1 (fully methylated) are represented using a gray color gradient. A practical feature of the tool allows the user to choose from different types of arrangement of the samples in the display: for instance, sorting by overall methylation level, by group, by unsupervised clustering or just following the order in which data were entered. In addition to the detailed plot, Methylation plotter produces a methylation profile plot that summarizes the status of the scrutinized region, a boxplot that sums up the differences between groups (if any) and a dendrogram that classifies the data by unsupervised clustering. Coupled with this analysis, descriptive statistics and testing for differences at both CpG and group levels are provided. The implementation is based in R/shiny, providing a highly dynamic user interface that generates quality graphics without the need of writing R code. Methylation plotter is freely available at http://gattaca.imppc.org:3838/methylation_plotter/. PMID:25260021

Mallona, Izaskun; Díez-Villanueva, Anna; Peinado, Miguel A

2014-01-01

400

Immunoaffinity Enrichment and Mass Spectrometry Analysis of Protein Methylation  

PubMed Central

Protein methylation is a common posttranslational modification that mostly occurs on arginine and lysine residues. Arginine methylation has been reported to regulate RNA processing, gene transcription, DNA damage repair, protein translocation, and signal transduction. Lysine methylation is best known to regulate histone function and is involved in epigenetic regulation of gene transcription. To better study protein methylation, we have developed highly specific antibodies against monomethyl arginine; asymmetric dimethyl arginine; and monomethyl, dimethyl, and trimethyl lysine motifs. These antibodies were used to perform immunoaffinity purification of methyl peptides followed by LC-MS/MS analysis to identify and quantify arginine and lysine methylation sites in several model studies. Overall, we identified over 1000 arginine methylation sites in human cell line and mouse tissues, and ?160 lysine methylation sites in human cell line HCT116. The number of methylation sites identified in this study exceeds those found in the literature to date. Detailed analysis of arginine-methylated proteins observed in mouse brain compared with those found in mouse embryo shows a tissue-specific distribution of arginine methylation, and extends the types of proteins that are known to be arginine methylated to include many new protein types. Many arginine-methylated proteins that we identified from the brain, including receptors, ion channels, transporters, and vesicle proteins, are involved in synaptic transmission, whereas the most abundant methylated proteins identified from mouse embryo are transcriptional regulators and RNA processing proteins. PMID:24129315

Guo, Ailan; Gu, Hongbo; Zhou, Jing; Mulhern, Daniel; Wang, Yi; Lee, Kimberly A.; Yang, Vicky; Aguiar, Mike; Kornhauser, Jon; Jia, Xiaoying; Ren, Jianmin; Beausoleil, Sean A.; Silva, Jeffrey C.; Vemulapalli, Vidyasiri; Bedford, Mark T.; Comb, Michael J.

2014-01-01

401

Scintillation proximity assay of arginine methylation.  

PubMed

Methylation of arginine residues, catalyzed by protein arginine methyltransferases (PRMTs), is one important protein posttranslational modification involved in epigenetic regulation of gene expression. A fast and effective assay for PRMT can provide valuable information for dissecting the biological functions of PRMTs, as well as for screening small-molecule inhibitors of arginine methylation. Currently, among the methods used for PRMT activity measurement, many contain laborious separation procedures, which restrict the applications of these assays for high-throughput screening (HTS) in drug discovery. The authors report here a mix-and-measure method to measure PRMT activity based on the principle of scintillation proximity assay (SPA). In this assay, (3)H-AdoMet was used as methyl donor, and biotin-modified histone H4 peptide served as a methylation substrate. Following the methylation reaction catalyzed by PRMTs, streptavidin-coated SPA beads were added to the reaction solution, and SPA signals were detected by a MicroBeta scintillation counter. No separation step is needed, which simplifies the assay procedure and greatly enhances the assay speed. Particularly, the miniaturization and robustness suggest that this method is suited for HTS of PRMT inhibitors. PMID:21821785

Wu, Jiang; Xie, Nan; Feng, You; Zheng, Y George

2012-02-01

402

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

PubMed Central

The modeling of the oxidation of methyl esters was investigated and the specific chemistry, which is due to the presence of the ester group in this class of molecules, is described. New reactions and rate parameters were defined and included in the software EXGAS for the automatic generation of kinetic mechanisms. Models generated with EXGAS were successfully validated against data from the literature (oxidation of methyl hexanoate and methyl heptanoate in a jet-stirred reactor) and a new set of experimental results for methyl decanoate. The oxidation of this last species was investigated in a jet-stirred reactor at temperatures from 500 to 1100 K, including the negative temperature coefficient region, under stoichiometric conditions, at a pressure of 1.06 bar and for a residence time of 1.5 s: more than 30 reaction products, including olefins, unsaturated esters, and cyclic ethers, were quantified and successfully simulated. Flow rate analysis showed that reactions pathways for the oxidation of methyl esters in the low-temperature range are similar to that of alkanes. PMID:23710076

Glaude, Pierre Alexandre; Herbinet, Olivier; Bax, Sarah; Biet, Joffrey; Warth, Valérie; Battin-Leclerc, Frédérique

2013-01-01

403

Histone lysine methylation and chromatin replication.  

PubMed

In eukaryotic organisms, the replication of the DNA sequence and its organization into chromatin are critical to maintain genome integrity. Chromatin components, such as histone variants and histone post-translational modifications, along with the higher-order chromatin structure, impact several DNA metabolic processes, including replication, transcription, and repair. In this review we focus on lysine methylation and the relationships between this histone mark and chromatin replication. We first describe studies implicating lysine methylation in regulating early steps in the replication process. We then discuss chromatin reassembly following replication fork passage, where the incorporation of a combination of newly synthesized histones and parental histones can impact the inheritance of lysine methylation marks on the daughter strands. Finally, we elaborate on how the inheritance of lysine methylation can impact maintenance of the chromatin landscape, using heterochromatin as a model chromatin domain, and we discuss the potential mechanisms involved in this process. This article is part of a Special Issue entitled: Methylation: A Multifaceted Modification - looking at transcription and beyond. PMID:24686120

Rivera, Carlos; Gurard-Levin, Zachary A; Almouzni, Geneviève; Loyola, Alejandra

2014-12-01

404

Prognostic DNA Methylation Markers for Prostate Cancer  

PubMed Central

Prostate cancer (PC) is the most commonly diagnosed neoplasm and the third most common cause of cancer-related death amongst men in the Western world. PC is a clinically highly heterogeneous disease, and distinction between aggressive and indolent disease is a major challenge for the management of PC. Currently, no biomarkers or prognostic tools are able to accurately predict tumor progression at the time of diagnosis. Thus, improved biomarkers for PC prognosis are urgently needed. This review focuses on the prognostic potential of DNA methylation biomarkers for PC. Epigenetic changes are hallmarks of PC and associated with malignant initiation as well as tumor progression. Moreover, DNA methylation is the most frequently studied epigenetic alteration in PC, and the prognostic potential of DNA methylation markers for PC has been demonstrated in multiple studies. The most promising methylation marker candidates identified so far include PITX2, C1orf114 (CCDC181) and the GABRE~miR-452~miR-224 locus, in addition to the three-gene signature AOX1/C1orf114/HAPLN3. Several other biomarker candidates have also been investigated, but with less stringent clinical validation and/or conflicting evidence regarding their possible prognostic value available at this time. Here, we review the current evidence for the prognostic potential of DNA methylation markers in PC. PMID:25238417

Strand, Siri H.; Orntoft, Torben F.; Sorensen, Karina D.

2014-01-01

405

Autism: a redox/methylation disorder.  

PubMed

While autism is still a mysterious developmental disorder, expansion of research efforts over the past 10 to 15 years has yielded a number of important clues implicating both genetic and environmental factors. We can now assert with a measure of confidence that contemporary autism reflects the combined impact of multiple environmental factors on the processes that regulate development in genetically vulnerable individuals. Since epigenetic regulation of gene expression is acknowledged as the most critical factor in development and DNA methylation (the addition of a carbon atom at discrete locations) is the fundamental event for epigenetic regulation, dysfunctional methylation can be considered as a likely cause of autism. Since methylation activity is highly sensitive to oxidative stress (an abnormal redox state) and many environmental factors promote oxidative stress, we have proposed a redox/methylation hypothesis for autism causation. The narrative herein describes the evolution of this hypothesis, which is essentially a series of linked discoveries about how the brain uniquely relies on oxidation and methylation to guide its development and to carry out its cognitive functions. PMID:24416710

Deth, Richard C

2013-11-01

406

DNA methylation, a hand behind neurodegenerative diseases  

PubMed Central

Epigenetic alterations represent a sort of functional modifications related to the genome that are not responsible for changes in the nucleotide sequence. DNA methylation is one of such epigenetic modifications that have been studied intensively for the past several decades. The transfer of a methyl group to the 5 position of a cytosine is the key feature of DNA methylation. A simple change as such can be caused by a variety of factors, which can be the cause of many serious diseases including several neurodegenerative diseases. In this review, we have reviewed and summarized recent progress regarding DNA methylation in four major neurodegenerative diseases: Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS). The studies of these four major neurodegenerative diseases conclude the strong suggestion of the important role DNA methylation plays in these diseases. However, each of these diseases has not yet been understood completely as details in some areas remain unclear, and will be investigated in future studies. We hope this review can provide new insights into the understanding of neurodegenerative diseases from the epigenetic perspective. PMID:24367332

Lu, Haoyang; Liu, Xinzhou; Deng, Yulin; Qing, Hong

2013-01-01

407

Histone Lysine Methylation in Diabetic Nephropathy  

PubMed Central

Diabetic nephropathy (DN) belongs to debilitating microvascular complications of diabetes and is the leading cause of end-stage renal diseases worldwide. Furthermore, outcomes from the DCCT/EDIC study showed that DN often persists and progresses despite intensive glucose control in many diabetes patients, possibly as a result of prior episode of hyperglycemia, which is called “metabolic memory.” The underlying mechanisms responsible for the development and progression of DN remain poorly understood. Activation of multiple signaling pathways and key transcription factors can lead to aberrant expression of DN-related pathologic genes in target renal cells. Increasing evidence suggests that epigenetic mechanisms in chromatin such as DNA methylation, histone acetylation, and methylation can influence the pathophysiology of DN and metabolic memory. Exciting researches from cell culture and experimental an