WorldWideScience

Sample records for vicinal methyl group

  1. Methylation diet and methyl group genetics in risk for adenomatous polyp occurrence

    Directory of Open Access Journals (Sweden)

    Mark Lucock

    2015-06-01

    Conclusion: A methylation diet influences methyl group synthesis in the regulation of blood homocysteine level, and is modulated by genetic interactions. Methylation-related nutrients also interact with key genes to modify risk of AP, a precursor of colorectal cancer. Independent of diet, two methylation-related genes (A2756G-MS and A66G-MSR were directly associated with AP occurrence.

  2. Inductive effect of methyl group in a series of methylated indoles: A ...

    Indian Academy of Sciences (India)

    Abstract. The inductive effect of methyl group has been quantified by expressing highest occupied molecular orbital (HOMO) and HOMO–1 energies of indole and a series of methylated indoles using a combination of graph theory (GT) and the Coulson–Longuett–Higgins perturbation method. By correlating these ...

  3. Spatial distribution of marine crenarchaeota group I in the vicinity of deep-sea hydrothermal systems.

    Science.gov (United States)

    Takai, Ken; Oida, Hanako; Suzuki, Yohey; Hirayama, Hisako; Nakagawa, Satoshi; Nunoura, Takuro; Inagaki, Fumio; Nealson, Kenneth H; Horikoshi, Koki

    2004-04-01

    Distribution profiles of marine crenarchaeota group I in the vicinity of deep-sea hydrothermal systems were mapped with culture-independent molecular techniques. Planktonic samples were obtained from the waters surrounding two geographically and geologically distinct hydrothermal systems, and the abundance of marine crenarchaeota group I was examined by 16S ribosomal DNA clone analysis, quantitative PCR, and whole-cell fluorescence in situ hybridization. A much higher proportion of marine crenarchaeota group I within the microbial community was detected in deep-sea hydrothermal environments than in normal deep and surface seawaters. The highest proportion was always obtained from the ambient seawater adjacent to hydrothermal emissions and chimneys but not from the hydrothermal plumes. These profiles were markedly different from the profiles of epsilon-Proteobacteria, which are abundant in the low temperatures of deep-sea hydrothermal environments.

  4. Are N-methyl groups of Tetramethylurea (TMU) Hydrophobic? A ...

    Indian Academy of Sciences (India)

    methyl groups of Tetramethylurea (TMU) Hydrophobic? A composition and temperature-dependent fluorescence spectroscopic investigation of TMU/water binary mixtures. SANDIPA INDRA RANJIT BISWAS. Regular Article Volume 128 Issue 5 ...

  5. Maternal Methyl-Group Donor Intake and Global DNA (HydroxyMethylation before and during Pregnancy

    Directory of Open Access Journals (Sweden)

    Sara Pauwels

    2016-08-01

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

  6. On adsorption of aluminium and methyl groups on silica for TMA/H2 ...

    Indian Academy of Sciences (India)

    Administrator

    hindered (shielded) by methyl groups where other methyl groups cannot get attached. Hence a small variation of. OH concentration will not affect the methyl group con- centration on the substrate surface. As the OH concentration decreases, the methyl group concentration need not decrease. This is because 15 is the.

  7. Methylation diet and methyl group genetics in risk for adenomatous polyp occurrence.

    Science.gov (United States)

    Lucock, Mark; Yates, Zoë; Martin, Charlotte; Choi, Jeong-Hwa; Beckett, Emma; Boyd, Lyndell; LeGras, Kathleen; Ng, Xiaowei; Skinner, Virginia; Wai, Ron; Kho, Jeremy; Roach, Paul; Veysey, Martin

    2015-06-01

    The aim of this study is to explore whether a methylation diet influences risk for adenomatous polyps (AP) either independently, or interactively with one-carbon metabolism-dependent gene variants, and whether such a diet modifies blood homocysteine, a biochemical phenotype closely related to the phenomenon of methylation. 249 subjects were examined using selective fluorescence, PCR and food frequency questionnaire to determine homocysteine, nine methylation-related gene polymorphisms, dietary methionine, 5-methyltetrahydrofolate, vitamins B6 and B12. 1). Both dietary methionine and 5-methyltetrahydrofolate intake are significantly associated with plasma homocysteine. 2). Dietary methionine is related to AP risk in 2R3R-TS wildtype subjects, while dietary B12 is similarly related to this phenotype in individuals heterozygous for C1420T-SHMT, A2756G-MS and 844ins68-CBS, and in those recessive for 2R3R-TS. 3). Dietary methionine has a marginal influence on plasma homocysteine level in C1420T-SHMT heterozygotes, while B6 exhibits the same effect on homocysteine in C776G-TCN2 homozygote recessive subjects. Natural 5-methyltetrahydrofolate intake is interesting: Wildtype A1298C-MTHFR, heterozygote C677T-MTHFR, wildtype A2756G-MS and recessive A66G-MSR individuals all show a significant reciprocal association with homocysteine. 4). Stepwise regression of all genotypes to predict risk for AP indicated A2756G-MS and A66G-MSR to be most relevant (p = 0.0176 and 0.0408 respectively). Results were corrected for age and gender. A methylation diet influences methyl group synthesis in the regulation of blood homocysteine level, and is modulated by genetic interactions. Methylation-related nutrients also interact with key genes to modify risk of AP, a precursor of colorectal cancer. Independent of diet, two methylation-related genes (A2756G-MS and A66G-MSR) were directly associated with AP occurrence.

  8. Group V adsorbate structures on vicinal Ge(001) surfaces determined from the optical spectrum

    Science.gov (United States)

    Banerjee, S.; Patterson, C. H.; McGilp, J. F.

    2017-06-01

    Vicinal Ge(001) is the standard substrate for the fabrication of high-performance solar cells by metal-organic vapour phase epitaxy, where growth of the III-V material on single domain Ge surfaces, with a single dimer orientation, minimizes the formation of anti-phase domain defects. Reflectance anisotropy spectroscopy has proved to be a powerful and sensitive optical probe of such anisotropic surface structures, but moving beyond fingerprinting to atomic structure determination from the optical spectra has been held back by the high computational cost. It is shown that an empirical, local-orbital-based hybrid density functional theory approach produces very good agreement between the theory and the experiment for (2 × 1)-As and (2 × 1)-Sb structures grown on vicinal Ge(001). These results, when taken together with previous work on Si interfaces, show that this computationally efficient approach is likely to prove to be an important general technique for determining the structure of anisotropic semiconductor surfaces and interfaces by comparing the experimental and calculated optical spectrum.

  9. Role of methyl group number on SOA formation from aromatic hydrocarbons photooxidation under low NOx conditions

    Science.gov (United States)

    Li, L.; Tang, P.; Nakao, S.; Chen, C.-L.; Cocker, D. R., III

    2015-11-01

    Substitution of methyl groups onto the aromatic ring determines the SOA formation from the aromatic hydrocarbon precursor. This study links the number of methyl groups on the aromatic ring to SOA formation from aromatic hydrocarbons photooxidation under low NOx conditions (HC / NO > 10 ppb C : ppb). Aromatic hydrocarbons with increasing numbers of methyl groups are systematically studied. SOA formation from pentamethylbenzene and hexamethylbenzene are reported for the first time. A decreasing SOA yield with increasing number of methyl groups is observed. Linear trends are found in both f44 vs. f43 and O / C vs. H / C for SOA from aromatic hydrocarbons with zero to six methyl groups. An SOA oxidation state predictive method based on benzene is used to examine the effect of added methyl groups on aromatic oxidation under low NOx conditions. Further, the impact of methyl group number on density and volatility of SOA from aromatic hydrocarbons is explored. Finally, a mechanism for methyl group impact on SOA formation is suggested. Overall, this work suggests as more methyl groups are attached on the aromatic ring, SOA products from these aromatic hydrocarbons become less oxidized per mass/carbon.

  10. Rayleigh-wave Group Velocity Tomography in the Vicinity of the Hawaiian Hotspot

    Science.gov (United States)

    Strader, A. E.; Laske, G.; Orcutt, J. A.; Wolfe, C. J.; Collins, J. A.; Solomon, S. C.; Detrick, R. S.; Bercovici, D.; Hauri, E. H.

    2009-12-01

    We present maps of long-period Rayleigh wave group velocity maps for the area spanned by the Hawaiian PLUME (Plume-Lithosphere Undersea Mantle Experiment) project. Specifically, we used observations from the second deployment of ocean-bottom and land broadband instruments that operated from April 2006 through May 2007. The recording network consisted of13 land stations with ten temporary and three observatory instruments and 38 ocean bottom sites that were equipped with 4-component broad-band instruments. With an average station spacing of approximately 200 km, this network had an aperture of nearly 1300 km. For this study, we used an efficient interactive screen tool that employs a multiple filtering technique to measure the frequency-dependent group velocity. The spectra are pre-whitened to reduce biasing effects at frequencies with strong dispersion. We established that the technique provides reliable results for the two-station approach used here, at frequencies between 7 and 60 mHz. Our analysis includes records from 182 shallow earthquakes with focal depth h00.01×1020 Nm, and surface wave magnitudes MS≥5.6. Six smaller events also have signal levels suitable for analysis. For initial dispersion quality and consistency checks, we inspected local group velocity maps obtained from 555 path-averaged group velocity curves for paths that cross the PLUME network. Occam-smoothed matrix inversions are performed for maps with 1° in latitude and longitude. The data are highly consistent at frequencies above 10 mHz. At frequencies below 25 mHz, there is an anomaly downstream of the island of Hawaii that intensifies with decreasing frequency. This result suggests a deep-seated structural anomaly. Group velocities at frequencies above 40 mHz also map with high fidelity. However, in an initial inversion for three-dimensional mantle shear velocity structure we discarded such data, as they are highly sensitive to bathymetry (which is well known and can be corrected for

  11. Rayleigh Wave Group Velocity Tomography of Siberia, China and the Vicinity

    Science.gov (United States)

    Wu, F. T.; Levshin, A. L.; Kozhevnikov, V. M.

    Rayleigh waves are used in a tomographic inversion to obtain group velocity maps of East Asia (40° E-160° E and 20° N-70° N). The period range studied is 30 to 70 seconds. Seismograms used for this study were recorded at CDSN stations, at a temporary broadband seismic array in Tibet, at several SRO stations, and Kirnos-equipped stations established in Asia by the former Soviet Union, in Siberia, in the Sakhalin and in Mongolia. Altogether more than 1200 paths were available in the tomographic inversion. The study area includes the Angara craton, the geologically ancient core of Asia, and the subsequently accreted units, the Altaids (a Paleozoic collision complex), the Sino-Korean platform (a chain of Archaen terranes separated by belts of active structures), the south China platform (a collage of Precambrian, Paleozoic and Mesozoic metamorphic and igneous terranes), as well as the Tibetan plateau (an active tectonic feature created in late Cenozoic through collision of the Indian subcontinent and the Asian continent). Many of these main units are recognizable in the tomographic images as distinctive units; Tibet appears as a prominent low velocity (about -15% from the average) structure, with western and central Tibet often appearing as the areas with the lowest velocities, the Central Asian fold-belt, and the Angara craton are consistently high group velocity areas. Some lesser tectonic features are also recognizable. For example, Lake Baikal is seen as a high velocity feature at periods greater than 40 seconds. However, the high group velocity feature does not stop near the southern end of Lake Baikal; it extends south-southwestward across Mongolia. The North China Plain, a part of the platform where extensional tectonics dominate, is an area of high velocities as a result of relatively thin crust. The south China block, the least tectonically active region of China, is generally an area of high velocity. For periods longer than 40 seconds, a NNE trending

  12. Oxidation of methyl groups by grass grubs and vertebrate liver enzymes

    Science.gov (United States)

    Hook, G. E. R.; Smith, J. N.

    1967-01-01

    1. Oxidation rates of p-nitrotoluene, p-acetamidotoluene and p-toluidine by intact grass grubs and vertebrate liver preparations were measured. 2. The effect of p-substitution in increasing the rate of conversion of the methyl into a carboxy group was in the order acetamido> nitro[unk] amino in mice and grass grubs. 3. Rates of oxidation of the N-methyl group in some alkylaryl N-methylcarbamates was measured and the effect of ring substituents in increasing the rate was in the order hydrogen> o-methyl or o-isopropyl> p-methyl or p-isopropyl> m-methyl or m-isopropyl. 4. Rates of oxidation of the N-methyl groups were similar to those of the p-substituted toluenes. PMID:6029608

  13. Folic acid, polymorphism of methyl-group metabolism genes, and DNA methylation in relation to GI carcinogenesis.

    Science.gov (United States)

    Fang, Jing Yuan; Xiao, Shu Dong

    2003-01-01

    DNA methylation is the main epigenetic modification after replication in humans. DNA (cytosine-5)-methyltransferase (DNMT) catalyzes the transfer of a methyl group from S-adenosyl-L-methionine (SAM) to C5 of cytosine within CpG dinucleotide sequences in the genomic DNA of higher eukaryotes. There is considerable evidence that aberrant DNA methylation plays an integral role in carcinogenesis. Folic acid or folate is crucial for normal DNA synthesis and can regulate DNA methylation, and through this, it affects cellular SAM levels. Folate deficiency results in DNA hypomethylation. Epidemiological studies have indicated that folic acid protects against gastrointestinal (GI) cancers. Methylene-tetrahydrofolate reductase (MTHFR) and methionine synthase (MS) are the enzymes involved in folate metabolism and are thought to influence DNA methylation. MTHFR is highly polymorphic, and the variant genotypes result in decreased MTHFR enzyme activity and lower plasma folate level. Two common MTHFR polymorphisms, 677CT (or 677TT) and A1298C, and an MS polymorphism, A-->G at 2756, have been identified. Most studies support an inverse association between folate status and the rate of colorectal adenomas and carcinomas. During human GI carcinogenesis, MTHFR is highly polymorphic, and the variant genotypes result in decreased MTHFR enzyme activity and lower plasma folate level, as well as aberrant methylation.

  14. Synthesis and photophysical properties of a poly(methyl methacrylate) polymer with carbazolyl side groups

    National Research Council Canada - National Science Library

    Tatiana D. Martins; Richard G. Weiss; Teresa D. Z. Atvars

    2008-01-01

    The photophysical properties of solutions and films of poly(methyl methacrylate) (PMMA) containing 1.6 mol % of randomly distributed pendant ethyl carbazolyl groups have been studied under steady-state and time-resolved conditions...

  15. A high resolution, inelastic neutron scattering investigation of tunnelling methyl groups in aspirin

    Science.gov (United States)

    Johnson, M. R.; Frick, B.; Trommsdorff, H. P.

    1996-08-01

    The tunnel frequency of protonated methyl groups in aspirin has been measured, by inelastic neutron scattering, at 2 K, to be 1.22 μeV. This result and the temperature dependence up to 42 K are in poor agreement with NMR measurements of deuterated methyl groups which conclude that the rotational potential is purely three-fold symmetric. The discrepancy is attributed to a six-fold contribution in the rotational potential for which justification is provided by a calculation of the rotational potential based on the room temperature crystal structure.

  16. Chemoselective Methylation of Phenolic Hydroxyl Group Prevents Quinone Methide Formation and Repolymerization During Lignin Depolymerization

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Kwang Ho; Dutta, Tanmoy; Walter, Eric D.; Isern, Nancy G.; Cort, John R.; Simmons, Blake A.; Singh, Seema

    2017-03-30

    Chemoselective blocking of the phenolic hydroxyl (Ar-OH) group by methylation was found to suppress secondary repolymerization and charring during lignin depolymerization. Methylation of Ar-OH prevents formation of reactive quinone methide intermediates, which are partly responsible for undesirable secondary repolymerization reactions. Instead, this structurally modified lignin produces more relatively low molecular weight products from lignin depolymerization compared to unmodified lignin. This result demonstrates that structural modification of lignin is desirable for production of low molecular weight phenolic products. This approach could be directed toward alteration of natural lignification processes to produce biomass more amenable to chemical depolymerization.

  17. Methyl group dynamics in glassy, polycrystalline, and liquid coenzyme Q10 studied by quasielastic neutron scattering

    Science.gov (United States)

    Smuda, Christoph; Busch, Sebastian; Wagner, Bernd; Unruh, Tobias

    2008-08-01

    The methyl group rotation of coenzyme Q10 confined in nanosized droplets was studied using quasielastic neutron scattering (QENS). Q10 as an oligoisoprene derivative with ten isoprene units can easily be supercooled in nanodroplets. Fixed window scans and QENS spectra at several temperatures of glassy Q10 were recorded to study the methyl group rotation which can be described by a logarithmic Gaussian distribution of hopping rates for temperatures below the glass transition temperature (Tg~200 K). A mean activation energy of 4.8 kJ/mol with a distribution width of 2.1 kJ/mol was obtained from the evaluation of the QENS spectra. A corresponding analysis of a fixed window scan yielded an average activation energy of 5.1 kJ/mol with a distribution width of 1.8 kJ/mol. The results are compared and discussed with those of chain deuterated polyisoprene-d5. For polycrystalline Q10, the QENS spectra could be described by the same model yielding a similar average activation energy as found for glassy Q10. However, no temperature dependence of the distribution width was observed. Based on the performed low-temperature measurements, the correlation times for the methyl group rotation were extrapolated to temperatures of liquid Q10. The complex dynamics of liquid Q10 could be described by a model yielding an apparent diffusion coefficient, the jump rate of the methyl groups, as well as an overall molecular rotational diffusion coefficient. The correlation times of the methyl group rotation in liquid Q10 at a given temperature T0 coincide with values determined in the glassy phase and extrapolated to T0.

  18. Altered metabolism of the methionine methyl group in the leukocytes of patients with schizophrenia

    Energy Technology Data Exchange (ETDEWEB)

    Ismail, L.; Sargent, T. III; Dobson, E.L.; Pollycove, M.

    1978-01-01

    Previous work has indicated that abnormal methylation processes may be associated with schizophrenia. In this study, leukocytes from patients with schizophrenia were incubated with methyl-/sup 14/C-L-methionine and the evolved /sup 14/CO/sub 2/ measured. With increasing concentration of methionine, the evolved /sup 14/CO/sub 2/ was lower in the patients than in normal control subjects. The incorporation of /sup 14/C into protein was the same in both groups, and when carboxyl-/sup 14/C-L-methionine was used the evolved /sup 14/CO/sub 2/ was the same in both groups, thus excluding the possibility that altered incorporation into protein or oxidation of the methionine molecule as a whole were responsible. The observed differences in methionine-methyl metabolism suggest that an abnormality in transmethylation processes or in oxidation of the methyl group to CO/sub 2/ is associated with schizophrenia. That this occurs in a peripheral tissue indicates that the abnormality is not restricted to the central nervous system.

  19. Possible Involvement of Hydrosulfide in B12-Dependent Methyl Group Transfer

    Directory of Open Access Journals (Sweden)

    John I. Toohey

    2017-04-01

    Full Text Available Evidence from several fields of investigation lead to the hypothesis that the sulfur atom is involved in vitamin B12-dependent methyl group transfer. To compile the evidence, it is necessary to briefly review the following fields: methylation, the new field of sulfane sulfur/hydrogen sulfide (S°/H2S, hydrosulfide derivatives of cobalamins, autoxidation of hydrosulfide radical, radical S-adenosylmethionine methyl transfer (RSMT, and methionine synthase (MS. Then, new reaction mechanisms for B12-dependent methyl group transfer are proposed; the mechanisms are facile and overcome difficulties that existed in previously-accepted mechanisms. Finally, the theory is applied to the effect of S°/H2S in nerve tissue involving the “hypomethylation theory” that was proposed 50 years ago to explain the neuropathology resulting from deficiency of vitamin B12 or folic acid. The conclusions are consistent with emerging evidence that sulfane sulfur/hydrogen sulfide may be beneficial in treating Alzheimer’s disease.

  20. Differential methylation between ethnic sub-groups reflects the effect of genetic ancestry and environmental exposures

    Science.gov (United States)

    Galanter, Joshua M; Gignoux, Christopher R; Oh, Sam S; Torgerson, Dara; Pino-Yanes, Maria; Thakur, Neeta; Eng, Celeste; Hu, Donglei; Huntsman, Scott; Farber, Harold J; Avila, Pedro C; Brigino-Buenaventura, Emerita; LeNoir, Michael A; Meade, Kelly; Serebrisky, Denise; Rodríguez-Cintrón, William; Kumar, Rajesh; Rodríguez-Santana, Jose R; Seibold, Max A; Borrell, Luisa N; Burchard, Esteban G; Zaitlen, Noah

    2017-01-01

    Populations are often divided categorically into distinct racial/ethnic groups based on social rather than biological constructs. Genetic ancestry has been suggested as an alternative to this categorization. Herein, we typed over 450,000 CpG sites in whole blood of 573 individuals of diverse Hispanic origin who also had high-density genotype data. We found that both self-identified ethnicity and genetically determined ancestry were each significantly associated with methylation levels at 916 and 194 CpGs, respectively, and that shared genomic ancestry accounted for a median of 75.7% (IQR 45.8% to 92%) of the variance in methylation associated with ethnicity. There was a significant enrichment (p=4.2×10-64) of ethnicity-associated sites amongst loci previously associated environmental exposures, particularly maternal smoking during pregnancy. We conclude that differential methylation between ethnic groups is partially explained by the shared genetic ancestry but that environmental factors not captured by ancestry significantly contribute to variation in methylation. DOI: http://dx.doi.org/10.7554/eLife.20532.001 PMID:28044981

  1. Spectroscopic investigation of the vibrational quasi-continuum arising from internal rotation of a methyl group

    Energy Technology Data Exchange (ETDEWEB)

    Hougen, J.T. [NIST, Gaithersburg, MD (United States)

    1993-12-01

    The goal of this project is to use spectroscopic techniques to investigate in detail phenomena involving the vibrational quasi-continuum in a simple physical system. Acetaldehyde was chosen for the study because: (i) methyl groups have been suggested to be important promotors of intramolecular vibrational relaxation, (ii) the internal rotation of a methyl group is an easily describle large-amplitude motion, which should retain its simple character even at high levels of excitation, and (iii) the aldehyde carbonyl group offers the possibility of both vibrational and electronic probing. The present investigation of the ground electronic state has three parts: (1) understanding the {open_quotes}isolated{close_quotes} internal-rotation motion below, at, and above the top of the torsional barrier, (2) understanding in detail traditional (bond stretching and bending) vibrational fundamental and overtone states, and (3) understanding interactions involving states with multiquantum excitations of at least one of these two kinds of motion.

  2. Methyl groups of thymine bases are important for nucleic acid recognition by DtxR.

    Science.gov (United States)

    Chen, C S; White, A; Love, J; Murphy, J R; Ringe, D

    2000-08-29

    The expression of diphtheria toxin is controlled by the diphtheria toxin repressor (DtxR). Under conditions of high iron concentration, DtxR binds the tox operator to inhibit transcription. To study how DNA binding specificity is achieved by this repressor, we solved the crystal structure of the nickel(II) activated DtxR(C102D) mutant complexed with a 43mer DNA duplex containing the DtxR consensus binding sequence. Structural analysis of this complex and comparison with a previously determined DtxR(C102D)-Ni(II)-tox operator ternary complex revealed unusual van der Waals interactions between Ser37/Pro39 of the repressor helix-turn-helix (HTH) motif and the methyl groups of specific thymine bases in the consensus binding sequence. Gel mobility shift assays utilizing deoxyuridine modified duplex DNA probes proved the importance of these interactions: the four methyl groups shown to interact with Ser37/Pro39 in the crystal structure contribute a total of 3.4 kcal/mol to binding energy. Thus, in addition to making base-specific hydrogen-bonding interactions to the DNA through its Gln43 residue, DtxR also recognizes methyl groups at certain positions in the DNA sequence with its Ser37 and Pro39 side chains, to achieve binding specificity toward its cognate operator sequences.

  3. Inelastic neutron scattering study of methyl groups rotation in some methylxanthines

    Science.gov (United States)

    Prager, M.; Pawlukojc, A.; Wischnewski, A.; Wuttke, J.

    2007-12-01

    The three isomeric dimethylxanthines and trimethylxanthine are studied by neutron spectroscopy up to energy transfers of 100meV at energy resolutions ranging from 0.7μeV to some meV. The loss of elastic intensity with increasing temperature can be modeled by quasielastic methyl rotation. The number of inequivalent methyl groups is in agreement with those of the room temperature crystal structures. Activation energies are obtained. In the case of theophylline, a doublet tunneling band is observed at 15.1 and 17.5μeV. In theobromine, a single tunneling band at 0.3μeV is found. Orientational disorder in caffeine leads to a 2.7μeV broad distribution of tunneling bands around the elastic line. At the same time, broad low energy phonon spectra characterize an orientational glassy state with weak methyl rotational potentials. Librational energies of the dimethylxanthines are clearly seen in the phonon densities of states. Rotational potentials can be derived which explain consistently all observables. While their symmetry in general is threefold, theophylline shows a close to sixfold potential reflecting a mirror symmetry.

  4. Turning cones off: the role of the 9-methyl group of retinal in red cones.

    Science.gov (United States)

    Estevez, Maureen E; Ala-Laurila, Petri; Crouch, Rosalie K; Cornwall, M Carter

    2006-12-01

    Our ability to see in bright light depends critically on the rapid rate at which cone photoreceptors detect and adapt to changes in illumination. This is achieved, in part, by their rapid response termination. In this study, we investigate the hypothesis that this rapid termination of the response in red cones is dependent on interactions between the 9-methyl group of retinal and red cone opsin, which are required for timely metarhodopsin (Meta) II decay. We used single-cell electrical recordings of flash responses to assess the kinetics of response termination and to calculate guanylyl cyclase (GC) rates in salamander red cones containing native visual pigment as well as visual pigment regenerated with 11-cis 9-demethyl retinal, an analogue of retinal in which the 9-methyl group is missing. After exposure to bright light that photoactivated more than approximately 0.2% of the pigment, red cones containing the analogue pigment had a slower recovery of both flash response amplitudes and GC rates (up to 10 times slower at high bleaches) than red cones containing 11-cis retinal. This finding is consistent with previously published biochemical data demonstrating that red cone opsin regenerated in vitro with 11-cis 9-demethyl retinal exhibited prolonged activation as a result of slowed Meta II decay. Our results suggest that two different mechanisms regulate the recovery of responsiveness in red cones after exposure to light. We propose a model in which the response recovery in red cones can be regulated (particularly at high light intensities) by the Meta II decay rate if that rate has been inhibited. In red cones, the interaction of the 9-methyl group of retinal with opsin promotes efficient Meta II decay and, thus, the rapid rate of recovery.

  5. Methyl group dynamics in a glass and its crystalline counterpart by neutron scattering

    CERN Document Server

    Moreno, A J; Colmenero, J; Frick, B

    2002-01-01

    Methyl group dynamics in the same sample of sodium acetate trihydrate in crystalline and glassy states have been investigated by neutron scattering. Measurements have been carried out in the whole temperature range covering the crossover from rotational tunneling to classical hopping. The results in the crystalline sample have been analyzed according to the usual single-particle model, while those in the glass were analyzed in terms of a broad Gaussian distribution of single-particle potentials, with a standard deviation of 205 K. The average barrier in the glass (417 K) takes, within the experimental error, the same value as the unique barrier in the crystal. (orig.)

  6. FLAMEnGO: a fuzzy logic approach for methyl group assignment using NOESY and paramagnetic relaxation enhancement data.

    Science.gov (United States)

    Chao, Fa-An; Shi, Lei; Masterson, Larry R; Veglia, Gianluigi

    2012-01-01

    Building on a recent method by Matthews and co-workers [1], we developed a new and efficient algorithm to assign methyl resonances from sparse and ambiguous NMR data. The new algorithm (FLAMEnGO: Fuzzy Logic Assignment of MEthyl GrOups) uses Monte Carlo sampling in conjunction with fuzzy logic to obtain the assignment of methyl resonances at high fidelity. Furthermore, we demonstrate that the inclusion of paramagnetic relaxation enhancement (PRE) data in the assignment strategy increases the percentage of correct assignments with sparse NOE data. Using synthetic tests and experimental data we show that this new approach provides up to ∼80% correct assignments with only 30% of methyl-methyl NOE data. In the experimental case of ubiquitin, PRE data from two spin labeled sites improve the percentage of assigned methyl groups up to ∼91%. This new strategy promises to further expand methyl group NMR spectroscopy to very large macromolecular systems. Copyright © 2011 Elsevier Inc. All rights reserved.

  7. Role of laccase from Coriolus versicolor MTCC-138 in selective oxidation of aromatic methyl group.

    Science.gov (United States)

    Chaurasia, Pankaj Kumar; Singh, Sunil Kumar; Bharati, Shashi Lata

    2014-01-01

    Now a day, laccases are the most promising enzymes in the area of biotechnology and synthesis. One of the best applications of laccases is the selective oxidation of aromatic methyl group to aldehyde group. Such transformations are valuable because it is difficult to stop the reaction at aldehyde stage. Chemical methods used for such biotransformations areexpensive and give poor yields. But, the laccase-catalyzed biotransformations of such type are non-expensive and yield is excellent. Authors have used crude laccase obtained from the liquid culture growth medium of fungal strain Coriolus versicolor MTCC-138 for the biotransformations of toluene, 3-nitrotoluene, and 4-chlorotoluene to benzaldehyde, 3-nitrobenzaldehyde, and 4-chlorobenzaldehyde, respectively, instead of purified laccase because purification process requires much time and cost. This communication reports that crude laccase can also be used in the place of purified laccase as effective biocatalyst.

  8. FLAMEnGO 2.0: an enhanced fuzzy logic algorithm for structure-based assignment of methyl group resonances.

    Science.gov (United States)

    Chao, Fa-An; Kim, Jonggul; Xia, Youlin; Milligan, Michael; Rowe, Nancy; Veglia, Gianluigi

    2014-08-01

    We present an enhanced version of the FLAMEnGO (Fuzzy Logic Assignment of Methyl Group) software, a structure-based method to assign methyl group resonances in large proteins. FLAMEnGO utilizes a fuzzy logic algorithm coupled with Monte Carlo sampling to obtain a probability-based assignment of the methyl group resonances. As an input, FLAMEnGO requires either the protein X-ray structure or an NMR structural ensemble including data such as methyl-methyl NOESY, paramagnetic relaxation enhancement (PRE), methine-methyl TOCSY data. Version 2.0 of this software (FLAMEnGO 2.0) has a user-friendly graphic interface and presents improved modules that enable the input of partial assignments and additional NMR restraints. We tested the performance of FLAMEnGO 2.0 on maltose binding protein (MBP) as well as the C-subunit of the cAMP-dependent protein kinase A (PKA-C). FLAMEnGO 2.0 can be used as a standalone method or to assist in the completion of partial resonance assignments and can be downloaded at www.chem.umn.edu/groups/veglia/forms/flamengo2-form.html. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. The effect of a methyl group incorporated in EDO-TTF

    Science.gov (United States)

    Shao, X. F.; Nakano, Y.; Saito, G.; Yakushi, K.; Koshihara, S.; Tanaka, K.; Yamochi, H.

    2010-06-01

    The introduction of a methyl group into ethylenedioxytetrathiafulvalene (EDO-TTF) greatly modified the molecular character as a component for the conducting complexes. While the pristine EDO-TTF almost exclusively formed head-to-tail type overlapping with the neighboring donor molecules in the complexes, the methyl substituted compound, MeEDO-TTF, showed both the head-to-head and head-to-tail overlapping patterns. In the former case, the donor molecules interacted with each other in a two-dimensional fashion to provide stable metals along with the charge-ordered complex which exhibited semiconductor-semiconductor first-order transition just above room temperature. The overlapping pattern of MeEDO-TTF directly corresponded to the electronic structure of the complex. In the case of head-to-tail packing patterns, the charge carriers were delocalized only in a quasi-one-dimensional column or in a multimer composed of the donor molecules. The comparison of the intermolecular overlap integrals calculated in the extended Hückel level suggested that at least the magnitude of ca. 10×10-3 is needed for the infinite chain or network of the conducting component molecules to exhibit metallic nature.

  10. SIRT1 affects DNA methylation of polycomb group protein target genes, a hotspot of the epigenetic shift observed in ageing

    OpenAIRE

    Wakeling, Luisa; Ions, Laura; Escolme, Suzanne; Cockell, Simon,; Su, Tianhong; Dey, Madhurima; Hampton, Emily; Jenkins, Gail; Wainwright, Linda; McKay, Jill; Ford, Dianne

    2015-01-01

    Background SIRT1 is likely to play a role in the extension in healthspan induced by dietary restriction. Actions of SIRT1 are pleiotropic, and effects on healthspan may include effects on DNA methylation. Polycomb group protein target genes (PCGTs) are suppressed by epigenetic mechanisms in stem cells, partly through the actions of the polycomb repressive complexes (PRCs), and have been shown previously to correspond with loci particularly susceptible to age-related changes in DNA methylation...

  11. Methylation of sulfhydryl groups: a new function for a family of small molecule plant O-methyltransferases

    Science.gov (United States)

    Coiner, Heather; Schröder, Gudrun; Wehinger, Elke; Liu, Chang-Jun; Noel, Joseph P.; Schwab, Wilfried; Schröder, Joachim

    2010-01-01

    Summary In plants, type I and II S-adenosyl-L-methionine-dependent O-methyltransferases (OMTs) catalyze most hydroxyl group methylations of small molecules. A homology-based RT-PCR strategy using Catharanthus roseus (Madagascar periwinkle) RNA previously identified six new type I plant OMT family members. We now describe the molecular and biochemical characterization of a seventh protein. It shares 56–58% identity with caffeic acid OMTs (COMTs), but it failed to methylate COMT substrates, and had no activity with flavonoids. However, the in vitro incubations revealed unusually high background levels without added substrates. A search for the responsible component revealed that the enzyme methylated dithiothreitol (DTT), the reducing agent added for enzyme stabilization. Unexpectedly, product analysis revealed that the methylation occurred on a sulfhydryl moiety, not on a hydroxyl group. Analysis of 34 compounds indicated a broad substrate range, with a preference for small hydrophobic molecules. Benzene thiol (Km 220 μM) and furfuryl thiol (Km 60 μM) were the best substrates (6–7-fold better than DTT). Small isosteric hydrophobic substrates with hydroxyl groups, like phenol and guaiacol, were also methylated, but the activities were at least 5-fold lower than with thiols. The enzyme was named C. roseus S-methyltransferase 1 (CrSMT1). Models based on the COMT crystal structure suggest that S-methylation is mechanistically identical to O-methylation. CrSMT1 so far is the only recognized example of an S-methyltransferase in this protein family. Its properties indicate that a few changes in key residues are sufficient to convert an OMT into a S-methyltransferase (SMT). Future functional investigations of plant methyltransferases should consider the possibility that the enzymes may direct methylation at sulfhydryl groups. PMID:16623883

  12. Specific labeling and assignment strategies of valine methyl groups for NMR studies of high molecular weight proteins

    Energy Technology Data Exchange (ETDEWEB)

    Mas, Guillaume; Crublet, Elodie [Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS) (France); Hamelin, Olivier [CNRS (France); Gans, Pierre; Boisbouvier, Jérôme, E-mail: jerome.boisbouvier@ibs.fr [Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS) (France)

    2013-09-28

    The specific protonation of valine and leucine methyl groups in proteins is typically achieved by overexpressing proteins in M9/D{sub 2}O medium supplemented with either labeled α-ketoisovalerate for the labeling of the four prochiral methyl groups or with 2-acetolactate for the stereospecific labeling of the valine and leucine side chains. However, when these labeling schemes are applied to large protein assemblies, significant overlap between the correlations of the valine and leucine methyl groups occurs, hampering the analysis of 2D methyl-TROSY spectra. Analysis of the leucine and valine biosynthesis pathways revealed that the incorporation of labeled precursors in the leucine pathway can be inhibited by the addition of exogenous l-leucine-d{sub 10}. We exploited this property to label stereospecifically the pro-R and pro-S methyl groups of valine with minimal scrambling to the leucine residues. This new labeling protocol was applied to the 468 kDa homododecameric peptidase TET2 to decrease the complexity of its NMR spectra. All of the pro-S valine methyl resonances of TET2 were assigned by combining mutagenesis with this innovative labeling approach. The assignments were transferred to the pro-R groups using an optimally labeled sample and a set of triple resonance experiments. This improved labeling scheme enables us to overcome the main limitation of overcrowding in the NMR spectra of prochiral methyl groups, which is a prerequisite for the site-specific measurement of the structural and dynamic parameters or for the study of interactions in very large protein assemblies.

  13. Photoinitiated polymerization of new hybrid monomer containing vinyl ether and (methyl) acryloyl groups

    Science.gov (United States)

    Diao, Cuimei; Zou, Yingquan

    2011-04-01

    The photopolymerization kinetics of 4-(vinyloxy)butyl methacrylate containing cationic and free radical polymerizable vinyl groups was studied by real-time Fourier transform infrared spectra (RT-FTIR) .The cationic polymerizable vinyl ether moieties(Vc) of the hybrid monomer in solution polymerized rapidly by exposure to UV light in presence of a cationic photoinitiator such as an iodonium salt or suflonium salt .High conversions, of 90%, were obtained for most of the systems investigated. The efficiency of the cationic photoinitiators in initiating the polymerization of the vinyl ether moieties (Vc) of the hybrid monomer was in the order: suflonium salt > iodonium salt . The free radical polymerizable methacrylate groups (Vr) of the hybrid monomer in solution polymerized by exposure to UV light in presence of a radical photoinitiator such as 2,4,6-trimethyl benzoyl diphenylphoshine oxide (TPO), 2-isopropyl thioxanthone (ITX) , Phenylbis(2,4,6-trimethylbenzoyl)phosphine oxide (Irgaure 819), 2-Methyl-4'-(methylthio)-2-morpholinopropiophenone (Irgaure 907). Among the photoinitiators , the best effect in initiating the polymerization of methacrylate groups (Vr) of the hybrid monomer is initiator Irgaure 907.

  14. Methyl Group Tunneling Rotation in the Lowest nπ* Triplet State of Toluquinone. An Optically Detected ENDOR, LAC and CR Study

    NARCIS (Netherlands)

    Lichtenbelt, Jan H.; Wiersma, Douwe A.

    1979-01-01

    In this paper we report and discuss the effects of methyl group tunneling rotation on the methyl proton ENDOR, LAC and CR spectra in the lowest triplet state of toluquinone at 1.8 K. From a detailed analysis of the ENDOR spectra in the lowest rotational state (A) we obtain for the methyl protons the

  15. Theory of long-lived nuclear spin states in methyl groups and quantum-rotor induced polarisation.

    Science.gov (United States)

    Dumez, Jean-Nicolas; Håkansson, Pär; Mamone, Salvatore; Meier, Benno; Stevanato, Gabriele; Hill-Cousins, Joseph T; Roy, Soumya Singha; Brown, Richard C D; Pileio, Giuseppe; Levitt, Malcolm H

    2015-01-28

    Long-lived nuclear spin states have a relaxation time much longer than the longitudinal relaxation time T1. Long-lived states extend significantly the time scales that may be probed with magnetic resonance, with possible applications to transport and binding studies, and to hyperpolarised imaging. Rapidly rotating methyl groups in solution may support a long-lived state, consisting of a population imbalance between states of different spin exchange symmetries. Here, we expand the formalism for describing the behaviour of long-lived nuclear spin states in methyl groups, with special attention to the hyperpolarisation effects observed in (13)CH3 groups upon rapidly converting a material with low-barrier methyl rotation from the cryogenic solid state to a room-temperature solution [M. Icker and S. Berger, J. Magn. Reson. 219, 1 (2012)]. We analyse the relaxation properties of methyl long-lived states using semi-classical relaxation theory. Numerical simulations are supplemented with a spherical-tensor analysis, which captures the essential properties of methyl long-lived states.

  16. Stable arylsilver compounds containing dimethylamino, (dimethylamino)methyl or methoxy groups at the aryl nucleus

    NARCIS (Netherlands)

    Koten, G. van; Leusink, A.J.; Noltes, J.G.

    1973-01-01

    The following organosilver compounds have been prepared from the corresponding lithium compounds and silver bromide : {2-[(dimethylamino)methyl]phenyl}silver, {2-[(dimethylamino)methyl]phenyl}silver.silver bromide, bis{[2-(dimethylamino)phenyl]silver} . silver bromide, (2, 6-dimethoxyphenyl)silver

  17. Hydroxy-directed diastereoselective installation of a methyl group on indalone models and spiroketal potential precursors for the bafilomycin A(1) C15-C25 subunit.

    Science.gov (United States)

    Poupon, Jean-Christophe; Lopez, Roman; Prunet, Joëlle; Férézou, Jean-Pierre

    2002-04-05

    Current efforts devoted to the synthesis of Bafilomycin A(1) led us to investigate a synthetic route through a spiroketal intermediate for the construction of the C15-C25 subunit. Preliminary studies for the diastereoselective installation of the methyl-16 cis with respect to the vicinal OH-15 group through radical opening of either siloxafuran intermediate 7 or cyclopropyl compounds 9 and 13 have been carried out using model compounds derived from commercial Indalone 6. In each case the expected "cis" diastereoisomer was obtained in good to excellent yield. Application of these results to Bafilomycin A(1) synthon led to the opposite "trans" stereoselectivity when alpha-carboxy- or alpha-keto-substituted spiroketals 4 or 19 were used. However, the expected potential intermediate has been obtained from the alpha-hydroxymethyl cyclopropanated synthon 21. A Barton-Motherwell xanthate radical deoxygenation-cylopropane opening methodology, followed by a hydroboration-oxidation of the exovinylic intermediate, delivered the expected product 22cis in high yield and excellent stereoselectivity.

  18. Catalytic Ester to Stannane Functional Group Interconversion via Decarbonylative Cross-Coupling of Methyl Esters

    KAUST Repository

    Yue, Huifeng

    2018-01-03

    An unprecedented conversion of methyl esters to stannanes was realized, providing access to a series of arylstannanes via nickel catalysis. Various common esters including ethyl, cyclohexyl, benzyl, and phenyl esters can undergo the newly developed decarbonylative stannylation reaction. The reaction shows broad substrate scope, can differentiate between different types of esters, and if applied in consecutive fashion, allows the transformation of methyl esters into aryl fluorides or biaryls via fluororination or arylation.

  19. The 9-methyl group of retinal is essential for rapid Meta II decay and phototransduction quenching in red cones.

    Science.gov (United States)

    Estevez, Maureen E; Kolesnikov, Alexander V; Ala-Laurila, Petri; Crouch, Rosalie K; Govardovskii, Victor I; Cornwall, M Carter

    2009-08-01

    Cone photoreceptors of the vertebrate retina terminate their response to light much faster than rod photoreceptors. However, the molecular mechanisms underlying this rapid response termination in cones are poorly understood. The experiments presented here tested two related hypotheses: first, that the rapid decay rate of metarhodopsin (Meta) II in red-sensitive cones depends on interactions between the 9-methyl group of retinal and the opsin part of the pigment molecule, and second, that rapid Meta II decay is critical for rapid recovery from saturation of red-sensitive cones after exposure to bright light. Microspectrophotometric measurements of pigment photolysis, microfluorometric measurements of retinol production, and single-cell electrophysiological recordings of flash responses of salamander cones were performed to test these hypotheses. In all cases, cones were bleached and their visual pigment was regenerated with either 11-cis retinal or with 11-cis 9-demethyl retinal, an analogue of retinal lacking the 9-methyl group. Meta II decay was four to five times slower and subsequent retinol production was three to four times slower in red-sensitive cones lacking the 9-methyl group of retinal. This was accompanied by a significant slowing of the recovery from saturation in cones lacking the 9-methyl group after exposure to bright (>0.1% visual pigment photoactivated) but not dim light. A mathematical model of the turn-off process of phototransduction revealed that the slower recovery of photoresponse can be explained by slower Meta decay of 9-demethyl visual pigment. These results demonstrate that the 9-methyl group of retinal is required for steric chromophore-opsin interactions that favor both the rapid decay of Meta II and the rapid response recovery after exposure to bright light in red-sensitive cones.

  20. Stereospecific assignments of the isopropyl methyl groups of the membrane protein OmpX in DHPC micelles.

    Science.gov (United States)

    Hilty, Christian; Wider, Gerhard; Fernández, César; Wüthrich, Kurt

    2003-12-01

    In NMR studies of large molecular structures, the number of conformational constraints based on NOE measurements is typically limited due to the need for partial deuteration. As a consequence, when using selective protonation of peripheral methyl groups on a perdeuterated background, stereospecific assignments of the diastereotopic methyl groups of Val and Leu can have a particularly large impact on the quality of the NMR structure determination. For example, 3D 15N- and 13C-resolved [1H,1H]-NOESY spectra of the E. Coli membrane protein OmpX in mixed micelles with DHPC, which have an overall molecular weight of about 60 kDa, showed that about 50% of all obtainable NOEs involve the diastereotopic methyl groups of Val and Leu. In this paper, we used biosynthetically-directed fractional 13C labeling of OmpX and [13C,1H]-HSQC spectroscopy to obtain stereospecific methyl assignments of Val and Leu in OmpX/DHPC. For practical purposes it is of interest that this data could be obtained without use of a deuterated background, and that combinations of NMR experiments have been found for obtaining the desired information either at a 1H frequency of 500 MHz, or with significantly reduced measuring time on a high-frequency instrument.

  1. Stereospecific assignments of the isopropyl methyl groups of the membrane protein OmpX in DHPC micelles

    Energy Technology Data Exchange (ETDEWEB)

    Hilty, Christian; Wider, Gerhard; Fernandez, Cesar; Wuethrich, Kurt [Institut fuer Molekularbiologie und Biophysik, Eidgenoessische Technische Hochschule Zuerich (Switzerland)], E-mail: wuthrich@mol.biol.ethz.ch

    2003-12-15

    In NMR studies of large molecular structures, the number of conformational constraints based on NOE measurements is typically limited due to the need for partial deuteration. As a consequence, when using selective protonation of peripheral methyl groups on a perdeuterated background, stereospecific assignments of the diastereotopic methyl groups of Val and Leu can have a particularly large impact on the quality of the NMR structure determination. For example, 3D {sup 15}N- and {sup 13}C-resolved [{sup 1}H,{sup 1}H]-NOESY spectra of the E. Coli membrane protein OmpX in mixed micelles with DHPC, which have an overall molecular weight of about 60 kDa, showed that about 50% of all obtainable NOEs involve the diastereotopic methyl groups of Val and Leu. In this paper, we used biosynthetically-directed fractional {sup 13}C labeling of OmpX and [{sup 13}C,{sup 1}H]-HSQC spectroscopy to obtain stereospecific methyl assignments of Val and Leu in OmpX/DHPC. For practical purposes it is of interest that this data could be obtained without use of a deuterated background, and that combinations of NMR experiments have been found for obtaining the desired information either at a {sup 1}H frequency of 500 MHz, or with significantly reduced measuring time on a high-frequency instrument.

  2. Microsatellite instability, MLH1 promoter methylation, and BRAF mutation analysis in sporadic colorectal cancers of different ethnic groups in Israel.

    Science.gov (United States)

    Vilkin, Alex; Niv, Yaron; Nagasaka, Takeshi; Morgenstern, Sarah; Levi, Zohar; Fireman, Zvi; Fuerst, Florentine; Goel, Ajay; Boland, C Richard

    2009-02-15

    The molecular mechanisms that underlie colorectal cancer (CRC) include microsatellite instability (MSI), chromosomal instability, and the CpG island methylator phenotype. There is evidence to suggest that CRC incidence varies among different ethnic populations worldwide. The authors of this report hypothesized that environmental factors and lifestyle differences among various ethnic groups may differentially influence the epigenetic regulation of tumor suppressor genes in CRC. In the current study, microdissection and DNA extraction were performed on 128 samples of CRC from Israeli patients (85 Jews and 43 Arabs). MSI analysis, mutL homolog 1 (MLH1) and mutS homolog 2 (MSH2) protein expression levels, and MLH1 promoter methylation were investigated by combined bisulfite restriction analysis. The v-raf murine sarcoma viral oncogene homolog B1 (BRAF) valine-to-glutamic acid mutation at residue 600 was investigated by direct DNA sequencing. High MSI (MSI-H), MLH1 methylation, and BRAF mutations were observed in 11.6%, 9.4%, and 23.5% of Jews, respectively, and in 16.2%, 17.6%, and 20.9% of Arabs, respectively (P value nonsignificant). MLH1 promoter methylation was observed in 22.6% of microsatellite-stable (MSS) tumors and in 53.8% of MSI-H tumors (P < .015). Extensive methylation (covering both 5' and 3' promoter regions) was present in all MSI-H tumors with loss of MLH1 expression. BRAF mutation was observed in 15.6% and 46.1% of MSS tumors and MSI-H tumors, respectively (P < .007). BRAF mutation was observed in 66%, 22.2%, and 14.7% of patients who had tumors with extensive MLH1 promoter methylation, methylation of the 5' region alone, or without methylation, respectively (P < .006). There was no difference in molecular signatures examined between Jewish and Arab patients with CRC in Israel. Extensive promoter methylation was associated with MLH1 inactivation, MSI, and BRAF mutation. (c) 2009 American Cancer Society.

  3. Cooperative effects of o- and m-methyl groups on the intramolecular charge-transfer emission properties of dibenzoylmethanatoboron difluorides.

    Science.gov (United States)

    Tanaka, Mirai; Muraoka, Shunsuke; Matsui, Yasunori; Ohta, Eisuke; Ogaki, Takuya; Mizuno, Kazuhiko; Ikeda, Hiroshi

    2017-06-14

    The photophysical properties of o-tolyl-, m-tolyl-, and p-xylyl-substituted asymmetric diaroylmethanatoboron difluorides in a mixture of CH2Cl2 and c-C6H12, and in the crystalline state were determined. In solution, the fluorescence (FL) properties of these substances are controlled by the position and number of methyl groups on the phenyl rings. An especially interesting finding is that FL from the p-xylyl derivative occurs from an excited state which possesses intramolecular charge-transfer character caused by the o- and m-methyl groups cooperatively. The results of X-ray crystallographic analysis reveal that these asymmetric diaroylmethanatoboron difluorides form dyads through orbital overlap of neighboring molecules. This phenomenon governs the unique FL properties of these substances in the solid state.

  4. Protein conformational exchange measured by {sup 1}H R{sub 1{rho}} relaxation dispersion of methyl groups

    Energy Technology Data Exchange (ETDEWEB)

    Weininger, Ulrich [Lund University, Department of Biophysical Chemistry, Center for Molecular Protein Science (Sweden); Blissing, Annica T.; Hennig, Janosch; Ahlner, Alexandra [Linkoeping University, Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology (Sweden); Liu, Zhihong; Vogel, Hans J. [University of Calgary, Department of Biological Sciences, Biochemistry Research Group (Canada); Akke, Mikael, E-mail: mikael.akke@bpc.liu.se [Lund University, Department of Biophysical Chemistry, Center for Molecular Protein Science (Sweden); Lundstroem, Patrik, E-mail: patlu@ifm.liu.se [Linkoeping University, Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology (Sweden)

    2013-09-15

    Activated dynamics plays a central role in protein function, where transitions between distinct conformations often underlie the switching between active and inactive states. The characteristic time scales of these transitions typically fall in the microsecond to millisecond range, which is amenable to investigations by NMR relaxation dispersion experiments. Processes at the faster end of this range are more challenging to study, because higher RF field strengths are required to achieve refocusing of the exchanging magnetization. Here we describe a rotating-frame relaxation dispersion experiment for {sup 1}H spins in methyl {sup 13}CHD{sub 2} groups, which improves the characterization of fast exchange processes. The influence of {sup 1}H-{sup 1}H rotating-frame nuclear Overhauser effects (ROE) is shown to be negligible, based on a comparison of R{sub 1{rho}} relaxation data acquired with tilt angles of 90 Degree-Sign and 35 Degree-Sign , in which the ROE is maximal and minimal, respectively, and on samples containing different {sup 1}H densities surrounding the monitored methyl groups. The method was applied to ubiquitin and the apo form of calmodulin. We find that ubiquitin does not exhibit any {sup 1}H relaxation dispersion of its methyl groups at 10 or 25 Degree-Sign C. By contrast, calmodulin shows significant conformational exchange of the methionine methyl groups in its C-terminal domain, as previously demonstrated by {sup 1}H and {sup 13}C CPMG experiments. The present R{sub 1{rho}} experiment extends the relaxation dispersion profile towards higher refocusing frequencies, which improves the definition of the exchange correlation time, compared to previous results.

  5. Quantum mechanical alternative to Arrhenius equation in the interpretation of proton spin-lattice relaxation data for the methyl groups in solids

    KAUST Repository

    Bernatowicz, Piotr

    2015-10-01

    Theory of nuclear spin-lattice relaxation in methyl groups in solids has been a recurring problem in nuclear magnetic resonance (NMR) spectroscopy. The current view is that, except for extreme cases of low torsional barriers where special quantum effects are at stake, the relaxation behaviour of the nuclear spins in methyl groups is controlled by thermally activated classical jumps of the methyl group between its three orientations. The temperature effects on the relaxation rates can be modelled by Arrhenius behaviour of the correlation time of the jump process. The entire variety of relaxation effects in protonated methyl groups has recently been given a consistently quantum mechanical explanation not invoking the jump model regardless of the temperature range. It exploits the damped quantum rotation (DQR) theory originally developed to describe NMR line shape effects for hindered methyl groups. In the DQR model, the incoherent dynamics of the methyl group include two quantum rate, i.e., coherence-damping processes. For proton relaxation only one of these processes is relevant. In this paper, temperature-dependent proton spin-lattice relaxation data for the methyl groups in polycrystalline methyltriphenyl silane and methyltriphenyl germanium, both deuterated in aromatic positions, are reported and interpreted in terms of the DQR model. A comparison with the conventional approach exploiting the phenomenological Arrhenius equation is made. The present observations provide further indications that incoherent motions of molecular moieties in condensed phase can retain quantum character over much broad temperature range than is commonly thought.

  6. A quantum mechanical alternative to the Arrhenius equation in the interpretation of proton spin-lattice relaxation data for the methyl groups in solids.

    Science.gov (United States)

    Bernatowicz, Piotr; Shkurenko, Aleksander; Osior, Agnieszka; Kamieński, Bohdan; Szymański, Sławomir

    2015-11-21

    The theory of nuclear spin-lattice relaxation in methyl groups in solids has been a recurring problem in nuclear magnetic resonance (NMR) spectroscopy. The current view is that, except for extreme cases of low torsional barriers where special quantum effects are at stake, the relaxation behaviour of the nuclear spins in methyl groups is controlled by thermally activated classical jumps of the methyl group between its three orientations. The temperature effects on the relaxation rates can be modelled by Arrhenius behaviour of the correlation time of the jump process. The entire variety of relaxation effects in protonated methyl groups have recently been given a consistent quantum mechanical explanation not invoking the jump model regardless of the temperature range. It exploits the damped quantum rotation (DQR) theory originally developed to describe NMR line shape effects for hindered methyl groups. In the DQR model, the incoherent dynamics of the methyl group include two quantum rate (i.e., coherence-damping) processes. For proton relaxation only one of these processes is relevant. In this paper, temperature-dependent proton spin-lattice relaxation data for the methyl groups in polycrystalline methyltriphenyl silane and methyltriphenyl germanium, both deuterated in aromatic positions, are reported and interpreted in terms of the DQR model. A comparison with the conventional approach exploiting the phenomenological Arrhenius equation is made. The present observations provide further indications that incoherent motions of molecular moieties in the condensed phase can retain quantum character over much broader temperature range than is commonly thought.

  7. Complex methyl group and hydrogen-bonded proton motions in terms of the Arrhenius and Schrödinger equations.

    Science.gov (United States)

    Latanowicz, L

    2008-01-01

    Equations for the temperature dependence of the spectral densities J(is)(m)(momega(I) +/-omega(T)), where m=1, 2, omega(I) and omega(T) are the resonance and tunnel splitting angular frequencies, in the presence of a complex motion, have been derived. The spin pairs of the protons or deuterons of the methyl group perform a complex motion consisting of three component motions. Two of them involve mass transportation over the barrier and through the barrier. They are characterized by k((H)) (Arrhenius) and k((T)) (Schrödinger) rate constants, respectively. The third motion causes fluctuations of the frequencies (nomega(I)+/-omega(T)) and it is related to the lifetime of the methyl spin at the energy level influenced by the rotor-bath interactions. These interactions induce rapid transitions, changing the symmetry of the torsional sublevels either from A to E or from E(a) to E(b). The correlation function for this third motion (k((omega)) rate constant) has been proposed by Müller-Warmuth et al. The spectral densities of the methyl group hindered rotation (k((H)), k((T)) and k((omega)) rate constants) differ from the spectral densities of the proton transfer (k((H)) and k((T)) rate constants) because three compound motions contribute to the complex motion of the methyl group. The recently derived equation [Formula: see text] , where [Formula: see text] and [Formula: see text] are the fraction and energy of particles with energies from zero to E(H), is taken into account in the calculations of the spectral densities. This equation follows from Maxwell's distribution of thermal energy. The spectral densities derived are applied to analyse the experimental temperature dependencies of proton and deuteron spin-lattice relaxation rate in solids containing the methyl group. A wide range of temperatures from zero Kelvin up to the melting point is considered. It has been established that the motion characterized by k((omega)) influences the spin-lattice relaxation up to the

  8. Effects of methyl group on aromatic hydrocarbons on the nanostructures and oxidative reactivity of combustion-generated soot

    KAUST Repository

    Guerrero Peña, Gerardo D.J.

    2016-07-23

    The substituted and unsubstituted aromatic hydrocarbons, present in transportation fuels such as gasoline and diesel, are thought to be responsible for most of the soot particles produced during their combustion. However, the effects of the substituted alkyl groups on the aromatic hydrocarbons on their sooting tendencies, and on the physical and chemical properties of soot produced from them are not well understood. In this work, the effect of the presence of methyl groups on aromatic hydrocarbons on their sooting propensity, and on the oxidative reactivity, morphology, and chemical composition of soot generated from them in diffusion flames is studied using benzene, toluene, and m-xylene as fuels. Several experimental techniques including high resolution transmission electron microscopy and X-ray diffraction are used to identify the morphological changes in soot, whereas the elemental and thermo-gravimetric analyses, electron energy loss spectroscopy, and Fourier transform infrared spectroscopy are used to study the changes in its chemical properties and reactivity. The activation energies for soot oxidation are calculated at different conversion levels, and a trend in the reactivity of soots from benzene, toluene and m-xylene is reported. It is observed that the sizes of primary particles and graphene-like sheets, and the concentrations of aliphatics and oxygenated groups in soot particles decreased with the addition of methyl group(s) on the aromatic ring. The physicochemical changes in soot are found to support the oxidative reactivity trends. © 2016 The Combustion Institute

  9. - Tunneling Matrix Formalism for - and Two-Methyl Molecules Based on the Extended Permutation-Inversion Group Idea and its Application to the Analyses of the Methyl-Torsional Rotational Spectra

    Science.gov (United States)

    Ohashi, Nobukimi; Kobayashi, Kaori; Fujitake, Masaharu

    2016-06-01

    Recently we reanalyzed the microwave absorption spectra of the trans-ethyl methyl ether molecule, state by state, in the ground vibrational, O-methyl torsional, C-methyl torsional and skeletal torsional states with the use of an IAM-like tunneling matrix formalism based on an extended permutation-inversion (PI) group idea, whose results appeared in Journal of Molecular Spectroscopy recently. Since a single rho-axis does not exist in trans-ethyl methyl ether that has two methyl-tops and the IAM formalism is not available as in the case of the one methyl-top molecule, we adopted instead an IAM-like (in other word, partial IAM) formalism. We will show the outline of the present formalism and the results of the spectral analyses briefly. We also would like to review the IAM formalism for the one top molecules based on the extended PI group, and show the result of the application to the spectral analysis. If possible, we would like to compare the IAM and IAM-like formalisms based on the extended PI group with the ERHAM formalism developed by Groner, especially, in the form of Hamiltonian matrix elements, and discuss about similarity and difference.

  10. The 6-amino-6-methyl-1,4-diazepine group as an ancillary ligand framework for neutral and cationic scandium and yttrium alkyls

    NARCIS (Netherlands)

    Ge, Shaozhong; Bambirra, Sergio; Meetsma, Auke; Hessen, Bart

    2006-01-01

    The 6-amino-6-methyl-1,4-diazepine framework is a readily available neutral 6-electron ligand moiety, suitable to support cationic group 3 metal alkyl catalysts; it also provides convenient access to tri- and tetradentate monoanionic ligand derivatives.

  11. High Glucose-Induced PC12 Cell Death by Increasing Glutamate Production and Decreasing Methyl Group Metabolism

    Directory of Open Access Journals (Sweden)

    Minjiang Chen

    2016-01-01

    Full Text Available Objective. High glucose- (HG- induced neuronal cell death is responsible for the development of diabetic neuropathy. However, the effect of HG on metabolism in neuronal cells is still unclear. Materials and Methods. The neural-crest derived PC12 cells were cultured for 72 h in the HG (75 mM or control (25 mM groups. We used NMR-based metabolomics to examine both intracellular and extracellular metabolic changes in HG-treated PC12 cells. Results. We found that the reduction in intracellular lactate may be due to excreting more lactate into the extracellular medium under HG condition. HG also induced the changes of other energy-related metabolites, such as an increased succinate and creatine phosphate. Our results also reveal that the synthesis of glutamate from the branched-chain amino acids (isoleucine and valine may be enhanced under HG. Increased levels of intracellular alanine, phenylalanine, myoinositol, and choline were observed in HG-treated PC12 cells. In addition, HG-induced decreases in intracellular dimethylamine, dimethylglycine, and 3-methylhistidine may indicate a downregulation of methyl group metabolism. Conclusions. Our metabolomic results suggest that HG-induced neuronal cell death may be attributed to a series of metabolic changes, involving energy metabolism, amino acids metabolism, osmoregulation and membrane metabolism, and methyl group metabolism.

  12. Synthesis and oxidation of CpIrIII compounds: functionalization of a Cp methyl group.

    Science.gov (United States)

    Park-Gehrke, Lisa S; Freudenthal, John; Kaminsky, Werner; Dipasquale, Antonio G; Mayer, James M

    2009-03-21

    [CpIrCl(2)](2) () and new CpIr(III)(L-L)X complexes (L-L = N-O or C-N chelating ligands; X = Cl, I, Me) have been prepared and their reactivity with two-electron chemical oxidants explored. Reaction of with PhI(OAc)(2) in wet solvents yields a new chloro-bridged dimer in which each of the Cp ligands has been singly acetoxylated to form [Cp(OAc)Ir(III)Cl(2)](2) () (Cp(OAc) = eta(5)-C(5)Me(4)CH(2)OAc). Complex and related carboxy- and alkoxy-functionalized Cp(OR) complexes can also be prepared from plus (PhIO)(n) and ROH. [Cp(OAc)Ir(III)Cl(2)](2) () and the methoxy analogue [Cp(OMe)Ir(III)Cl(2)](2) () have been structurally characterized. Treatment of [CpIrCl(2)](2) () with 2-phenylpyridine yields CpIr(III)(ppy)Cl () (ppy = cyclometallated 2-phenylpyridyl) which is readily converted to its iodide and methyl analogues CpIr(III)(ppy)I and CpIr(III)(ppy)Me (). CpIr(III) complexes were also prepared with N-O chelating ligands derived from anthranilic acid (2-aminobenzoic acid) and alpha-aminoisobutyric acid (H(2)NCMe(2)COOH), ligands chosen to be relatively oxidation resistant. These complexes and were reacted with potential two-electron oxidants including PhI(OAc)(2), hexachlorocyclohexadienone (C(6)Cl(6)O), N-fluoro-2,4,6-trimethylpyridinium (Me(3)pyF(+)), [Me(3)O]BF(4) and MeOTf (OTf = triflate, CF(3)SO(3)). Iridium(V) complexes were not observed or implicated in these reactions, despite the similarity of the potential products to known CpIr(V) species. The carbon electrophiles [Me(3)O]BF(4) and MeOTf appear to react preferentially at the N-O ligands, to give methyl esters in some cases. Overall, the results indicate that Cp is not inert under oxidizing conditions and is therefore not a good supporting ligand for oxidizing organometallic complexes.

  13. Biotransformation of Bicyclic Halolactones with a Methyl Group in the Cyclohexane Ring into Hydroxylactones and Their Biological Activity.

    Science.gov (United States)

    Wińska, Katarzyna; Grabarczyk, Małgorzata; Mączka, Wanda; Żarowska, Barbara; Maciejewska, Gabriela; Dancewicz, Katarzyna; Gabryś, Beata; Szumny, Antoni; Anioł, Mirosław

    2016-10-31

    The aim of this study was the chemical synthesis of a series of halo- and unsaturated lactones, as well as their microbial transformation products. Finally some of their biological activities were assessed. Three bicyclic halolactones with a methyl group in the cyclohexane ring were obtained from the corresponding γ,δ-unsaturated ester during a two-step synthesis. These lactones were subjected to screening biotransformation using twenty two fungal strains. These strains were tested on their ability to transform halolactones into new hydroxylactones. Among the six strains able to catalyze hydrolytic dehalogenation, only two ( Fusarium equiseti , AM22 and Yarrowia lipolytica , AM71) gave a product in a high yield. Moreover, one strain ( Penicillium wermiculatum , AM30) introduced the hydroxy group on the cyclohexane ring without removing the halogen atom. The biological activity of five of the obtained lactones was tested. Some of these compounds exhibited growth inhibition against bacteria, yeasts and fungi and deterrent activity against peach-potato aphid.

  14. 2-[3-Furyl(hydroxy)methyl]-2,3-dimethylcyclohexanone.

    Science.gov (United States)

    García, Esther; Mendoza, Virgilio; Guzmán, José Agustín; Maldonado Graniel, Luis Angel; Hernández-Ortega, Simón

    2002-06-01

    Contribution No. 1750 of the Instituto de Quimica, UNAM, Mexico. In the molecule of the title compound, C(13)H(18)O(3), there is a syn relationship between the two vicinal methyl groups. The six-membered ring adopts a chair conformation, with one equatorial and two axial groups, and the furyl group is almost parallel to the ketone group. Intermolecular hydrogen bonds [O[bond]H...O[double bond]C 2.814 (3) A] form chains along [100].

  15. Photoinduced nuclear spin conversion of methyl groups of single molecules; Photoinduzierte Kernspinkonversion von Methylgruppen an einzelnen Molekuelen. Lochbrenn- und Einzelmolekuelspektroskopie an Terrylen und Methylderivaten

    Energy Technology Data Exchange (ETDEWEB)

    Sigl, A.

    2007-12-28

    A methyl group is an outstanding quantum system due to its special symmetry properties. The threefold rotation around one of its bond is isomorphic to the group of even permutations of the remaining protons, a property which imposes severe quantum restrictions on the system, for instance a strict correlation of rotational states with nuclear spin states. The resulting long lifetimes of the rotational tunneling states of the methyl group can be exploited for applying certain high resolution optical techniques, like hole burning or single molecule spectroscopy to optically switch the methyl group from one tunneling state to another therebye changing the nuclear spin of the protons. One goal of the thesis was to perform this switching in single methyl groups. To this end the methyl group was attached to a chromophoric system, in the present case terrylene, which is well suited for single molecule spectroscopy as well as for hole burning. Experiments were performed with the bare terrylene molecule in a hexadecane lattice which served as a reference system, with alphamethyl terrylene and betamethyl terrylene, both embedded in hexadecane, too. A single molecular probe is a highly sensitive detector for dynamic lattice instabilities. Already the bare terrylene probe showed a wealth of interesting local dynamic effects of the hexadecane lattice which could be well acounted for by the assumption of two nearly degenerate sites with rather different optical and thermal properties, all of which could be determined in a quantitative fashion. As to the methylated terrylene systems, the experiments verified that for betamethyl terrylene it is indeed possible to measure rotational tunneling events in single methyl groups. However, the spectral patterns obtained was much more complicated than expected pointing to the presence of three spectroscopically different methyl groups. In order to achieve a definite assignement, molecular mechanics simulations of the terrylene probes in the

  16. Polymethylated [Fe(η6-arene)2]2+ dications: methyl-group rearrangements and application of the EINS mechanism.

    Science.gov (United States)

    Štíbr, Bohumil; Bakardjiev, Mario; Hájková, Zuzana; Holub, Josef; Padělková, Zdenka; Růžička, Aleš; Kennedy, John D

    2011-06-14

    Reactions between the methylated arenes ArMe(n) [where ArMe(n) = C(6)Me(n)H((6-n)), and n = 1-6] and FeCl(2) in heptane at 90 °C in the presence of anhydrous AlCl(3) give, for the arenes with n = 1-5, extensive isomerisations and disproportionations involving the methyl groups on the arene rings, and the formation of mixtures of [Fe(ArMe(n))(2)](2+) dications that defy separation into pure species. GC-MS studies of AlCl(3)/mesitylene and AlCl(3)/durene reactions in the absence of FeCl(2) (90 °C, 2 h) allow quantitative assessments of the rearrangements, and the EINS mechanism (electrophile-induced nucleophilic substitution) is applied to rationalise the phenomena. By contrast, ArMe(n) / FeCl(2) /AlCl(3) reactions in heptane for 24-36 h at room-temperature proceed with no rearrangements, allowing the synthesis of the complete series of pure [Fe(ArMen)](2+) cations in yields of 48-71%. The pure compounds are characterised by (1)H NMR spectroscopy and electrospray-ionization mass-spectrometry (ESI-MS), and the structures of [Fe(m-xylene)(2)][PF(6)](2) and [Fe(durene)(2)][PF(6)](2) are established by single-crystal X-ray diffraction analyses.

  17. In Search of the Perfect Photocage: Structure-Reactivity Relationships in meso-Methyl BODIPY Photoremovable Protecting Groups.

    Science.gov (United States)

    Slanina, Tomáš; Shrestha, Pradeep; Palao, Eduardo; Kand, Dnyaneshwar; Peterson, Julie A; Dutton, Andrew S; Rubinstein, Naama; Weinstain, Roy; Winter, Arthur H; Klán, Petr

    2017-10-25

    A detailed investigation of the photophysical parameters and photochemical reactivity of meso-methyl BODIPY photoremovable protecting groups was accomplished through systematic variation of the leaving group (LG) and core substituents as well as substitutions at boron. Efficiencies of the LG release were evaluated using both steady-state and transient absorption spectroscopies as well as computational analyses to identify the optimal structural features. We find that the quantum yields for photorelease with this photocage are highly sensitive to substituent effects. In particular, we find that the quantum yields of photorelease are improved with derivatives with higher intersystem crossing quantum yields, which can be promoted by core heavy atoms. Moreover, release quantum yields are dramatically improved by boron alkylation, whereas alkylation in the meso-methyl position has no effect. Better LGs are released considerably more efficiently than poorer LGs. We find that these substituent effects are additive, for example, a 2,6-diiodo-B-dimethyl BODIPY photocage features quantum yields of 28% for the mediocre LG acetate and a 95% quantum yield of release for chloride. The high chemical and quantum yields combined with the outstanding absorption properties of BODIPY dyes lead to photocages with uncaging cross sections over 10 000 M -1 cm -1 , values that surpass cross sections of related photocages absorbing visible light. These new photocages, which absorb strongly near the second harmonic of an Nd:YAG laser (532 nm), hold promise for manipulating and interrogating biological and material systems with the high spatiotemporal control provided by pulsed laser irradiation, while avoiding the phototoxicity problems encountered with many UV-absorbing photocages. More generally, the insights gained from this structure-reactivity relationship may aid in the development of new highly efficient photoreactions.

  18. THz and mid-IR spectroscopy of interstellar ice analogs: methyl and carboxylic acid groups.

    Science.gov (United States)

    Ioppolo, S; McGuire, B A; Allodi, M A; Blake, G A

    2014-01-01

    A fundamental problem in astrochemistry concerns the synthesis and survival of complex organic molecules (COMs) throughout the process of star and planet formation. While it is generally accepted that most complex molecules and prebiotic species form in the solid phase on icy grain particles, a complete understanding of the formation pathways is still largely lacking. To take full advantage of the enormous number of available THz observations (e.g., Herschel Space Observatory, SOFIA, and ALMA), laboratory analogs must be studied systematically. Here, we present the THz (0.3-7.5 THz; 10-250 cm(-1)) and mid-IR (400-4000 cm(-1)) spectra of astrophysically-relevant species that share the same functional groups, including formic acid (HCOOH) and acetic acid (CH3COOH), and acetaldehyde (CH3CHO) and acetone ((CH3)2CO), compared to more abundant interstellar molecules such as water (H2O), methanol (CH3OH), and carbon monoxide (CO). A suite of pure and mixed binary ices are discussed. The effects on the spectra due to the composition and the structure of the ice at different temperatures are shown. Our results demonstrate that THz spectra are sensitive to reversible and irreversible transformations within the ice caused by thermal processing, suggesting that THz spectra can be used to study the composition, structure, and thermal history of interstellar ices. Moreover, the THz spectrum of an individual species depends on the functional group(s) within that molecule. Thus, future THz studies of different functional groups will help in characterizing the chemistry and physics of the interstellar medium (ISM).

  19. Synthesis and Biotransformation of Bicyclic Unsaturated Lactones with Three or Four Methyl Groups.

    Science.gov (United States)

    Wińska, Katarzyna; Grabarczyk, Małgorzata; Mączka, Wanda; Kondas, Adrianna; Maciejewska, Gabriela; Bonikowski, Radosław; Anioł, Mirosław

    2017-01-17

    The aim of this study was to obtain new unsaturated lactones by chemical synthesis and their microbial transformations using fungal strains. Some of these strains were able to transform unsaturated lactones into different hydroxy or epoxy derivatives. Strains of Syncephalastrum racemosum and Absidia cylindrospora gave products with a hydroxy group introduced into a tertiary carbon, while the Penicillium vermiculatum strain hydroxylated primary carbons. The Syncephalastrum racemosum strain hydroxylated both substrates in an allylic position. Using the Absidia cylindrospora and Penicillium vermiculatum strains led to the obtained epoxylactones. The structures of all lactones were established on the basis of spectroscopic data.

  20. Cultivar-Specific Changes in Primary and Secondary Metabolites in Pak Choi (Brassica Rapa, Chinensis Group by Methyl Jasmonate

    Directory of Open Access Journals (Sweden)

    Moo Jung Kim

    2017-05-01

    Full Text Available Glucosinolates, their hydrolysis products and primary metabolites were analyzed in five pak choi cultivars to determine the effect of methyl jasmonate (MeJA on metabolite flux from primary metabolites to glucosinolates and their hydrolysis products. Among detected glucosinolates (total 14 glucosinolates; 9 aliphatic, 4 indole and 1 aromatic glucosinolates, indole glucosinolate concentrations (153–229% and their hydrolysis products increased with MeJA treatment. Changes in the total isothiocyanates by MeJA were associated with epithiospecifier protein activity estimated as nitrile formation. Goitrin, a goitrogenic compound, significantly decreased by MeJA treatment in all cultivars. Changes in glucosinolates, especially aliphatic, significantly differed among cultivars. Primary metabolites including amino acids, organic acids and sugars also changed with MeJA treatment in a cultivar-specific manner. A decreased sugar level suggests that they might be a carbon source for secondary metabolite biosynthesis in MeJA-treated pak choi. The result of the present study suggests that MeJA can be an effective agent to elevate indole glucosinolates and their hydrolysis products and to reduce a goitrogenic compound in pak choi. The total glucosinolate concentration was the highest in “Chinese cabbage” in the control group (32.5 µmol/g DW, but indole glucosinolates increased the greatest in “Asian” when treated with MeJA.

  1. Nonclassical dynamics of the methyl group in 1,1,1-triphenylethane. Evidence from powder 1H NMR spectra

    KAUST Repository

    Osior, Agnieszka

    2017-03-14

    According to the damped quantum rotation (DQR) theory, hindered rotation of methyl groups, evidenced in nuclear magnetic resonance (NMR) line shapes, is a nonclassical process. It comprises a number of quantum-rate processes measured by two different quantum-rate constants. The classical jump model employing only one rate constant is reproduced if these quantum constants happen to be equal. The values of their ratio, or the nonclassicallity coefficient, determined hitherto from NMR spectra of single crystals and solutions range from about 1.20 to 1.30 in the latter case to above 5.0 in the former, with the value of 1 corresponding to the jump model. Presently, first systematic investigations of the DQR effects in wide-line NMR spectra of a powder sample are reported. For 1,1,1-triphenylethane deuterated in the aromatic positions, the relevant line-shape effects were monitored in the range 99–121 K. The values of the nonclassicality coefficient dropping from 2.7 to 1.7 were evaluated in line shape fits to the experimental powder spectra from the range 99–108 K. At these temperatures, the fits with the conventional line-shape model are visibly inferior to the DQR fits. Using a theoretical model reported earlier, a semiquantitative interpretation of the DQR parameters evaluated from the spectra is given. It is shown that the DQR effects as such can be detected in wide-line NMR spectra of powdered samples, which are relatively facile to measure. However, a fully quantitative picture of these effects can only be obtained from the much more demanding experiments on single crystals.

  2. The importance of a single methyl group in determining the reaction chemistry of pentamethylcyclopentadienyl cyclooctatetraenyl uranium metallocenes.

    Science.gov (United States)

    Takase, Michael K; Ziller, Joseph W; Evans, William J

    2011-04-18

    The steric factors that allow trivalent [(C(5)Me(5))(3)U] (1) to function as a three-electron reductant with C(8)H(8) to form tetravalent [{(C(5)Me(5))(C(8)H(8))U}(2)(μ-C(8)H(8))] (2) have been explored by examining the synthesis and reactivity of the intermediate, "[(C(5)Me(5))(2)(C(8)H(8))U]" (3), and the slightly less crowded analogues, [(C(5)Me(5))(C(5)Me(4)H)(C(8)H(8))U] and [(C(5)Me(4)H)(2)(C(8)H(8))U], that have, successively one less methyl group. The reaction of [{(C(5)Me(5))(C(8)H(8))U(μ-OTf)}(2)] (4; OTf=OSO(2) CF(3)) with two equivalents of KC(5)Me(5) in THF gave ring-opening to "[(C(5)Me(5))(C(8)H(8))U{O(CH(2))(4)(C(5) Me(5))}]" consistent with in situ formation of 3. Reaction of 4 with two and four equivalents of KC(5)Me(4)H generates two equivalents of [(C(5)Me(5))(C(5)Me(4)H)(C(8)H(8))U] (5) and [(C(5)Me(4)H)(2)(C(8)H(8))U] (6), respectively, which in contrast to 3 were isolable. Tetravalent 5 reduces phenazine and PhEEPh (E=S, Se, and Te) to form the tetravalent uranium reduction products, [{(C(5)Me(5))(C(8)H(8))U}(2)(μ-C(12)H(8)N(2))] (7), [{(C(5)Me(5))(C(8)H(8))U}(2)(μ-SPh)(2)] (8), [{(C(5)Me(5))(C(8)H(8))U}(2)(μ-SePh)(2)] (9), and [{(C(5)Me(5))(C(8)H(8))U}(2)(μ-TePh)(2)] (10), consistent with sterically induced reduction. In contrast, the less sterically crowded 6 does not react with these substrates. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Nicotinamide, NAD(P(H, and Methyl-Group Homeostasis Evolved and Became a Determinant of Ageing Diseases: Hypotheses and Lessons from Pellagra

    Directory of Open Access Journals (Sweden)

    Adrian C. Williams

    2012-01-01

    Full Text Available Compartmentalized redox faults are common to ageing diseases. Dietary constituents are catabolized to NAD(H donating electrons producing proton-based bioenergy in coevolved, cross-species and cross-organ networks. Nicotinamide and NAD deficiency from poor diet or high expenditure causes pellagra, an ageing and dementing disorder with lost robustness to infection and stress. Nicotinamide and stress induce Nicotinamide-N-methyltransferase (NNMT improving choline retention but consume methyl groups. High NNMT activity is linked to Parkinson’s, cancers, and diseases of affluence. Optimising nicotinamide and choline/methyl group availability is important for brain development and increased during our evolution raising metabolic and methylome ceilings through dietary/metabolic symbiotic means but strict energy constraints remain and life-history tradeoffs are the rule. An optimal energy, NAD and methyl group supply, avoiding hypo and hyper-vitaminoses nicotinamide and choline, is important to healthy ageing and avoids utilising double-edged symbionts or uncontrolled autophagy or reversions to fermentation reactions in inflammatory and cancerous tissue that all redistribute NAD(P(H, but incur high allostatic costs.

  4. The differential localization of a methyl group confers a different anti-breast cancer activity to two triterpenes present in olives.

    Science.gov (United States)

    Sánchez-Quesada, Cristina; López-Biedma, Alicia; Gaforio, José J

    2015-01-01

    Uvaol (UV) and erythrodiol (ER) are two triterpenic dialcohols present in the minor fraction of virgin olive oil, in leaves and in the drupe of olives. These triterpenes possess the same chemical structure and differ only in the location of a methyl group. It has been reported that they have antitumoral effects in leukemic cells, in skin mice tumours and, finally, in astrocytoma cells, but there are no evidences about their effects in highly invasive human breast cancer cells and human epithelial breast cells. For this purpose, we have evaluated their cytotoxic activities as well as their effects on cell proliferation, cell cycle profile, apoptotic induction, oxidative stress and DNA oxidative damage in both highly invasive human breast cancer cells (MDA-MB-231) and human epithelial breast cells (MCF10A). UV and ER showed different effects in normal and breast cancer cells, whereas both compounds possess the same structure, except for the location of a methyl group. UV protects from damage to DNA in both cell lines, whereas ER enhances damage to DNA in these cell lines. Thus, ER promotes apoptosis and arrests cell cycle in human epithelial breast cells. Hence, both compounds differ in their action in human breast cells apparently by the different location of only a methyl group.

  5. Synthesis and biochemical properties of 6-bromoandrostenedione derivatives with a 2,2-dimethyl or 2-methyl group as aromatase inhibitors.

    Science.gov (United States)

    Numazawa, Mitsuteru; Handa, Wakako; Yamada, Keiko

    2004-11-01

    To gain insight into the mechanism for irreversible inactivation of aromatase by 6beta-bromoandrostenedione (1), one of the earliest discovered suicide substrates, in relation to the catalytic function of the enzyme, the 2,2-dimethyl derivative of compound 1, steroid 4, and its 6alpha-isomer 5, as well as 2-methyl-1,4-diene steroid 8 and its 6alpha-bromide 10, were synthesized. All of the steroids inhibited aromatase activity in human placental microsomes with apparent K(i)'s ranging between 10 and 81 nM. The 2,2-dimethyl-6beta- and 6alpha-bromo steroids 4 and 5 were extremely powerful inhibitors (K(i): 14 and 10 nM, respectively), but these two did not cause a time-dependent inactivation of aromatase in the presence of NADPH; in contrast, the 2-methyl-1,4-diene steroids 8 and 10 caused time-dependent inactivation with apparent k(inact) of 0.035 and 0.071 min(-1), respectively, in a suicide manner. These results indicate that the 2,2-dimethyl function of the 6beta-bromide 4 would prevent the inactivation of aromatase caused by inhibitor 1 in a suicide manner, probably through steric activity, whereas the 2-methyl group of steroid 8 did not significantly affect the suicidal inactivation by the parent 1,4-diene steroid, a typical suicide substrate.

  6. Hydrogen atoms in acetylsalicylic acid (Aspirin): the librating methyl group and probing the potential well in the hydrogen-bonded dimer

    Science.gov (United States)

    Wilson, Chick C.

    2001-02-01

    The structure of acetylsalicylic acid (2-(acetoyloxy)benzoic acid; Aspirin) has been studied by variable temperature single crystal neutron diffraction. The usual large torsional librational motion of the terminal methyl group is observed and its temperature dependence analysed using a simple model for the potential, yielding the force constant and barrier height for this motion. In addition, asymmetry of the scattering density of the proton involved in the hydrogen bond forming the carboxylic acid dimer motif is observed at temperatures above 200 K. This asymmetry is discussed in terms of its possible implications for the shape of the hydrogen bonding potential well.

  7. The Reactivity of 1-Methyl Group of Guaiazulenes for Oxidation by Quinones; Kinonkei sankazai ni taisuru guaiazuren no 1-mechiruki no hannosei

    Energy Technology Data Exchange (ETDEWEB)

    Okajima, Toshiya.; Konomi, Yuuko.; Kurokawa, Shinji. [Saga University, Saga (Japan). Faculty of Culture and Education

    1999-04-10

    Previously, we have reported the methodology for chemical conversion of guaiazulene (7-isopropyl-1,4-dimethylazulene,1) to 7-isopropyl-4-methylazulene-1-carbaldehyde (4) by protecting-deprotecting technique of reactive 3-position. Inthe synthetic scheme, DDQ (2,3-dichloro-5,6-dicyano-p-benzo-quinone, 5c) was used to convert unreactive 1-methyl group into formyi one. Computational calculation (RHF/3-21G//AM1) suggented that (1) {omicron}-chloranil (6b) is also effective as the oxidant instead of DDQ, which decomposes to highly toxic hydrogen syanide (HCN), and (2) three weaker oxidants (p-benzoquinone (5a), and p-chloranil (5b), and {omicron}-bebzoquinone (6a) do not oxidize the desired reactants. In accordance with these prediction, 3-trichloroaacetyl derivative (2d,Z--COCCl{sub 3}) was successfully converted to the corresponding 1-formyl derivative (3,Z=-COCCl{sub 3}) in 90% yield, when treated with 3-equimolar {omicron}-chloranil. Moreover, the treatment of 2d with latter three oxidants gave no 1-formyl derivative. The oxidation of 1-*methyl group of azulene derivatives by quinones is considered to be thermodynamicall controlled, according to the same tendency between the theoretical predictions and the experimental results. This study provided a good example of successful prediction of experimental results by simple application of computational technique in organic syntesis. (authoe)

  8. Are Vicinal Metal Surfaces Stable?

    DEFF Research Database (Denmark)

    Frenken, J. W. M.; Stoltze, Per

    1999-01-01

    We use effective medium theory to demonstrate that the energies of many metal surfaces are lowered when these surfaces are replaced by facets with lower-index orientations. This implies that the low-temperature equilibrium shapes of many metal crystals should be heavily faceted. The predicted ins...... instability of vicinal metal surfaces is at variance with the almost generally observed stability of these surfaces. We argue that the unstable orientations undergo a defaceting transition at relatively low temperatures, driven by the high vibrational entropy of steps....

  9. Isolation of two N-monosubstituted protoporphyrins, bearing either the whole drug or a methyl group on the pyrrole nitrogen atom, from liver of mice given griseofulvin.

    Science.gov (United States)

    Holley, A E; Frater, Y; Gibbs, A H; De Matteis, F; Lamb, J H; Farmer, P B; Naylor, S

    1991-01-01

    1. A hepatic green pigment with inhibitory properties towards the enzyme ferrochelatase has been isolated from the liver of mice treated with griseofulvin and identified as N-methylprotoporphyrin. 2. All four structural isomers of N-methylprotoporphyrin have been demonstrated to be present, NA, where ring A of protoporphyrin IX is N-methylated, being the predominant isomer. 3. In addition to N-methylprotoporphyrin, a second green pigment, present in far greater amounts, was also isolated from the liver of griseofulvin-treated mice. This second green pigment is also an N-monosubstituted protoporphyrin, but in this case the substituent on the pyrrole nitrogen atom appears to be intact griseofulvin rather than a methyl group. 4. The fragmentation of this adduct in tandem m.s. studies suggests that griseofulvin is bound to the pyrrole nitrogen through one of its carbon atoms and further suggests that N-methylprotoporphyrin may arise as a secondary product from the major griseofulvin pigment. PMID:2012610

  10. The cross-metathesis of methyl oleate with cis-2-butene-1,4-diyl diacetate and the influence of protecting groups

    Directory of Open Access Journals (Sweden)

    Jessica Pérez Gomes

    2011-01-01

    Full Text Available Background: α,ω-Difunctional substrates are useful intermediates for polymer synthesis. An attractive, sustainable and selective (but as yet unused method in the chemical industry is the oleochemical cross-metathesis with preferably symmetric functionalised substrates. The current study explores the cross-metathesis of methyl oleate (1 with cis-2-butene-1,4-diyl diacetate (2 starting from renewable resources and quite inexpensive base chemicals.Results: This cross-metathesis reaction was carried out with several phosphine and N-heterocyclic carbene ruthenium catalysts. The reaction conditions were optimised for high conversions in combination with high cross-metathesis selectivity. The influence of protecting groups present in the substrates on the necessary catalyst loading was also investigated.Conclusions: The value-added methyl 11-acetoxyundec-9-enoate (3 and undec-2-enyl acetate (4 are accessed with nearly quantitative oleochemical conversions and high cross-metathesis selectivity under mild reaction conditions. These two cross-metathesis products can be potentially used as functional monomers for diverse sustainable polymers.

  11. Chemo- and Regioselective Oxidation of Secondary Alcohols in Vicinal Diols

    NARCIS (Netherlands)

    Eisink, Niek; Minnaard, Adriaan; Witte, Martin

    Oxidation of secondary hydroxyl groups in vicinal diols enables the straightforward functionalization of biomolecules and biomaterials. The resulting hydroxy ketone can for example be used to form derivatives, such as the epimeric alcohol and imines, and it may be employed for chemical probe

  12. Bioactive Steroids with Methyl Ester Group in the Side Chain from a Reef Soft Coral Sinularia brassica Cultured in a Tank

    Directory of Open Access Journals (Sweden)

    Chiung-Yao Huang

    2017-09-01

    Full Text Available A continuing chemical investigation of the ethyl acetate (EtOAc extract of a reef soft coral Sinularia brassica, which was cultured in a tank, afforded four new steroids with methyl ester groups, sinubrasones A–D (1–4 for the first time. In particular, 1 possesses a β-D-xylopyranose. The structures of the new compounds were elucidated on the basis of spectroscopic analyses. The cytotoxicities of compounds 1–4 against the proliferation of a limited panel of cancer cell lines were assayed. The anti-inflammatory activities of these new compounds 1–4 were also evaluated by measuring their ability to suppress superoxide anion generation and elastase release in N-formyl-methionyl-leucyl-phenylalanine/cytochalasin B (fMLP/CB-induced human neutrophils. Compounds 2 and 3 were shown to exhibit significant cytotoxicity, and compounds 3 and 4 were also found to display attracting anti-inflammatory activities.

  13. Theoretical Investigation of C-H Vibrational Spectroscopy. 1. Modeling of Methyl and Methylene Groups of Ethanol with Different Conformers.

    Science.gov (United States)

    Wang, Lin; Ishiyama, Tatsuya; Morita, Akihiro

    2017-09-14

    A flexible and polarizable molecular model of ethanol is developed to extend our investigation of thermodynamic, structural, and vibrational properties of the liquid and interface. A molecular dynamics (MD) simulation with the present model confirmed that this model well reproduces a number of properties of liquid ethanol, including density, heat of vaporization, surface tension, molecular dipole moment, and trans/gauche ratio. In particular, the present model can describe vibrational IR, Raman, and sum frequency generation (SFG) spectra of ethanol and partially deuterated analogues with reliable accuracy. The improved accuracy is largely attributed to proper modeling of the conformational dependence and the intramolecular couplings including Fermi resonance in C-H vibrations. Precise dependence of torsional motions is found to be critical in representing vibrational spectra of the C-H bending. This model allows for further vibrational analysis of complicated alkyl groups widely observed in various organic molecules with MD simulation.

  14. Effects of donor-acceptor groups on the structural and electronic properties of 4-(methoxymethyl)-6-methyl-5-nitro-2-oxo-1,2-dihydropyridine-3-carbonitrile.

    Science.gov (United States)

    Gümüş, Hacer Pir; Tamer, Ömer; Avcı, Davut; Atalay, Yusuf

    2014-11-11

    Quantum chemical calculations on the geometric parameters, harmonic vibrational wavenumbers and 1H and 13C nuclear magnetic resonance (NMR) chemical shifts values of 4-(methoxymethyl)-6-methyl-5-nitro-2-oxo-1,2-dihydropyridine-3-carbonitrile [C9H9N3O4] molecule in ground state were performed using the ab initio HF and density functional theory (DFT/B3LYP) methods with 6-311++G(d,p) basis set. The results of optimized molecular structure were presented and compared with X-ray diffraction results. The theoretical vibrational frequencies and 1H and 13C NMR chemical shifts values were compared with experimental values of the investigated molecule. The observed and calculated values were found to be in good agreement. Since the title compound contains different electron-donor and -acceptor groups as well as lone pair electrons, and multiple bonds, the effects of these groups on the structural and electronic properties are found out. In addition, conformational, natural bond orbital (NBO), nonlinear optical (NLO) analysis, frontier molecular orbital energies, molecular surfaces, Mulliken charges and atomic polar tensor based charges were investigated using HF and DFT methods. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Methyl 2-(5-methyl-3-methyl-sulfinyl-1-benzofuran-2-yl)acetate.

    Science.gov (United States)

    Choi, Hong Dae; Seo, Pil Ja; Son, Byeng Wha; Lee, Uk

    2008-08-06

    The title compound, C(13)H(14)O(4)S, was prepared by oxidation of methyl 2-(5-methyl-3-methyl-sulfanyl-1-benzofuran-2-yl)acetate with 3-chloro-peroxy-benzoic acid. The O atom and methyl group of the methyl-sulfinyl substituent lie on opposite sides of the plane of the benzofuran system. The crystal structure is stabilized by inter-molecular aromatic π-π inter-actions between the benzene rings of neighbouring mol-ecules, with a centroid-centroid separation of 3.841 (3) Å.

  16. Characterization of an antagonistic switch between histone H3 lysine 27 methylation and acetylation in the transcriptional regulation of Polycomb group target genes.

    Science.gov (United States)

    Pasini, Diego; Malatesta, Martina; Jung, Hye Ryung; Walfridsson, Julian; Willer, Anton; Olsson, Linda; Skotte, Julie; Wutz, Anton; Porse, Bo; Jensen, Ole Nørregaard; Helin, Kristian

    2010-08-01

    Polycomb group (PcG) proteins are transcriptional repressors, which regulate proliferation and cell fate decisions during development, and their deregulated expression is a frequent event in human tumours. The Polycomb repressive complex 2 (PRC2) catalyzes trimethylation (me3) of histone H3 lysine 27 (K27), and it is believed that this activity mediates transcriptional repression. Despite the recent progress in understanding PcG function, the molecular mechanisms by which the PcG proteins repress transcription, as well as the mechanisms that lead to the activation of PcG target genes are poorly understood. To gain insight into these mechanisms, we have determined the global changes in histone modifications in embryonic stem (ES) cells lacking the PcG protein Suz12 that is essential for PRC2 activity. We show that loss of PRC2 activity results in a global increase in H3K27 acetylation. The methylation to acetylation switch correlates with the transcriptional activation of PcG target genes, both during ES cell differentiation and in MLL-AF9-transduced hematopoietic stem cells. Moreover, we provide evidence that the acetylation of H3K27 is catalyzed by the acetyltransferases p300 and CBP. Based on these data, we propose that the PcG proteins in part repress transcription by preventing the binding of acetyltransferases to PcG target genes.

  17. Effect of the Antibiotic Neomycin on the Toxicity of the Glycoside Vicine in Rats

    National Research Council Canada - National Science Library

    Arbid, Mahmoud S; Koriem, Khaled M. M; Asaad, Gihan F; Megahed, Hoda A

    2013-01-01

    .... Hemoglobin (Hb) concentration, hematocrit (Hct) value, and red blood cells (RBCs) count were significantly decreased after injection of vicine and the improvement of these values in the group pretreated with neomycin...

  18. Habitat--Monterey Canyon and Vicinity, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for the habitat map of the seafloor of the Monterey Canyon and Vicinity map area, California. The vector data file is included in...

  19. Contours--Monterey Canyon and Vicinity, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents bathymetric contours for several seafloor maps of the Monterey Canyon and Vicinity map area, California. The raster data file is...

  20. Scrambling free combinatorial labeling of alanine-β, isoleucine-δ1, leucine-proS and valine-proS methyl groups for the detection of long range NOEs

    Energy Technology Data Exchange (ETDEWEB)

    Kerfah, Rime [NMR-Bio, IBS/CEA (France); Plevin, Michael J. [University of York, Department of Biology (United Kingdom); Pessey, Ombeline [Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS) (France); Hamelin, Olivier [CNRS (France); Gans, Pierre; Boisbouvier, Jerome, E-mail: jerome.boisbouvier@ibs.fr [Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS) (France)

    2015-01-15

    Specific isotopic labeling of methyl groups in proteins has greatly extended the applicability of solution NMR spectroscopy. Simultaneous labeling of the methyl groups of several different amino acid types can offer a larger number of useful probes that can be used for structural characterisations of challenging proteins. Herein, we propose an improved AILV methyl-labeling protocol in which L and V are stereo-specifically labeled. We show that 2-ketobutyrate cannot be combined with Ala and 2-acetolactate (for the stereo-specific labeling of L and V) as this results in co-incorporation incompatibility and isotopic scrambling. Thus, we developed a robust and cost-effective enzymatic synthesis of the isoleucine precursor, 2-hydroxy-2-(1′-[{sup 2}H{sub 2}], 2′-[{sup 13}C])ethyl-3-keto-4-[{sup 2}H{sub 3}]butanoic acid, as well as an incorporation protocol that eliminates metabolic leakage. We show that application of this labeling scheme to a large 82 kDa protein permits the detection of long-range {sup 1}H–{sup 1}H NOE cross-peaks between methyl probes separated by up to 10 Å.

  1. Mechanism and site of inhibition of AMPA receptors: substitution of one and two methyl groups at the 4-aminophenyl ring of 2,3-benzodiazepine and implications in the "E" site.

    Science.gov (United States)

    Wang, Congzhou; Wu, Andrew; Shen, Yu-Chuan; Ettari, Roberta; Grasso, Silvana; Niu, Li

    2015-08-19

    2,3-Benzodiazepines are a well-known group of compounds for their potential antagonism against AMPA receptors. It has been previously reported that the inhibitory effect of 2,3-benzodiazepine derivatives with a 7,8-ethylenedioxy moiety can be enhanced by simply adding a chlorine atom at position 3 of the 4-aminophenyl ring. Here we report that adding a methyl group at position 3 on the 4-aminophenyl ring, termed as BDZ-11-7, can similarly enhance the inhibitory activity, as compared with the unsubstituted one or BDZ-11-2. Our kinetic studies have shown that BDZ-11-7 is a noncompetitive antagonist of GluA2Q homomeric receptors and prefers to inhibit the closed-channel state. However, adding another methyl group at position 5 on the 4-aminophenyl ring, termed as BDZ-11-6, fails to yield extra inhibition on GluA2Q receptors. Instead, BDZ-11-6 exhibits a diminished inhibition of GluA2Q. Site interaction test indicates the two compounds, BDZ-11-6 and BDZ-11-7, bind to the same site on GluA2Q, which is also the binding site for their prototype, BDZ-11-2. Based on the results from this and our earlier studies, we propose that the binding site that accommodates the 4-aminophenyl ring must contain two interactive points, with one preferring polar groups like chlorine and the other preferring nonpolar groups such as a methyl group. Either adding a chlorine or a methyl group may enhance the inhibitory activity of 2,3-benzodiazepine derivatives with a 7,8-ethylenedioxy moiety. Adding any two of the same group on positions 3 and 5 of the 4-aminophenyl ring, however, significantly reduces the interaction between these 2,3-benzodiazepines and their binding site, because one group is always repelled by one interactive point. We predict therefore that adding a chlorine atom at position 3 and a methyl group at position 5 of the 4-aminophenyl ring of 2,3-benzodiazepine derivatives with a 7,8-ethylenedioxy moiety may produce a new compound that is more potent.

  2. Triage of Atypical Glandular Cell by SOX1 and POU4F3 Methylation: A Taiwanese Gynecologic Oncology Group (TGOG Study.

    Directory of Open Access Journals (Sweden)

    Cheng-Chang Chang

    Full Text Available Invasive procedures including loop electrosurgical excision, cervical conization, and endometrial sampling are often recommended when atypical glandular cells (AGC are detected on Pap smear with unsatisfactory colposcopy. These invasive procedures may result in patient anxiety, increased medical expense, and increasing the risk of preterm delivery in subsequent pregnancies. This study was performed to assess methylation biomarkers in the triage of AGC on Pap smear for invasive procedures.We conducted a multicenter study in 13 medical centers in Taiwan from May 2012 to May 2014. A total of 55 samples diagnosed "AGC not otherwise specified" (AGC-NOS were included. All patients with AGC underwent colposcopy, cervical biopsy, endometrial sampling, and conization if indicated. Multiplex quantitative methylation-specific polymerase chain reaction (QMSPCR was performed. Sensitivity, specificity, and accuracy were calculated for detecting CIN3+ and endometrial complex hyperplasia.In 55 patients with AGC, the sensitivity for methylated (m SOX1m, PAX1 m, ZNF582m,PTPRRm, AJAP1m, HS3ST2m, and POU4F3m for detecting CIN3+ and endometrial complex hyperplasia lesions was 100, 86, 71, 86, 86, 57, and 100%; specificity was 67, 79, 85, 50, 52, 96, and 52%, respectively. Testing for high risk-HPV had a sensitivity of 57% and specificity of 75% for CIN3+ and endometrial complex hyperplasia lesions.Methylated (m SOX1m and POU4F3m could be new methylation biomarkers for detection of CIN3+ and endometrial complex hyperplasia in AGC. Women with AGC and positive SOX1m / POU4F3m, colposcopy, cervical conization or endometrial sampling should be considered.

  3. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  4. Methylation-mediated repression of microRNA-129-2 suppresses cell aggressiveness by inhibiting high mobility group box 1 in human hepatocellular carcinoma.

    Science.gov (United States)

    Liu, Zhikui; Dou, Changwei; Yao, Bowen; Xu, Meng; Ding, Linglong; Wang, Yufeng; Jia, Yuli; Li, Qing; Zhang, Hongyong; Tu, Kangsheng; Song, Tao; Liu, Qingguang

    2016-06-14

    Aberrant expression of microRNAs (miRNAs) and its dysfunction have been revealed as crucial modulators of cancer initiation and progression. MiR-129-2 has been reported to play a tumor suppressive role in different human malignancies. Here, we demonstrated that miR-129-2 was significantly decreased in hepatocellular carcinoma (HCC) tissues and cell lines. Furthermore, miR-129-2 was expressed at significant lower levels in aggressive and recurrent tumor tissues. Clinical analysis indicated that miR-129-2 expression was inversely correlated with venous infiltration, high Edmondson-Steiner grading and advanced tumor-node-metastasis (TNM) stage in HCC. Notably, miR-129-2 was an independent prognostic factor for indicating overall survival (OS) and disease-free survival (DFS) of HCC patients. Ectopic expression of miR-129-2 inhibited cell migration and invasion in vitro and in vivo. Furthermore, we confirmed that high mobility group box 1 (HMGB1) was a direct target of miR-129-2, and it abrogated the function of miR-129-2 in HCC. Mechanistic investigations showed that miR-129-2 overexpression inhibited AKT phosphorylation at Ser473 and decreased the expression of matrix metalloproteinase2/9 (MMP2/9). Upregulation of p-AKT abolished the decreased cell migration and invasion induced by miR-129-2 in HCC. Whereas inhibition of Akt phosphorylation significantly decreased HMGB1-enhanced HCC cell migration and invasion. Moreover, we found that miR-129-2 was downregulated by DNA methylation, and demethylation of miR-129-2 increased miR-129-2 expression in HCC cells and resulted in significant inhibitory effects on cell migration and invasion. In conclusion, miR-129-2 may serve as a prognostic indicator for HCC patients and exerts tumor suppressive role, at least in part, by inhibiting HMGB1.

  5. Methylated β-Cyclodextrins

    DEFF Research Database (Denmark)

    Schönbeck, Jens Christian Sidney; Westh, Peter; Madsen, Jens Christian

    2011-01-01

    groups at O2 promote complexation by extending the hydrophobic cavity. Like in the case of 2-hydroxypropylated cyclodextrins, the methyl substituents cause an increased release of ordered water from the hydration shell of the bile salts, resulting in a strong increase in both the enthalpy and the entropy...

  6. Secondary methylation of yeast ribosomal precursor RNA

    National Research Council Canada - National Science Library

    Brand, R C; Klootwijk, J; Van Steenbergen, T J; De Kok, A J; Planta, R J

    1977-01-01

    .... From the total of 37 ribose and 6 base-methyl groups found in 26-S rRNA, the two copies of the base-methylated nucleoside m3U as well as the doubly methylated sequence Um-Gm psi are not yet present...

  7. Thermally Activated Paramagnets from Diamagnetic Polymers of Biphenyl-3,5-diyl Bis(tert-butyl Nitroxides Carrying Methyl and Fluoro Groups at the 2’- and 5’-Positions

    Directory of Open Access Journals (Sweden)

    Toru Yoshitake

    2016-03-01

    Full Text Available Three new biradicals—2’,5’-dimethyl-, 2’-fluoro-5’-methyl-, and 5’-fluoro-2’-methyl- biphenyl-3,5-diyl bis(tert-butyl nitroxides—were synthesized. The magnetic susceptibility measurements revealed their diamagnetism below and around room temperature. The nitroxide groups are located close to each other in an intermolecular fashion to form a weakly covalent head-to-tail (NO2 ring. Biradical molecules are connected on both radical sites, constructing a diamagnetic chain. The dimethyl derivative underwent a structural phase transition at 83 °C, clarified via differential scanning calorimetry and powder X-ray diffraction, and a paramagnetic solid phase with S = 1 irreversibly appeared. The other analogues exhibited a similar irreversible upsurge of the magnetic susceptibility on heating, but the transition was characterized as the melting.

  8. Electronic transport in methylated fragments of DNA

    Science.gov (United States)

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

    2015-11-01

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

  9. Electronic transport in methylated fragments of DNA

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, M. L. de; Oliveira, J. I. N.; Lima Neto, J. X.; Gomes, C. E. M.; Fulco, U. L., E-mail: umbertofulco@gmail.com; Albuquerque, E. L. [Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN (Brazil); Freire, V. N. [Departamento de Física, Universidade Federal do Ceará, 60455-760 Fortaleza, CE (Brazil); Caetano, E. W. S. [Instituto Federal de Educação, Ciência e Tecnologia do Ceará, 60040-531 Fortaleza, CE (Brazil); Moura, F. A. B. F. de; Lyra, M. L. [Instituto de Física, Universidade Federal de Alagoas, 57072-900 Maceió-AL (Brazil)

    2015-11-16

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

  10. Efficacy and safety profile of a topical methyl salicylate and menthol patch in adult patients with mild to moderate muscle strain: a randomized, double-blind, parallel-group, placebo-controlled, multicenter study.

    Science.gov (United States)

    Higashi, Yoshinobu; Kiuchi, Takehito; Furuta, Kenichi

    2010-01-01

    An occlusive patch formulation containing 10% methyl salicylate and 3% l-menthol was recently approved by the US Food and Drug Administration for the treatment of mild to moderate pain. Despite widespread use of counterirritants, including methyl salicylate and menthol, for topical pain relief, published efficacy and safety data regarding the use of the agents alone or in combination are limited. The goal of this study was to determine the efficacy and safety profile of a patch containing 10% methyl salicylate and 3% l-menthol compared with a placebo patch in adult patients with mild to moderate muscle strain. Eligible patients were men or women aged >or=18 years with a clinical diagnosis of mild to moderate muscle strain. Patients were randomly assigned to receive either 1 active patch or 1 placebo patch applied to the skin at the affected area (ie, shoulder, upper back, upper arm, neck, calf, thigh, forearm, abdomen). Pain intensity was assessed on a 100-mm visual analog scale while at rest and with movement for 12 hours after patch application. The primary efficacy end point was the summed pain intensity difference score through 8 hours (SPID8) with movement. Analyses included use of descriptive statistics and an ANOVA model. Safety data, including adverse events, and secondary efficacy end points were also evaluated. A total of 208 patients (104 men, 104 women; age range, 18-78 years) were randomized to 1 of 2 study groups (105 in the active-patch group [mean age, 37.3 years], 103 in the placebo-patch group [mean age, 38.1 years]). The primary efficacy analysis (SPID8 with movement) indicated that patients receiving the active patch experienced significantly greater pain relief (approximately 40%) than those patients receiving a placebo patch (mean [SD], 182.6 [131.2] vs 130.1 [144.1]; P = 0.005). Analysis of the per-protocol population also found significantly more relief (P = 0.024) in the active-patch group (176.2 [131.4]; n = 92) versus the placebo

  11. Rubipodanin A, the First Natural N-Desmonomethyl Rubiaceae-Type Cyclopeptide from Rubia podantha, Indicating an Important Role of the N9-Methyl Group in the Conformation and Bioactivity.

    Directory of Open Access Journals (Sweden)

    Zhe Wang

    Full Text Available One new cyclic hexapeptide named rubipodanin A (1, which is the first identified natural N-desmonomethyl Rubiaceae-type cyclopeptide, together with six known Rubiaceae-type cyclopeptides (2-7 were obtained using the TLC cyclopeptide protosite detection method with ninhydrin from the roots and rhizomes of Rubia podantha. The cyclopeptide structures were elucidated by extensive spectroscopic analysis, including 1D-NMR, 2D-NMR, IR, UV and MS. The solution conformation and biological activities of 1 and RA-V (4 were evaluated, and the results demonstrated that the N9-methyl group plays a vital role in the maintenance of the conformation and bioactivity.

  12. Methylation-Specific PCR Unraveled

    Directory of Open Access Journals (Sweden)

    Sarah Derks

    2004-01-01

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

  13. Flocculation of diatomite by methylated egg albumin

    OpenAIRE

    Seki, Hideshi; Suzuki, Akira

    2003-01-01

    A common and inexpensive protein, egg albumin, was applied to the solid-liquid separation or flocculation of diatomite. Egg albumin was methylated in a 0.1 M HCl methyl alcohol solution at room temperature. About 90% of the carboxylic groups of egg albumin could be methylated within 24 h. The adsorption of egg albumin to diatomite at pH6.8 was remarkably enhanced by methylation. The adsorption constant of methylated egg albumin to diatomite at 30°C was about 100-fold larger than that of nativ...

  14. Methyl Halide Production by Fungi

    Science.gov (United States)

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

    2005-12-01

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

  15. Self-assembled nanostructures on vicinal surfaces

    Science.gov (United States)

    Petrovykh, Dmitri Yourievich

    2000-10-01

    One of the first methods for visualizing crystal planes and atomic steps has been step decoration with gold on alkali-halide surfaces. An impressive body of work has been conducted since then on the role of steps in controlling surface diffusion and adsorption rates, catalytic and chemical activity, and other physical and chemical surface properties. Due to these special characteristics, vicinal surfaces offer an approach for creating self-assembled structures with one or more dimensions on nanometer scale. The storage and communications industries have been revolutionized by applications of two-dimensional electron gas confined in thin films, so an interest in one and zero-dimensional systems is not surprising. This work demonstrates how macroscopic amounts of low-dimensional structures can be produced by self-assembly using stepped surfaces as nanometer-scale templates. High-quality templates of step arrays can be prepared on vicinal Si(111) surfaces. Sub-monolayer CaF2/Si(111) heteroepitaxial growth is examined in a series of experiments. A new growth mode is observed in addition to the ones typical in three dimensions. With increasing coverage, the growth front changes from rough to smooth geometry, driven by the elastic interactions between the multiple growth fronts and the surface steps. The mechanism is thus unique to the two-dimensional growth on stepped surfaces. The possible arrangements of the CaF2 self-assembled nanostructures are arrays of stripes or islands, both interesting as potential masks for silicon nanolithography. Anisotropic surface reconstructions, such as Ca and Au induced 3 x 1 and 5 x 2 on Si(111), are effectively self-assembled one-dimensional atomic chains. Reconstructions are single-domain on vicinal surfaces and with odd electron count a metallic one-dimensional state is expected in both the above examples. However in angular-resolved photoemission both appear as semiconductors, and Au-Si(111)5 x 2 exhibits a continuous one

  16. On-Chip DNA Methylation Analysis Using Osmium Complexation

    Directory of Open Access Journals (Sweden)

    Kaori Sugizaki

    2011-01-01

    Full Text Available The development of a reaction for detecting the presence/absence of one methyl group in a long DNA strand is a chemically and biologically challenging research subject. A newly designed chemical assay on a chip for the typing of DNA methylation has been developed. A methylation-detection probe fixed at the bottom of microwells was crosslinked with methylated DNA mediated by osmium complexation and contributes to selective amplification of methylated DNA.

  17. Mechanism of Inhibition of the GluA2 AMPA Receptor Channel Opening by Talampanel and Its Enantiomer: The Stereochemistry of the 4-Methyl Group on the Diazepine Ring of 2,3-Benzodiazepine Derivatives

    Science.gov (United States)

    2013-01-01

    Stereoselectivity of 2,3-benzodiazepine compounds provides a unique way for the design of stereoisomers as more selective and more potent inhibitors as drug candidates for treatment of the neurological diseases involving excessive activity of AMPA receptors. Here we investigate a pair of enantiomers known as Talampanel and its (+) counterpart about their mechanism of inhibition and selectivity toward four AMPA receptor subunits or GluA1–4. We show that Talampanel is the eutomer with the endismic ratio being 14 for the closed-channel and 10 for the open-channel state of GluA2. Kinetic evidence supports that Talampanel is a noncompetitive inhibitor and it binds to the same site for those 2,3-benzodiazepine compounds with the C-4 methyl group on the diazepine ring. This site, which we term as the “M” site, recognizes preferentially those 2,3-benzodiazepine compounds with the C-4 methyl group being in the R configuration, as in the chemical structure of Talampanel. Given that Talampanel inhibits GluA1 and GluA2, but is virtually ineffective on the GluA3 and GluA4 AMPA receptor subunits, we hypothesize that the “M” site(s) on GluA1 and GluA2 to which Talampanel binds is different from that on GluA3 and GluA4. If the molecular properties of the AMPA receptors and Talampanel are used for selecting an inhibitor as a single drug candidate for controlling the activity of all AMPA receptors in vivo, Talampanel is not ideal. Our results further suggest that addition of longer acyl groups to the N-3 position should produce more potent 2,3-benzodiazepine inhibitors for the “M” site. PMID:23402301

  18. Comparison and evaluation of five types of imidazole-modified silica adsorbents for the removal of 2,4-dinitrophenol from water samples with the methyl group at different positions of imidazolium ring

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhike, E-mail: wzk@htu.cn; Ye, Cunling; Li, Juan; Wang, Heping; Zhang, Han

    2013-09-15

    Highlights: • Five imidazole-modified silica adsorbents were synthesized. • The five adsorbents are of primary anion-exchange and electrostatic nature. • The electrostatic nature was affected by the methyl group of imidazolium ring. • The five adsorbents are suitable for adsorption of 2,4-DNP with low pK{sub a} value. • The adsorbent was regenerated and reused ten times by washings with HCl and water. -- Abstract: The objective of this work was to improve the understanding the influence of the methyl group at different positions of imidazolium ring on the adsorption behaviors of imidazole-modified silica adsorbents. Five adsorbents named as SilprImCl, SilprM{sub 1}ImCl, SilprM{sub 2}ImCl, SilprM{sub 4}ImCl and SilprM{sub 1}M{sub 2}ImCl were synthesized using imidazole, 1-methylimidazole, 2-methylimidazole, 4-methylimidazole and 1,2-dimethylimidazole, respectively. These adsorbents were characterized by scanning electron microscope, infrared spectra, thermogravimetric analysis, elemental analysis and BET analysis. Firstly, phenol, 2-nitrophenol (2-NP), 3-nitrophenol (3-NP), 4-nitrophenol (4-NP) and 2,4-dinitrophenol (2,4-DNP) were used as adsorbates to investigate the selectivity of SilprImCl and its adsorption capacities followed the order of 2,4-DNP ≫ 4-NP > 2-NP ≫ 3-NP > phenol. Therefore, 2,4-DNP was used to investigate the adsorption behaviors of the five adsorbents. It was inferred that the adsorbents are of primary anion-exchange and electrostatic nature. The electrostatic nature was affected significantly by the methyl group at different positions of imidazolium ring. The adsorbed amounts of 2,4-DNP decreased in the order of: SilprM{sub 1}M{sub 2}ImCl ≈ SilprM{sub 1}ImCl > SilprM{sub 4}ImCl > SilprM{sub 2}ImCl > SilprImCl. The adsorption–elution experiments indicated that 2,4-DNP can be removed from aqueous solutions by a SilprM{sub 4}ImCl packed column and the recovery of 91.6% was obtained. The adsorbent could be regenerated and reused

  19. Methyl 2-(5-bromo-3-methyl-sulfinyl-1-benzofuran-2-yl)acetate.

    Science.gov (United States)

    Choi, Hong Dae; Seo, Pil Ja; Son, Byeng Wha; Lee, Uk

    2008-11-20

    The title compound, C(12)H(11)BrO(4)S, was synthesized by the oxidation of methyl 2-(5-bromo-3-methyl-sulfanyl-1-benzofuran-2-yl)acetate with 3-chloro-peroxy-benzoic acid. The O atom and the methyl group of the methyl-sulfinyl substituent lie on opposite sides of the plane of the benzofuran ring system. The crystal structure is stabilized by C-H⋯π inter-actions, involving a methyl H atom and the benzene ring of a neighbouring mol-ecule, and by weak inter-molecular C-H⋯O hydrogen bonds.

  20. Dehydrogenative [2 + 2 + 1] Heteroannulation Using a Methyl Group as a One-Carbon Unit: Access to Pyrazolo[3,4-c]quinolines.

    Science.gov (United States)

    Deng, Guo-Bo; Li, Hai-Bing; Yang, Xu-Heng; Song, Ren-Jie; Hu, Ming; Li, Jin-Heng

    2016-05-06

    A practical and straightforward access to pyrazolo[3,4-c]quinolines by molecular sieve mediated dehydrogenative [2 + 2 + 1] heteroannulation of N-(o-alkenylaryl)imines with aryldiazonium salts is described using a sp(3)-hybrid carbon atom as a one-carbon unit. The reaction enables the formation of three new chemical bonds, a C-C bond and two C-N bonds, in a single reaction and features simple operation and excellent functional group tolerance.

  1. The Synthesis of Methyl Salicylate: Amine Diazotization.

    Science.gov (United States)

    Zanger, Murray; McKee, James R.

    1988-01-01

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

  2. Determining the energetics of vicinal perovskite oxide surfaces

    NARCIS (Netherlands)

    Wessels, W.A.; Bollmann, Tjeerd Rogier Johannes; Koster, Gertjan; Zandvliet, Henricus J.W.; Rijnders, Augustinus J.H.M.

    2017-01-01

    The energetics of vicinal SrTiO3(001) and DyScO3(110), prototypical perovskite vicinal surfaces, has been studied using topographic atomic force microscopy imaging. The kink formation and strain relaxation energies are extracted from a statistical analysis of the step meandering. Both perovskite

  3. Methylation Linear Discriminant Analysis (MLDA for identifying differentially methylated CpG islands

    Directory of Open Access Journals (Sweden)

    Vass J Keith

    2008-08-01

    Full Text Available Abstract Background Hypermethylation of promoter CpG islands is strongly correlated to transcriptional gene silencing and epigenetic maintenance of the silenced state. As well as its role in tumor development, CpG island methylation contributes to the acquisition of resistance to chemotherapy. Differential Methylation Hybridisation (DMH is one technique used for genome-wide DNA methylation analysis. The study of such microarray data sets should ideally account for the specific biological features of DNA methylation and the non-symmetrical distribution of the ratios of unmethylated and methylated sequences hybridised on the array. We have therefore developed a novel algorithm tailored to this type of data, Methylation Linear Discriminant Analysis (MLDA. Results MLDA was programmed in R (version 2.7.0 and the package is available at CRAN 1. This approach utilizes linear regression models of non-normalised hybridisation data to define methylation status. Log-transformed signal intensities of unmethylated controls on the microarray are used as a reference. The signal intensities of DNA samples digested with methylation sensitive restriction enzymes and mock digested are then transformed to the likelihood of a locus being methylated using this reference. We tested the ability of MLDA to identify loci differentially methylated as analysed by DMH between cisplatin sensitive and resistant ovarian cancer cell lines. MLDA identified 115 differentially methylated loci and 23 out of 26 of these loci have been independently validated by Methylation Specific PCR and/or bisulphite pyrosequencing. Conclusion MLDA has advantages for analyzing methylation data from CpG island microarrays, since there is a clear rational for the definition of methylation status, it uses DMH data without between-group normalisation and is less influenced by cross-hybridisation of loci. The MLDA algorithm successfully identified differentially methylated loci between two classes of

  4. From vicinal to rough crystal surfaces

    Science.gov (United States)

    Balibar, S.; Guthmann, C.; Rolley, E.

    1993-06-01

    One generally expects the properties of a vicinal surface to be independent of the existence of steps as soon as these steps overlap, i.e. when their mutual distance is smaller than their width. By using the roughening theory by Nozières and Gallet [1], we show that, at least for surfaces weakly coupled to the lattice, this overlap occurs for distances significantly larger than the commonly defined width. Our prediction is supported by an analysis of the various measurements of the angular variation of the surface stiffness of helium crystals, which were performed by Wolf et al. [2], Andreeva et al. [3] and Babkin et al. [4]. As a consequence, the interaction between crystal steps should be studied on vicinal surfaces with a much smaller tilt angle than previously thought. This article is also an opportunity to return to the relation between the step width and the correlation length on smooth surfaces, as well as to the treatment of the various finite size effects which occur in the problem of roughening. We finally reconsider how the weak coupling hypothesis applies to the case of helium crystals. On s'attend généralement à ce que les propriétés d'une surface vicinale ne soient plus contrôlées par l'existence des marches lorsque celles-ci se recouvrent, donc lorsque leur distance mutuelle devient inférieure à leur largeur. En reprenant la théorie de la transition rugueuse élaborée par Nozières et Gallet [1], nous montrons que, pour des surfaces faiblement couplées au réseau cristallin, ce recouvrement doit se produire pour des distances nettement plus grandes que la largeur (telle qu'elle est habituellement définie). Notre prédiction est confirmée par l'analyse des différentes mesures de la variation angulaire de la rigidité de surface des cristaux d'hélium réalisées par Wolf et al. [2], Andreeva et al. [3] and Babkin et al. [4]. Il s'ensuit que l'étude de l'interaction entre marches cristallines doit être effectuée sur des surfaces

  5. Inter-individual variation in DNA methylation is largely restricted to tissue-specific differentially methylated regions in maize.

    Science.gov (United States)

    Lauria, Massimiliano; Echegoyen-Nava, Rodrigo Antonio; Rodríguez-Ríos, Dalia; Zaina, Silvio; Lund, Gertrud

    2017-02-23

    Variation in DNA methylation across distinct genetic populations, or in response to specific biotic or abiotic stimuli, has typically been studied in leaf DNA from pooled individuals using either reduced representation bisulfite sequencing, whole genome bisulfite sequencing (WGBS) or methylation sensitive amplified polymorphism (MSAP). The latter represents a useful alterative when sample size is large, or when analysing methylation changes in genomes that have yet to be sequenced. In this study we compared variation in methylation across ten individual leaf and endosperm samples from maize hybrid and inbred lines using MSAP. We also addressed the methodological implications of analysing methylation variation using pooled versus individual DNA samples, in addition to the validity of MSAP compared to WGBS. Finally, we analysed a subset of variable and non-variable fragments with respect to genomic location, vicinity to repetitive elements and expression patterns across leaf and endosperm tissues. On average, 30% of individuals showed inter-individual methylation variation, mostly of leaf and endosperm-specific differentially methylated DNA regions. With the exception of low frequency demethylation events, the bulk of inter-individual methylation variation (84 and 80% in leaf and endosperm, respectively) was effectively captured in DNA from pooled individuals. Furthermore, available genome-wide methylation data largely confirmed MSAP leaf methylation profiles. Most variable methylation that mapped within genes was associated with CG methylation, and many of such genes showed tissue-specific expression profiles. Finally, we found that the hAT DNA transposon was the most common class II transposable element found in close proximity to variable DNA regions. The relevance of our results with respect to future studies of methylation variation is the following: firstly, the finding that inter-individual methylation variation is largely restricted to tissue

  6. Dissociation dynamics of methylal

    Energy Technology Data Exchange (ETDEWEB)

    Beaud, P.; Frey, H.-M.; Gerber, T.; Mischler, B.; Radi, P.P.; Tzannis, A.-P. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1999-08-01

    The dissociation of methylal is investigated using mass spectrometry, combined with a pyrolytic radical source and femtosecond pump probe experiments. Based on preliminary results two reaction paths of methylal dissociation are proposed and discussed. (author) 4 fig., 3 refs.

  7. Flocculation of diatomite by methylated egg albumin.

    Science.gov (United States)

    Seki, Hideshi; Suzuki, Akira

    2003-07-01

    A common and inexpensive protein, egg albumin, was applied to the solid-liquid separation or flocculation of diatomite. Egg albumin was methylated in a 0.05 M HCl methyl alcohol solution at room temperature. About 90% of the carboxylic groups of egg albumin could be methylated within 24 h. The adsorption of egg albumin onto diatomite at pH 6.8 was remarkably enhanced by methylation. The adsorption constant of methylated egg albumin to diatomite at 30 degrees C was about 100-fold larger than that of native egg albumin; however, the adsorption constant of methylated egg albumin decreased to about 1/100 with temperature decreasing from 30 to 6 degrees C. The saturated adsorption amount of egg albumin was also increased by the methylation. The flocculating ability of methylated egg albumin was examined with a diatomite suspension at 6 and 30 degrees C in the pH range from pH 2 to 11. The diatomite suspension was effectively flocculated by the addition of small amounts of methylated egg albumin (only 0.5-1 wt% against diatomite) over a wide pH range from pH 3 to 10.

  8. Colorectal Cancer "Methylator Phenotype": Fact or Artifact?

    Directory of Open Access Journals (Sweden)

    Charles Anacleto

    2005-04-01

    Full Text Available It has been proposed that human colorectal tumors can be classified into two groups: one in which methylation is rare, and another with methylation of several loci associated with a "CpG island methylated phenotype (CIMP," characterized by preferential proximal location in the colon, but otherwise poorly defined. There is considerable overlap between this putative methylator phenotype and the well-known mutator phenotype associated with microsatellite instability (MSI. We have examined hypermethylation of the promoter region of five genes (DAPK, MGMT, hMLH1, p16INK4a, and p14ARF in 106 primary colorectal cancers. A graph depicting the frequency of methylated loci in the series of tumors showed a continuous, monotonically decreasing distribution quite different from the previously claimed discontinuity. We observed a significant association between the presence of three or more methylated loci and the proximal location of the tumors. However, if we remove from analysis the tumors with hMLH1 methylation or those with MSI, the significance vanishes, suggesting that the association between multiple methylations and proximal location was indirect due to the correlation with MSI. Thus, our data do not support the independent existence of the so-called methylator phenotype and suggest that it rather may represent a statistical artifact caused by confounding of associations.

  9. Methyl transfer in chemotaxis toward sugars by Bacillus subtilis.

    OpenAIRE

    Thoelke, M S; Casper, J M; Ordal, G W

    1990-01-01

    Like amino acids, the sugars glucose and the nonmetabolizable 2-deoxyglucose caused a turnover of methyl groups on the methyl-accepting chemotaxis proteins. These sugars also caused methanol formation on addition. Thus, in contrast to chemotaxis in Escherichia coli, taxis to phosphotransferase sugars by Bacillus subtilis utilizes the methyl-accepting chemotaxis proteins.

  10. Methylation of hemoglobin to enhance flocculant performance

    Science.gov (United States)

    An inexpensive bioflocculant, bovine hemoglobin (Hb), has been covalently modified through methylation of the side chain carboxyl groups of aspartic and glutamic acid residues to improve its flocculation activity. Potentiometric titration of the recovered products showed approximately 28% degree of ...

  11. Parental smoking in the vicinity of children and tobacco control policies in the European region.

    Science.gov (United States)

    Kovess, Viviane; Pilowsky, Daniel J; Boyd, Anders; Pez, Ondine; Bitfoi, Adina; Carta, Mauro; Eke, Ceyda; Golitz, Dietmar; Kuijpers, Rowella; Lesinskiene, Sigita; Mihova, Zlatka; Otten, Roy; Susser, Ezra

    2013-01-01

    To ascertain patterns of parental smoking in the vicinity of children in Eastern and Western Europe and their relation to Tobacco Control Scale (TCS) scores. Data on parental smoking patterns were obtained from the School Child Mental Health Europe (SCMHE), a 2010 cross-sectional survey of 5141 school children aged 6 to 11 years and their parents in six countries: Germany, Netherlands, Lithuania, Romania, Bulgaria and Turkey ranked by TCS into three level categories toward tobacco control policies. A slightly higher proportion of Eastern compared to Western European mothers (42.4 vs. 35.1%) were currently smoking in but the difference was not statistically significant after adjusting for maternal age and maternal educational attainment. About a fifth (19.3%) and a tenth (10.0%) of Eastern and Western European mothers, respectively, smoked in the vicinity of their children, and the difference was significant even after adjustment for potential confounders (pParents with the highest educational attainment were significantly less likely to smoke in the vicinity of their children than those with the lowest attainment. After control of these covariates lax tobacco control policies, compared to intermediate policies, were associated with a 50% increase in the likelihood of maternal smoking in the vicinity of children adjusted odds ratio (AOR) = 1.52 and 1.64. Among fathers, however, the relationship with paternal smoking and TCS seems more complex since strict policy increases the risk as well AOR = 1,40. Only one country, however belongs to the strict group. Tobacco control policies seem to have influenced maternal smoking behaviors overall to a limited degree and smoking in the vicinity of children to a much greater degree. Children living in European countries with lax tobacco control policies are more likely to be exposed to second hand smoking from maternal and paternal smoking.

  12. Parental smoking in the vicinity of children and tobacco control policies in the European region.

    Directory of Open Access Journals (Sweden)

    Viviane Kovess

    Full Text Available OBJECTIVE: To ascertain patterns of parental smoking in the vicinity of children in Eastern and Western Europe and their relation to Tobacco Control Scale (TCS scores. METHODS: Data on parental smoking patterns were obtained from the School Child Mental Health Europe (SCMHE, a 2010 cross-sectional survey of 5141 school children aged 6 to 11 years and their parents in six countries: Germany, Netherlands, Lithuania, Romania, Bulgaria and Turkey ranked by TCS into three level categories toward tobacco control policies. RESULTS: A slightly higher proportion of Eastern compared to Western European mothers (42.4 vs. 35.1% were currently smoking in but the difference was not statistically significant after adjusting for maternal age and maternal educational attainment. About a fifth (19.3% and a tenth (10.0% of Eastern and Western European mothers, respectively, smoked in the vicinity of their children, and the difference was significant even after adjustment for potential confounders (p<0.001. Parents with the highest educational attainment were significantly less likely to smoke in the vicinity of their children than those with the lowest attainment. After control of these covariates lax tobacco control policies, compared to intermediate policies, were associated with a 50% increase in the likelihood of maternal smoking in the vicinity of children adjusted odds ratio (AOR = 1.52 and 1.64. Among fathers, however, the relationship with paternal smoking and TCS seems more complex since strict policy increases the risk as well AOR = 1,40. Only one country, however belongs to the strict group. SIGNIFICANCE: Tobacco control policies seem to have influenced maternal smoking behaviors overall to a limited degree and smoking in the vicinity of children to a much greater degree. Children living in European countries with lax tobacco control policies are more likely to be exposed to second hand smoking from maternal and paternal smoking.

  13. Faults--Drakes Bay and Vicinity Map Area, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data of faults for the geologic and geomorphologic map of the Drakes Bay and Vicinity map area, California. The vector data file is...

  14. BackscatterB [EM300]--Monterey Canyon and Vicinity, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for the acoustic-backscatter map of Monterey Canyon and Vicinity map area, California. Backscatter data are provided as separate...

  15. BackscatterC [7125]--Monterey Canyon and Vicinity, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for the acoustic-backscatter map of Monterey Canyon and Vicinity map area, California. Backscatter data are provided as separate...

  16. Folds--Monterey Canyon and Vicinity Map Area, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for the folds for the geologic and geomorphic map of Monterey Canyon and Vicinity, California. The vector data file is included in...

  17. Backscatter A [8101]--Drakes Bay and Vicinity, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for the acoustic-backscatter map of Drakes bay and Vicinity map area, California. Backscatter data are provided as separate grids...

  18. Backscatter C [7125]--Drakes Bay and Vicinity, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for the acoustic-backscatter map of Drakes bay and Vicinity map area, California. Backscatter data are provided as separate grids...

  19. Faults--Monterey Canyon and Vicinity Map Area, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for the faults for the geologic and geomorphic map of Monterey Canyon and Vicinity, California. The vector data file is included in...

  20. establishment of background radiation dose rate in the vicinity

    African Journals Online (AJOL)

    nb

    .ac.tz). *Permanent address: Department of Physics, University of Dodoma. P. O. Box 339 Dodoma. ABSTRACT. The absorbed dose rate in air in the vicinity of the proposed Manyoni uranium mining project located in Singida region, Tanzania, ...

  1. Folds--Drakes Bay and Vicinity Map Area, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data of folds for the geologic and geomorphologic map of the Drakes Bay and Vicinity map area, California. The vector data file is...

  2. Paleoshorelines--Monterey Canyon and Vicinity Map Area, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for the paleoshorelines for the geologic and geomorphic map of Monterey Canyon and Vicinity, California. The vector data file is...

  3. Aerial survey of sea otters in the Cordova vicinity

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The movement of significantly large numbers of sea otters into the Cordova vicinity has generated a local storm of protest concerning the ability of sea otters to...

  4. Theoretical studies on the reaction of mono- and ditriflate derivatives of 1,4:3,6-dianhydro- d-mannitol with trimethylamine—Can a quaternary ammonium salt be a source of the methyl group?

    Science.gov (United States)

    Bednarko, Justyna; Wielińska, Justyna; Sikora, Karol; Liberek, Beata; Nowacki, Andrzej

    2016-01-01

    DFT studies on the mechanism of the formation of "gemini" quaternary ammonium salts in the reaction of 1,4:3,6-dianhydro- d-mannitol ditriflate derivative with trimethylamine and its subsequent conversion to tertiary amine through the methyl-transfer reaction are discussed. Two alternative reaction pathways are presented in the gas phase and in ethanol. Additionally, the transformation of the monotriflate derivative of 1,4:3,6-dianhydro- d-mannitol into the single quaternary ammonium salt is presented. Two functionals (B3LYP, M062X) and two basis sets (6-31+G** and 6-311++G**) were used for the calculations. The effect of the substituent attached to the five-membered rings at the C2 (and/or C5) carbon atom on the activation barrier is described. The trimethylammonium group bond to the five-membered ring greatly reduces the activation barrier height. The preferred reaction pathway for the conversions was established. Including the London dispersion in the calculations increases the stabilization of all the points on the potential energy surface in relation to individual reactants.

  5. Submesoscale Dispersion in the Vicinity of the Deepwater Horizon Spill

    Science.gov (United States)

    2014-09-02

    RESPONSIBLE PERSON 19b. TELEPHONE NUMBER (Include area code) 11-03-2014 Journal Article Submesoscale dispersion in the vicinity of the Deepwater ...ecosystems, society, and the economy as evidenced by the Deepwater Horizon oil spill in the Gulf of Mexico in 2010 and the Fukushima nuclear plant...vicinity of the Deepwater Horizon spill Andrew C. Pojea, Tamay M. Özgökmenb,1, Bruce L. Lipphardt, Jr.c, Brian K. Hausb, Edward H. Ryanb, Angelique C

  6. MAJOR OIL PLAYS IN UTAH AND VICINITY

    Energy Technology Data Exchange (ETDEWEB)

    Thomas C. Chidsey; Craig D. Morgan; Kevin McClure; Grant C. Willis

    2003-09-01

    Arizona. Outcrop analogs are found in the stratigraphically equivalent Navajo Sandstone of southern Utah which displays large-scale dunal cross-strata with excellent reservoir properties and interdunal features such as oases, wadi, and playa lithofacies with poor reservoir properties. Hydrocarbons in the Paradox Formation are stratigraphically trapped in carbonate buildups (or phylloid-algal mounds). Similar carbonate buildups are exposed in the Paradox along the San Juan River of southeastern Utah. Reservoir-quality porosity may develop in the types of facies associated with buildups such as troughs, detrital wedges, and fans, identified from these outcrops. When combined with subsurface geological and production data, these outcrop analogs can improve (1) development drilling and production strategies such as horizontal drilling, (2) reservoir-simulation models, (3) reserve calculations, and (4) design and implementation of secondary/tertiary oil recovery programs and other best practices used in the oil fields of Utah and vicinity. During this quarter, technology transfer activities consisted of exhibiting the project plans, objectives, and products at a booth at the 2003 annual convention of the American Association of Petroleum Geologists. The project home page was updated on the Utah Geological Survey Internet web site.

  7. Allele specific expression and methylation in the bumblebee, Bombus terrestris

    Directory of Open Access Journals (Sweden)

    Zoë Lonsdale

    2017-09-01

    Full Text Available The social hymenoptera are emerging as models for epigenetics. DNA methylation, the addition of a methyl group, is a common epigenetic marker. In mammals and flowering plants methylation affects allele specific expression. There is contradictory evidence for the role of methylation on allele specific expression in social insects. The aim of this paper is to investigate allele specific expression and monoallelic methylation in the bumblebee, Bombus terrestris. We found nineteen genes that were both monoallelically methylated and monoallelically expressed in a single bee. Fourteen of these genes express the hypermethylated allele, while the other five express the hypomethylated allele. We also searched for allele specific expression in twenty-nine published RNA-seq libraries. We found 555 loci with allele-specific expression. We discuss our results with reference to the functional role of methylation in gene expression in insects and in the as yet unquantified role of genetic cis effects in insect allele specific methylation and expression.

  8. Electrochemical biosensing strategies for DNA methylation analysis.

    Science.gov (United States)

    Hossain, Tanvir; Mahmudunnabi, Golam; Masud, Mostafa Kamal; Islam, Md Nazmul; Ooi, Lezanne; Konstantinov, Konstantin; Hossain, Md Shahriar Al; Martinac, Boris; Alici, Gursel; Nguyen, Nam-Trung; Shiddiky, Muhammad J A

    2017-08-15

    DNA methylation is one of the key epigenetic modifications of DNA that results from the enzymatic addition of a methyl group at the fifth carbon of the cytosine base. It plays a crucial role in cellular development, genomic stability and gene expression. Aberrant DNA methylation is responsible for the pathogenesis of many diseases including cancers. Over the past several decades, many methodologies have been developed to detect DNA methylation. These methodologies range from classical molecular biology and optical approaches, such as bisulfite sequencing, microarrays, quantitative real-time PCR, colorimetry, Raman spectroscopy to the more recent electrochemical approaches. Among these, electrochemical approaches offer sensitive, simple, specific, rapid, and cost-effective analysis of DNA methylation. Additionally, electrochemical methods are highly amenable to miniaturization and possess the potential to be multiplexed. In recent years, several reviews have provided information on the detection strategies of DNA methylation. However, to date, there is no comprehensive evaluation of electrochemical DNA methylation detection strategies. Herein, we address the recent developments of electrochemical DNA methylation detection approaches. Furthermore, we highlight the major technical and biological challenges involved in these strategies and provide suggestions for the future direction of this important field. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Optical biosensing strategies for DNA methylation analysis.

    Science.gov (United States)

    Nazmul Islam, Md; Yadav, Sharda; Hakimul Haque, Md; Munaz, Ahmed; Islam, Farhadul; Al Hossain, Md Shahriar; Gopalan, Vinod; Lam, Alfred K; Nguyen, Nam-Trung; Shiddiky, Muhammad J A

    2017-06-15

    DNA methylation is an epigenetic modification of DNA, where a methyl group is added at the fifth carbon of the cytosine base to form 5 methyl cytosine (5mC) without altering the DNA sequences. It plays important roles in regulating many cellular processes by modulating key genes expression. Alteration in DNA methylation patterns becomes particularly important in the aetiology of different diseases including cancers. Abnormal methylation pattern could contribute to the pathogenesis of cancer either by silencing key tumor suppressor genes or by activating oncogenes. Thus, DNA methylation biosensing can help in the better understanding of cancer prognosis and diagnosis and aid the development of therapies. Over the last few decades, a plethora of optical detection techniques have been developed for analyzing DNA methylation using fluorescence, Raman spectroscopy, surface plasmon resonance (SPR), electrochemiluminescence and colorimetric readouts. This paper aims to comprehensively review the optical strategies for DNA methylation detection. We also present an overview of the remaining challenges of optical strategies that still need to be focused along with the lesson learnt while working with these techniques. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Epigenetic DNA Methylation Linked to Social Dominance.

    Directory of Open Access Journals (Sweden)

    Kapa Lenkov

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

  11. Major Oil Plays in Utah and Vicinity

    Energy Technology Data Exchange (ETDEWEB)

    Thomas C. Chidsey; Craig D. Morgan; Kevin McClure; Douglas A. Sprinkel; Roger L. Bon; Hellmut H. Doelling

    2003-12-31

    fractured and sealed by overlying argillaceous and non-fractured units. The best outcrop analogs for Twin Creek reservoirs are found at Devils Slide and near the town of Peoa, Utah, where fractures in dense, homogeneous non-porous limestone beds are in contact with the basal siltstone units (containing sealed fractures) of the overlying units. The shallow marine, Mississippian Leadville Limestone is a major oil and gas reservoir in the Paradox Basin of Utah and Colorado. Hydrocarbons are produced from basement-involved, northwest-trending structural traps with closure on both anticlines and faults. Excellent outcrops of Leadville-equivalent rocks are found along the south flank of the Uinta Mountains, Utah. For example, like the Leadville, the Mississippian Madison Limestone contains zones of solution breccia, fractures, and facies variations. When combined with subsurface geological and production data, these outcrop analogs can improve (1) development drilling and production strategies such as horizontal drilling, (2) reservoir-simulation models, (3) reserve calculations, and (4) design and implementation of secondary/tertiary oil recovery programs and other best practices used in the oil fields of Utah and vicinity. In the southern Green River Formation play of the Uinta Basin, optimal drilling, development, and production practices consist of: (1) owning drilling rigs and frac holding tanks; (2) perforating sandstone beds with more than 8 percent neutron porosity and stimulate with separate fracture treatments; (3) placing completed wells on primary production using artificial lift; (4) converting wells relatively soon to secondary waterflooding maintaining reservoir pressure above the bubble point to maximize oil recovery; (5) developing waterflood units using an alternating injector--producer pattern on 40-acre (16-ha) spacing; and (6) recompleting producing wells by perforating all beds that are productive in the waterflood unit. As part of technology transfer

  12. Methyl 2-(5-chloro-3-methyl-sulfinyl-1-benzofuran-2-yl)acetate.

    Science.gov (United States)

    Choi, Hong Dae; Seo, Pil Ja; Son, Byeng Wha; Lee, Uk

    2008-10-18

    The title compound, C(12)H(11)ClO(4)S, was prepared by the oxidation of methyl 2-(5-chloro-3-methyl-sulfanyl-1-benzofuran-2-yl)acetate with 3-chloro-peroxy-benzoic acid. The O atom and the methyl group of the methyl-sulfinyl substituent lie on opposite sides of the plane of the benzofuran fragment. The crystal structure is stabilized by aromatic π-π inter-actions between the benzene rings of neighbouring mol-ecules [centroid-to-centroid distance = 3.809 (2) Å], and by C-H⋯π inter-actions between a methyl H atom and the furan ring of an adjacent mol-ecule. In addition, the crystal structure exhibits inter-molecular C-H⋯O hydrogen bonds.

  13. DNA methylation in plants.

    Science.gov (United States)

    Vanyushin, B F

    2006-01-01

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

  14. Dietary and lifestyle factors of DNA methylation.

    Science.gov (United States)

    Lim, Unhee; Song, Min-Ae

    2012-01-01

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

  15. Chirped Pulse Microwave Spectroscopy on Methyl Butanoate

    Science.gov (United States)

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

    2016-06-01

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

  16. Bathymetry of the Republic of the Marshall Islands and vicinity

    Science.gov (United States)

    Hein, James R.; Wong, Florence L.; Mosier, Dan L.

    1999-01-01

    The bathymetric map of the Republic of the Marshall Islands and vicinity is bounded by a window of latitude 3 to 17 degrees North, longitude 153 to 175 degrees East. The map was compiled from surveys conducted by the USGS, Korean Ocean Research and Development Institute, and published gridded data. In addition to national jurisdictions, island and atoll coastlines are indicated on the map.

  17. Methylation of Eugenol Using Dimethyl Carbonate and Bentonite as Catalyst

    Directory of Open Access Journals (Sweden)

    Dina Asnawati

    2015-11-01

    Full Text Available Eugenol is a compound with a variety of reactive functional groups such as allyl, hydroxy and methoxy. The presence of the functional groups brings eugenol possible to undertake the transformation into various derivative compounds with diverse activities. One of the simple and possible transformations is methylation or alkylation. Commonly, methyl halides and dimethyl sulphate are used as methylation agent. However, those kinds of methylation agents are toxic and carcinogenic. In this research dimethyl carbonate, an alternative methylation agent is used, because of its low toxicity, green, and economic. The synthesis has been carried out by using a catalyst. Bentonite was activated by heating to a temperature using 300 °C. Methylation was shown by the formation of a light yellow liquid (25.71% yield. The structures of products were characterized by GC-MS and obtained a compound, namely bis eugenol (4-allyl-2-methoxyphenoxy methane (2.37% yield.

  18. Genome-wide methylation profiling identifies novel methylated genes in neuroblastoma tumors.

    Science.gov (United States)

    Olsson, Maja; Beck, Stephan; Kogner, Per; Martinsson, Tommy; Carén, Helena

    2016-01-01

    Neuroblastoma is a very heterogeneous tumor of childhood. The clinical spectra range from very aggressive metastatic disease to spontaneous regression, even without therapy. Aberrant DNA methylation pattern is a common feature of most cancers. For neuroblastoma, it has been demonstrated both for single genes as well as genome-wide, where a so-called methylator phenotype has been described. Here, we present a study using Illumina 450K methylation arrays on 60 neuroblastoma tumors. We show that aggressive tumors, characterized by International Neuroblastoma Risk Group (INRG) as stage M, are hypermethylated compared to low-grade tumors. On the contrary, INRG stage L tumors display more non-CpG methylation. The genes with the highest number of hypermethylated CpG sites in INRG M tumors are TERT, PCDHGA4, DLX5, and DLX6-AS1. Gene ontology analysis showed a representation of neuronal tumor relevant gene functions among the differentially methylated genes. For validation, we used a set of independent tumors previously analyzed with the Illumina 27K methylation arrays, which confirmed the differentially methylated sites. Top candidate genes with aberrant methylation were analyzed for altered gene expression through the R2 platform ( http://r2.amc.nl), and for correlations between methylation and gene expression in a public dataset. Altered expression in nonsurvivors was found for the genes B3GALT4 and KIAA1949, CLIC5, DLX6-AS, TERT, and PIRT, and strongest correlations were found for TRIM36, KIAA0513, and PIRT. Our data indicate that methylation profiling can be used for patient stratification and informs on epigenetically deregulated genes with the potential of increasing our knowledge about the underlying mechanisms of tumor development.

  19. Identification of functionally methylated regions based on discriminant analysis through integrating methylation and gene expression data.

    Science.gov (United States)

    Zhang, Yuanyuan; Zhang, Junying

    2015-07-01

    DNA methylation is essential not only in cellular differentiation but also in diseases. Identification of differentially methylated patterns between case and control groups is important in understanding the mechanism and possible functionality of complex diseases. We propose a method to find possible functionally methylated regions which not only are differentially methylated but also have an effect on gene expression. It integrates methylation and gene expression data and is based on distance discriminant analysis (DDA). In the procedure of identifying differentially methylated regions (DMRs), we do not need to cluster methylation sites or partition the genome in advance. Therefore, the identified DMRs have a larger coverage than those of bump hunting and Ong's methods. Furthermore, through incorporating gene expression data as a complementary source, whether these DMRs are functional is determined through estimating the difference of the corresponding genes. Through a comparison of our approach with bump hunting and Ong's methods for simulation data, it is shown that our method is more powerful in identifying DMRs which have a larger distance in the genome, or only consist of a few sites and have higher sensitivity and specificity. Also, our method is more robust to heterogeneity of data. Applied to different real datasets, we find that most of the functional DMRs are hyper-methylated and located at CpG rich regions (e.g. islands, TSS200 and TSS1500), consistent with the fact that the methylation levels of CpG islands are higher in tumors than normal. Through comparing and analyzing the results of different datasets, we find that the change of methylation in some regions may be related to diseases through changing expression of the corresponding genes, and show the effectiveness of our method.

  20. DNA methylation abnormalities in congenital heart disease.

    Science.gov (United States)

    Serra-Juhé, Clara; Cuscó, Ivon; Homs, Aïda; Flores, Raquel; Torán, Núria; Pérez-Jurado, Luis A

    2015-01-01

    Congenital heart defects represent the most common malformation at birth, occurring also in ∼50% of individuals with Down syndrome. Congenital heart defects are thought to have multifactorial etiology, but the main causes are largely unknown. We have explored the global methylation profile of fetal heart DNA in comparison to blood DNA from control subjects: an absolute correlation with the type of tissue was detected. Pathway analysis revealed a significant enrichment of differential methylation at genes related to muscle contraction and cardiomyopathies in the developing heart DNA. We have also searched for abnormal methylation profiles on developing heart-tissue DNA of syndromic and non-syndromic congenital heart defects. On average, 3 regions with aberrant methylation were detected per sample and 18 regions were found differentially methylated between groups. Several epimutations were detected in candidate genes involved in growth regulation, apoptosis and folate pathway. A likely pathogenic hypermethylation of several intragenic sites at the MSX1 gene, involved in outflow tract morphogenesis, was found in a fetus with isolated heart malformation. In addition, hypermethylation of the GATA4 gene was present in fetuses with Down syndrome with or without congenital heart defects, as well as in fetuses with isolated heart malformations. Expression deregulation of the abnormally methylated genes was detected. Our data indicate that epigenetic alterations of relevant genes are present in developing heart DNA in fetuses with both isolated and syndromic heart malformations. These epimutations likely contribute to the pathogenesis of the malformation by cis-acting effects on gene expression.

  1. Decreased Fecundity and Sperm DNA Methylation Patterns

    Science.gov (United States)

    Jenkins, Timothy G.; Aston, Kenneth I.; Meyer, Tyson D.; Hotaling, James M.; Shamsi, Monis B.; Johnstone, Erica B.; Cox, Kyley J.; Stanford, Joseph B.; Porucznik, Christina A.; Carrell, Douglas T.

    2016-01-01

    Objective To evaluate the relationship between epigenetic patterns in sperm and fecundity. Design Prospective study of couples trying to conceive, utilizing semen samples collected through the HOPE study, at the University of Utah. Setting Academic Andrology and IVF Laboratory Patients DNA methylation alterations associated with fecundity were analyzed in 124 semen samples. 27 semen samples from couples who conceived within 2 months of attempting a pregnancy and a total of 29 semen samples from couples who were unable to achieve a pregnancy within 12 months were analyzed to identify regions of interest. Interventions None. Main Outcome Measures Genome-wide assessment of differential sperm DNA methylation and standard semen analysis. Results No differences in sperm count, sperm morphology, or semen volume were observed between the patients achieving a pregnancy within 2 months of study time and those not obtaining a pregnancy within 12 months. However, using data from the Human Methylation 450k array analysis we did identify 2 genomic regions with significantly decreased (FDR <0.01) methylation and 3 genomic regions with significantly increased methylation in the “failure-to-conceive” group. Interestingly, the only two sites where decreased methylation was associated with reduced fecundity are at closely related genes known to be expressed in sperm, HSPA1L and HSPA1B. Conclusions Our data suggest that there are genomic loci where DNA methylation alterations are associated with decreased fecundity. We have thus identified candidate loci for future study to verify these results and investigate the causative or contributory relationship between altered sperm methylation and decreased fecundity. PMID:26453269

  2. Relationship between methylation status of vitamin D-related genes, vitamin D levels, and methyl-donor biochemistry

    Directory of Open Access Journals (Sweden)

    Emma Louise Beckett

    2016-12-01

    Full Text Available Vitamin D is known for its role in the regulation of gene expression via the vitamin D receptor, a nuclear transcription factor. More recently, a role for vitamin D in regulating DNA methylation has been identified as an additional mechanism of modulation of gene expression. How methylation status influences vitamin D metabolism and response pathways is not yet clear. Therefore, we aimed to assess the relationship between plasma 25-hydroxycholecalciferol (25(OHD and the methylation status of vitamin D metabolism enzyme genes (CYP2R1, CYP27B1 and CYP24A1 and the vitamin D receptor gene (VDR. This analysis was conducted in the context of dietary vitamin D, and background methyl donor related biochemistry, with adjustment for several dietary and lifestyle variables. Percentage methylation at CpG sites was assessed in peripheral blood cells using methylation sensitive and dependent enzymes and qPCR. Standard analytical techniques were used to determine plasma 25(OHD and homocysteine, and serum folate and B12, with the relationship to methylation status assessed using multi-variable regression analysis. CYP2R1 and VDR methylation were found to be independent predictors of plasma 25(OHD, when adjusted for vitamin D intake and other lifestyle variables. CYP24A1 was related to plasma 25(OHD directly, but not in the context of vitamin D intake. Methyl-group donor biochemistry was associated with the methylation status of some genes, but did not alter the relationship between methylation and plasma 25(OHD. Modulation of methylation status of CYP2R1, CYP24A1 and VDR in response to plasma 25(OHD may be part of feedback loops involved in maintaining vitamin D homeostasis, and may explain a portion of the variance in plasma 25(OHD levels in response to intake and sun exposure. Methyl-group donor biochemistry, while a potential independent modulator, did not alter this effect.

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

    Science.gov (United States)

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

    2015-08-15

    Methylated arsenic can be found in virtually all earth surface environments. So far, however, little information has been collected regarding their removal by coagulation. In this study, the removal of monomethylarsenate (MMA) and dimethylarsenate (DMA) from drinking water by coagulation was investigated from the viewpoint of methyl substitution. Results indicated that FeCl3 was more efficient than AlCl3 and polyaluminum chloride (PACl) in methylated As removal. For the initial arsenic concentration of 200 μg/L, an FeCl3 dosage of 0.2 mmol Fe/L was sufficient to attain about 95% removal of MMA, while a dosage of 0.6 mmol Fe/L achieved about 57% removal of DMA. Arsenic removal efficiency was negatively correlated with the degree of methyl substitution. With the increase in methyl group number, the quantity of negatively charged arsenic species decreased and molecular size increased, leading to the decrease of methylated As removal by coagulation. Adsorption on preformed hydroxide flocs was the major mechanism during coagulation. Both FTIR and XPS results indicated that the As−O group of As might substitute the O−H group of Fe/Al hydroxide to form a Fe/Al−O−As complex. Furthermore, the use of traditional oxidants and coagulation aids exhibited limited help for improving coagulation removal of DMA. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Genetic control of methyl halide production in Arabidopsis.

    Science.gov (United States)

    Rhew, Robert C; Østergaard, Lars; Saltzman, Eric S; Yanofsky, Martin F

    2003-10-14

    Methyl chloride (CH(3)Cl) and methyl bromide (CH(3)Br) are the primary carriers of natural chlorine and bromine, respectively, to the stratosphere, where they catalyze the destruction of ozone, whereas methyl iodide (CH(3)I) influences aerosol formation and ozone loss in the boundary layer. CH(3)Br is also an agricultural pesticide whose use is regulated by international agreement. Despite the economic and environmental importance of these methyl halides, their natural sources and biological production mechanisms are poorly understood. Besides CH(3)Br fumigation, important sources include oceans, biomass burning, tropical plants, salt marshes, and certain crops and fungi. Here, we demonstrate that the model plant Arabidopsis thaliana produces and emits methyl halides and that the enzyme primarily responsible for the production is encoded by the HARMLESS TO OZONE LAYER (HOL) gene. The encoded protein belongs to a group of methyltransferases capable of catalyzing the S-adenosyl-L-methionine (SAM)-dependent methylation of chloride (Cl(-)), bromide (Br(-)), and iodide (I(-)) to produce methyl halides. In mutant plants with the HOL gene disrupted, methyl halide production is largely eliminated. A phylogenetic analysis with the HOL gene suggests that the ability to produce methyl halides is widespread among vascular plants. This approach provides a genetic basis for understanding and predicting patterns of methyl halide production by plants.

  5. Radiation Field in the Vicinity of the Collider Center

    Energy Technology Data Exchange (ETDEWEB)

    Stevens, A. J. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    1994-10-26

    The Collider Center and the adjoining cryogenic support building are unique among the buildings close to the collider tunnel because these are locations where the occupancy by non-radiation workers is high. This note describes calculations of the dose equivalent from local beam loss at both the nearest point of these buildings to the collider ring and on the berm in the vicinity of these buildings.

  6. Environmental surveillance in the vicinity of Hanford for January 1968

    Energy Technology Data Exchange (ETDEWEB)

    Wooldridge, C.B. (ed.)

    1968-04-15

    The concentrations of most radionuclides in the vicinity of Hanford during January 1968 were below comparable measurements for a year ago. Slightly increased concentrations of I-131 in Richland drinking water were observed during the last two weeks of the month. Radioiodine detected in several milk samples (maximum 25 pCi/l) was attributed to fallout from an announced nuclear weapons test of December 24, 1967. Increased beta activities on air filters were also attributed to fallout.

  7. Adsorption of egg albumin onto methylated yeast biomass

    OpenAIRE

    Seki, Hideshi; Suzuki, Akira; Maruyama, Hideo

    2004-01-01

    A new biosorbent, methylated yeast (MeYE), was prepared for the adsorptive separation of proteins from aqueous solutions. Yeast was methylated in a 0.1 M HCl methyl alcohol solution at room temperature. About 80% of the carboxylic groups of yeast could be methylated within 9 h. The adsorption of egg albumin to MeYE was studied to evaluate the protein adsorption ability of MeYE. At near neutral pH, egg albumin was scarcely adsorbed to unmethylated yeast and the adsorption amount of egg albumin...

  8. DNA methylation in an engineered heart tissue model of cardiac hypertrophy: common signatures and effects of DNA methylation inhibitors.

    Science.gov (United States)

    Stenzig, Justus; Hirt, Marc N; Löser, Alexandra; Bartholdt, Lena M; Hensel, Jan-Tobias; Werner, Tessa R; Riemenschneider, Mona; Indenbirken, Daniela; Guenther, Thomas; Müller, Christian; Hübner, Norbert; Stoll, Monika; Eschenhagen, Thomas

    2016-01-01

    DNA methylation affects transcriptional regulation and constitutes a drug target in cancer biology. In cardiac hypertrophy, DNA methylation may control the fetal gene program. We therefore investigated DNA methylation signatures and their dynamics in an in vitro model of cardiac hypertrophy based on engineered heart tissue (EHT). We exposed EHTs from neonatal rat cardiomyocytes to a 12-fold increased afterload (AE) or to phenylephrine (PE 20 µM) and compared DNA methylation signatures to control EHT by pull-down assay and DNA methylation microarray. A 7-day intervention sufficed to induce contractile dysfunction and significantly decrease promoter methylation of hypertrophy-associated upregulated genes such as Nppa (encoding ANP) and Acta1 (α-skeletal actin) in both intervention groups. To evaluate whether pathological consequences of AE are affected by inhibiting de novo DNA methylation we applied AE in the absence and presence of DNA methyltransferase (DNMT) inhibitors: 5-aza-2'-deoxycytidine (aza, 100 µM, nucleosidic inhibitor), RG108 (60 µM, non-nucleosidic) or methylene disalicylic acid (MDSA, 25 µM, non-nucleosidic). Aza had no effect on EHT function, but RG108 and MDSA partially prevented the detrimental consequences of AE on force, contraction and relaxation velocity. RG108 reduced AE-induced Atp2a2 (SERCA2a) promoter methylation. The results provide evidence for dynamic DNA methylation in cardiac hypertrophy and warrant further investigation of the potential of DNA methylation in the treatment of cardiac hypertrophy.

  9. Kinetics and mechanism of the oxidation of some vicinal and non ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 115; Issue 2. Kinetics and ... Kinetics of oxidation of five vicinal and four non-vicinal diols, and two of their monoethers, by tetrabutylammonium tribromide (TBATB) has been studied. The vicinal diols ... Department of Chemistry, JNV University, Jodhpur 342 005, India ...

  10. Genome methylation patterns across castes and generations in a parasitoid wasp.

    Science.gov (United States)

    Shaham, Roei; Ben-Shlomo, Rachel; Motro, Uzi; Keasar, Tamar

    2016-11-01

    Environmental influences shape phenotypes within and across generations, often through DNA methylations that modify gene expression. Methylations were proposed to mediate caste and task allocation in some eusocial insects, but how an insect's environment affects DNA methylation in its offspring is yet unknown. We characterized parental effects on methylation profiles in the polyembryonic parasitoid wasp Copidosoma koehleri, as well as methylation patterns associated with its simple caste system. We used methylation-sensitive amplified fragment length polymorphism (MS-AFLP) to compare methylation patterns, among (1) reproductive and soldier larvae; and (2) offspring (larvae, pupae, and adults) of wasps that were reared at either high or low larval density and mated in the four possible combinations. Methylation frequencies were similar across castes, but the profiles of methylated fragments differed significantly. Parental rearing density did not affect methylation frequencies in the offspring at any developmental stage. Principal coordinate analysis indicated no significant differences in methylation profiles among the four crossbreeding groups and the three developmental stages. Nevertheless, a clustering analysis, performed on a subset of the fragments, revealed similar methylation patterns in larvae, pupae, and adults in two of the four parental crosses. Nine fragments were methylated at two cytosine sites in all larvae, and five others were methylated at two sites in all adults. Thus, DNA methylations correlate with within-generation phenotypic plasticity due to caste. However, their association with developmental stage and with transgenerational epigenetic effects is not clearly supported.

  11. The identification of specific methylation patterns across different cancers.

    Science.gov (United States)

    Zhang, Chunlong; Zhao, Hongyan; Li, Jie; Liu, Hongbo; Wang, Fang; Wei, Yanjun; Su, Jianzhong; Zhang, Dongwei; Liu, Tiefu; Zhang, Yan

    2015-01-01

    Abnormal DNA methylation is known as playing an important role in the tumorgenesis. It is helpful for distinguishing the specificity of diagnosis and therapeutic targets for cancers based on characteristics of DNA methylation patterns across cancers. High throughput DNA methylation analysis provides the possibility to comprehensively filter the epigenetics diversity across various cancers. We integrated whole-genome methylation data detected in 798 samples from seven cancers. The hierarchical clustering revealed the existence of cancer-specific methylation pattern. Then we identified 331 differentially methylated genes across these cancers, most of which (266) were specifically differential methylation in unique cancer. A DNA methylation correlation network (DMCN) was built based on the methylation correlation between these genes. It was shown the hubs in the DMCN were inclined to cancer-specific genes in seven cancers. Further survival analysis using the part of genes in the DMCN revealed high-risk group and low-risk group were distinguished by seven biomarkers (PCDHB15, WBSCR17, IGF1, GYPC, CYGB, ACTG2, and PRRT1) in breast cancer and eight biomarkers (ZBTB32, OR51B4, CCL8, TMEFF2, SALL3, GPSM1, MAGEA8, and SALL1) in colon cancer, respectively. At last, a protein-protein interaction network was introduced to verify the biological function of differentially methylated genes. It was shown that MAP3K14, PTN, ACVR1 and HCK sharing different DNA methylation and gene expression across cancers were relatively high degree distribution in PPI network. The study suggested that not only the identified cancer-specific genes provided reference for individual treatment but also the relationship across cancers could be explained by differential DNA methylation.

  12. DNA methylation in obesity

    Directory of Open Access Journals (Sweden)

    Małgorzata Pokrywka

    2014-11-01

    Full Text Available 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.

  13. High-temperature measurements of the reactions of OH with small methyl esters: methyl formate, methyl acetate, methyl propanoate, and methyl butanoate.

    Science.gov (United States)

    Lam, King-Yiu; Davidson, David F; Hanson, Ronald K

    2012-12-20

    The overall rate constants for the reactions of hydroxyl radicals (OH) with four small methyl esters, namely methyl formate (CH(3)OCHO), methyl acetate (CH(3)OC(O)CH(3)), methyl propanoate (CH(3)OC(O)C(2)H(5)), and methyl butanoate (CH(3)OC(O)C(3)H(7)), were investigated behind reflected shock waves using UV laser absorption of OH radicals near 306.69 nm. Test gas mixtures of individual methyl esters and tert-butyl hydroperoxide (TBHP), a fast source of OH at elevated temperatures, diluted in argon were shock-heated to temperatures spanning from 876 to 1371 K at pressures near 1.5 atm. The overall rate constants were determined by matching the measured OH time-histories with the computed profiles from the comprehensive chemical kinetic mechanisms of Dooley et al. (2010) and Dooley et al. (2008), which were originally developed for the oxidation of methyl formate and methyl butanoate, respectively. These measured values can be expressed in Arrhenius form as k(CH(3)OCHO+OH) = 2.56 × 10(13) exp(-2026/T) cm(3) mol(-1) s(-1), k(CH(3)OC(O)CH(3)+OH) = 3.59 × 10(13) exp(-2438/T) cm(3) mol(-1) s(-1), k(CH(3)OC(O)C(2)H(5)+OH) = 6.65 × 10(13) exp(-2539/T) cm(3) mol(-1) s(-1), and k(CH(3)OC(O)C(3)H(7)+OH) = 1.13 × 10(14) exp(-2515/T) cm(3) mol(-1) s(-1) over the temperature ranges studied. Detailed error analyses were performed to estimate the overall uncertainties of these reactions, and the estimated (2σ) uncertainties were found to be ±29% at 913 K and ±18% at 1289 K for k(CH(3)OCHO+OH), ± 29% at 930 K and ±17% at 1299 K for k(CH(3)OC(O)CH(3)+OH), ± 25% at 909 K and ±17% at 1341 K for k(CH(3)OC(O)C2H(5)+OH), and ±24% at 925 K and ±16% at 1320 K for k(CH(3)OC(O)C(3)H(7)+OH). We believe these are the first direct high-temperature rate constant measurements for the reactions of OH with these small methyl esters. These measured rate constants were also compared with the estimated values employed in different comprehensive kinetic mechanisms. Additionally, the

  14. Apoptosis and DNA Methylation

    Directory of Open Access Journals (Sweden)

    Richard R. Meehan

    2011-04-01

    Full Text Available Epigenetic mechanisms assist in maintaining gene expression patterns and cellular properties in developing and adult tissues. The molecular pathology of disease states frequently includes perturbation of DNA and histone methylation patterns, which can activate apoptotic pathways associated with maintenance of genome integrity. This perspective focuses on the pathways linking DNA methyltransferases and methyl-CpG binding proteins to apoptosis, and includes new bioinformatic analyses to characterize the evolutionary origin of two G/T mismatch-specific thymine DNA glycosylases, MBD4 and TDG.

  15. Atmospheric BTEX concentrations in the vicinity of the crude oil refinery of the Baltic region.

    Science.gov (United States)

    Baltrėnas, Pranas; Baltrėnaitė, Edita; Serevičienė, Vaida; Pereira, Paulo

    2011-11-01

    Among chemical industries, petroleum refineries have been identified as large emitters of a wide variety of pollutants. Benzene, toluene, ethylbenzene, and xylene (BTEX) form an important group of aromatic volatile organic compounds (VOCs) because of their role in the troposphere chemistry and the risk posed to human health. A very large crude oil refinery of the Baltic States (200,000 bbl/day) is situated in the northern, rural part of Lithuania, 10 km from the town of Mažeikiai (Lithuania). The objectives of this study were: (1) to determine of atmospheric levels of BTEX in the region rural and urban parts at the vicinity of the crude oil refinery; and (2) to investigate the effect of meteorological parameters (wind speed, wind direction, temperature, pressure, humidity) on the concentrations measured. The averaged concentration of benzene varied from 2.12 ppbv in the rural areas to 2.75 ppbv in the urban areas where the traffic was determined to be a dominant source of BTEX emissions. Our study showed that concentration of benzene, as strictly regulated air pollutant by EU Directive 2008/50/EC, did not exceed the limit of 5 ppbv in the region in the vicinity of the crude oil refinery during the investigated period. No significant change in air quality in the vicinity of the oil refinery was discovered, however, an impact of the industry on the background air quality was detected. The T/B ratio (0.50-0.81) that was much lower than 2.0, identified other sources of pollution than traffic.

  16. Correlation between RAGE gene promoter methylation and diabetic retinal inflammation.

    Science.gov (United States)

    Kan, Shifeng; Wu, Jing; Sun, Chengxi; Hao, Jing; Wu, Zhen

    2018-01-01

    The methylation status of the receptor for advanced glycation end products (RAGE) gene promoter in peripheral blood mononuclear cells (PBMCs) of type 2 diabetic retinopathy (DR) patients was evaluated to investigate the correlation between RAGE gene promoter methylation and diabetic retinal inflammation. Eighty patients admitted and diagnosed as type 2 DR in Qilu Hospital, Shandong University during the period from October, 2013 to October, 2015 were enrolled in this study. They were the observation group and 40 healthy subjects were enrolled in the control group. PBMCs were collected from patients using density gradient centrifugation, and the methylation status of RAGE gene promoters was detected using methylation-specific PCP (MSP). Interleukin-1β (IL-1β), IL-6 and tumor necrosis factor-α (TNF-α) levels of in the serum were measured using enzyme-linked immunosorbent assay (ELISA). PBMCs in patients with positive RAGE gene promoter methylation were isolated and cultured and RAGE gene promoter methylation was inhibited using the demethylating agent, 5'-aza-2'-deoxycytidine (5-aza-dC). The methylation status of RAGE gene promoters in PBMCs was detected via MSP. IL-1β, IL-6 and TNF-α levels in the supernatant of PBMC culture solution were evaluated using ELISA. MSP results showed that there were 26 cases (32.50%) of RAGE gene promoter methylation in PBMCs in DR patients. RAGE gene promoters were methylated in all normal healthy subjects. IL-1β, IL-6 and TNF-α levels in serum for positive RAGE gene promoter methylation group were significantly lower than those in negative RAGE gene promoter methylation group (pRAGE gene promoter methylation of PBMCs in patients with positive RAGE gene promoter methylation. The inhibition of methylation in RAGE gene promoter increased the levels of IL-1β, IL-6 and TNF-α in supernatant of culture solution. In conclusion, RAGE gene promoter hypomethylation was detected in DR patients, indicating that RAGE gene promoter

  17. Whole-genome methylation caller designed for methyl-DNA ...

    African Journals Online (AJOL)

    DNA methylation is an indispensable epigenetic modification required for regulating the expression of mammalian genomes. Continued efforts have been made to unravel the methylation states genome-wide, featuring the methyl-DNA immunoprecipitation (MeDIP) coupled with next-generation sequencing. Our method ...

  18. Patterns of DNA methylation in animals: an ecotoxicological perspective.

    Science.gov (United States)

    Head, Jessica A

    2014-07-01

    DNA methylation refers to the addition of a methyl group to nucleotides within DNA. As with other epigenetic endpoints, patterns of DNA methylation are susceptible to alterations due to exposure to environmental stressors, including contaminants. These alterations can persist in the absence of the initial stressor as cells divide, and can even be inherited between generations if they occur in the germ line. Although our knowledge concerning patterns of DNA methylation in animals is increasing, there remains a gap in the literature when it comes to species outside of those typically used for biomedical research. Here, I review the literature relating to DNA methylation in an array of taxa (mammals, fish, birds, amphibians, reptiles, and invertebrates) and discuss these data from an ecotoxicological perspective. The pattern and extent of DNA methylation is well conserved across species of vertebrates; methylation appears mainly on cytosine residues within a CpG context, and much of the genome is methylated, with the notable exception of cytosines within CpG islands in the promoters of genes. Highly methylated genes in vertebrates tend to be transcriptionally repressed. However, large differences occur between classes of vertebrates in terms of the timing and nature of reprogramming and genomic imprinting: epigenetic processes that establish patterns of DNA methylation in the early embryo and which are sensitive to environmental stress. In invertebrates, patterns of DNA methylation are extremely variable and differ significantly from the condition observed in vertebrates. Some invertebrate genomes exhibit no DNA methylation while others are methylated to a level that is comparable to vertebrates. Additionally, DNA methylation may have different functions in invertebrates, e.g., alternative splicing. This variability in basic patterns of DNA methylation among species during sensitive periods of development suggests that responses to epigenetically active environmental

  19. Electromagnetic fields in the vicinity of DECT cordless telephones and mobile phones

    Directory of Open Access Journals (Sweden)

    Paweł Mamrot

    2015-12-01

    Full Text Available Background: Mobile telephones belong to the most frequently used personal devices. In their surroundings they produce the electromagnetic field (EMF, in which exposure range there are not only users but also nearby bystanders. The aim of the investigations and EMF measurements in the vicinity of phones was to identify the electric field levels with regard to various working modes. Material and methods: Twelve sets of DECT (digital enhanced cordless telecommunications cordless phones (12 base units and 15 handsets, 21 mobile telephones produced by different manufactures, and 16 smartphones in various applications, (including multimedia in the conditions of daily use in living rooms were measured. Measurements were taken using the point method in predetermined distances of 0.05–1 m from the devices without the presence of users. Results: In the vicinity of DECT cordless phone handsets, electric field strength ranged from 0.26 to 2.30 V/m in the distance of 0.05 m – 0.18–0.26 V/m (1 m. In surroundings of DECT cordless telephones base units the values of EMF were from 1.78–5.44 V/m (0.05 m to 0.19– 0.41 V/m (1 m. In the vicinity of mobile phones working in GSM mode with voice transmission, the electric field strength ranged from 2.34–9.14 V/m (0.05 m to 0.18–0.47 V/m (1 m while in the vicinity of mobile phones working in WCDMA (Wideband Code Division Multiple Access mode the electric field strength ranged from 0.22–1.83 V/m (0.05 m to 0.18–0.20 V/m (1 m. Conclusions: The mean values of the electric field strength for each group of devices, mobile phones and DECT wireless phones sets do not exceed the reference value of 7 V/m, adopted as the limit for general public exposure. Med Pr 2015;66(6:803–814

  20. DNA Methylation and Cancer Diagnosis

    Science.gov (United States)

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

    2013-01-01

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

  1. The impact of methylation quantitative trait loci (mQTLs) on active smoking-related DNA methylation changes.

    Science.gov (United States)

    Gao, Xu; Thomsen, Hauke; Zhang, Yan; Breitling, Lutz Philipp; Brenner, Hermann

    2017-01-01

    Methylation quantitative trait loci (mQTLs) are the genetic variants that may affect the DNA methylation patterns of CpG sites. However, their roles in influencing the disturbances of smoking-related epigenetic changes have not been well established. This study was conducted to address whether mQTLs exist in the vicinity of smoking-related CpG sites (± 50 kb) and to examine their associations with smoking exposure and all-cause mortality in older adults. We obtained DNA methylation profiles in whole blood samples by Illumina Infinium Human Methylation 450 BeadChip array of two independent subsamples of the ESTHER study (discovery set, n = 581; validation set, n = 368) and their corresponding genotyping data using the Illumina Infinium OncoArray BeadChip. After correction for multiple testing (FDR), we successfully identified that 70 out of 151 previously reported smoking-related CpG sites were significantly associated with 192 SNPs within the 50 kb search window of each locus. The 192 mQTLs significantly influenced the active smoking-related DNA methylation changes, with percentage changes ranging from 0.01 to 18.96%, especially for the weakly/moderately smoking-related CpG sites. However, these identified mQTLs were not directly associated with active smoking exposure or all-cause mortality. Our findings clearly demonstrated that if not dealt with properly, the mQTLs might impair the power of epigenetic-based models of smoking exposure to a certain extent. In addition, such genetic variants could be the key factor to distinguish between the heritable and smoking-induced impact on epigenome disparities. These mQTLs are of special importance when DNA methylation markers measured by Illumina Infinium assay are used for any comparative population studies related to smoking-related cancers and chronic diseases.

  2. DNA methylation-based variation between human populations.

    Science.gov (United States)

    Kader, Farzeen; Ghai, Meenu

    2017-02-01

    Several studies have proved that DNA methylation affects regulation of gene expression and development. Epigenome-wide studies have reported variation in methylation patterns between populations, including Caucasians, non-Caucasians (Blacks), Hispanics, Arabs, and numerous populations of the African continent. Not only has DNA methylation differences shown to impact externally visible characteristics, but is also a potential biomarker for underlying racial health disparities between human populations. Ethnicity-related methylation differences set their mark during early embryonic development. Genetic variations, such as single-nucleotide polymorphisms and environmental factors, such as age, dietary folate, socioeconomic status, and smoking, impacts DNA methylation levels, which reciprocally impacts expression of phenotypes. Studies show that it is necessary to address these external influences when attempting to differentiate between populations since the relative impacts of these factors on the human methylome remain uncertain. The present review summarises several reported attempts to establish the contribution of differential DNA methylation to natural human variation, and shows that DNA methylation could represent new opportunities for risk stratification and prevention of several diseases amongst populations world-wide. Variation of methylation patterns between human populations is an exciting prospect which inspires further valuable research to apply the concept in routine medical and forensic casework. However, trans-generational inheritance needs to be quantified to decipher the proportion of variation contributed by DNA methylation. The future holds thorough evaluation of the epigenome to understand quantification, heritability, and the effect of DNA methylation on phenotypes. In addition, methylation profiling of the same ethnic groups across geographical locations will shed light on conserved methylation differences in populations.

  3. Scheme Transformations in the Vicinity of an Infrared Fixed Point

    DEFF Research Database (Denmark)

    Ryttov, Thomas; Shrock, Robert

    2012-01-01

    We analyze the effect of scheme transformations in the vicinity of an exact or approximate infrared fixed point in an asymptotically free gauge theory with fermions. We show that there is far less freedom in carrying out such scheme transformations in this case than at an ultraviolet fixed point....... We construct a transformation from the $\\bar{MS}$ scheme to a scheme with a vanishing three-loop term in the $\\beta$ function and use this to assess the scheme dependence of an infrared fixed point in SU($N$) theories with fermions. Implications for the anomalous dimension of the fermion bilinear...

  4. Reelin (RELN) DNA methylation in the peripheral blood of schizophrenia.

    Science.gov (United States)

    Nabil Fikri, Rahim Mohd; Norlelawati, A Talib; Nour El-Huda, Abdul Rahim; Hanisah, Mohd Noor; Kartini, Abdullah; Norsidah, Kuzaifah; Nor Zamzila, Abdullah

    2017-05-01

    The epigenetic changes of RELN that are involved in the development of dopaminergic neurons may fit the developmental theory of schizophrenia. However, evidence regarding the association of RELN DNA methylation with schizophrenia is far from sufficient, as studies have only been conducted on a few limited brain samples. As DNA methylation in the peripheral blood may mirror the changes taking place in the brain, the use of peripheral blood for a DNA methylation study in schizophrenia is feasible due to the scarcity of brain samples. Therefore, the aim of our study was to examine the relationship of DNA methylation levels of RELN promoters with schizophrenia using genomic DNA derived from the peripheral blood of patients with the disorder. The case control studies consisted of 110 schizophrenia participants and 122 healthy controls who had been recruited from the same district. After bisufhite conversion, the methylation levels of the DNA samples were calculated based on their differences of the Cq values assayed using the highly sensitive real-time MethyLight TaqMan ® procedure. A significantly higher level of methylation of the RELN promoter was found in patients with schizophrenia compared to controls (p = 0.005) and also in males compared with females (p = 0.004). Subsequently, the RELN expression of the methylated group was 25 fold less than that of the non-methylated group. Based upon the assumption of parallel methylation changes in the brain and peripheral blood, we concluded that RELN DNA methylation might contribute to the pathogenesis of schizophrenia. However, the definite effects of methylation on RELN function during development and also in adult life still require further elaboration. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Chiral methyl-branched pheromones.

    Science.gov (United States)

    Ando, Tetsu; Yamakawa, Rei

    2015-07-01

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

  6. Health effects of living in the vicinity of the landfills

    Directory of Open Access Journals (Sweden)

    Katarzyna Lar

    2013-12-01

    Full Text Available Landfill sites are the easiest, the cheapest and the most common way of waste management and disposal. In the face of the increasing amount of waste, the dynamics of globalization and urbanization process, waste management is an important issue of ecological policy in highly developed countries. Landfill sites intensify environmental threats for the neighborhood and give rise to toxic substances which impair human health being released from the landfills. These are persistent organic pollutants (POPs, heavy metals and also biological gas, bioaerosols, bacteria and viruses. Scientists have conducted a lot of research to evaluate the impact of landfill sites on human health living in their vicinity. They found increased occurrence of congenital anomalies, increased risk of certain cancers and low birth weight of infants. The results of the studies didn’t deliver absolute proof of relation between the impact of landfill sites on the induction of cancer and other diseases. There is a necessity to conduct further research to evaluate the impact of landfill sites on people health living in the vicinity

  7. Energetic particle fluxes in vicinity of Jupiter's moon Europa

    Science.gov (United States)

    Podzolko, Mikhail; Getselev, Igor; Gubar, Yuriy; Veselovsky, Igor

    Currently several projects of sending research space vehicles to Jupiter and its Galilean moons in 2020 are being developed. In particular, Russian Space Agency proposed the project of Europa lander. During the mission the spacecraft will be affected by charged particles of various origins. The greatest hazard will originate from powerful Jupiter's radiation belts, especially during the time of spacecraft operation near Europa and on its surface. The absorbed radiation dose during 2 months in Europa's orbit under shielding compared to that for "Galileo" spacecraft will amount to almost 1 megarad, the major contribution to it will originate from relativistic electrons. However, near Europa part of the charged particle flux will be shaded by the moon. Obviously, fluxes of particles of all energies on its surface will be lower by at least 2 times, than in the same point of space without Europa. But furthermore, the reduction of the fluxes in vicinity of Europa is nonuniform, and differs for the surface and the low-altitude orbit. This is caused by several factors: the complexity of particle trajectories near Europa and in Jupiter's magnetosphere in general, difference of Europa's orbital plane from Jupiter's geomagnetic equator plane, certain disturbance of Jupiter's magnetic field in vicinity of Europa, possible influence of electric fields and Europa's tenuous atmosphere. In the current study computations of energetic particle flux distribution near Europa and on its surface are made, taking into account several of the above-mentioned factors.

  8. DNA methylation dynamics in neurogenesis

    Science.gov (United States)

    Wang, Zhiqin; Tang, Beisha; He, Yuquan; Jin, Peng

    2016-01-01

    Neurogenesis is not limited to the embryonic stage, but continually proceeds in the adult brain throughout life. Epigenetic mechanisms, including DNA methylation, histone modification and noncoding RNA, play important roles in neurogenesis. For decades, DNA methylation was thought to be a stable modification, except for demethylation in the early embryo. In recent years, DNA methylation has proved to be dynamic during development. In this review, we summarize the latest understanding about DNA methylation dynamics in neurogenesis, including the roles of different methylation forms (5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine), as well as their ‘writers’, ‘readers’ and interactions with histone modifications. PMID:26950681

  9. DNA methylation and healthy human aging.

    Science.gov (United States)

    Jones, Meaghan J; Goodman, Sarah J; Kobor, Michael S

    2015-12-01

    The process of aging results in a host of changes at the cellular and molecular levels, which include senescence, telomere shortening, and changes in gene expression. Epigenetic patterns also change over the lifespan, suggesting that epigenetic changes may constitute an important component of the aging process. The epigenetic mark that has been most highly studied is DNA methylation, the presence of methyl groups at CpG dinucleotides. These dinucleotides are often located near gene promoters and associate with gene expression levels. Early studies indicated that global levels of DNA methylation increase over the first few years of life and then decrease beginning in late adulthood. Recently, with the advent of microarray and next-generation sequencing technologies, increases in variability of DNA methylation with age have been observed, and a number of site-specific patterns have been identified. It has also been shown that certain CpG sites are highly associated with age, to the extent that prediction models using a small number of these sites can accurately predict the chronological age of the donor. Together, these observations point to the existence of two phenomena that both contribute to age-related DNA methylation changes: epigenetic drift and the epigenetic clock. In this review, we focus on healthy human aging throughout the lifetime and discuss the dynamics of DNA methylation as well as how interactions between the genome, environment, and the epigenome influence aging rates. We also discuss the impact of determining 'epigenetic age' for human health and outline some important caveats to existing and future studies. © 2015 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.

  10. Radical SAM-Mediated Methylation of Ribosomal RNA

    Science.gov (United States)

    Stojkovic, Vanja; Fujimori, Danica Galonić

    2015-01-01

    Post-transcriptional modifications of RNA play an important role in a wide range of biological processes. In ribosomal RNA (rRNA), methylation of nucleotide bases is the predominant modification. In recent years, methylation of adenosine 2503 (A2503) in bacterial 23S rRNA has attracted significant attention due to both the unusual regioselectivity of the methyl group incorporation, as well as the pathophysiological roles of the resultant methylations. Specifically, A2503 is methylated at the C2 and C8 positions of the adenine ring, and the introduced modifications have a profound impact on translational fidelity and antibiotic resistance, respectively. These modifications are performed by RlmN and Cfr, two members, of the recently discovered class of radical S-adenosylmethionine (radical SAM) methylsynthases. Here, we present several methods that can be used to evaluate the activity of these enzymes, under both in vivo and in vitro conditions. PMID:26253978

  11. Methylation in hepatocellular carcinoma

    Directory of Open Access Journals (Sweden)

    Regina M. Santella

    2007-02-01

    Full Text Available

    The development of HCC is a complex, multistep, multistage process. The molecular pathogenesis of HCC appears to involve multiple genetic aberrations in the molecular control of hepatocyte proliferation, differentiation and death and the maintenance of genomic integrity. This process is influenced by the cumulative activation and inactivation of oncogenes, tumor suppressor genes and other genes. p53, a tumor suppressor gene, is the most frequently mutated gene in human cancers. There is also a striking sequence specific binding and induction of mutations by AFB1 at codon 249 of p53 in HCC.

    Epigenetic alterations are also involved in cancer development and progression. Methylation of promoter CpG islands is associated with inhibition of transcriptional initiation and permanent silencing of downstream genes.

    It is now known that most important tumor suppressor genes are inactivated, not only by mutations and deletions but also by promoter methylation. Several studies indicated that p16, p15, RASSF1A, MGMT, and GSTP1 promoter hypermethylation are prevalent in HCC. In addition, geographic variation in the methylation status of tumor DNA indicates that environmental factors may influence the frequent and concordant degree of hypermethylation in multiple genes in HCC and that epigeneticenvironmental interactions may be involved in hepatocarcinogenesis. We have found significant relationships between promoter methylation and AFB1-DNA adducts confirming the impact of environmental exposures on gene methylation.

    DNA isolated from serum or plasma of cancer patients frequently contains the same genetic and

  12. DNA methylation characteristics of primary melanomas with distinct biological behaviour.

    Directory of Open Access Journals (Sweden)

    Szilvia Ecsedi

    Full Text Available In melanoma, the presence of promoter related hypermethylation has previously been reported, however, no methylation-based distinction has been drawn among the diverse melanoma subtypes. Here, we investigated DNA methylation changes associated with melanoma progression and links between methylation patterns and other types of somatic alterations, including the most frequent mutations and DNA copy number changes. Our results revealed that the methylome, presenting in early stage samples and associated with the BRAF(V600E mutation, gradually decreased in the medium and late stages of the disease. An inverse relationship among the other predefined groups and promoter methylation was also revealed except for histologic subtype, whereas the more aggressive, nodular subtype melanomas exhibited hypermethylation as well. The Breslow thickness, which is a continuous variable, allowed for the most precise insight into how promoter methylation decreases from stage to stage. Integrating our methylation results with a high-throughput copy number alteration dataset, local correlations were detected in the MYB and EYA4 genes. With regard to the effects of DNA hypermethylation on melanoma patients' survival, correcting for clinical cofounders, only the KIT gene was associated with a lower overall survival rate. In this study, we demonstrate the strong influence of promoter localized DNA methylation changes on melanoma initiation and show how hypermethylation decreases in melanomas associated with less favourable clinical outcomes. Furthermore, we establish the methylation pattern as part of an integrated apparatus of somatic DNA alterations.

  13. Genome-Wide Analysis of DNA Methylation in Human Amnion

    Directory of Open Access Journals (Sweden)

    Jinsil Kim

    2013-01-01

    Full Text Available The amnion is a specialized tissue in contact with the amniotic fluid, which is in a constantly changing state. To investigate the importance of epigenetic events in this tissue in the physiology and pathophysiology of pregnancy, we performed genome-wide DNA methylation profiling of human amnion from term (with and without labor and preterm deliveries. Using the Illumina Infinium HumanMethylation27 BeadChip, we identified genes exhibiting differential methylation associated with normal labor and preterm birth. Functional analysis of the differentially methylated genes revealed biologically relevant enriched gene sets. Bisulfite sequencing analysis of the promoter region of the oxytocin receptor (OXTR gene detected two CpG dinucleotides showing significant methylation differences among the three groups of samples. Hypermethylation of the CpG island of the solute carrier family 30 member 3 (SLC30A3 gene in preterm amnion was confirmed by methylation-specific PCR. This work provides preliminary evidence that DNA methylation changes in the amnion may be at least partially involved in the physiological process of labor and the etiology of preterm birth and suggests that DNA methylation profiles, in combination with other biological data, may provide valuable insight into the mechanisms underlying normal and pathological pregnancies.

  14. Genetic variants of methyl metabolizing enzymes and epigenetic regulators: Associations with promoter CpG island hypermethylation in colorectal cancer

    NARCIS (Netherlands)

    Vogel, S. de; Wouters, K.A.D.; Gottschalk, R.W.H.; Schooten, F.J. van; Goeij, A.F.P.M. de; Bruïne, A.P. de; Goldbohm, R.A.; Brandt, P.A. van den; Weijenberg, M.P.; Engeland, M. van

    2009-01-01

    Aberrant DNA methylation affects carcinogenesis of colorectal cancer. Folate metabolizing enzymes may influence the bioavailability of methyl groups, whereas DNA and histone methyltransferases are involved in epigenetic regulation of gene expression. We studied associations of genetic variants of

  15. Quantifying Mapping Orbit Performance in the Vicinity of Primitive Bodies

    Science.gov (United States)

    Pavlak, Thomas A.; Broschart, Stephen B.; Lantoine, Gregory

    2015-01-01

    Predicting and quantifying the capability of mapping orbits in the vicinity of primitive bodies is challenging given the complex orbit geometries that exist and the irregular shape of the bodies themselves. This paper employs various quantitative metrics to characterize the performance and relative effectiveness of various types of mapping orbits including terminator, quasi-terminator, hovering, ping pong, and conic-like trajectories. Metrics of interest include surface area coverage, lighting conditions, and the variety of viewing angles achieved. The metrics discussed in this investigation are intended to enable mission designers and project stakeholders to better characterize candidate mapping orbits during preliminary mission formulation activities. The goal of this investigation is to understand the trade space associated with carrying out remote sensing campaigns at small primitive bodies in the context of a robotic space mission. Specifically, this study seeks to understand the surface viewing geometries, ranges, etc. that are available from several commonly proposed mapping orbits architectures

  16. Particle transport in the vicinity of divertor separatrix

    Science.gov (United States)

    Nishimura, Y.; Lyu, J. C.

    2017-10-01

    Guiding center orbit following code in a tokamak edge geometry is developed which connects straight field line coordinate system (away from the separatrix) and Cartesian coordinate system (in the vicinity of the separatrix) smoothly in the equation of motion. In the presence of magnetic stochasticity charged particles in the closed magnetic field line region can be transported to the open field line region and then hit the divertor plates within several toroidal transits. Our preliminary studies suggest finite heat load both on the inner and outer divertor plates. Energy spectrum of particles reaching the plates (which differs from that of the bulk plasma) as function of imposed magnetic stochasticity, is analyzed. This work is supported by Taiwan MOST 104-2112-M-006-019.

  17. DNA methylation program during development.

    Science.gov (United States)

    Zhou, Feng C

    2012-12-01

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

  18. Transformation of o-xylene to o-methyl benzoic acid by a denitrifying enrichment culture using toluene as the primary substrate.

    Science.gov (United States)

    Jørgensen, C; Nielsen, B; Jensen, B K; Mortensen, E

    1995-06-01

    A highly enriched denitrifying mixed culture transformed o-xylene co-metabolically along with toluene by methyl group oxidation. o-Methyl benzaldehyde and o-methyl benzoic acid accumulated transiently as metabolic products of o-xylene transformation. Transformation of o-methyl benzyl alcohol and o-methyl benzaldehyde occurred independently of toluene degradation and resulted in the formation of a compound coeluting with o-methyl benzoic acid on a gas chromatograph. The co-metabolic relationship between toluene and o-xylene could be attributed to a mechanism linked to the initial oxidation of the methyl group.

  19. Variation in DNA methylation of the oxytocin receptor gene predicts children's resilience to prenatal stress.

    Science.gov (United States)

    Milaniak, Izabela; Cecil, Charlotte A M; Barker, Edward D; Relton, Caroline L; Gaunt, Tom R; McArdle, Wendy; Jaffee, Sara R

    2017-12-01

    Emerging research in epigenetics has shown that there is variability in how environmental exposures "get under the skin" through mechanisms like DNA methylation to influence gene expression that may lead to differential adaptations to stress. This is the first study to examine prospectively the relationship between DNA methylation at birth and resilience to prenatal environmental stressors in several domains (conduct, hyperactivity, emotional problems, and global symptomatology) in middle childhood. We focused on DNA methylation in the vicinity of the oxytocin receptor (OXTR) gene as it has been previously associated with impairments in social-cognitive processes that may underlie a wide range of childhood psychopathology. Participants were 91 youth exposed to pre- and postnatal adversity with established conduct problem trajectories drawn from the Avon Longitudinal Study of Parents and Children. Consistent with our hypothesis, OXTR DNA methylation was predictive of resilience in the conduct problems domain in middle childhood. DNA methylation profiles did not predict resilience in domains of emotional, hyperactivity, and global symptomatology, suggesting a potential role for OXTR in the development of conduct problems in particular. However, individuals who were resilient to conduct problems were also broadly resilient across multiple domains. Therefore, future research should elucidate the biological pathways between OXTR DNA methylation and gene expression and its relation to impairments in social behavior.

  20. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Pedersen, Marianne Terndrup

    2011-01-01

    a role in transcriptional repression. TET1 binds a significant proportion of Polycomb group target genes. Furthermore, TET1 associates and colocalizes with the SIN3A co-repressor complex. We propose that TET1 fine-tunes transcription, opposes aberrant DNA methylation at CpG-rich sequences and thereby...... contributes to the regulation of DNA methylation fidelity.......Enzymes catalysing the methylation of the 5-position of cytosine (mC) have essential roles in regulating gene expression and maintaining cellular identity. Recently, TET1 was found to hydroxylate the methyl group of mC, converting it to 5-hydroxymethyl cytosine (hmC). Here we show that TET1 binds...

  1. Comparative analysis of rubber seed methyl ester with other methyl ...

    African Journals Online (AJOL)

    The important properties of biodiesel such as specific gravity, flash point, cloud point and pour point were determined and compared with that of diesel. Other properties such as kinematic viscosity sulphur content, Aniline point and Acid value of rubber seed methyl ester were deduced and compared with other methyl esters.

  2. Penggunaan Biosorben Biji Pepaya Sebagai Penjerap Zat Warna Methyl Orange, Methyl Violet dan Methyl Red

    OpenAIRE

    Ranita, Lara Indra

    2017-01-01

    120405009 Biosorben adalah bahan yang memiliki banyak pori dimana proses adsorpsi berlangsung pada dinding pori atau terjadi pada daerah tertentu di dalam partikel tersebut. Biosorben dari biji pepaya digunakan untuk menyerap zat warna tekstil, yaitu methyl orange, methyl violet dan methyl red. Tujuan dari penelitian ini adalah mempelajari pengaruh waktu adsorpsi dan massa biosorben terhadap kemampuan daya serap zat warna. Penelitian ini menggunakan biji pepaya sebagai ba...

  3. [Effect of Baihu Guizhi decoction on characteristic methylation genes expression of pyretic arthralgia rat model].

    Science.gov (United States)

    Chen, Huan; Ju, Shao-Hua; Wei, Jiang-Ping; Fu, Wen-Jun; Zheng, Hang; Xu, Shi-Jun

    2017-01-01

    To investigate the characteristic methylation genes of pyretic arthralgia model in hot and dampness environment and the regulation effect of Baihu Guizhi decoction on this characteristic methylation genes. Plantar injection of CFA was used in hot and dampness environment to induce the pyretic arthralgia rat models. From 15th day after modeling, Baihu Guizhi decoction was given for 30 days. Foot volume was detected every 4 days after modeling, and HE staining was used to detect the histopathology of all rats' ankle joint at day 45.MeDIP-Seq sequencing method was used to detect the methylation level of knee joint synovial, and the method of difference sets was used to screen the characteristic methylation genesinpyretic arthralgia models.The contents of IL-1β, IL-17, TNF-α, EGF, IL-12p70, IL-4, IL-6 and IFN-γ in serum were measured by using suspension chips. The mRNA expression level of characteristic methylation genes was measured by qRT-PCR. The results suggested that as compared with adjuvant arthritis rat models(AA), the foot swelling and histopathology inpyretic arthralgia models (PA) were only slightly increased. As compared with normal group (NG), the wholegenome CpG island in both AA and PA groups was kept in a lower methylation state, furthermore, the methylation level was lowest in PA group; with 705 difference methylation genes in AA group and 2 418 difference methylation genes in PA group. As compared with AA, there were 1 287 difference methylation genes, including 974 down-regulated methylation genesand 313 up-regulated methylation genes. This difference methylation genes were mostly enriched in 32 KEGG pathways. Moreover, there were 52 characteristic methylation genes of PA models in promoter region, including 36 down-regulatedmethylation genes and 16 up-regulatedmethylation genes. After drug intervention, Baihu Guizhi decoction improved the foot swelling and pathological injury in PA models, significantly decreased the levels of IL-1β, TNF-α, EGF

  4. MethylRAD: a simple and scalable method for genome-wide DNA methylation profiling using methylation-dependent restriction enzymes.

    Science.gov (United States)

    Wang, Shi; Lv, Jia; Zhang, Lingling; Dou, Jinzhuang; Sun, Yan; Li, Xue; Fu, Xiaoteng; Dou, Huaiqian; Mao, Junxia; Hu, Xiaoli; Bao, Zhenmin

    2015-11-01

    Characterization of dynamic DNA methylomes in diverse phylogenetic groups has attracted growing interest for a better understanding of the evolution of DNA methylation as well as its function and biological significance in eukaryotes. Sequencing-based methods are promising in fulfilling this task. However, none of the currently available methods offers the 'perfect solution', and they have limitations that prevent their application in the less studied phylogenetic groups. The recently discovered Mrr-like enzymes are appealing for new method development, owing to their ability to collect 32-bp methylated DNA fragments from the whole genome for high-throughput sequencing. Here, we have developed a simple and scalable DNA methylation profiling method (called MethylRAD) using Mrr-like enzymes. MethylRAD allows for de novo (reference-free) methylation analysis, extremely low DNA input (e.g. 1 ng) and adjustment of tag density, all of which are still unattainable for most widely used methylation profiling methods such as RRBS and MeDIP. We performed extensive analyses to validate the power and accuracy of our method in both model (plant Arabidopsis thaliana) and non-model (scallop Patinopecten yessoensis) species. We further demonstrated its great utility in identification of a gene (LPCAT1) that is potentially crucial for carotenoid accumulation in scallop adductor muscle. MethylRAD has several advantages over existing tools and fills a void in the current epigenomic toolkit by providing a universal tool that can be used for diverse research applications, e.g. from model to non-model species, from ordinary to precious samples and from small to large genomes, but at an affordable cost. © 2015 The Authors.

  5. DNA methylation as a biomarker for preeclampsia.

    Science.gov (United States)

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

    2014-10-01

    Preeclampsia contributes significantly to pregnancy-associated morbidity and mortality as well as future risk of cardiovascular disease in mother and offspring, and preeclampsia in offspring. The lack of reliable methods for early detection limits the opportunities for prevention, diagnosis, and timely treatment. The purpose of this study was to explore distinct DNA methylation patterns associated with preeclampsia in both maternal cells and fetal-derived tissue that represent potential biomarkers to predict future preeclampsia and inheritance in children. A convenience sample of nulliparous women (N = 55) in the first trimester of pregnancy was recruited for this prospective study. Genome-wide DNA methylation was quantified in first-trimester maternal peripheral white blood cells and placental chorionic tissue from normotensive women and those with preeclampsia (n = 6/group). Late-onset preeclampsia developed in 12.7% of women. Significant differences in DNA methylation were identified in 207 individual linked cytosine and guanine (CpG) sites in maternal white blood cells collected in the first trimester (132 sites with gain and 75 sites with loss of methylation), which were common to approximately 75% of the differentially methylated CpG sites identified in chorionic tissue of fetal origin. This study is the first to identify maternal epigenetic targets and common targets in fetal-derived tissue that represent putative biomarkers for early detection and heritable risk of preeclampsia. Findings may pave the way for diagnosis of preeclampsia prior to its clinical presentation and acute damaging effects, and the potential for prevention of the detrimental long-term sequelae. © The Author(s) 2013.

  6. DNA Methylation as a Biomarker for Preeclampsia

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-10-01

    Background: Preeclampsia contributes significantly to pregnancy-associated morbidity and mortality as well as future risk of cardiovascular disease in mother and offspring, and preeclampsia in offspring. The lack of reliable methods for early detection limits the opportunities for prevention, diagnosis, and timely treatment. Purpose: The purpose of this study was to explore distinct DNA methylation patterns associated with preeclampsia in both maternal cells and fetal-derived tissue that represent potential biomarkers to predict future preeclampsia and inheritance in children. Method: A convenience sample of nulliparous women (N = 55) in the first trimester of pregnancy was recruited for this prospective study. Genome-wide DNA methylation was quantified in first-trimester maternal peripheral white blood cells and placental chorionic tissue from normotensive women and those with preeclampsia (n = 6/group). Results: Late-onset preeclampsia developed in 12.7% of women. Significant differences in DNA methylation were identified in 207 individual linked cytosine and guanine (CpG) sites in maternal white blood cells collected in the first trimester (132 sites with gain and 75 sites with loss of methylation), which were common to approximately 75% of the differentially methylated CpG sites identified in chorionic tissue of fetal origin. Conclusion: This study is the first to identify maternal epigenetic targets and common targets in fetal-derived tissue that represent putative biomarkers for early detection and heritable risk of preeclampsia. Findings may pave the way for diagnosis of preeclampsia prior to its clinical presentation and acute damaging effects, and the potential for prevention of the detrimental long-term sequelae.

  7. 33 CFR 110.190 - Tortugas Harbor, in vicinity of Garden Key, Dry Tortugas, Fla.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Tortugas Harbor, in vicinity of Garden Key, Dry Tortugas, Fla. 110.190 Section 110.190 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.190 Tortugas Harbor, in vicinity of Garden Key, Dry Tortugas,...

  8. Photodissociation of methyl formate: Conical intersections, roaming and triple fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Lin, King-Chuen; Tsai, Po-Yu [Department of Chemistry, National Taiwan University, Taipei 106, Taiwan (China); Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan (China); Chao, Meng-Hsuan [Department of Chemistry, National Taiwan University, Taipei 106, Taiwan (China); Kasai, Toshio [Department of Chemistry, National Taiwan University, Taipei 106, Taiwan (China); Graduate School of Science, Department of Chemistry, Osaka University, Toyonaka, 560-0043 Osaka (Japan); Lombardi, Andrea [Dipartimento di Chimica, Università di Perugia, 06123 Perugia (Italy); Palazzetti, Federico [Scuola Normale Superiore, 56126 Pisa (Italy); Aquilanti, Vincenzo [Dipartimento di Chimica, Università di Perugia, 06123 Perugia (Italy); Consiglio Nazionale delle Ricerche, Istituto di Struttura della Materia, 00016 Roma (Italy)

    2015-12-31

    The photodissociation channels of methyl formate have been extensively investigated by two different advanced experimental techniques, ion imaging and Fourier-Transform-Infrared emission spectroscopy, combined with quantum chemical calculations and molecular dynamics simulations. Our aim is to characterize the role of alternative routes to the conventional transition-state mediated pathway: the roaming and the triple fragmentation processes. The photolysis experiments, carried out at a range of laser wavelengths in the vicinity of the triple fragmentation threshold, beside the simulation of large bunches of classical trajectories with different initial conditions, have shown that both mechanisms share a common path that involves a conical intersection during the relaxation process from the electronic excited state S{sub 1} to the ground state S{sub 0}.

  9. Adsorption of egg albumin onto methylated yeast biomass.

    Science.gov (United States)

    Seki, Hideshi; Suzuki, Akira; Maruyama, Hideo

    2004-02-15

    A new biosorbent, methylated yeast (MeYE), was prepared for the adsorptive separation of proteins from aqueous solutions. Yeast was methylated in a 0.1 M HCl methyl alcohol solution at room temperature. About 80% of the carboxylic groups of yeast could be methylated within 9 h. The adsorption of egg albumin onto MeYE was studied to evaluate the protein adsorption ability of MeYE. At near neutral pH, egg albumin was scarcely adsorbed onto unmethylated yeast and the adsorbed amount of egg albumin increased with increasing methylation degree. The amount of egg albumin adsorbed onto MeYE increased with increasing pH from 4 to 7 and steeply decreased above pH 7. The Langmuir isotherm was applied to determine the apparent adsorption constant and the saturated adsorbed amount of egg albumin on MeYE. Both the apparent adsorption constant and the saturated adsorbed amount increased with the degree of methylation. The saturated adsorbed amount of egg albumin onto MeYE having methylation degree 77% was 8.41 x 10(-6) mol g(-1) or 0.378 gg(-1) at near neutral pH.

  10. Recent patents of DNA methylation biomarkers in gastrointestinal oncology.

    Science.gov (United States)

    Corvalan, Alejandro H; Maturana, Maria J

    2010-11-01

    Gastrointestinal malignancies are among the most common malignancies worldwide. Advances in technology and treatment have improved diagnosis and monitoring of these tumors. As a consequence, identification of new biomarkers that can be applied at different levels of disease is urgently needed. DNA methylation is a process in which cytosines acquire a methyl group in 5' position only if they are followed by a guanine. An emerging catalog of specific genes inactivated by DNA methylation in gastrointestinal tumors has been established. In this review we will give a brief overview of the main sources of DNA used to investigate methylation biomarkers and several related patents. One of these is related to multiple genes that predict the risk of development of esophageal adenocarcinoma. Another evaluated methylation status of 24 genes to find one frequently methylated in primary tumors as well as plasma samples from gastric cancer patients. Others patented the epigenetic silencing of miR-342 as a promissory biomarker for colorectal carcinoma. Thus the new field of DNA methylation biomarkers holds the promise of better methods for screening, early detection, disease progression and outcome predictor of therapy response in gastrointestinal oncology.

  11. Scintillation proximity assay for measurement of RNA methylation.

    Science.gov (United States)

    Baker, Matthew R; Zarubica, Tamara; Wright, H Tonie; Rife, Jason P

    2009-03-01

    Methylation of RNA by methyltransferases is a phylogenetically ubiquitous post-transcriptional modification that occurs most extensively in transfer RNA (tRNA) and ribosomal RNA (rRNA). Biochemical characterization of RNA methyltransferase enzymes and their methylated product RNA or RNA-protein complexes is usually done by measuring the incorporation of radiolabeled methyl groups into the product over time. This has traditionally required the separation of radiolabeled product from radiolabeled methyl donor through a filter binding assay. We have adapted and optimized a scintillation proximity assay (SPA) to replace the more costly, wasteful and cumbersome filter binding assay and demonstrate its utility in studies of three distinct methyltransferases, RmtA, KsgA and ErmC'. In vitro, RmtA and KsgA methylate different bases in 16S rRNA in 30S ribosomal particles, while ErmC' most efficiently methylates protein-depleted or protein-free 23S rRNA. This assay does not utilize engineered affinity tags that are often required in SPA, and is capable of detecting either radiolabeled RNA or RNA-protein complex. We show that this method is suitable for quantitating extent of RNA methylation or active RNA methyltransferase, and for testing RNA-methyltransferase inhibitors. This assay can be carried out with techniques routinely used in a typical biochemistry laboratory or could be easily adapted for a high throughput screening format.

  12. Methods of DNA methylation detection

    Science.gov (United States)

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

    2010-01-01

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

  13. DNA methylation in metabolic disorders

    DEFF Research Database (Denmark)

    Barres, Romain; Zierath, Juleen R

    2011-01-01

    DNA methylation is a major epigenetic modification that controls gene expression in physiologic and pathologic states. Metabolic diseases such as diabetes and obesity are associated with profound alterations in gene expression that are caused by genetic and environmental factors. Recent reports...... have provided evidence that environmental factors at all ages could modify DNA methylation in somatic tissues, which suggests that DNA methylation is a more dynamic process than previously appreciated. Because of the importance of lifestyle factors in metabolic disorders, DNA methylation provides...... a mechanism by which environmental factors, including diet and exercise, can modify genetic predisposition to disease. This article considers the current evidence that defines a role for DNA methylation in metabolic disorders....

  14. DNA Methylation in Schizophrenia.

    Science.gov (United States)

    Pries, Lotta-Katrin; Gülöksüz, Sinan; Kenis, Gunter

    2017-01-01

    Schizophrenia is a highly heritable psychiatric condition that displays a complex phenotype. A multitude of genetic susceptibility loci have now been identified, but these fail to explain the high heritability estimates of schizophrenia. In addition, epidemiologically relevant environmental risk factors for schizophrenia may lead to permanent changes in brain function. In conjunction with genetic liability, these environmental risk factors-likely through epigenetic mechanisms-may give rise to schizophrenia, a clinical syndrome characterized by florid psychotic symptoms and moderate to severe cognitive impairment. These pathophysiological features point to the involvement of epigenetic processes. Recently, a wave of studies examining aberrant DNA modifications in schizophrenia was published. This chapter aims to comprehensively review the current findings, from both candidate gene studies and genome-wide approaches, on DNA methylation changes in schizophrenia.

  15. DNA Methylation in Thyroid Tumorigenesis

    Energy Technology Data Exchange (ETDEWEB)

    Stephen, Josena K., E-mail: jstephe2@hfhs.org [Department of Otolaryngology/Head and Neck Surgery, Henry Ford Hospital, Detroit, MI 48202 (United States); Chitale, Dhananjay [Department of Pathology, Henry Ford Hospital, Detroit, MI 48202 (United States); Narra, Vinod [Essex Surgical Associates, PC, Beverly, MA 01915 (United States); Chen, Kang Mei; Sawhney, Raja; Worsham, Maria J. [Department of Otolaryngology/Head and Neck Surgery, Henry Ford Hospital, Detroit, MI 48202 (United States)

    2011-03-29

    Thyroid cancer is the most common endocrine cancer with 1,690 deaths each year. There are four main types of which the papillary and follicular types together account for >90% followed by medullary cancers with 3% to 5% and anaplastic carcinomas making up <3%. Epigenetic events of DNA hypermethylation are emerging as promising molecular targets for cancer detection. Our immediate and long term goal is to identify DNA methylation markers for early detection of thyroid cancer. This pilot study comprised of 21 patients to include 11 papillary thyroid cancers (PTC), 2 follicular thyroid cancers (FTC), 5 normal thyroid cases, and 3 hyperthyroid cases. Aberrant promoter methylation was examined in 24 tumor suppressor genes using the methylation specific multiplex ligation-dependent probe amplification (MS-MLPA) assay and in the NIS gene using methylation-specific PCR (MSP). The frequently methylated genes were CASP8 (17/21), RASSF1 (16/21) and NIS (9/21). In the normal samples, CASP8, RASSF1 and NIS were methylated in 5/5, 4/5 and 1/5 respectively. In the hyperthyroid samples, CASP8, RASSF1 and NIS were methylated in 3/3, 2/3 and 1/3 respectively. In the thyroid cancers, CASP8, RASSF1, and NIS were methylated in 9/13, 10/13, and 7/13 respectively. CASP8, RASSF1 and NIS were also methylated in concurrently present normal thyroid tissue in 3/11, 4/11 and 3/11 matched thyroid cancer cases (matched for presence of both normal thyroid tissue and thyroid cancer), respectively. Our data suggests that aberrant methylation of CASP8, RASSF1, and NIS maybe an early change in thyroid tumorigenesis regardless of cell type.

  16. Data on metals biomonitoring in the body of schoolchildren in the vicinity of a heavily industrialized site

    Directory of Open Access Journals (Sweden)

    Raheleh Kafaei

    2017-06-01

    Full Text Available This data is obtained from analyzing the concentration of metals include Al, Co, Cr, Cu, Fe, Mo, Pb, and Zn in the urine of schoolchildren in Asalouyeh city in vicinity to a heavily industrialized site and comparison with a reference city. The significance of sex groups on urine metal level was evaluated through this data. The urinary content of metals was measured by inductively coupled plasma atomic emission spectroscopy (ICP-OES. Statistical analyze of data were done by Mann–Whitney test. The herein presented date could beneficial for health assessment of gas and petrochemical companies.

  17. Protective effects of vitamins C and E against hepatotoxicity induced by methyl parathion in rats.

    Science.gov (United States)

    Uzunhisarcikli, Meltem; Kalender, Yusuf

    2011-10-01

    Male rats were given vitamins C+E, methyl parathion, or both daily via gavage for seven weeks. Body weight was decreased while liver weight increased significantly at the end of fourth and seventh weeks in the methyl parathion- and methyl parathion plus vitamin-treated groups. Serum total protein, albumin, triglyceride, low density lipoprotein-cholesterol (VLDL-cholesterol) levels decreased, and serum alkaline phosphatase (ALP), alanine aminotransferase (ALT), aspartate aminotransferase (AST), γ-glutamyl-transferase (GGT), lactate dehydrogenase (LDH), and total cholesterol levels increased significantly in the methyl parathion- and the methyl parathion plus vitamin-treated rats. There was a statistically significant difference for all biochemical parameters when the methyl parathion plus vitamin-treated group was compared with methyl parathion-treated group. In electron microscopic investigation, cytopathological alterations were observed in hepatocytes of the methyl parathion- and the methyl parathion plus vitamin-treated rats. As a result, methyl parathion-induced hepatotoxicity is reduced by vitamins C+E, but vitamins C+E did not provide complete protection. Copyright © 2011 Elsevier Inc. All rights reserved.

  18. On the role of steric clashes in methylation control of restriction endonuclease activity.

    Science.gov (United States)

    Mierzejewska, Karolina; Bochtler, Matthias; Czapinska, Honorata

    2016-01-08

    Restriction-modification systems digest non-methylated invading DNA, while protecting host DNA against the endonuclease activity by methylation. It is widely believed that the methylated DNA would not 'fit' into the binding site of the endonuclease in the productive orientation, and thus steric clashes should account for most of the protection. We test this concept statistically by grafting methyl groups in silico onto non-methylated DNA in co-crystal structures with restriction endonucleases. Clash scores are significantly higher for protective than non-protective methylation (P < 0.05% according to the Wilcoxon rank sum test). Structural data alone are sufficient to distinguish between protective and non-protective DNA methylation with 90% confidence and decision thresholds of 1.1 Å and 48 Å(3) for the most severe distance-based and cumulative volume-based clash with the protein, respectively (0.1 Å was deducted from each interatomic distance to allow for coordinate errors). The most severe clashes are more pronounced for protective methyl groups attached to the nitrogen atoms (N6-methyladenines and N4-methylcytosines) than for C5-methyl groups on cytosines. Cumulative clashes are comparable for all three types of protective methylation. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. The effect of catechol O-methylation on radical scavenging characteristics of quercetin and luteolin, a mechanistic insight

    NARCIS (Netherlands)

    Lemanska, K.; Woude, van der H.; Szymusiak, H.; Boersma, M.G.; Gliszczynska-Swiglo, A.; Rietjens, I.M.C.M.; Tyrakowska, B.

    2004-01-01

    The biological effect of flavonoids can be modulated in vivo due to metabolism. The O-methylation of the catechol group in the molecule by catechol O-methyl transferase is one of the important metabolic pathways of flavonoids. In the present study, the consequences of catechol O-methylation for the

  20. N-Methyl-N-nitroso-p-toluenesulfonamide

    Directory of Open Access Journals (Sweden)

    Kartik Rai

    2014-07-01

    Full Text Available The crystal structure of the title compound, C8H10N2O3S, displays predominant C—H...O hydrogen-bonding and π–π stacking interactions. The hydrogen bonds are between the O atoms of the sulfonyl group and H atoms on methyl groups. The π–π stacking interactions occur between adjacent aromatic rings, with a centroid–centroid distance of 3.868 (11 Å. These interactions lead to the formation of chains parallel to (101.

  1. The interplay between environmental factors and DNA methylation in psychotic disorders : Environmental orchestration of the epigenome

    NARCIS (Netherlands)

    Houtepen, LC|info:eu-repo/dai/nl/413662802

    2016-01-01

    Introduction: Environmental exposures during early- life increase the risk of developing a psychotic disorder, but it remains unclear how early life events can have such persistent later life consequences. DNA methylation is the addition of a methyl group to a DNA base and is part of a group of

  2. DNA methylation pathways and their crosstalk with histone methylation

    Science.gov (United States)

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

    2015-01-01

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

  3. Distinct high-profile methylated genes in colorectal cancer.

    Directory of Open Access Journals (Sweden)

    Pooneh Mokarram

    Full Text Available BACKGROUND: Mutations and promoters' methylation of a set of candidate cancer genes (CAN genes are associated with progression of colorectal cancer (CRC. We hypothesized that these genes' promoters are inactivated through epigenetic silencing and may show a different profile in high-risk populations. We investigated the status of CAN gene methylation and CHD5 protein expression in African American CRC tissue microarrays (TMA using immunohistochemical staining. METHODOLOGY/PRINCIPAL FINDINGS: The promoter methylation status of the CAN genes was studied by methylation-specific PCR (MSP in 51 Iranians (a white population and 51 African Americans (AA. Microsatellite instability (MSI was analyzed as well. The differential frequency of methylation for each gene was tested by chi-square analysis between the two groups based on matched age and sex. CHD5 protein expression was evaluated in moderate to well differentiated and poorly differentiated carcinomas compared to matched normal tissue using TMA. In addition, the correlation between these epigenetic biomarkers and various clinicopathological factors, including, age, location, and stage of the disease were analyzed. Seventy-seven and 34% of tumors were distal in Iranian and African American patients, respectively. In both populations, the percentage of methylation was >65% for SYNE1, MMP2, APC2, GPNMB, EVL, PTPRD, and STARD8, whereas methylation was <50% for LGR6, RET, CD109, and RNF. The difference in methylation between the two populations was statistically significant for CHD5, ICAM5 and GPNMB. Thirty-one percent AA tumors showed MSI-H, compared to 28% in Iranians. CONCLUSIONS/SIGNIFICANCE: A significantly higher methylation rate was found for GPNMB, ICAM5, and CHD5 genes in AA patients compared to Iranians. These genes might play a role in the high incidence and aggressiveness of CRC in the AA population. The hypermethylation of the CAN genes can be considered as a marker of colon carcinogenesis.

  4. DNA methylation: hemodialysis versus hemodiafiltration.

    Science.gov (United States)

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

    2015-04-01

    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 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. © 2014 The Authors. Therapeutic Apheresis and Dialysis © 2014 International Society for Apheresis.

  5. Evidence for widespread genomic methylation in the migratory locust, Locusta migratoria (Orthoptera: Acrididae.

    Directory of Open Access Journals (Sweden)

    Katie L Robinson

    Full Text Available The importance of DNA methylation in mammalian and plant systems is well established. In recent years there has been renewed interest in DNA methylation in insects. Accumulating evidence, both from mammals and insects, points towards an emerging role for DNA methylation in the regulation of phenotypic plasticity. The migratory locust (Locusta migratoria is a model organism for the study of phenotypic plasticity. Despite this, there is little information available about the degree to which the genome is methylated in this species and genes encoding methylation machinery have not been previously identified. We therefore undertook an initial investigation to establish the presence of a functional DNA methylation system in L. migratoria. We found that the migratory locust possesses genes that putatively encode methylation machinery (DNA methyltransferases and a methyl-binding domain protein and exhibits genomic methylation, some of which appears to be localised to repetitive regions of the genome. We have also identified a distinct group of genes within the L. migratoria genome that appear to have been historically methylated and show some possible functional differentiation. These results will facilitate more detailed research into the functional significance of DNA methylation in locusts.

  6. Comprehensive analysis of preeclampsia-associated DNA methylation in the placenta.

    Directory of Open Access Journals (Sweden)

    Tianjiao Chu

    Full Text Available A small number of recent reports have suggested that altered placental DNA methylation may be associated with early onset preeclampsia. It is important that further studies be undertaken to confirm and develop these findings. We therefore undertook a systematic analysis of DNA methylation patterns in placental tissue from 24 women with preeclampsia and 24 with uncomplicated pregnancy outcome.We analyzed the DNA methylation status of approximately 27,000 CpG sites in placental tissues in a massively parallel fashion using an oligonucleotide microarray. Follow up analysis of DNA methylation at specific CpG loci was performed using the Epityper MassArray approach and high-throughput bisulfite sequencing.Preeclampsia-specific DNA methylation changes were identified in placental tissue samples irrespective of gestational age of delivery. In addition, we identified a group of CpG sites within specific gene sequences that were only altered in early onset-preeclampsia (EOPET although these DNA methylation changes did not correlate with altered mRNA transcription. We found evidence that fetal gender influences DNA methylation at autosomal loci but could find no clear association between DNA methylation and gestational age.Preeclampsia is associated with altered placental DNA methylation. Fetal gender should be carefully considered during the design of future studies in which placental DNA is analyzed at the level of DNA methylation. Further large-scale analyses of preeclampsia-associated DNA methylation are necessary.

  7. Antichaperone activity and heme degradation effect of methyl tert-butyl ether (MTBE) on normal and diabetic hemoglobins.

    Science.gov (United States)

    Najdegerami, Ismaeil Hossein; Maghami, Parvaneh; Sheikh-Hasani, Vahid; Hosseinzadeh, Ghader; Sheibani, Nader; Moosavi-Movahedi, Ali A

    2017-05-01

    Because of the extensive use of methyl tert-butyl ether (MTBE) as an additive to increase the octane quality of gasoline, the environmental pollution by this compound has increased in recent decades. Environmental release of MTBE may lead to its entry to the blood stream through inhalation or drinking of contaminated water, and its interactions with biological molecules such as proteins. The present study was proposed to comparatively investigate the interactions of MTBE with hemoglobin (Hb) from diabetic and nondiabetic individuals using various spectroscopic methods including UV-visible, fluorescence, chemiluminescence, and circular dichroism. These results demonstrated the effects of MTBE on heme degradation of Hb and the reaction of these degradation products with water generating reactive oxygen species. Interaction of Hb with MTBE enhanced its aggregation rate and decreased lag time, indicating the antichaperone activity of MTBE upon interaction with Hb. Furthermore, the diabetic Hb showed more severe effects of MTBE, including heme degradation, reactive oxygen species production, unfolding, and antichaperone behavior than the nondiabetic Hb. The results from molecular docking suggested that the special interaction site of MTBE in the vicinity of Hb heme group is responsible for heme degradation. Copyright © 2016 John Wiley & Sons, Ltd.

  8. Selective hydrodeoxygenation of cyclic vicinal diols to cyclic alcohols over tungsten oxide-palladium catalysts.

    Science.gov (United States)

    Amada, Yasushi; Ota, Nobuhiko; Tamura, Masazumi; Nakagawa, Yoshinao; Tomishige, Keiichi

    2014-08-01

    Hydrodeoxygenation of cyclic vicinal diols such as 1,4-anhydroerythritol was conducted over catalysts containing both a noble metal and a group 5-7 transition-metal oxide. The combination of Pd and WOx allowed the removal of one of the two OH groups selectively. 3-Hydroxytetrahydrofuran was obtained from 1,4-anhydroerythritol in 72 and 74% yield over WOx -Pd/C and WOx -Pd/ZrO2 , respectively. The WOx -Pd/ZrO2 catalyst was reusable without significant loss of activity if the catalyst was calcined as a method of regeneration. Characterization of WOx -Pd/C with temperature-programmed reduction, X-ray diffraction, and transmission electron microscopy/energy-dispersive X-ray spectroscopy suggested that Pd metal particles approximately 9 nm in size were formed on amorphous tungsten oxide particles. A reaction mechanism was proposed on the basis of kinetics, reaction results with tungsten oxides under an atmosphere of Ar, and density functional theory calculations. A tetravalent tungsten center (W(IV) ) was formed by reduction of WO3 with the Pd catalyst and H2 , and this center served as the reductant for partial hydrodeoxygenation. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Variations in the Intragene Methylation Profiles Hallmark Induced Pluripotency

    Science.gov (United States)

    Druzhkov, Pavel; Zolotykh, Nikolay; Meyerov, Iosif; Alsaedi, Ahmed; Shutova, Maria; Ivanchenko, Mikhail; Zaikin, Alexey

    2015-01-01

    We demonstrate the potential of differentiating embryonic and induced pluripotent stem cells by the regularized linear and decision tree machine learning classification algorithms, based on a number of intragene methylation measures. The resulting average accuracy of classification has been proven to be above 95%, which overcomes the earlier achievements. We propose a constructive and transparent method of feature selection based on classifier accuracy. Enrichment analysis reveals statistically meaningful presence of stemness group and cancer discriminating genes among the selected best classifying features. These findings stimulate the further research on the functional consequences of these differences in methylation patterns. The presented approach can be broadly used to discriminate the cells of different phenotype or in different state by their methylation profiles, identify groups of genes constituting multifeature classifiers, and assess enrichment of these groups by the sets of genes with a functionality of interest. PMID:26618180

  10. Variations in the Intragene Methylation Profiles Hallmark Induced Pluripotency

    Directory of Open Access Journals (Sweden)

    Pavel Druzhkov

    2015-01-01

    Full Text Available We demonstrate the potential of differentiating embryonic and induced pluripotent stem cells by the regularized linear and decision tree machine learning classification algorithms, based on a number of intragene methylation measures. The resulting average accuracy of classification has been proven to be above 95%, which overcomes the earlier achievements. We propose a constructive and transparent method of feature selection based on classifier accuracy. Enrichment analysis reveals statistically meaningful presence of stemness group and cancer discriminating genes among the selected best classifying features. These findings stimulate the further research on the functional consequences of these differences in methylation patterns. The presented approach can be broadly used to discriminate the cells of different phenotype or in different state by their methylation profiles, identify groups of genes constituting multifeature classifiers, and assess enrichment of these groups by the sets of genes with a functionality of interest.

  11. Managing nematodes without methyl bromide.

    Science.gov (United States)

    Zasada, Inga A; Halbrendt, John M; Kokalis-Burelle, Nancy; LaMondia, James; McKenry, Michael V; Noling, Joe W

    2010-01-01

    Methyl bromide is an effective pre-plant soil fumigant used to control nematodes in many high-input, high-value crops in the United States, including vegetables, nursery plants, ornamentals, tree fruits, strawberries, and grapes. Because methyl bromide has provided a reliable return on investment for nematode control, many of these commodities have standardized their production practices based on the use of this chemical and will be negatively impacted if effective and economical alternatives are not identified. Alternative control measures based on other chemicals, genetic resistance, and cultural practices require a greater knowledge of nematode biology to achieve satisfactory results. Here, we provide an overview of nematode management practices that we believe will be relied upon heavily in U.S. high-value crop production systems in a world without methyl bromide. Included are case studies of U.S. high-value crop production systems to demonstrate how nematode management practices other than methyl bromide may be incorporated.

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

    Science.gov (United States)

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

    2013-12-01

    An europium β-diketonate complex with a dipyrazolyltriazine derivative ligand, Eu(TTA)3DPBT, has been incorporated into poly(methyl methacryate) (PMMA). The influence of temperature on its luminescence properties has been investigated. The fluorescence emission spectra and luminescence lifetimes showed temperature sensitivity. The analysis of the relative intensity ratio (R) of (5)D0 → (7)F2 to (5)D0 → (7)F1 transition and Judd-Ofelt experimental intensity parameters Ω2 indicated that the local structure and asymmetry in the vicinity of europium ions show no obvious change when the temperature is increased. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. Methylated genes as new cancer biomarkers

    DEFF Research Database (Denmark)

    Brunner, Nils; Duffy, M.J; Napieralski, R.

    2009-01-01

    that measurement of the methylation status of the promoter regions of specific genes can aid early detection of cancer, determine prognosis and predict therapy responses. Promising DNA methylation biomarkers include the use of methylated GSTP1 for aiding the early diagnosis of prostate cancer, methylated PITX2...

  14. DNA methylation analysis in human cancer

    OpenAIRE

    O'Sullivan, Eileen; Goggins, Michael

    2013-01-01

    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.

  15. Cigarette smoking and DNA methylation

    Directory of Open Access Journals (Sweden)

    Ken W.K Lee

    2013-07-01

    Full Text Available DNA methylation is the most studied epigenetic modification, capable of controlling gene expression in the contexts of normal traits or diseases. It is highly dynamic during early embryogenesis and remains relatively stable throughout life, and such patterns are intricately related to human development. DNA methylation is a quantitative trait determined by a complex interplay of genetic and environmental factors. Genetic variants at a specific locus can influence both regional and distant DNA methylation. The environment can have varying effects on DNA methylation depending on when the exposure occurs, such as during prenatal life or during adulthood. In particular, cigarette smoking in the context of both current smoking and prenatal exposure is a strong modifier of DNA methylation. Epigenome-wide association studies have uncovered candidate genes associated with cigarette smoking that have biologically relevant functions in the etiology of smoking-related diseases. As such, DNA methylation is a potential mechanistic link between current smoking and cancer, as well as prenatal cigarette-smoke exposure and the development of adult chronic diseases.

  16. Construction of Differential-Methylation Subtractive Library

    Directory of Open Access Journals (Sweden)

    Wei Hu

    2014-01-01

    Full Text Available Stress-induced ROS changes DNA methylation patterns. A protocol combining methylation-sensitive restriction endonuclease (MS-RE digestion with suppression subtractive hybridization (SSH to construct the differential-methylation subtractive library was developed for finding genes regulated by methylation mechanism under cold stress. The total efficiency of target fragment detection was 74.64%. DNA methylation analysis demonstrated the methylation status of target fragments changed after low temperature or DNA methyltransferase inhibitor treatment. Transcription level analysis indicated that demethylation of DNA promotes gene expression level. The results proved that our protocol was reliable and efficient to obtain gene fragments in differential-methylation status.

  17. To What Extent Does DNA Methylation Affect Phenotypic Variation in Cattle?

    Directory of Open Access Journals (Sweden)

    Stephanie McKAY

    2015-07-01

    Full Text Available DNA methylation is an environmentally influenced epigenetic modification that regulates gene transcription and has the potential to influence variation in economically important phenotypes in agricultural species. We have utilized a novel approach to evaluate the relationship between genetic and epigenetic variation and downstream phenotypes. To begin with, we have integrated RNA-Seq and methyl binding domain sequencing (MBD-Seq data in order to determine the extent to which DNA methylation affects phenotypic variation in economically important traits of cattle. MBD-Seq is a technique that involves the sample enrichment of methylated genomic regions followed by their next-generation sequencing. This study utilized Illumina next generation sequencing technology to perform both RNA-Seq and MBD-Seq. NextGENe software (SoftGenetics, State College, PA was employed for quality trimming and aligning the sequence reads to the UMD3.1 bovine reference genome, generating counts of matched reads and methylated peak identification. Subsequently, we identified and quantified genome-wide methylated regions and characterized the extent of differential methylation and differential expression between two groups of animals with extreme phenotypes. The program edgeR from the R software package (version 3.0.1 was employed for identifying differentially methylated regions and regions of differential expression. Finally, Partial Correlation with Information Theory (PCIT was performed to identify transcripts and methylation events that exhibit differential hubbing. A differential hub is defined as a gene network hub that is more highly connected in one treatment group than the other. This analysis produced every possible pair-wise interaction that subsequently enabled us to look at network interactions of how methylation affects expression. (co-expression, co-methylation, methylation x expression. Genomic regions of interest derived from this analysis were then aligned

  18. A photochemical source of methyl chloride in saline waters.

    Science.gov (United States)

    Moore, Robert M

    2008-03-15

    It is shown experimentallythatthe methoxy group in simple lignin-like molecules can be the source of the methyl group in CH3Cl produced by a photochemical reaction in an aqueous solution of chloride. Terrestrially derived colored dissolved organic matter (CDOM) in river water also yields CH3Cl through a photochemical process in a chloride solution. CDOM extracted from subsurface ocean waters showed some ability to enhance photochemical production of CH3Cl while CDOM from surface water showed no effect. Reactions of the kind described in this paper may be contributors to the marine source of methyl chloride and possibly other alkyl halides.

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

    Science.gov (United States)

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

    2015-05-18

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

  20. BackscatterA [USGS SWATH]--Monterey Canyon and Vicinity, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for the acoustic-backscatter map of Monterey Canyon and Vicinity map area, California. Backscatter data are provided as separate...

  1. BackscatterD [CSUMB Swath]--Monterey Canyon and Vicinity, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for the acoustic-backscatter map of Monterey Canyon and Vicinity map area, California. Backscatter data are provided as separate...

  2. Digital Geologic Map of Rocky Mountain National Park and Vicinity, Colorado (NPS, GRD, GRE, ROMO)

    Data.gov (United States)

    National Park Service, Department of the Interior — The Digital Geologic Map of Rocky Mountain National Park and Vicinity, Coloradois comprised of GIS data layers, two ancillary GIS tables, a Windows Help File with...

  3. Geology and geomorphology--Drakes Bay and Vicinity Bay Map Area, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for the geologic and geomorphic map of the Drakes Bay and Vicinity map area, California. The polygon shapefile is included in...

  4. Basalt microlapilli in deep sea sediments of Indian Ocean in the vicinity of Vityaz fracture zone

    Digital Repository Service at National Institute of Oceanography (India)

    Nath, B.N.; Iyer, S.D.

    Two cores recovered from the flanks of Mid-India oceanic ridge in the vicinity of Vityaz fracture zone consist of discrete pyroclastic layers at various depths. These layers are composed of coarse-grained, angular basaltic microlapilli in which...

  5. Digital Geologic Map of Great Basin National Park and Vicinity, Nevada (NPS, GRD, GRE, GRBA)

    Data.gov (United States)

    National Park Service, Department of the Interior — The Digital Geologic Map of Great Basin National Park and Vicinity, Nevada is composed of GIS data layers, two ancillary GIS tables, a Windows Help File with...

  6. Geology and geomorphology--Monterey Canyon and Vicinity Map Area, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for the geologic and geomorphic map of Monterey Canyon and Vicinity, California. The vector data file is included in...

  7. Life in wind turbines vicinity, effects on health – a review

    Directory of Open Access Journals (Sweden)

    Krystyna Pawlas

    2012-12-01

    Full Text Available The paper presents a short review of scientific papers , and other sources concerning health effects of exposure to noise, infrasounds, electromagnetic radiation and mechanical hazards induced in dwellers living in vicinity of wind farm.

  8. Allele-specific, age-dependent and BMI-associated DNA methylation of human MCHR1.

    Directory of Open Access Journals (Sweden)

    Stefanie Stepanow

    Full Text Available BACKGROUND: Melanin-concentrating hormone receptor 1 (MCHR1 plays a significant role in regulation of energy balance, food intake, physical activity and body weight in humans and rodents. Several association studies for human obesity showed contrary results concerning the SNPs rs133072 (G/A and rs133073 (T/C, which localize to the first exon of MCHR1. The variations constitute two main haplotypes (GT, AC. Both SNPs affect CpG dinucleotides, whereby each haplotype contains a potential methylation site at one of the two SNP positions. In addition, 15 CpGs in close vicinity of these SNPs constitute a weak CpG island. Here, we studied whether DNA methylation in this sequence context may contribute to population- and age-specific effects of MCHR1 alleles in obesity. PRINCIPAL FINDINGS: We analyzed DNA methylation of a 315 bp region of MCHR1 encompassing rs133072 and rs133073 and the CpG island in blood samples of 49 individuals by bisulfite sequencing. The AC haplotype shows a significantly higher methylation level than the GT haplotype. This allele-specific methylation is age-dependent. In young individuals (20-30 years the difference in DNA methylation between haplotypes is significant; whereas in individuals older than 60 years it is not detectable. Interestingly, the GT allele shows a decrease in methylation status with increasing BMI, whereas the methylation of the AC allele is not associated with this phenotype. Heterozygous lymphoblastoid cell lines show the same pattern of allele-specific DNA methylation. The cell line, which exhibits the highest difference in methylation levels between both haplotypes, also shows allele-specific transcription of MCHR1, which can be abolished by treatment with the DNA methylase inhibitor 5-aza-2'-deoxycytidine. CONCLUSIONS: We show that DNA methylation at MCHR1 is allele-specific, age-dependent, BMI-associated and affects transcription. Conceivably, this epigenetic regulation contributes to the age- and

  9. Selective carboxyl methylation of structurally altered calmodulins in Xenopus oocytes

    Energy Technology Data Exchange (ETDEWEB)

    Desrosiers, R.R.; Romanik, E.A.; O' Connor, C.M. (Worcester Foundation for Experimental Biology, Shrewsbury, MA (USA))

    1990-12-05

    The eucaryotic protein carboxyl methyltransferase specifically modifies atypical D-aspartyl and L-isoaspartyl residues which are generated spontaneously as proteins age. The selectivity of the enzyme for altered proteins in intact cells was explored by co-injecting Xenopus laevis oocytes with S-adenosyl-L-(methyl-3H)methionine and structurally altered calmodulins generated during a 14-day preincubation in vitro. Control experiments indicated that the oocyte protein carboxyl methyltransferase was not saturated with endogenous substrates, since protein carboxyl methylation rates could be stimulated up to 8-fold by increasing concentrations of injected calmodulin. The oocyte protein carboxyl methyltransferase showed strong selectivities for bovine brain and bacterially synthesized calmodulins which had been preincubated in the presence of 1 mM EDTA relative to calmodulins which had been preincubated with 1 mM CaCl2. Radioactive methyl groups were incorporated into base-stable linkages with recombinant calmodulin as well as into carboxyl methyl esters following its microinjection into oocytes. This base-stable radioactivity most likely represents the trimethylation of lysine 115, a highly conserved post-translational modification which is present in bovine and Xenopus but not in bacterially synthesized calmodulin. Endogenous oocyte calmodulin incorporates radioactivity into both carboxyl methyl esters and into base-stable linkages following microinjection of oocytes with S-adenosyl-(methyl-3H)methionine alone. The rate of oocyte calmodulin carboxyl methylation in injected oocytes is calculated to be similar to that of lysine 115 trimethylation, suggesting that the rate of calmodulin carboxyl methylation is similar to that of calmodulin synthesis. At steady state, oocyte calmodulin contains approximately 0.0002 esters/mol of protein, which turn over rapidly.

  10. Transformation of Tertiary Benzyl Alcohols into the Vicinal Halo-Substituted Derivatives Using N-Halosuccinimides

    Directory of Open Access Journals (Sweden)

    Njomza Ajvazi

    2016-10-01

    Full Text Available The efficiency of direct conversion of tertiary alcohols bearing a β-hydrogen atom to vicinal halohydrins—chlorohydrins and bromohydrins—under green reaction conditions was tested preliminarily on model tertiary benzyl alcohols. Tertiary alcohols were successfully directly halogenated to vicinal halohydrins with N-halosuccinimide in aqueous media. The efficiency of the reaction in water was significantly improved in the presence of sodium dodecyl sulphate as the surfactant.

  11. LINE-1 methylation status and its association with tetralogy of fallot in infants

    Science.gov (United States)

    2012-01-01

    Background Methylation levels of long interspersed nucleotide elements (LINE-1) are representative of genome-wide methylation status and play an important role in maintaining genomic stability and gene expression. To derive insight into the association between genome-wide methylation status and tetralogy of fallot (TOF), we compared the methylation status of LINE-1 element between TOF patients and controls. The methylation of the NKX 2–5, HAND 1, and TBX 20 promoter regions was also evaluated. Methods Genomic DNA from right ventricular tissue samples was obtained from 32 patients with TOF and 15 control subjects. Sequenom MassARRAY platform was performed to examine the methylation levels of LINE-1, NKX2-5, HAND1 and TBX20. Mann–Whitney U test was used to compare differences in methylation levels between two groups. Results The methylation level of LINE-1 was significantly lower in patients with TOF, with a median of 57.95% (interquartile range [IQR]: 56.10%–60.04%), as opposed to 59.70% in controls (IQR: 59.00%–61.30%; P = 0.0021). The highest LINE-1 methylation level was 61.3%. The risk of TOF increased in subjects with the lowest methylation levels (less than or equal to 59.0%; OR = 14.7, 95% CI: 1.8–117.7, P = 0.014) and in those with medium methylation levels (59.0%–61.3%; OR = 2.0, 95% CI: 0.3–14.2, P = 0.65). An ROC curve analysis showed a relatively high accuracy of using the LINE-1 methylation level in predicting the presence of TOF (AUC = 0.78, 95% CI: 0.65–0.91; P = 0.002). The association of the LINE-1 methylation level with TOF was only observed in males (P = 0.006) and not in females (P = 0.25). Neither age nor gender was found to be associated with the LINE-1 methylation level in patients or controls. Higher methylation levels of NKX2-5 and HAND1 and lower methylation levels of TBX20 were also observed in patients with TOF than in controls. No association was found between the methylation levels of

  12. Inhibition of radical reactions for an improved potassium tert-butoxide-promoted (11) C-methylation strategy for the synthesis of α-(11) C-methyl amino acids.

    Science.gov (United States)

    Suzuki, Chie; Kato, Koichi; Tsuji, Atsushi B; Zhang, Ming-Rong; Arano, Yasushi; Saga, Tsuneo

    2015-03-01

    α-(11) C-Methyl amino acids are useful tools for biological imaging studies. However, a robust procedure for the labeling of amino acids has not yet been established. In this study, the (11) C-methylation of Schiff-base-activated α-amino acid derivatives has been optimized for the radiosynthesis of various α-(11) C-methyl amino acids. The benzophenone imine analog of methyl 2-amino butyrate was (11) C-methylated with [(11) C]methyl iodide following its initial deprotonation with potassium tert-butoxide (KOtBu). The use of an alternative base such as tetrabutylammonium fluoride, triethylamine, and 1,8-diazabicyclo[5.4.0]undec-7-ene did not result in the (11) C-methylated product. Furthermore, the KOtBu-promoted (11) C-methylation of the Schiff-base-activated amino acid analog was enhanced by the addition of 1,2,4,5-tetramethoxybenzene or 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) and inhibited by the addition of 1,10-phenanthroline. These results suggest that inhibition of radical generation induced by KOtBu improves the α-(11) C-methylation of the Schiff-base-activated amino acids. The addition of a mixture of KOtBu and TEMPO to a solution of Schiff-base-activated amino acid ester and [(11) C]methyl iodide provided optimal results, and the tert-butyl ester and benzophenone imine groups could be readily hydrolyzed to give the desired α-(11) C-methyl amino acids with a high radiochemical conversion. This strategy could be readily applied to the synthesis of other α-(11) C-methyl amino acids. Copyright © 2015 John Wiley & Sons, Ltd.

  13. Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots

    DEFF Research Database (Denmark)

    Ingerslev, Lars R; Donkin, Ida; Fabre, Odile

    2018-01-01

    Remodeling of the sperm epigenome by lifestyle factors before conception could account for altered metabolism in the next generation offspring. Here, we hypothesized that endurance training changes the epigenome of human spermatozoa. Using small RNA (sRNA) sequencing and reduced representation...... bisulfite sequencing (RRBS), we, respectively, investigated sRNA expression and DNA methylation in pure fractions of motile spermatozoa collected from young healthy individuals before, after 6 weeks of endurance training and after 3 months without exercise. Expression of 8 PIWI interacting RNA were changed...... by exercise training. RRBS analysis revealed 330 differentially methylated regions (DMRs) after training and 303 DMRs after the detraining period, which were, in both conditions, enriched at close vicinity of transcription start sites. Ontology analysis of genes located at proximity of DMRs returned terms...

  14. Past pregnancy outcomes among women living in the vicinity of a lead smelter in Kosovo, Yugoslavia

    Energy Technology Data Exchange (ETDEWEB)

    Murphy, M.J.; Graziano, J.H.; Popovac, D.; Kline, J.K.; Mehmeti, A.; Factor-Litvak, P.; Ahmedi, G.; Shrout, P.; Rajovic, B.; Nenezic, D.U.; (Columbia Univ., New York, NY (USA))

    1990-01-01

    This analysis compares the rates of spontaneous abortion among women living in the vicinity of a lead smelter with those of women living in a town where blood lead levels were low. Data derive from the obstetric histories of both groups of women obtained while seeking prenatal care for a later pregnancy. A total of 639 women (304 exposed, 335 unexposed) had at least one previous pregnancy and lived at the same address since their first pregnancy. The geometric mean blood lead concentrations in the sample at the time of the interviews were 0.77 mumol/L in the exposed town and 0.25 mumol/L in the unexposed town. The rates of spontaneous abortions in first pregnancies were similar, with 16.4 percent of women in the exposed town and 14.0 percent in the unexposed town reporting loss. The adjusted odds ratio relating town of residence to spontaneous abortion was 1.1 (95% CI = 0.9, 1.4). This analysis represents the first systematic attempt to seek an association between environmental lead exposure and spontaneous abortion. As such, the failure to find a positive association strongly suggests that at the levels of exposure represented in our sample, such an association does not exist.

  15. The Bolgary IX settlement – a site of the Ananyino finale in the vicinity of Perm

    Directory of Open Access Journals (Sweden)

    Vasilyeva Anastasia V.

    2015-06-01

    Full Text Available The article presents materials recovered from the Bolgary IX settlement, attributed to the late Ananyino group of sites, discovered in the vicinity of the city of Perm on the left bank of the Kama River. The structures thus found were interpreted by the authors as, presumably, a dwelling (? and a cult building. The pre-Ananyino cult buildings are well known by two hillforts – Zuevy Klychi-1 on the Lower Kama and Argyzh on the Vyatka River. Small clay figurines, arrow heads, spindle whorls, small oblational cups and household ceramics were found within the cult buildings. Household ceramics are represented by some typical late Ananyino vessel forms: mainly bowls with a closed throat, sometimes with profiled pronounced neck. Some vessels have a collar on the rim. Ornamentation of the vessels includes versatile corded, combed and recessed compositions. The Bolgary IX material culture is considered in complex with simultaneous Protasy burial ground, which is located on a nearby promontory and has similar ceramics among the grave goods. This complex of sites (the settlement and the burial ground is dated back to 3rd-2nd centuries BC and is related by the authors to the period of transition from the Ananyino to the Glyadenovo cultures in the Kama River region.

  16. Phonon interactions with methyl radicals in single crystals

    Directory of Open Access Journals (Sweden)

    James W. Wells

    2017-04-01

    Full Text Available The high temperature ESR spectra’s anomalous appearance at very low temperatures for the methyl radical created in single crystals is explained by magnetic dipole interactions with neighboring protons. These protons acting via phonon vibrations induce resonant oscillations with the methyl group to establish a very temperature sensitive ‘‘relaxation’’ mode that allows the higher energy ‘‘E’’ state electrons with spin 12 to ‘‘decay’’ into ‘‘A’’ spin 12 states. Because of the amplitude amplification with temperature, the ‘‘E’’ state population is depleted and the ‘‘A’’ state population augmented to produce the high temperature ESR spectrum. This phenomenon is found to be valid for all but the very highest barriers to methyl group tunneling. In support, a time dependent spin population study shows this temperature evolution in the state populations under this perturbation.

  17. A review of bacterial methyl halide degradation: biochemistry, genetics and molecular ecology

    Science.gov (United States)

    McDonald, I.R.; Warner, K.L.; McAnulla, C.; Woodall, C.A.; Oremland, R.S.; Murrell, J.C.

    2002-01-01

    Methyl halide-degrading bacteria are a diverse group of organisms that are found in both terrestrial and marine environments. They potentially play an important role in mitigating ozone depletion resulting from methyl chloride and methyl bromide emissions. The first step in the pathway(s) of methyl halide degradation involves a methyltransferase and, recently, the presence of this pathway has been studied in a number of bacteria. This paper reviews the biochemistry and genetics of methyl halide utilization in the aerobic bacteria Methylobacterium chloromethanicum CM4T, Hyphomicrobium chloromethanicum CM2T, Aminobacter strain IMB-1 and Aminobacter strain CC495. These bacteria are able to use methyl halides as a sole source of carbon and energy, are all members of the α-Proteobacteria and were isolated from a variety of polluted and pristine terrestrial environments. An understanding of the genetics of these bacteria identified a unique gene (cmuA) involved in the degradation of methyl halides, which codes for a protein (CmuA) with unique methyltransferase and corrinoid functions. This unique functional gene, cmuA, is being used to develop molecular ecology techniques to examine the diversity and distribution of methyl halide-utilizing bacteria in the environment and hopefully to understand their role in methyl halide degradation in different environments. These techniques will also enable the detection of potentially novel methyl halide-degrading bacteria.

  18. Methyl-donor deficiency due to chemically induced glutathione depletion.

    Science.gov (United States)

    Lertratanangkoon, K; Orkiszewski, R S; Scimeca, J M

    1996-03-01

    Dietary deficiency of methionine (Met) is known to deplete cellular Met and cause DNA hypomethylation, but depletion of Met and impairment in methylation due to chemically induced glutathione (GSH) depletion has escaped recognition. In this study, the effect of GSH depletion on the Met pool and methylation capability was examined after bromobenzene (BB), a model GSH-depleting hepatotoxin, was administered to the Syrian hamster. An i.p. dose of BB (800 mg/kg) caused a rapid and extensive depletion of liver GSH; approximately 68% of the initial concentration was depleted during the first hour. The lowest level of GSH, only 4% of the control, was detected at 5 h. GSH depletion was accompanied by a prompt increase in liver Met during the first hour. This initial increase was followed by an extensive depletion during the next 4 h. At 5 h after BB, liver Met was 12% below the control value, and it remained around this concentration throughout the 24-h experiment. To further confirm these results, the endogenous Met pool was labeled with deuterated Met. The administration of (L)- Met-methyl-d(3) to the Syrian hamster after GSH had been depleted by BB resulted in a significant protection of the liver against necrosis. The protection was accompanied by a marked incorporation of deuterated Met into the liver Met pool. The incorporation, which was determined by gas chromatography-mass spectrometry, shows BB dose dependence. Approximately 53% of the liver Met was labeled when a toxic BB dose (800 mg/kg) was used, while only 25% incorporation was found for the nontoxic dose (100 mg/kg). These results were different from the controls, where only 15% incorporation was found. The differences in the incorporation indicate that there are differences in the degree of utilization and/or depletion of Met in these hamsters, and these differences apparently are dependent upon the degree of toxicity and GSH depletion. The marked incorporation of deuterated Met in the high-dose group was

  19. Landsat - SRTM Shaded Relief Comparison, Los Angeles and Vicinity

    Science.gov (United States)

    2002-01-01

    Digital elevation models (DEMs), such as those produced by the Shuttle Radar Topography Mission (SRTM), allow user-controlled visualization of the Earth's landforms that is not possible using satellite imagery alone. This three-view comparison shows Los Angeles, Calif., and vicinity, with a Landsat image (only) on the left, a shaded relief rendering of the SRTM DEM on the right, and a merge of the two data sets in the middle. Note that topographic expression in the Landsat image alone is very subtle due to the fairly high sun angle (63 degrees above the horizon) during the satellite overflight in late morning of a mid-Spring day (May 4, 2001). In contrast, computer generated topographic shading of the DEM provides a pure and bold image of topographic expression with a user specified illumination direction. The middle image shows how combining the Landsat and DEM shaded relief can result in a topographically enhanced satellite image in which the information content of both data sets is merged into a single view.Landsat has been providing visible and infrared views of the Earth since 1972. SRTM elevation data matches the 30-meter (98-foot) resolution of most Landsat images and helps in analyzing the large and growing Landsat image archive, managed by the U.S. Geological Survey (USGS).Elevation data used in this image was acquired by the Shuttle Radar Topography Mission (SRTM) aboard the Space Shuttle Endeavour, launched on Feb. 11, 2000. SRTM used the same radar instrument that comprised the Spaceborne Imaging Radar-C/X-Band Synthetic Aperture Radar (SIR-C/X-SAR) that flew twice on the Space Shuttle Endeavour in 1994. SRTM was designed to collect 3-D measurements of the Earth's surface. To collect the 3-D data, engineers added a 60-meter (approximately 200-foot) mast, installed additional C-band and X-band antennas, and improved tracking and navigation devices. The mission is a cooperative project between NASA, the National Imagery and Mapping Agency (NIMA) of the U

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

    Science.gov (United States)

    Choi, Sang-Woon; Tammen, Stephanie A; Liu, Zhenhua; Friso, Simonetta

    2015-08-01

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

  1. Ancestry dependent DNA methylation and influence of maternal nutrition.

    Directory of Open Access Journals (Sweden)

    Khyobeni Mozhui

    Full Text Available There is extensive variation in DNA methylation between individuals and ethnic groups. These differences arise from a combination of genetic and non-genetic influences and potential modifiers include nutritional cues, early life experience, and social and physical environments. Here we compare genome-wide DNA methylation in neonatal cord blood from African American (AA; N = 112 and European American (EA; N = 91 participants of the CANDLE Study (Conditions Affecting Neurocognitive Development and Learning in Early Childhood. Our goal is to determine if there are replicable ancestry-specific methylation patterns that may implicate risk factors for diseases that have differential prevalence between populations. To identify the most robust ancestry-specific CpG sites, we replicate our results in lymphoblastoid cell lines from Yoruba African and CEPH European panels of HapMap. We also evaluate the influence of maternal nutrition--specifically, plasma levels of vitamin D and folate during pregnancy--on methylation in newborns. We define stable ancestry-dependent methylation of genes that include tumor suppressors and cell cycle regulators (e.g., APC, BRCA1, MCC. Overall, there is lower global methylation in African ancestral groups. Plasma levels of 25-hydroxy vitamin D are also considerably lower among AA mothers and about 60% of AA and 40% of EA mothers have concentrations below 20 ng/ml. Using a weighted correlation analysis, we define a network of CpG sites that is jointly modulated by ancestry and maternal vitamin D. Our results show that differences in DNA methylation patterns are remarkably stable and maternal micronutrients can exert an influence on the child epigenome.

  2. Methylation effect on the ohmic resistance of a poly-GC DNA-like chain

    Science.gov (United States)

    de Moura, F. A. B. F.; Lyra, M. L.; de Almeida, M. L.; Ourique, G. S.; Fulco, U. L.; Albuquerque, E. L.

    2016-10-01

    We determine, by using a tight-binding model Hamiltonian, the characteristic current-voltage (IxV) curves of a 5-methylated cytosine single strand poly-GC DNA-like finite segment, considering the methyl groups attached laterally to a random fraction of the cytosine basis. Striking, we found that the methylation significantly impacts the ohmic resistance (R) of the DNA-like segments, indicating that measurements of R can be used as a biosensor tool to probe the presence of anomalous methylation.

  3. Nonlinear relativistic plasma resonance: Renormalization group approach

    Energy Technology Data Exchange (ETDEWEB)

    Metelskii, I. I., E-mail: metelski@lebedev.ru [Russian Academy of Sciences, Lebedev Physical Institute (Russian Federation); Kovalev, V. F., E-mail: vfkvvfkv@gmail.com [Dukhov All-Russian Research Institute of Automatics (Russian Federation); Bychenkov, V. Yu., E-mail: bychenk@lebedev.ru [Russian Academy of Sciences, Lebedev Physical Institute (Russian Federation)

    2017-02-15

    An analytical solution to the nonlinear set of equations describing the electron dynamics and electric field structure in the vicinity of the critical density in a nonuniform plasma is constructed using the renormalization group approach with allowance for relativistic effects of electron motion. It is demonstrated that the obtained solution describes two regimes of plasma oscillations in the vicinity of the plasma resonance— stationary and nonstationary. For the stationary regime, the spatiotemporal and spectral characteristics of the resonantly enhanced electric field are investigated in detail and the effect of the relativistic nonlinearity on the spatial localization of the energy of the plasma relativistic field is considered. The applicability limits of the obtained solution, which are determined by the conditions of plasma wave breaking in the vicinity of the resonance, are established and analyzed in detail for typical laser and plasma parameters. The applicability limits of the earlier developed nonrelativistic theories are refined.

  4. DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia

    DEFF Research Database (Denmark)

    Nordlund, Jessica; Bäcklin, Christofer L; Zachariadis, Vasilios

    2015-01-01

    BACKGROUND: We present a method that utilizes DNA methylation profiling for prediction of the cytogenetic subtypes of acute lymphoblastic leukemia (ALL) cells from pediatric ALL patients. The primary aim of our study was to improve risk stratification of ALL patients into treatment groups using DNA...... methylation as a complement to current diagnostic methods. A secondary aim was to gain insight into the functional role of DNA methylation in ALL. RESULTS: We used the methylation status of ~450,000 CpG sites in 546 well-characterized patients with T-ALL or seven recurrent B-cell precursor ALL subtypes...... methylation classification to screen for subtype membership of 210 patients with undefined karyotype (normal or no result) or non-recurrent cytogenetic aberrations ('other' subtype). Nearly half (n = 106) of the patients lacking cytogenetic subgrouping displayed highly similar methylation profiles...

  5. Influence of the Near Molecular Vicinity on the Temperature Regulated Fluorescence Response of Poly(N-vinylcaprolactam

    Directory of Open Access Journals (Sweden)

    Anne Enzenberg

    2016-03-01

    Full Text Available A series of new fluorescent dye bearing monomers, including glycomonomers, based on maleamide and maleic esteramide was synthesized. The dye monomers were incorporated by radical copolymerization into thermo-responsive poly(N‑vinyl-caprolactam that displays a lower critical solution temperature (LCST in aqueous solution. The effects of the local molecular environment on the polymers’ luminescence, in particular on the fluorescence intensity and the extent of solvatochromism, were investigated below as well as above the phase transition. By attaching substituents of varying size and polarity in the close vicinity of the fluorophore, and by varying the spacer groups connecting the dyes to the polymer backbone, we explored the underlying structure–property relationships, in order to establish rules for successful sensor designs, e.g., for molecular thermometers. Most importantly, spacer groups of sufficient length separating the fluorophore from the polymer backbone proved to be crucial for obtaining pronounced temperature regulated fluorescence responses.

  6. Are N-methyl groups of Tetramethylurea (TMU) Hydrophobic? A ...

    Indian Academy of Sciences (India)

    Lakowicz J R 1999 In Principles of Fluorescence Spec- troscopy (New York: Kluwer Academic). 56. Galley W C and Purkey R M 1970 Proc. Natl. Acad. Sci. U.S.A. 67 1116. 57. Demchenko A P 2002 Luminescence 17 19. 58. Arêas E P G, Arêas J A G, Hamburger J, Peticolas W L and Santos P S 1996 J. Colloid Interface Sci.

  7. Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia

    DEFF Research Database (Denmark)

    Nordlund, Jessica; Bäcklin, Christofer L; Wahlberg, Per

    2013-01-01

    cells at relapse, compared with matched samples at diagnosis. Analysis of relapse-free survival identified CpG sites with subtype-specific differential methylation that divided the patients into different risk groups, depending on their methylation status. CONCLUSIONS: Our results suggest an important...

  8. Folate and DNA Methylation: A Review of Molecular Mechanisms and the Evidence for Folate’s Role12

    Science.gov (United States)

    Crider, Krista S.; Yang, Thomas P.; Berry, Robert J; Bailey, Lynn B.

    2012-01-01

    DNA methylation is an epigenetic modification critical to normal genome regulation and development. The vitamin folate is a key source of the one carbon group used to methylate DNA. Because normal mammalian development is dependent on DNA methylation, there is enormous interest in assessing the potential for changes in folate intake to modulate DNA methylation both as a biomarker for folate status and as a mechanistic link to developmental disorders and chronic diseases including cancer. This review highlights the role of DNA methylation in normal genome function, how it can be altered, and the evidence of the role of folate/folic acid in these processes. PMID:22332098

  9. Negative regulation of DNA methylation in plants.

    Science.gov (United States)

    Saze, Hidetoshi; Sasaki, Taku; Kakutani, Tetsuji

    2008-01-01

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

  10. Promoter histone H3 lysine 9 di-methylation is associated with DNA methylation and aberrant expression of p16 in gastric cancer cells.

    Science.gov (United States)

    Meng, Chun-Feng; Zhu, Xin-Jiang; Peng, Guo; Dai, Dong-Qiu

    2009-11-01

    In the course of gastric cancer development, gene silencing by DNA hypermethylation is an important mechanism. While DNA methylation often co-exists with histone modifications to regulate gene expression, the function of histone modifications in gene silencing in gastric cancer has not been evaluated in detail. p16, a well-known tumor suppressor gene, is frequently silenced in DNA hypermethylation manner in gastric cancer. Accordingly, we chose p16 to clarify whether there is a correlation among histone H3 lysine 9 (H3-K9) di-methylation, H3-K9 acetylation, DNA methylation and p16 expression in human gastric cancer. Three gastric cancer cells, MKN-45, SGC-7901 and BGC-823, were treated with 5-aza-2'-deoxycytidine (5-Aza-dC) and/or trichostatin A (TSA). We investigated p16 promoter DNA methylation status, p16 mRNA levels, regional and global levels of di-methyl-H3-K9 and acetyl-H3-K9 in four groups: i) 5-Aza-dC, ii) TSA, iii) the combination of 5-Aza-dC and TSA and iv) control group with no treatments. p16 silencing is characterized by DNA hypermethylation, H3-K9 hypoacetylation and H3-K9 hypermethylation at the promoter region. Treatment with TSA, increased H3-K9 acetylation at the hypermethylated promoter, but did not affect H3-K9 di-methylation or p16 expression. By contrast, treatment with 5-Aza-dC, reduced H3-K9 di-methylation, increased H3-K9 acetylation at the hypermethylated promoter and reactivated the expression of p16. Combined treatment restored the expression of p16 synergistically. In addition, 5-Aza-dC and the combined treatment did not result in global alteration of H3-K9 di-methylation. These results suggest that H3-K9 di-methylation, H3-K9 acetylation and DNA methylation work in combination to silence p16 in gastric cancer. The decreased H3-K9 di-methylation correlates with DNA demethylation and reactivation of p16. H3-K9 di-methylation as well as DNA methylation related to p16 silencing is limited to the promoter region. In addition to its effect

  11. Association of CXCL12 gene promoter methylation with periodontitis in patients with diabetes mellitus type 2.

    Science.gov (United States)

    Grdović, Nevena; Rajić, Jovana; Petrović, Sanja Matić; Dinić, Svetlana; Uskoković, Aleksandra; Mihailović, Mirjana; Jovanović, Jelena Arambašić; Tolić, Anja; Pucar, Ana; Milašin, Jelena; Vidaković, Melita

    2016-12-01

    CXCL12 is widely expressed, constitutive chemokine involved in tissue repair and regeneration, while the extent of its expression is important in various chronic inflammatory conditions. Involvement of DNA methylation in CXCL12 gene suppression (CXCL12) has been shown in malignancy and some autoimmune diseases. The aim of this study was to investigate whether the alterations in DNA methylation of CXCL12 are also involved in progression of periodontitis in combination with diabetes, as these chronic inflammatory conditions are strongly interrelated. Study included 72 subjects divided in three groups: healthy control (C, n=21), periodontitis (P, n=29) and diabetes/periodontitis group (D/P, n=22). DNA extracted from epithelial cells obtained by sterile cotton swabs from buccal mucosa was subjected to methylation specific polymerase chain reaction (MSP) to obtain DNA methylation pattern of CXCL12 promoter. CXCL12 promoter was predominantly unmethylated in all groups. However, increase in the frequency of the methylated form and increase in percent of methylation of CXCL12 promoter in periodontitis and diabetes/periodontitis group compared to control group were found, although without statistical significance. However, statistically significant increase in Tm of MSP products in diabetes/periodontitis group was observed. Correlation analysis revealed statistically significant relationship between the extent of DNA methylation of the CXCL12 promoter and periodontal parameters, as well as between DNA methylation of CXCL12 and glycosylated hemoglobin. Presented results suggest that chronic inflammation contributes to the change of CXCL12 DNA methylation in buccal cells and that DNA methylation profile of CXCL12 promoter plays important role in development and progression of periodontal disease. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Whole genome methylation profiles as independent markers of survival in stage IIIC melanoma patients

    Directory of Open Access Journals (Sweden)

    Sigalotti Luca

    2012-09-01

    Full Text Available Abstract Background The clinical course of cutaneous melanoma (CM can differ significantly for patients with identical stages of disease, defined clinico-pathologically, and no molecular markers differentiate patients with such a diverse prognosis. This study aimed to define the prognostic value of whole genome DNA methylation profiles in stage III CM. Methods Genome-wide methylation profiles were evaluated by the Illumina Human Methylation 27 BeadChip assay in short-term neoplastic cell cultures from 45 stage IIIC CM patients. Unsupervised K-means partitioning clustering was exploited to sort patients into 2 groups based on their methylation profiles. Methylation patterns related to the discovered groups were determined using the nearest shrunken centroid classification algorithm. The impact of genome-wide methylation patterns on overall survival (OS was assessed using Cox regression and Kaplan-Meier analyses. Results Unsupervised K-means partitioning by whole genome methylation profiles identified classes with significantly different OS in stage IIIC CM patients. Patients with a “favorable” methylation profile had increased OS (P = 0.001, log-rank = 10.2 by Kaplan-Meier analysis. Median OS of stage IIIC patients with a “favorable” vs. “unfavorable” methylation profile were 31.5 and 10.4 months, respectively. The 5 year OS for stage IIIC patients with a “favorable” methylation profile was 41.2% as compared to 0% for patients with an “unfavorable” methylation profile. Among the variables examined by multivariate Cox regression analysis, classification defined by methylation profile was the only predictor of OS (Hazard Ratio = 2.41, for “unfavorable” methylation profile; 95% Confidence Interval: 1.02-5.70; P = 0.045. A 17 gene methylation signature able to correctly assign prognosis (overall error rate = 0 in stage IIIC patients on the basis of distinct methylation-defined groups was also identified

  13. An integrative analysis of DNA methylation and RNA-Seq data for human heart, kidney and liver

    Directory of Open Access Journals (Sweden)

    Xie Linglin

    2011-12-01

    Full Text Available Abstract Background Many groups, including our own, have proposed the use of DNA methylation profiles as biomarkers for various disease states. While much research has been done identifying DNA methylation signatures in cancer vs. normal etc., we still lack sufficient knowledge of the role that differential methylation plays during normal cellular differentiation and tissue specification. We also need thorough, genome level studies to determine the meaning of methylation of individual CpG dinucleotides in terms of gene expression. Results In this study, we have used (insert statistical method here to compile unique DNA methylation signatures from normal human heart, lung, and kidney using the Illumina Infinium 27 K methylation arraysand compared those to gene expression by RNA sequencing. We have identified unique signatures of global DNA methylation for human heart, kidney and liver, and showed that DNA methylation data can be used to correctly classify various tissues. It indicates that DNA methylation reflects tissue specificity and may play an important role in tissue differentiation. The integrative analysis of methylation and RNA-Seq data showed that gene methylation and its transcriptional levels were comprehensively correlated. The location of methylation markers in terms of distance to transcription start site and CpG island showed no effects on the regulation of gene expression by DNA methylation in normal tissues. Conclusions This study showed that an integrative analysis of methylation array and RNA-Seq data can be utilized to discover the global regulation of gene expression by DNA methylation and suggests that DNA methylation plays an important role in normal tissue differentiation via modulation of gene expression.

  14. Noninteracting, vicinal frustrated P/B-Lewis pair at the norbornane framework: synthesis, characterization, and reactions.

    Science.gov (United States)

    Sajid, Muhammad; Kehr, Gerald; Wiegand, Thomas; Eckert, Hellmut; Schwickert, Christian; Pöttgen, Rainer; Cardenas, Allan Jay P; Warren, Timothy H; Fröhlich, Roland; Daniliuc, Constantin G; Erker, Gerhard

    2013-06-19

    Hydroboration of dimesitylnorbornenylphosphane with Piers' borane [HB(C6F5)2] gave the frustrated Lewis pair (FLP) 4 in good yield. It has the -PMes2 Lewis base attached at the 2-endo position and the -B(C6F5)2 group 3-exo oriented at the norbornane framework. The vicinal FLP 4 was shown by X-ray diffraction and by spectroscopy to be a rare example of an intramolecular noninteracting pair of a Lewis acid and Lewis base functionality. The FLP 4 rapidly splits dihydrogen heterolytically at ambient temperature to yield the phosphonium/hydrido borate zwitterion 5. It adds to the carbonyl group of benzaldehyde and to carbon dioxide to yield the adducts 6 and 7, respectively. Compounds 5-7 were characterized by X-ray diffraction. Compound 4 adds to the S═O function of sulfur dioxide to give a pair of diastereomeric heterocyclic six-membered ring products due to the newly formed sulfur chirality center, annulated with the norbornane skeleton, which were investigated by (31)P/(11)B single and double resonance solid state NMR experiments. Compound 8 was also characterized by X-ray diffraction. The FLP 4 undergoes a clean N,N-addition to nitric oxide (NO) to give a norbornane annulated five-membered heterocyclic persistent FLP-NO aminoxyl radical 12 (characterized, e.g., by X-ray diffraction and EPR spectroscopy). Additionally, the FLP radical was characterized by (1)H solid state NMR spectroscopy. The radical 12 undergoes a H-atom abstraction reaction with 1,4-cyclohexadiene to yield the respective diamagnetic FLP-NOH product 13, which was also characterized by X-ray diffraction and solid state NMR spectroscopy.

  15. Histone methylations in heart development, congenital and adult heart diseases

    OpenAIRE

    Zhang, Qing-Jun; Liu, Zhi-Ping

    2015-01-01

    Heart development comprises myocyte specification, differentiation and cardiac morphogenesis. These processes are regulated by a group of core cardiac transcription factors in a coordinated temporal and spatial manner. Histone methylation is an emerging epigenetic mechanism for regulating gene transcription. Interplay among cardiac transcription factors and histone lysine modifiers plays important role in heart development. Aberrant expression and mutation of the histone lysine modifiers duri...

  16. O-Alkylated heavy atom carbohydrate probes for protein X-ray crystallography: Studies towards the synthesis of methyl 2-O-methyl-L-selenofucopyranoside

    Directory of Open Access Journals (Sweden)

    Roman Sommer

    2016-12-01

    Full Text Available Selenoglycosides are used as reactive glycosyl donors in the syntheses of oligosaccharides. In addition, such heavy atom analogs of natural glycosides are useful tools for structure determination of their lectin receptors using X-ray crystallography. Some lectins, e.g., members of the tectonin family, only bind to carbohydrate epitopes with O-alkylated ring hydroxy groups. In this context, we report the first synthesis of an O-methylated selenoglycoside, specifically methyl 2-O-methyl-L-selenofucopyranoside, a ligand of the lectin tectonin-2 from the mushroom Laccaria bicolor. The synthetic route required a strategic revision and further optimization due to the intrinsic lability of alkyl selenoglycosides, in particular for the labile fucose. Here, we describe a successful synthetic access to methyl 2-O-methyl-L-selenofucopyranoside in 9 linear steps and 26% overall yield starting from allyl L-fucopyranoside.

  17. MGMT, GATA6, CD81, DR4, and CASP8 gene promoter methylation in glioblastoma

    Directory of Open Access Journals (Sweden)

    Skiriute Daina

    2012-06-01

    Full Text Available Abstract Background Methylation of promoter region is the major mechanism affecting gene expression in tumors. Recent methylome studies of brain tumors revealed a list of new epigenetically modified genes. Our aim was to study promoter methylation of newly identified epigenetically silenced genes together with already known epigenetic markers and evaluate its separate and concomitant role in glioblastoma genesis and patient outcome. Methods The methylation status of MGMT, CD81, GATA6, DR4, and CASP8 in 76 patients with primary glioblastomas was investigated. Methylation-specific PCR reaction was performed using bisulfite treated DNA. Evaluating glioblastoma patient survival time after operation, patient data and gene methylation effect on survival was estimated using survival analysis. Results The overwhelming majority (97.3% of tumors were methylated in at least one of five genes tested. In glioblastoma specimens gene methylation was observed as follows: MGMT in 51.3%, GATA6 in 68.4%, CD81 in 46.1%, DR4 in 41.3% and CASP8 in 56.8% of tumors. Methylation of MGMT was associated with younger patient age (p CASP8 with older (p MGMT methylation was significantly more frequent event in patient group who survived longer than 36 months after operation (p CASP8 was more frequent in patients who survived shorter than 36 months (p MGMT, GATA6 and CASP8 as independent predictors for glioblastoma patient outcome (p MGMT and GATA6 were independent predictors for patient survival in younger patients’ group, while there were no significant associations observed in older patients’ group when adjusted for therapy. Conclusions High methylation frequency of tested genes shows heterogeneity of glioblastoma epigenome and the importance of MGMT, GATA6 and CASP8 genes methylation in glioblastoma patient outcome.

  18. Investigation of correlations between DNA methylation, suicidal behavior and aging.

    Science.gov (United States)

    Jeremian, Richie; Chen, Yi-An; De Luca, Vincenzo; Vincent, John B; Kennedy, James L; Zai, Clement C; Strauss, John

    2017-02-01

    Suicidal behavior (SB) is a major cause of mortality for patients diagnosed with bipolar disorder (BD). In this study, we investigated epigenetic differences in BD participants with and without a history of SB. We used suicidality scores constructed from Schedule for Clinical Assessments in Neuropsychiatry (SCAN) interview questions about suicidal thought and behavior to identify individuals from a BD cohort of n=452; participants with the most extreme high (H-SB, n=18) and most extreme low (L-SB, n=22) scores were used as cases and controls, respectively. Epigenome-wide DNA methylation patterns were compared between the two groups using the Illumina Infinium Human Methylation 450 BeadChip microarray. DNA methylation age was compared to chronological tissue age. We observed highly significant differences in methylation between cases and controls in three genomic regions enriched for epigenetic modifications corresponding to gene regulatory regions. BD participants with a history of SB showed less overall methylation in the 5' untranslated region of Membrane palmitoylated protein 4 (MPP4) (P=7.42×10(-7) ) and in intron 3 of TRE2/BUB2/CDC16 domain family member 16 (TBC1D16) (P=6.47×10(-7) ), while exon 1 of Nucleoporin 133 (NUP133) was less methylated in controls (P=1.17x10(-6) ). Moreover, we observed a greater correlation between DNA methylation age and tissue age in controls (r=.91, Psuicide attempters. Despite the small sample size, our proof-of-concept study highlights the potential for epigenetic factors to be useful in understanding the molecular underpinnings of suicide with the ultimate aim of its prevention. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  19. Abundance of genes involved in mercury methylation in oceanic environments

    Science.gov (United States)

    Palumbo, A. V.; Podar, M.; Gilmour, C. C.; Brandt, C. C.; Brown, S. D.; Crable, B. R.; Weighill, D.; Jacobson, D. A.; Somenahally, A. C.; Elias, D. A.

    2016-02-01

    The distribution and diversity of genes involved in mercury methylation in oceanic environments is of interest in determining the source of mercury in ocean environments and may have predictive value for mercury methylation rates. The highly conserved hgcAB genes involved in mercury methylation provide an avenue for evaluating the genetic potential for mercury methylation. The genes are sporadically present in a few diverse groups of bacteria and Archaea including Deltaproteobacteria, Firmicutes and Archaea and of over 7000 sequenced species they are only present in about 100 genomes. Examination of sequence data from methylators and non-methylators indicates that these genes are associated with other genes involved in metal transformations and transport. We examined hgcAB presence in over 3500 microbial metagenomes (from all environments) and found the hgcAB genes were present in anaerobic oceanic environments but not in aerobic layers of the open ocean. The genes were common in sediments from marine, coastal and estuarine sources as well as polluted environments. The genes were rare, found in 7 of 138 samples, in metagenomes from the pelagic water column including profiles though the oxygen minimum zone. Other oxic and sub-oxic coastal waters also demonstrated a lack of hgcAB genes including the OMZ in the Eastern North Pacific Ocean. There were some unique hgcA like unique sequences found in metagenomes from depth in the Pacific and Southern Atlantic Ocean. Coastal "dead zone" waters may be important sources of MeHg as the hgcAB genes were abundant in the anoxic waters of a stratified fjord. The genes were absent in microbiomes from vertebrates but were in invertebrate microbiomes However, oceanic species were underrepresented in these samples. Climate change could provide an additional flux of MeHg to the oceans as we found the most abundant representation of hgcAB genes in arctic permafrost. Thus warming could increase flux of methyl mercury to arctic waters.

  20. Evolution of DNA Methylation across Insects

    Science.gov (United States)

    Vogel, Kevin J.; Moore, Allen J.; Schmitz, Robert J.

    2017-01-01

    DNA methylation contributes to gene and transcriptional regulation in eukaryotes, and therefore has been hypothesized to facilitate the evolution of plastic traits such as sociality in insects. However, DNA methylation is sparsely studied in insects. Therefore, we documented patterns of DNA methylation across a wide diversity of insects. We predicted that underlying enzymatic machinery is concordant with patterns of DNA methylation. Finally, given the suggestion that DNA methylation facilitated social evolution in Hymenoptera, we tested the hypothesis that the DNA methylation system will be associated with presence/absence of sociality among other insect orders. We found DNA methylation to be widespread, detected in all orders examined except Diptera (flies). Whole genome bisulfite sequencing showed that orders differed in levels of DNA methylation. Hymenopteran (ants, bees, wasps and sawflies) had some of the lowest levels, including several potential losses. Blattodea (cockroaches and termites) show all possible patterns, including a potential loss of DNA methylation in a eusocial species whereas solitary species had the highest levels. Species with DNA methylation do not always possess the typical enzymatic machinery. We identified a gene duplication event in the maintenance DNA methyltransferase 1 (DNMT1) that is shared by some Hymenoptera, and paralogs have experienced divergent, nonneutral evolution. This diversity and nonneutral evolution of underlying machinery suggests alternative DNA methylation pathways may exist. Phylogenetically corrected comparisons revealed no evidence that supports evolutionary association between sociality and DNA methylation. Future functional studies will be required to advance our understanding of DNA methylation in insects. PMID:28025279

  1. Reaction pathways of the dissociation of methylal: A DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Frey, H.-M.; Beaud, P.; Gerber, T.; Mischler, B.; Radi, P.P.; Tzannis, A.-P. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1999-08-01

    Schemata for modelling combustion processes do not yet include reaction rates for oxygenated fuels like methylal (DMM) which is considered as an additive or replacement for diesel due to its low sooting propensity. Density functional theory (DFT) studies of the possible reaction pathways for different dissociation steps of methylal are presented. Cleavage of a hydrogen bond to the methoxy group or the central carbon atom were simulated at the BLYP/6-311++G{sup **} level of theory. The results are compared to the experiment when dissociating and/or ionising DMM with femtosecond pulses. (author) 1 fig., 1 tab., 1 ref.

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

    Science.gov (United States)

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

    2009-04-01

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

  3. Laser pointing in the vicinity of jet engine plumes

    NARCIS (Netherlands)

    Schleijpen, H.M.A.

    2010-01-01

    Target tracking and laser-based pointing from airborne platforms can be degraded significantly by the propagation environment around an airborne platform including zones of severe turbulence generated by rotor downwash and engine exhausts. This is the topic of the EDA study group ERG 108.019 on

  4. Laser pointing in the vicinity of jet engine plumes

    NARCIS (Netherlands)

    Schleijpen, H.M.A.

    2009-01-01

    Target tracking and laser-based pointing from airborne platforms can be degraded significantly by the propagation environment around an airborne platform including zones of severe turbulence generated by rotor downwash and engine exhausts. This is the topic of the EDA study group ERG 108.019 on

  5. Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    You Wanhui

    2012-04-01

    Full Text Available Abstract Background In plants, transposons and non-protein-coding repeats are epigenetically silenced by CG and non-CG methylation. This pattern of methylation is mediated in part by small RNAs and two specialized RNA polymerases, termed Pol IV and Pol V, in a process called RNA-directed DNA methylation. By contrast, many protein-coding genes transcribed by Pol II contain in their gene bodies exclusively CG methylation that is independent of small RNAs and Pol IV/Pol V activities. It is unclear how the different methylation machineries distinguish between transposons and genes. Here we report on a group of atypical genes that display in their coding region a transposon-like methylation pattern, which is associated with gene silencing in sporophytic tissues. Results We performed a methylation-sensitive amplification polymorphism analysis to search for targets of RNA-directed DNA methylation in Arabidopsis thaliana and identified several members of a gene family encoding cysteine-rich peptides (CRPs. In leaves, the CRP genes are silent and their coding regions contain dense, transposon-like methylation in CG, CHG and CHH contexts, which depends partly on the Pol IV/Pol V pathway and small RNAs. Methylation in the coding region is reduced, however, in the synergid cells of the female gametophyte, where the CRP genes are specifically expressed. Further demonstrating that expressed CRP genes lack gene body methylation, a CRP4-GFP fusion gene under the control of the constitutive 35 S promoter remains unmethylated in leaves and is transcribed to produce a translatable mRNA. By contrast, a CRP4-GFP fusion gene under the control of a CRP4 promoter fragment acquires CG and non-CG methylation in the CRP coding region in leaves similar to the silent endogenous CRP4 gene. Conclusions Unlike CG methylation in gene bodies, which does not dramatically affect Pol II transcription, combined CG and non-CG methylation in CRP coding regions is likely to

  6. Bacterial production of methyl ketones

    Energy Technology Data Exchange (ETDEWEB)

    Beller, Harry R.; Goh, Ee-Been

    2017-01-31

    The present invention relates to methods and compositions for increasing production of methyl ketones in a genetically modified host cell that overproduces .beta.-ketoacyl-CoAs through a re-engineered .beta.-oxidation pathway and overexpresses FadM.

  7. Histone Lysine Methylation and Neurodevelopmental Disorders

    Directory of Open Access Journals (Sweden)

    Jeong-Hoon Kim

    2017-06-01

    Full Text Available Methylation of several lysine residues of histones is a crucial mechanism for relatively long-term regulation of genomic activity. Recent molecular biological studies have demonstrated that the function of histone methylation is more diverse and complex than previously thought. Moreover, studies using newly available genomics techniques, such as exome sequencing, have identified an increasing number of histone lysine methylation-related genes as intellectual disability-associated genes, which highlights the importance of accurate control of histone methylation during neurogenesis. However, given the functional diversity and complexity of histone methylation within the cell, the study of the molecular basis of histone methylation-related neurodevelopmental disorders is currently still in its infancy. Here, we review the latest studies that revealed the pathological implications of alterations in histone methylation status in the context of various neurodevelopmental disorders and propose possible therapeutic application of epigenetic compounds regulating histone methylation status for the treatment of these diseases.

  8. DNA methylation and epigenetic inheritance during plant gametogenesis.

    Science.gov (United States)

    Takeda, Shin; Paszkowski, Jerzy

    2006-02-01

    In plants, newly acquired epigenetic states of transcriptional gene activity are readily transmitted to the progeny. This is in contrast to mammals, where only rare cases of transgenerational inheritance of new epigenetic traits have been reported (FASEB J 12:949-957, 1998; Nat Genet 23:314-318, 1999; Proc Natl Acad Sci U S A 100:2538-2543, 2003). Epigenetic inheritance in plants seems to rely on cytosine methylation maintained through meiosis and postmeiotic mitoses, giving rise to gametophytes. In particular, maintenance of CpG methylation ((m)CpG) appears to play a central role, guiding the distribution of other epigenetic signals such as histone H3 methylation and non-CpG DNA methylation. The evolutionarily conserved DNA methyltransferase MET1 is responsible for copying (m)CpG patterns through DNA replication in the gametophytic phase. The importance of gametophytic MET1 activity is illustrated by the phenotypes of met1 mutants that are severely compromised in the accuracy of epigenetic inheritance during gametogenesis. This includes elimination of imprinting at paternally silent loci such as FWA or MEDEA (MEA). The importance of DNA methylation in gametophytic imprinting has been reinforced by the discovery of DEMETER (DME), encoding putative DNA glycosylase involved in the removal of (m)C. DME opposes transcriptional silencing associated with imprinting activities of the MEA/FIE polycomb group complex.

  9. Differential DNA Methylation Analysis without a Reference Genome.

    Science.gov (United States)

    Klughammer, Johanna; Datlinger, Paul; Printz, Dieter; Sheffield, Nathan C; Farlik, Matthias; Hadler, Johanna; Fritsch, Gerhard; Bock, Christoph

    2015-12-22

    Genome-wide DNA methylation mapping uncovers epigenetic changes associated with animal development, environmental adaptation, and species evolution. To address the lack of high-throughput methods for DNA methylation analysis in non-model organisms, we developed an integrated approach for studying DNA methylation differences independent of a reference genome. Experimentally, our method relies on an optimized 96-well protocol for reduced representation bisulfite sequencing (RRBS), which we have validated in nine species (human, mouse, rat, cow, dog, chicken, carp, sea bass, and zebrafish). Bioinformatically, we developed the RefFreeDMA software to deduce ad hoc genomes directly from RRBS reads and to pinpoint differentially methylated regions between samples or groups of individuals (http://RefFreeDMA.computational-epigenetics.org). The identified regions are interpreted using motif enrichment analysis and/or cross-mapping to annotated genomes. We validated our method by reference-free analysis of cell-type-specific DNA methylation in the blood of human, cow, and carp. In summary, we present a cost-effective method for epigenome analysis in ecology and evolution, which enables epigenome-wide association studies in natural populations and species without a reference genome. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  10. Differential DNA Methylation Analysis without a Reference Genome

    Directory of Open Access Journals (Sweden)

    Johanna Klughammer

    2015-12-01

    Full Text Available Genome-wide DNA methylation mapping uncovers epigenetic changes associated with animal development, environmental adaptation, and species evolution. To address the lack of high-throughput methods for DNA methylation analysis in non-model organisms, we developed an integrated approach for studying DNA methylation differences independent of a reference genome. Experimentally, our method relies on an optimized 96-well protocol for reduced representation bisulfite sequencing (RRBS, which we have validated in nine species (human, mouse, rat, cow, dog, chicken, carp, sea bass, and zebrafish. Bioinformatically, we developed the RefFreeDMA software to deduce ad hoc genomes directly from RRBS reads and to pinpoint differentially methylated regions between samples or groups of individuals (http://RefFreeDMA.computational-epigenetics.org. The identified regions are interpreted using motif enrichment analysis and/or cross-mapping to annotated genomes. We validated our method by reference-free analysis of cell-type-specific DNA methylation in the blood of human, cow, and carp. In summary, we present a cost-effective method for epigenome analysis in ecology and evolution, which enables epigenome-wide association studies in natural populations and species without a reference genome.

  11. Intragenic DNA methylation: implications of this epigenetic mechanism for cancer research.

    Science.gov (United States)

    Shenker, N; Flanagan, J M

    2012-01-17

    Epigenetics is the study of all mechanisms that regulate gene transcription and genome stability that are maintained throughout the cell division, but do not include the DNA sequence itself. The best-studied epigenetic mechanism to date is DNA methylation, where methyl groups are added to the cytosine base within cytosine-guanine dinucleotides (CpG sites). CpGs are frequently clustered in high density (CpG islands (CGIs)) at the promoter of over half of all genes. Current knowledge of transcriptional regulation by DNA methylation centres on its role at the promoter where unmethylated CGIs are present at most actively transcribed genes, whereas hypermethylation of the promoter results in gene repression. Over the last 5 years, research has gradually incorporated a broader understanding that methylation patterns across the gene (so-called intragenic or gene body methylation) may have a role in transcriptional regulation and efficiency. Numerous genome-wide DNA methylation profiling studies now support this notion, although whether DNA methylation patterns are a cause or consequence of other regulatory mechanisms is not yet clear. This review will examine the evidence for the function of intragenic methylation in gene transcription, and discuss the significance of this in carcinogenesis and for the future use of therapies targeted against DNA methylation.

  12. Overlapping signatures of chronic pain in the DNA methylation landscape of prefrontal cortex and peripheral T cells

    Science.gov (United States)

    Massart, Renaud; Dymov, Sergiy; Millecamps, Magali; Suderman, Matthew; Gregoire, Stephanie; Koenigs, Kevin; Alvarado, Sebastian; Tajerian, Maral; Stone, Laura S.; Szyf, Moshe

    2016-01-01

    We tested the hypothesis that epigenetic mechanisms in the brain and the immune system are associated with chronic pain. Genome-wide DNA methylation assessed in 9 months post nerve-injury (SNI) and Sham rats, in the prefrontal cortex (PFC) as well as in T cells revealed a vast difference in the DNA methylation landscape in the brain between the groups and a remarkable overlap (72%) between differentially methylated probes in T cells and prefrontal cortex. DNA methylation states in the PFC showed robust correlation with pain score of animals in several genes involved in pain. Finally, only 11 differentially methylated probes in T cells were sufficient to distinguish SNI or Sham individual rats. This study supports the plausibility of DNA methylation involvement in chronic pain and demonstrates the potential feasibility of DNA methylation markers in T cells as noninvasive biomarkers of chronic pain susceptibility. PMID:26817950

  13. Variation in genomic methylation in natural populations of chinese white poplar.

    Directory of Open Access Journals (Sweden)

    Kaifeng Ma

    Full Text Available BACKGROUND: It is thought that methylcytosine can be inherited through meiosis and mitosis, and that epigenetic variation may be under genetic control or correlation may be caused by neutral drift. However, DNA methylation also varies with tissue, developmental stage, and environmental factors. Eliminating these factors, we analyzed the levels and patterns, diversity and structure of genomic methylcytosine in the xylem of nine natural populations of Chinese white poplar. PRINCIPAL FINDINGS: On average, the relative total methylation and non-methylation levels were approximately 26.567% and 42.708% (P<0.001, respectively. Also, the relative CNG methylation level was higher than the relative CG methylation level. The relative methylation/non-methylation levels were significantly different among the nine natural populations. Epigenetic diversity ranged from 0.811 (Gansu to 1.211 (Shaanxi, and the coefficients of epigenetic differentiation (GST  = 0.159 were assessed by Shannon's diversity index. Co-inertia analysis indicated that methylation-sensitive polymorphism (MSP and genomic methylation pattern (CG-CNG profiles gave similar distributions. Using a between-group eigen analysis, we found that the Hebei and Shanxi populations were independent of each other, but the Henan population intersected with the other populations, to some degree. CONCLUSIONS: Genome methylation in Populus tomentosa presented tissue-specific characteristics and the relative 5'-CCGG methylation level was higher in xylem than in leaves. Meanwhile, the genome methylation in the xylem shows great epigenetic variation and could be fixed and inherited though mitosis. Compared to genetic structure, data suggest that epigenetic and genetic variation do not completely match.

  14. The effect of poly(methyl methacrylate) surface treatments on the adhesion of silicone-based resilient denture liners.

    Science.gov (United States)

    Cavalcanti, Yuri Wanderley; Bertolini, Martinna Mendonça; Cury, Altair Antoninha Del Bel; da Silva, Wander José

    2014-12-01

    Different surface treatment protocols of poly(methyl methacrylate) have been proposed to improve the adhesion of silicone-based resilient denture liners to poly(methyl methacrylate) surfaces. The purpose of this study was to evaluate the effect of different poly(methyl methacrylate) surface treatments on the adhesion of silicone-based resilient denture liners. Poly(methyl methacrylate) specimens were prepared and divided into 4 treatment groups: no treatment (control), methyl methacrylate for 180 seconds, acetone for 30 seconds, and ethyl acetate for 60 seconds. Poly(methyl methacrylate) disks (30.0 × 5.0 mm; n = 10) were evaluated regarding surface roughness and surface free energy. To evaluate tensile bond strength, the resilient material was applied between 2 treated poly(methyl methacrylate) bars (60.0 × 5.0 × 5.0 mm; n = 20 for each group) to form a 2-mm-thick layer. Data were analyzed by 1-way ANOVA and the Tukey honestly significant difference tests (α = .05). A Pearson correlation test verified the influence of surface properties on tensile bond strength. Failure type was assessed, and the poly(methyl methacrylate) surface treatment modifications were visualized with scanning electron microscopy. The surface roughness was increased (P methyl methacrylate treatment. For the acetone and ethyl acetate groups, the surface free energy decreased (P methyl methacrylate and ethyl acetate groups (P methyl methacrylate presented a cleaner surface, whereas the ethyl acetate treatment produced a porous topography. The methyl methacrylate and ethyl acetate surface treatment protocols improved the adhesion of a silicone-based resilient denture liner to poly(methyl methacrylate). Copyright © 2014 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

  15. Unidirectional lateral nanowire formation during the epitaxial growth of GaAsBi on vicinal substrates

    Science.gov (United States)

    Collar, Kristen N.; Li, Jincheng; Jiao, Wenyuan; Kong, Wei; Brown, April S.

    2018-01-01

    We report on enhanced control of the growth of lateral GaAs nanowires (NWs) embedded in epitaxial (100) GaAsBi thin films enabled by the use of vicinal substrates and the growth-condition dependent role of Bi as a surfactant. Enhanced step-flow growth is achieved through the use of vicinal substrates and yields unidirectional nanowire growth. The addition of Bi during GaAsBi growth enhances Ga adatom diffusion anisotropy and modifies incorporation rates at steps in comparison to GaAs growth yielding lower density but longer NWs. The NWs grown on vicinal substrates grew unidirectionally towards the misorientation direction when Bi was present. The III/V flux ratio significantly impacts the size, shape and density of the resulting NWs. These results suggest that utilizing growth conditions which enhance step-flow growth enable enhanced control of lateral nanostructures.

  16. Experimental photophysical characterization of fluorophores in the vicinity of gold nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Rosa, J P; Baptista, P V [CIGMH, Departamento de Ciencias da Vida, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal); Lima, J C, E-mail: pmvb@fct.unl.pt, E-mail: lima@dq.fct.unl.pt [REQUIMTE, Departamento de Quimica, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal)

    2011-10-14

    We propose an experimental-based tool for dealing with fluorescence modulation close to nanoparticles for application in studies of fluorophores in the vicinity of gold nanoparticles (AuNPs), typically addressed via theoretical models. We performed a photophysical characterization of fluorophores in the vicinity of AuNPs, showing that correct {Phi}{sub F} determination suffers from a local pH effect, and address the observed radiative enhancement. Our approach is based on the experimental assurance that the reference fluorophores are in the same optical conditions as those of the AuNP-fluorophore conjugates. We demonstrate the relevance for introducing corrections for the inner filter effect and the reabsorption of the emitted light caused by AuNPs. The proposed approach could circumvent the need for theoretical based corrections and allow for more accurate determination of fluorescence emission in the vicinity of gold nanoparticles.

  17. Cost-Performance Parametrics for Transporting Small Packages to the Mars Vicinity

    Science.gov (United States)

    McCleskey, C.; Lepsch, Roger A.; Martin, J.; Popescu, M.

    2015-01-01

    This paper explores the costs and performance required to deliver a small-sized payload package (CubeSat-sized, for instance) to various transportation nodes en route to Mars and near-Mars destinations (such as Mars moons, Phobos and Deimos). Needed is a contemporary assessment and summary compilation of transportation metrics that factor both performance and affordability of modern and emerging delivery capabilities. The paper brings together: (a) required mass transport gear ratios in delivering payload from Earths surface to the Mars vicinity, (b) the cyclical energy required for delivery, and (c) the affordability and availability of various means of transporting material across various Earth-Moon vicinity and Near-Mars vicinity nodes relevant to Mars transportation. Examples for unit deliveries are computed and tabulated, using a CubeSat as a unit, for periodic near-Mars delivery campaign scenarios.

  18. Effects of DNA methylation inhibitors and conventional antidepressants on mice behaviour and brain DNA methylation levels.

    Science.gov (United States)

    Sales, Amanda Juliana; Joca, Sâmia Regiane Lourenço

    2016-02-01

    Stress increases DNA methylation and decreases the expression of genes involved in neural plasticity, while treatment with DNA methyltransferase inhibitors (DNMTi) increases gene expression and induces antidepressant-like effects in preclinical models. Therefore, the aim of the present work was to further investigate the potential antidepressant-like effect induced by DNMTi by evaluating the behavioural effects induced by associating DNMTi treatment with conventional antidepressant drugs in mice submitted to the forced swimming test (FST). In addition, brain levels of DNA methylation were also investigated. Mice received systemic injections of 5-aza-2'-deoxycytidine (5-AzaD, 0.1, 0.2 mg/kg), RG108 (0.1, 0.2, 0.4 mg/kg), desipramine (DES, 2.5, 5, 10 mg/kg) or fluoxetine (FLX, 5, 10, 20, 30 mg/kg) and were submitted to the FST or to the open field test (OFT). Additional groups received a combination of subeffective doses of 5-AzaD or RG108 (DNMTi) with subeffective doses of DES or FLX (antidepressants). Subeffective doses of RG108 (0.1 mg/kg) or 5-AzaD (0.1 mg/kg) in association with subeffective doses of DES (2.5 mg/kg) or FLX (10 mg/kg) induced significant antidepressant-like effects. Effective doses of RG108 (0.2 mg/kg), 5-AzaD (0.2 mg/kg), DES (10 mg/kg) and FLX (20 mg/kg) atenuated stress-induced changes in DNA methylation levels in the hippocampus and prefrontal cortex. None of the treatments induced locomotor effects in the OFT. These results suggest that DNMTi potentiate the behavioural effects of antidepressant drugs in the FST and that antidepressants, as well as DNMTi, are able to modulate stress-induced changes in DNA methylation in brain regions closely associated with the neurobiology of depression.

  19. Identification of DNA methylation biomarkers from Infinium arrays

    Directory of Open Access Journals (Sweden)

    Richard D Emes

    2012-08-01

    Full Text Available Epigenetic modifications of DNA, such as cytosine methylation are differentially abundant in diseases such as cancer. A goal for clinical research is finding sites that are differentially methylated between groups of samples to act as potential biomarkers for disease outcome. However, clinical samples are often limited in availability, represent a heterogeneous collection of cells or are of uncertain clinical class. Array based methods for identification of methylation provide a cost effective method to survey a proportion of the methylome at single base resolution. The Illumina Infinium array has become a popular and reliable high throughput method in this field and are proving useful in the identification of biomarkers for disease. Here, we compare a commonly used statistical test with a new intuitive and flexible computational approach to quickly detect differentially methylated sites. The method rapidly identifies and ranks candidate lists with greatest inter-group variability whilst controlling for intra-group variability. Intuitive and biologically relevant filters can be imposed to quickly identify sites and genes of interest.

  20. Hydrogen bond docking site competition in methyl esters.

    Science.gov (United States)

    Zhao, Hailiang; Tang, Shanshan; Du, Lin

    2017-06-15

    The OH⋯O hydrogen bonds in the 2,2,2-trifluoroethanol (TFE)-methyl ester complexes in the gas phase have been investigated by FTIR spectroscopy and DFT calculations. Methyl formate (MF), methyl acetate (MA), and methyl trifluoroacetate (MTFA) were chosen as the hydrogen bond acceptors. A dominant inter-molecular hydrogen bond was formed between the OH group of TFE and different docking sites in the methyl esters (carbonyl oxygen or ester oxygen). The competition of the two docking sites decides the structure and spectral properties of the complexes. On the basis of the observed red shifts of the OH-stretching transition with respect to the TFE monomer, the order of the hydrogen bond strength can be sorted as TFE-MA (119cm-1)>TFE-MF (93cm-1)>TFE-MTFA (44cm-1). Combining the experimental infrared spectra with the DFT calculations, the Gibbs free energies of formation were determined to be 1.5, 4.5 and 8.6kJmol-1 for TFE-MA, TFE-MF and TFE-MTFA, respectively. The hydrogen bonding in the MTFA complex is much weaker than those of the TFE-MA and TFE-MF complexes due to the effect of the CF3 substitution on MTFA, while the replacement of an H atom with a CH3 group in methyl ester only slightly increases the hydrogen bond strength. Topological analysis and localized molecular orbital energy decomposition analysis was also applied to compare the interactions in the complexes. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Hydrogen bond docking site competition in methyl esters

    Science.gov (United States)

    Zhao, Hailiang; Tang, Shanshan; Du, Lin

    2017-06-01

    The Osbnd H ⋯ O hydrogen bonds in the 2,2,2-trifluoroethanol (TFE)-methyl ester complexes in the gas phase have been investigated by FTIR spectroscopy and DFT calculations. Methyl formate (MF), methyl acetate (MA), and methyl trifluoroacetate (MTFA) were chosen as the hydrogen bond acceptors. A dominant inter-molecular hydrogen bond was formed between the OH group of TFE and different docking sites in the methyl esters (carbonyl oxygen or ester oxygen). The competition of the two docking sites decides the structure and spectral properties of the complexes. On the basis of the observed red shifts of the OH-stretching transition with respect to the TFE monomer, the order of the hydrogen bond strength can be sorted as TFE-MA (119 cm- 1) > TFE-MF (93 cm- 1) > TFE-MTFA (44 cm- 1). Combining the experimental infrared spectra with the DFT calculations, the Gibbs free energies of formation were determined to be 1.5, 4.5 and 8.6 kJ mol- 1 for TFE-MA, TFE-MF and TFE-MTFA, respectively. The hydrogen bonding in the MTFA complex is much weaker than those of the TFE-MA and TFE-MF complexes due to the effect of the CF3 substitution on MTFA, while the replacement of an H atom with a CH3 group in methyl ester only slightly increases the hydrogen bond strength. Topological analysis and localized molecular orbital energy decomposition analysis was also applied to compare the interactions in the complexes.

  2. Methyl-donor nutrients inhibit breast cancer cell growth.

    Science.gov (United States)

    Park, Chung S; Cho, Kyongshin; Bae, Dong R; Joo, Nam E; Kim, Hyung H; Mabasa, Lawrence; Fowler, Andrea W

    2008-01-01

    Lipotropes (methyl group containing nutrients, including methionine, choline, folate, and vitamin B(12)) are dietary methyl donors and cofactors that are involved in one-carbon metabolism, which is important for genomic DNA methylation reactions and nucleic acid synthesis. One-carbon metabolism provides methyl groups for all biological methylation pathways and is highly dependent on dietary supplementation of methyl nutrients. Nutrition is an important determinant of breast cancer risk and tumor behavior, and dietary intervention may be an effective approach to prevent breast cancer. Apoptosis is important for the regulation of homeostasis and tumorigenesis. The anti-apoptotic protein Bcl-2 may be a regulatory target in cancer therapy; controlling or modulating its expression may be a therapeutic strategy against breast cancer. In this study, the effects of lipotrope supplementation on the growth and death of human breast cancer cell lines T47D and MCF-7 were examined and found to inhibit growth of both T47D and MCF-7 cells. Furthermore, the ratios of apoptotic cells to the total number of cells were approximately 44% and 34% higher in the lipotrope-supplemented treatments of T47D and MCF-7 cancer cells, respectively, compared with the control treatments. More importantly, Bcl-2 protein expression was decreased by approximately 25% from lipotrope supplementation in T47D cells, suggesting that lipotropes can induce breast cancer cell death by direct downregulation of Bcl-2 protein expression. Cancer treatment failure is often correlated with Bcl-2 protein upregulation. These data may be useful in the development of effective nutritional strategies to prevent and reduce breast cancer in humans.

  3. Methyl fluorosulfonyldifluoroacetate (MFSDA): An Underutilised Reagent for Trifluoromethylation.

    Science.gov (United States)

    Clarke, Sarah L; McGlacken, Gerard P

    2017-01-26

    The introduction of fluorine groups to pharmaceutical compounds can have a dramatic effect on the lipophilicity and metabolic stability of the molecule in vivo. Around 20 % of drugs contain at least one fluorine atom. The trifluoromethyl group is known to have beneficial effects and can dramatically affect the biological activity when substituted for a methyl group, for example. In any case, the direct and late-stage introduction of a trifluoromethyl group is a powerful transformation in the tool box of the medicinal chemist. The use of methyl fluorosulfonyldifluoroacetate (MFSDA) as a relatively inexpensive reagent for trifluoromethylation was first reported in 1989; however, in our opinion it has been somewhat underutilised. Herein, a comprehensive review of trifluoromethylation using MFSDA is reported, which we hope will further expose readers to this useful reagent. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Science.gov (United States)

    2010-07-01

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

  5. Quantitative DNA Methylation Profiling in Cancer.

    Science.gov (United States)

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

    2016-01-01

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

  6. miRNAting control of DNA methylation

    Indian Academy of Sciences (India)

    miRNAting control of DNA methylation. ASHWANI JHA and RAVI SHANKAR. Supplementary figure 1. Enrichment analysis of the genes methylated in the presence of IDNl1 and/or IDNl2 for molecular function and biological process. Supplementary figure 2. Enrichment analysis of the genes methylated by DRM2 for ...

  7. The role of methylation in urological tumours

    NARCIS (Netherlands)

    Heijden, A.G. van der

    2013-01-01

    Alterations in DNA methylation have been described in human cancer for more than thirty years now. Since the last decade DNA methylation gets more and more important in cancer research. In this review the different alterations of DNA methylation are discussed in testicular germ cell tumours,

  8. Whole-genome DNA methylation characteristics in pediatric precursor B cell acute lymphoblastic leukemia (BCP ALL.

    Directory of Open Access Journals (Sweden)

    Radosław Chaber

    Full Text Available In addition to genetic alterations, epigenetic abnormalities have been shown to underlie the pathogenesis of acute lymphoblastic leukemia (ALL-the most common pediatric cancer. The purpose of this study was to characterize the whole genome DNA methylation profile in children with precursor B-cell ALL (BCP ALL and to compare this profile with methylation observed in normal bone marrow samples. Additional efforts were made to correlate the observed methylation patterns with selected clinical features. We assessed DNA methylation from bone marrow samples obtained from 38 children with BCP ALL at the time of diagnosis along with 4 samples of normal bone marrow cells as controls using Infinium MethylationEPIC BeadChip Array. Patients were diagnosed and stratified into prognosis groups according to the BFM ALL IC 2009 protocol. The analysis of differentially methylated sites across the genome as well as promoter methylation profiles allowed clear separation of the leukemic and control samples into two clusters. 86.6% of the promoter-associated differentially methylated sites were hypermethylated in BCP ALL. Seven sites were found to correlate with the BFM ALL IC 2009 high risk group. Amongst these, one was located within the gene body of the MBP gene and another was within the promoter region- PSMF1 gene. Differentially methylated sites that were significantly related with subsets of patients with ETV6-RUNX1 fusion and hyperdiploidy. The analyzed translocations and change of genes' sequence context does not affect methylation and methylation seems not to be a mechanism for the regulation of expression of the resulting fusion genes.

  9. The role of cytosine methylation on charge transport through a DNA strand

    Science.gov (United States)

    Qi, Jianqing; Govind, Niranjan; Anantram, M. P.

    2015-09-01

    Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Using density functional theory and the Landauer-Büttiker method, we study the electronic properties and charge transport through an eight base-pair methylated DNA strand and its native counterpart. We first analyze the effect of cytosine methylation on the tight-binding parameters of two DNA strands and then model the transmission of the electrons and conductance through the strands both with and without decoherence. We find that the main difference of the tight-binding parameters between the native DNA and the methylated DNA lies in the on-site energies of (methylated) cytosine bases. The intra- and inter-strand hopping integrals between two nearest neighboring guanine base and (methylated) cytosine base also change with the addition of the methyl groups. Our calculations show that in the phase-coherent limit, the transmission of the methylated strand is close to the native strand when the energy is nearby the highest occupied molecular orbital level and larger than the native strand by 5 times in the bandgap. The trend in transmission also holds in the presence of the decoherence with the same rate. The lower conductance for the methylated strand in the experiment is suggested to be caused by the more stable structure due to the introduction of the methyl groups. We also study the role of the exchange-correlation functional and the effect of contact coupling by choosing coupling strengths ranging from weak to strong coupling limit.

  10. Characteristics of DNA methylation changes induced by traffic-related air pollution.

    Science.gov (United States)

    Ding, Rui; Jin, Yongtang; Liu, Xinneng; Zhu, Ziyi; Zhang, Yuan; Wang, Ting; Xu, Yinchun

    2016-01-15

    Traffic-related air pollution (TRAP) is a potential risk factor for numerous respiratory disorders, including lung cancer, while alteration of DNA methylation may be one of the underlying mechanisms. However, the effects of TRAP mixtures on DNA methylation have not been investigated. We have studied the effects of brief or prolonged TRAP exposures on DNA methylation in the rat. The exposures were performed in spring and autumn, with identical study procedures. In each season, healthy Wistar rats were exposed to TRAP at for 4 h, 7 d, 14 d, or 28 d. Global DNA methylation (LINE-1 and Alu) and specific gene methylation (p16(CDKN2A), APC, and iNOS) in the DNA from blood and lung tissues were quantified by pyrosequencing. Multiple linear regression was applied to assess the influence of air pollutants on DNA methylation levels. The levels of PM2.5, PM10, and NO2 in the high and moderate groups were significantly higher than in the control group. The DNA methylation levels were not significantly different between spring and autumn. When spring and autumn data were analyzed together, PM2.5, PM10, and NO2 exposures were associated with changes in%5mC (95% CI) in LINE-1, iNOS, p16(CDKN2A), and APC ranging from -0.088 (-0.150, -0.026) to 0.102 (0.049, 0.154) per 1 μg/m(3) increase in the pollutant concentration. Prolonged exposure to a high level of TRAP was negatively associated with LINE-1 and iNOS methylation, and positively associated with APC methylations in the DNA from lung tissues but not blood. These findings show that TRAP exposure is associated with decreased methylation of LINE-1 and iNOS, and increased methylation of p16(CDKN2A) and APC. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. The role of cytosine methylation on charge transport through a DNA strand

    Energy Technology Data Exchange (ETDEWEB)

    Qi, Jianqing, E-mail: jqqi@uw.edu; Anantram, M. P., E-mail: anantmp@uw.edu [Department of Electrical Engineering, University of Washington, Seattle, Washington 98195-2500 (United States); Govind, Niranjan, E-mail: niri.govind@pnnl.gov [William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States)

    2015-09-07

    Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Using density functional theory and the Landauer-Büttiker method, we study the electronic properties and charge transport through an eight base-pair methylated DNA strand and its native counterpart. We first analyze the effect of cytosine methylation on the tight-binding parameters of two DNA strands and then model the transmission of the electrons and conductance through the strands both with and without decoherence. We find that the main difference of the tight-binding parameters between the native DNA and the methylated DNA lies in the on-site energies of (methylated) cytosine bases. The intra- and inter-strand hopping integrals between two nearest neighboring guanine base and (methylated) cytosine base also change with the addition of the methyl groups. Our calculations show that in the phase-coherent limit, the transmission of the methylated strand is close to the native strand when the energy is nearby the highest occupied molecular orbital level and larger than the native strand by 5 times in the bandgap. The trend in transmission also holds in the presence of the decoherence with the same rate. The lower conductance for the methylated strand in the experiment is suggested to be caused by the more stable structure due to the introduction of the methyl groups. We also study the role of the exchange-correlation functional and the effect of contact coupling by choosing coupling strengths ranging from weak to strong coupling limit.

  12. Chemical characterization of atmospheric particles and source apportionment in the vicinity of a steelmaking industry

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, S.M., E-mail: smarta@ctn.ist.utl.pt [Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 139.7 km, 2695-066 Bobadela LRS (Portugal); Lage, J. [Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 139.7 km, 2695-066 Bobadela LRS (Portugal); Fernández, B. [Global R& D, ArcelorMittal, Avilés (Spain); Garcia, S. [Instituto de Soldadura e Qualidade, Av. Prof. Dr. Cavaco Silva, 33, 2740-120 Porto Salvo (Portugal); Reis, M.A.; Chaves, P.C. [Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 139.7 km, 2695-066 Bobadela LRS (Portugal)

    2015-07-15

    The objective of this work was to provide a chemical characterization of atmospheric particles collected in the vicinity of a steelmaking industry and to identify the sources that affect PM{sub 10} levels. A total of 94 PM samples were collected in two sampling campaigns that occurred in February and June/July of 2011. PM{sub 2.5} and PM{sub 2.5–10} were analyzed for a total of 22 elements by Instrumental Neutron Activation Analysis and Particle Induced X-ray Emission. The concentrations of water soluble ions in PM{sub 10} were measured by Ion Chromatography and Indophenol-Blue Spectrophotometry. Positive Matrix Factorization receptor model was used to identify sources of particulate matter and to determine their mass contribution to PM{sub 10}. Seven main groups of sources were identified: marine aerosol identified by Na and Cl (22%), steelmaking and sinter plant represented by As, Cr, Cu, Fe, Ni, Mn, Pb, Sb and Zn (11%), sinter plant stack identified by NH{sub 4}{sup +}, K and Pb (12%), an unidentified Br source (1.8%), secondary aerosol from coke making and blast furnace (19%), fugitive emissions from the handling of raw material, sinter plant and vehicles dust resuspension identified by Al, Ca, La, Si, Ti and V (14%) and sinter plant and blast furnace associated essentially with Fe and Mn (21%). - Highlights: • Emissions from steelworks are very complex. • The larger steelworks contribution to PM{sub 10} was from blast furnace and sinter plant. • Sinter plant stack emissions contributed for 12% of the PM{sub 10} mass. • Secondary aerosol from coke making and blast furnace contributed for 19% of the PM{sub 10}. • Fugitive dust emissions highly contribute to PM{sub 10} mass.

  13. The Nature of Surface States on Vicinal Cu (775): An STM and Photoemission Study

    OpenAIRE

    Zaki, Nader; Knox, Kevin; Osgood, Richard M.; Johnson, Peter D.; Fujii, Jun; Vobornik, Ivana; Panaccione, Giancarlo

    2014-01-01

    We report ARPES and a set of in situ STM measurements on a narrow-terrace-width vicinal Cu(111) crystal surface, Cu(775), whose vicinal cut lies close to the transition between terrace and step modulation. These measurements show sharp zone-folding (or Umklapp) features with a periodicity in k||, indicating that the predominant reference plane is that of Cu(775), i.e. that the surface is predominately step-modulated. Our measurements also show variation in Umklapp intensity with photon energy...

  14. 2-Bromo-2-methyl-N-p-tolylpropanamide

    Directory of Open Access Journals (Sweden)

    Rodolfo Moreno-Fuquen

    2011-06-01

    Full Text Available In the title molecule, C11H14BrNO, there is twist between the mean plane of the amide group and the benzene ring [C(=O—N—C...;C torsion angle = −31.2 (5°]. In the crystal, intermolecular N—H...O and weak C—H...O hydrogen bonds link molecules into chains along [100]. The methyl group H atoms are disordered over two sets of sites with equal occupancy.

  15. DNA methylation signatures in cord blood of ICSI children.

    Science.gov (United States)

    El Hajj, Nady; Haertle, Larissa; Dittrich, Marcus; Denk, Sarah; Lehnen, Harald; Hahn, Thomas; Schorsch, Martin; Haaf, Thomas

    2017-08-01

    Does ICSI induce specific DNA methylation changes in the resulting offspring? Although several thousand analyzed CpG sites (throughout the genome) displayed significant between-group methylation differences, both ICSI and spontaneously conceived children varied within the normal range of methylation variation. Children conceived by ART have increased risks for medical problems at birth and to the extent of present knowledge also in later life (i.e. impaired metabolic and cardiovascular functions). One plausible mechanism mediating these ART effects are epigenetic changes originating in the germ cells and/or early embryos and persisting during further development. We compared the cord blood methylomes and candidate gene methylation patterns of newborns conceived through ICSI or spontaneously. Umbilical cord bloods were obtained from healthy newborn singletons conceived spontaneously (53 samples), through ICSI (89) or IVF (34). Bisulfite-converted DNA samples of 48 ICSI and 46 control pregnancies were used for genome-wide analyses with Illumina's 450K methylation arrays. Candidate genes from the methylation screen were analyzed in all three groups by bisulfite pyrosequencing. Altogether, 4730 (0.11%) of 428 227 analyzed CpG sites exhibited significant between-group methylation differences, but all with small (β studied in more detail by bisulfite pyrosequencing. ATG4C and SNORD114-9 could be validated in an independent ICSI group, following adjustment for maternal age and other confounding factors. ATG4C was also significant in the IVF group. N/A. The observed epigenetic effects are small and there are numerous potential confounding factors such as parental age and infertility. Although our study meets current standards for epigenetic screens, sample size is still two orders of magnitude below that of genome-wide association studies. Our study suggests an impact of ICSI on the offspring's epigenome(s), which may contribute to phenotypic variation and disease

  16. Proximal methylation features associated with nonrandom changes in gene body methylation

    OpenAIRE

    Picard, Colette L.; Gehring, Mary

    2017-01-01

    Background Gene body methylation at CG dinucleotides is a widely conserved feature of methylated genomes but remains poorly understood. The Arabidopsis thaliana strain Cvi has depleted gene body methylation relative to the reference strain Col. Here, we leverage this natural epigenetic difference to investigate gene body methylation stability. Results Recombinant inbred lines derived from Col and Cvi were used to examine the transmission of distinct gene body methylation states. The vast majo...

  17. Identification of endometrial cancer methylation features using combined methylation analysis methods.

    Directory of Open Access Journals (Sweden)

    Michael P Trimarchi

    Full Text Available DNA methylation is a stable epigenetic mark that is frequently altered in tumors. DNA methylation features are attractive biomarkers for disease states given the stability of DNA methylation in living cells and in biologic specimens typically available for analysis. Widespread accumulation of methylation in regulatory elements in some cancers (specifically the CpG island methylator phenotype, CIMP can play an important role in tumorigenesis. High resolution assessment of CIMP for the entire genome, however, remains cost prohibitive and requires quantities of DNA not available for many tissue samples of interest. Genome-wide scans of methylation have been undertaken for large numbers of tumors, and higher resolution analyses for a limited number of cancer specimens. Methods for analyzing such large datasets and integrating findings from different studies continue to evolve. An approach for comparison of findings from a genome-wide assessment of the methylated component of tumor DNA and more widely applied methylation scans was developed.Methylomes for 76 primary endometrial cancer and 12 normal endometrial samples were generated using methylated fragment capture and second generation sequencing, MethylCap-seq. Publically available Infinium HumanMethylation 450 data from The Cancer Genome Atlas (TCGA were compared to MethylCap-seq data.Analysis of methylation in promoter CpG islands (CGIs identified a subset of tumors with a methylator phenotype. We used a two-stage approach to develop a 13-region methylation signature associated with a "hypermethylator state." High level methylation for the 13-region methylation signatures was associated with mismatch repair deficiency, high mutation rate, and low somatic copy number alteration in the TCGA test set. In addition, the signature devised showed good agreement with previously described methylation clusters devised by TCGA.We identified a methylation signature for a "hypermethylator phenotype" in

  18. DNA methylation of methylation complex genes in relation to stress and genome-wide methylation in mother-newborn dyads.

    Science.gov (United States)

    Clukay, Christopher J; Hughes, David A; Rodney, Nicole C; Kertes, Darlene A; Mulligan, Connie J

    2017-10-13

    Early life stress is known to have enduring biological effects, particularly with respect to health. Epigenetic modifications, such as DNA methylation, are a possible mechanism to mediate the biological effect of stress. We previously found correlations between maternal stress, newborn birthweight, and genome-wide measures of DNA methylation. Here we investigate ten genes related to the methylation/demethylation complex in order to better understand the impact of stress on health. DNA methylation and genetic variants at methylation/demethylation genes were assayed. Mean methylation measures were constructed for each gene and tested, in addition to genetic variants, for association with maternal stress measures based on interview and survey data (chronic stress and war trauma), maternal venous, and newborn cord genome-wide mean methylation (GMM), and birthweight. After cell type correction, we found multiple pairwise associations between war trauma, maternal GMM, maternal methylation at DNMT1, DNMT3A, TET3, and MBD2, and birthweight. The association of maternal GMM and maternal methylation at DNMT1, DNMT3A, TET3, and MBD2 is consistent with the role of these genes in establishing, maintaining and altering genome-wide methylation patterns, in some cases in response to stress. DNMT1 produces one of the primary enzymes that reproduces methylation patterns during DNA replication. DNMT3A and TET3 have been implicated in genome-wide hypomethylation in response to glucocorticoid hormones. Although we cannot determine the directionality of the genic and genome-wide changes in methylation, our results suggest that altered methylation of specific methylation genes may be part of the molecular mechanism underlying the human biological response to stress. © 2017 Wiley Periodicals, Inc.

  19. Methyl (E-2-({2-[(E-(hydroxyiminomethyl]phenoxy}methyl-3-(4-methylphenylacrylate

    Directory of Open Access Journals (Sweden)

    G. Ganesh

    2012-06-01

    Full Text Available In the title compound, C19H19NO4, the dihedral angle between the mean planes through the benzene rings is 82.18 (7°. The C=N double bond is trans-configured. The molecules are linked into centrosymmetric dimers via pairs of O—H...N hydrogen bonds with the motif R22(6. The crystal packing also features C—H...O interactions. The methyl group attached to one of the aromatic rings is disordered over two almost equally occupied positions [occpancy ratio = 0.51 (4:0.49 (4].

  20. 2-Ethyl 4-methyl 5-ethyl-3-methyl-1H-pyrrole-2,4-dicarboxylate

    Directory of Open Access Journals (Sweden)

    Gui-Fen Lu

    2012-02-01

    Full Text Available The title pyrrole derivative compound, C12H17NO4, was synthesized from methyl 3-oxopentanoate by a Knorr-type reaction and contains a pyrrole ring to which two diagonal alkoxycarbonyl groups and two diagonal alkyl substituents are attached. The methylcarbonyl and ethylcarbonyl substituents are approximately co-planar with the pyrrole ring, making dihedral angles of 5.64 (2 and 3.44 (1°, respectively. In the crystal, adjacent molecules are assembled by pairs of N—H...O hydrogen bonds into dimers in a head-to-head mode.

  1. DNA methylation increases throughout Arabidopsis development.

    Science.gov (United States)

    Ruiz-García, L; Cervera, M T; Martínez-Zapater, J M

    2005-10-01

    We used amplified fragment length polymorphisms (AFLP) to analyze the stability of DNA methylation throughout Arabidopsis development. AFLP can detect genome-wide changes in cytosine methylation produced by DNA demethylation agents, such as 5-azacytidine, or specific mutations at the DDM1 locus. In both cases, cytosine demethylation is associated with a general increase in the presence of amplified fragments. Using this approach, we followed DNA methylation at methylation sensitive restriction sites throughout Arabidopsis development. The results show a progressive DNA methylation trend from cotyledons to vegetative organs to reproductive organs.

  2. The forest melliferous flora in the vicinity of Blace, Serbia

    Directory of Open Access Journals (Sweden)

    Perišić Snežana

    2004-01-01

    Full Text Available Melliferous plant species in the forests near Blace (South Serbia were investigated in order to estimate the significance, contribution, quality and ecological characteristics of representatives of the apiflora as potential nectar and pollen sources, the elements of bee pasturage. The significance of melliferous plants was determined on the basis of nectar and pollen production intensity, as well as by following blooming periods. According to adaptations to moisture, light, and temperature, melliferous species can be relegated to eight groups and six subgroups. Out of the total number of melliferous species in the investigated area (223, the forest apiflora accounted for 82 species (36,77%. The species with highest nectar and/or pollen production are: Alnus glutinosa, Corylus avellana, Paulownia tomentosa, Picea abies, Prunus tenella, Robinia pseudoacacia, species of the genera Salix, Tilia, and Campanula, Atropa bella-donna, Calamintha officinalis, Glechoma hederacea, Pulmonaria officinalis, Salvia glutinosa and Valeriana officinalis.

  3. Proximal methylation features associated with nonrandom changes in gene body methylation.

    Science.gov (United States)

    Picard, Colette L; Gehring, Mary

    2017-04-26

    Gene body methylation at CG dinucleotides is a widely conserved feature of methylated genomes but remains poorly understood. The Arabidopsis thaliana strain Cvi has depleted gene body methylation relative to the reference strain Col. Here, we leverage this natural epigenetic difference to investigate gene body methylation stability. Recombinant inbred lines derived from Col and Cvi were used to examine the transmission of distinct gene body methylation states. The vast majority of genic CG methylation patterns are faithfully transmitted over nine generations according to parental genotype, with only 1-4% of CGs either losing or gaining methylation relative to the parent. Genic CGs that fail to maintain the parental methylation state are shared among independent lines, suggesting that these are not random occurrences. We use a logistic regression framework to identify features that best predict sites that fail to maintain parental methylation state. Intermediate levels of CG methylation around a dynamic CG site and high methylation variability across many A. thaliana strains at that site are the strongest predictors. These data suggest that the dynamic CGs we identify are not specific to the Col-Cvi recombinant inbred lines but have an epigenetic state that is inherently less stable within the A. thaliana species. Extending this, variably methylated genic CGs in maize and Brachypodium distachyon are also associated with intermediate local CG methylation. These results provide new insights into the features determining the inheritance of gene body methylation and demonstrate that two different methylation equilibria can be maintained within single individuals.

  4. Geology and ground water of the Savannah River Plant and vicinity, South Carolina

    Science.gov (United States)

    Siple, George E.

    1967-01-01

    The area described in this report covers approximately 2,600 square miles in west-central South Carolina and includes the site of the Savannah River Plant, a major production facility of the U.S. Atomic Energy Commission. The climate, surface drainage, and land forms of the study area are typical of the southern part of the Atlantic Coastal Plain. Precipitation is normally abundant and fairly evenly distributed throughout the year, and the mean annual temperature is moderately warm (64?F). The major streams that drain the area (the Savannah, Salkehatchie, and Edisto Rivers) have low gradients and flow in a southeasterly direction toward the Atlantic Ocean. Surface features of the area include narrow, flat-bottomed, steep-sided valleys and broad gently rolling interfluvial areas. Those parts of the Coastal Plain included within the report area can be subdivided into the Aiken Plateau, the Congaree Sandhills, and the Coastal Terraces. The area is underlain by a sequence of unconsolidated and partly consolidated sediments of Late Cretaceous, Tertiary, and Quaternary age. The unconsolidated sediments were deposited unconformably on a basement of igneous and metamorphic rocks of Precambrian and Paleozoic age and sedimentary rocks of Triassic age. The basement rocks are similar to the granite-diorite complex of the Charlotte Belt, the metamorphosed rocks of the Carolina Slate Belt, and the consolidated sediments of the Newark Group. The unconsolidated sediments strike about N. 60 ? E. and dip 6-20 feet per mile to the southeast. They form a wedge-shaped mass that increases in thickness toward the southeast to slightly more than 1,200 feet in the vicinity of Allendale, S.C., on the southeast or downdip side of the study area. The oldest or lowermost unconsolidated sedimentary unit, the Tuscaloosa Formation of Late Cretaceous age, is overlain in the subsurface by beds that are also probably Late Cretaceous in age and that herein are named the Ellenton Formation. The Upper

  5. "An Investigation on Methylation Methods of Hesperidin "

    Directory of Open Access Journals (Sweden)

    Fatemeh Fathiazad

    2004-07-01

    Full Text Available Since hesperidin is a poor water soluble compound, in pharmaceutical formulations its methylated derivatives (hesperidin methyl chalcone, HMC are used. The aim of this study was to establish an efficient methylation method for preparation of hesperidin methyl derivatives. For this purpose hesperidin was isolated from tangerine peel, purified and its methyl derivatives were prepared using three different techniques, i.e. diazomethane, methyl iodide-sodium hydride and dimethylsulfate. The efficiency of the methods was evaluated in terms of the percentage of unchanged and intact hesperidin in the final methylated products the and amount of unchanged hesperidin was an indication of the better efficiency of the method. A reversed phase HPLC method was also developed for determination and quantification of hesperidin in the final methylated products .The method involved the use of a Shim pack CLC-ODS column, a mixture of methanol-phosphate buffer (37:63, v/v of pH = 2.6 as a mobile phase in an isocratic mode at a flow rate of 1 ml/min and UV detection at 280 nm. The results showed that methylation with methyl iodide-sodium hydride have the highest efficiency among different methylation methods.

  6. Methylated genes as new cancer biomarkers.

    LENUS (Irish Health Repository)

    Duffy, M J

    2012-02-01

    Aberrant hypermethylation of promoter regions in specific genes is a key event in the formation and progression of cancer. In at least some situations, these aberrant alterations occur early in the formation of malignancy and appear to be tumour specific. Multiple reports have suggested that measurement of the methylation status of the promoter regions of specific genes can aid early detection of cancer, determine prognosis and predict therapy responses. Promising DNA methylation biomarkers include the use of methylated GSTP1 for aiding the early diagnosis of prostate cancer, methylated PITX2 for predicting outcome in lymph node-negative breast cancer patients and methylated MGMT in predicting benefit from alkylating agents in patients with glioblastomas. However, prior to clinical utilisation, these findings require validation in prospective clinical studies. Furthermore, assays for measuring gene methylation need to be standardised, simplified and evaluated in external quality assurance programmes. It is concluded that methylated genes have the potential to provide a new generation of cancer biomarkers.

  7. The effects of diet, genetics and chemicals on toxicity and aberrant DNA methylation: an introduction.

    Science.gov (United States)

    Poirier, Lionel A

    2002-08-01

    In the early 1930s, the group of Banting and Best showed that the choline moiety of lecithin was responsible for the prevention of the fatty livers produced in pancreatectomized dogs treated with insulin. This was the first study linking abnormal methyl metabolism with disease. Since then, deficiencies of each of the four essential dietary sources of methyl groups (choline, methionine, vitamin B-12 and folic acid) have been associated with increased risk of a number of diseases. Choline-deficient diets were shown to enhance liver tumor formation in rats, and such diets frequently were found to lead to atherosclerosis. Although methionine deficiency per se was not extensively studied in vivo, its metabolic antagonist ethionine did cause liver cancer and pancreatic toxicity in rodents. Deficiencies of vitamin B-12 and of folic acid have long been shown to cause neurological disturbances and birth defects both in humans and in experimental animals. In 1969 inborn errors of metabolism leading to the accumulation of the demethylated metabolite of methionine, homocysteine, were proposed as contributing to the early onset of atherosclerosis. Before 1990, numerous studies described the abnormal methylation of DNA in tumors and transformed cells. Less frequently investigated, however, were the exogenous and endogenous agents leading to such abnormal methylation. These included genetic variants among rodent strains and the methyl-deficient diets that caused liver cancer. In addition, several chemicals, particularly carcinogens, were shown to alter DNA methylation. The possible links between chemically induced alterations in DNA methylation and development of other diseases were little explored. However, by 1990, a chain of causality had been established in experimental carcinogenesis linking dietary methyl deficiency with methyl insufficiency in vivo, as well as with the abnormal methylation of DNA and of specific genes. Also during this period, the diminished activity of

  8. Thermal Decomposition of Methyl Esters in Biodiesel Fuel: Kinetics, Mechanisms and Products

    Science.gov (United States)

    Chai, Ming

    Biodiesel continues to enjoy increasing popularity. However, recent studies on carbonyl compounds emissions from biodiesel fuel are inconclusive. Emissions of carbonyl compounds from petroleum diesel fuels were compared to emissions from pure biodiesel fuels and petroleum-biodiesel blends used in a non-road diesel generator. The concentration of total carbonyl compounds was the highest when the engine was idling. The carbonyl emissions, as well as ozone formation potential, from biodiesel fuel blends were higher than those emitted from petroleum diesel fuel. The sulfur content of diesel fuel and the source of biodiesel fuel were not found to have a significant impact on emissions of carbonyl compounds. Mechanism parameters of the thermal decomposition of biodiesel-range methyl esters were obtained from the results of thermal gravimetric analysis (TGA). The overall reaction orders are between 0.49 and 0.71 and the energies of activation are between 59.9 and 101.3 kJ/mole. Methyl esters in air have lower activation energies than those in nitrogen. Methyl linoleate has the lowest activation energy, followed by methyl oleate, and methyl stearate. The pyrolysis and oxidation of the three methyl esters were investigated using a semi-isothermal tubular flow reactor. The profiles of major products versus reaction temperature are presented. In the pyrolysis of methyl stearate, the primary reaction pathway is the decarboxylic reaction at the methyl ester functional group. Methyl oleate's products indicate more reactions on its carbon-carbon double bond. Methyl linoleate shows highest reactivity among the three methyl esters, and 87 products were detected. The oxidation of three methyl esters resulted in more products in all compound classes, and 55, 114, and 127 products were detected, respectively. The oxidation of methyl esters includes decarboxylation on ester group. The methyl ester's carbon chain could be oxidized as a hydrocarbon compound and form oxidized esters and

  9. Methylation of DNA in cancer.

    Science.gov (United States)

    Watanabe, Yoshihisa; Maekawa, Masato

    2010-01-01

    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. Global changes in the epigenetic landscape are a hallmark of cancer. Methylation of cytosine bases in DNA provides a layer of epigenetic control in many eukaryotes that has important implications for normal biology and disease. DNA methylation is a crucial epigenetic modification of the genome that is involved in regulating many cellular processes. These include embryonic development, transcription, chromatin structure, X-chromosome inactivation, genomic imprinting, and chromosome stability. Consistent with these important roles, a growing number of human diseases including cancer have been found to be associated with aberrant DNA methylation. Recent advancements in the rapidly evolving field of cancer epigenetics have described extensive reprogramming of every component of the epigenetic machinery in cancer, such as DNA demethylation. Hypomethylation of the genome largely affects the intergenic and intronic regions of the DNA, particularly repeat sequences and transposable elements, and it is believed to result in chromosomal instability and increased mutation events. Therefore, we propose that R/G-chromosome band boundaries, which correspond with the early/late-switch regions of replication timing and a transition in relative GC content, correspond to "unstable" genomic regions in which concentrated occurrences of repetitive sequences and transposable elements including LINE and Alu elements are hypomethylated during tumorigenesis. In this review, we discuss the current understanding of alterations in DNA methylation composing the epigenetic landscape that occurs in cancer compared with normal cells, the roles of these changes in cancer initiation and progression, and the potential use of this knowledge in designing more

  10. New Synthesis, Structure and Analgesic Properties of Methyl 1-R-4-Methyl-2,2-Dioxo-1H-2λ6,1-Benzothiazine-3-Carboxylates

    Directory of Open Access Journals (Sweden)

    Liliana Azotla-Cruz

    2017-01-01

    Full Text Available According to the principles of the methodology of bioisosteric replacements a series of methyl 1-R-4-methyl-2,2-dioxo-1H-2λ6,1-benzothiazine-3-carboxylates has been obtained as potential analgesics. In addition, a fundamentally new strategy for the synthesis of compounds of this chemical class involving the introduction of N-alkyl substituent at the final stage in 2,1-benzothiazine nucleus already formed has been proposed. Using nuclear magnetic resonance (NMR spectroscopy, mass spectrometry and X-ray diffraction analysis it has been proven that in the DMSO/K2CO3 system the reaction of methyl 4-methyl-2,2-dioxo-1H-2λ6,1-benzothiazine-3-carboxylate and alkyl halides leads to formation of N-substituted derivatives with good yields regardless of the structure of the alkylating agent. The peculiarities of NMR (1Н and 13С spectra of the compounds synthesized, their mass spectrometric behavior and the spatial structure are discussed. In N-benzyl derivative the ability to form a monosolvate with methanol has been found. According to the results of the pharmacological testing conducted on the model of the thermal tail-flick it has been determined that replacement of 4-ОН-group in methyl 1-R-4-hydroxy-2,2-dioxo-1H-2λ6,1-benzothiazine-3-carboxylates for the methyl group is actually bioisosteric since all methyl 1-R-4-methyl-2,2-dioxo-1H-2λ6,1-benzothiazine-3-carboxylates synthesized demonstrated a statistically significant analgesic effect. The majority of the substances can inhibit the thermal pain response much more effective than piroxicam in the same dose. Under the same conditions as an analgesic the N-methyl-substituted analog exceeds not only piroxicam, but more active meloxicam as well. Therefore, it deserves in-depth biological studies on other experimental models.

  11. New Synthesis, Structure and Analgesic Properties of Methyl 1-R-4-Methyl-2,2-Dioxo-1H-2λ6,1-Benzothiazine-3-Carboxylates

    Science.gov (United States)

    Azotla-Cruz, Liliana; Lijanova, Irina V.; Ukrainets, Igor V.; Likhanova, Natalya V.; Olivares-Xometl, Octavio; Bereznyakova, Natalya L.

    2017-01-01

    According to the principles of the methodology of bioisosteric replacements a series of methyl 1-R-4-methyl-2,2-dioxo-1H-2λ6,1-benzothiazine-3-carboxylates has been obtained as potential analgesics. In addition, a fundamentally new strategy for the synthesis of compounds of this chemical class involving the introduction of N-alkyl substituent at the final stage in 2,1-benzothiazine nucleus already formed has been proposed. Using nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry and X-ray diffraction analysis it has been proven that in the DMSO/K2CO3 system the reaction of methyl 4-methyl-2,2-dioxo-1H-2λ6,1-benzothiazine-3-carboxylate and alkyl halides leads to formation of N-substituted derivatives with good yields regardless of the structure of the alkylating agent. The peculiarities of NMR (1Н and 13С) spectra of the compounds synthesized, their mass spectrometric behavior and the spatial structure are discussed. In N-benzyl derivative the ability to form a monosolvate with methanol has been found. According to the results of the pharmacological testing conducted on the model of the thermal tail-flick it has been determined that replacement of 4-ОН-group in methyl 1-R-4-hydroxy-2,2-dioxo-1H-2λ6,1-benzothiazine-3-carboxylates for the methyl group is actually bioisosteric since all methyl 1-R-4-methyl-2,2-dioxo-1H-2λ6,1-benzothiazine-3-carboxylates synthesized demonstrated a statistically significant analgesic effect. The majority of the substances can inhibit the thermal pain response much more effective than piroxicam in the same dose. Under the same conditions as an analgesic the N-methyl-substituted analog exceeds not only piroxicam, but more active meloxicam as well. Therefore, it deserves in-depth biological studies on other experimental models. PMID:28085092

  12. New Synthesis, Structure and Analgesic Properties of Methyl 1-R-4-Methyl-2,2-Dioxo-1H-2λ⁶,1-Benzothiazine-3-Carboxylates.

    Science.gov (United States)

    Azotla-Cruz, Liliana; Lijanova, Irina V; Ukrainets, Igor V; Likhanova, Natalya V; Olivares-Xometl, Octavio; Bereznyakova, Natalya L

    2017-01-12

    According to the principles of the methodology of bioisosteric replacements a series of methyl 1-R-4-methyl-2,2-dioxo-1H-2λ⁶,1-benzothiazine-3-carboxylates has been obtained as potential analgesics. In addition, a fundamentally new strategy for the synthesis of compounds of this chemical class involving the introduction of N-alkyl substituent at the final stage in 2,1-benzothiazine nucleus already formed has been proposed. Using nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry and X-ray diffraction analysis it has been proven that in the DMSO/K₂CO₃ system the reaction of methyl 4-methyl-2,2-dioxo-1H-2λ⁶,1-benzothiazine-3-carboxylate and alkyl halides leads to formation of N-substituted derivatives with good yields regardless of the structure of the alkylating agent. The peculiarities of NMR (¹Н and 13С) spectra of the compounds synthesized, their mass spectrometric behavior and the spatial structure are discussed. In N-benzyl derivative the ability to form a monosolvate with methanol has been found. According to the results of the pharmacological testing conducted on the model of the thermal tail-flick it has been determined that replacement of 4-ОН-group in methyl 1-R-4-hydroxy-2,2-dioxo-1H-2λ⁶,1-benzothiazine-3-carboxylates for the methyl group is actually bioisosteric since all methyl 1-R-4-methyl-2,2-dioxo-1H-2λ⁶,1-benzothiazine-3-carboxylates synthesized demonstrated a statistically significant analgesic effect. The majority of the substances can inhibit the thermal pain response much more effective than piroxicam in the same dose. Under the same conditions as an analgesic the N-methyl-substituted analog exceeds not only piroxicam, but more active meloxicam as well. Therefore, it deserves in-depth biological studies on other experimental models.

  13. Distinctive Klf4 mutants determine preference for DNA methylation status

    Energy Technology Data Exchange (ETDEWEB)

    Hashimoto, Hideharu; Wang, Dongxue; Steves, Alyse N.; Jin, Peng; Blumenthal, Robert M.; Zhang, Xing; Cheng, Xiaodong

    2016-09-04

    Reprogramming of mammalian genome methylation is critically important but poorly understood. Klf4, a transcription factor directing reprogramming, contains a DNA binding domain with three consecutive C2H2 zinc fingers. Klf4 recognizes CpG or TpG within a specific sequence. Mouse Klf4 DNA binding domain has roughly equal affinity for methylated CpG or TpG, and slightly lower affinity for unmodified CpG. The structural basis for this key preference is unclear, though the side chain of Glu446 is known to contact the methyl group of 5-methylcytosine (5mC) or thymine (5-methyluracil). We examined the role of Glu446 by mutagenesis. Substituting Glu446 with aspartate (E446D) resulted in preference for unmodified cytosine, due to decreased affinity for 5mC. In contrast, substituting Glu446 with proline (E446P) increased affinity for 5mC by two orders of magnitude. Structural analysis revealed hydrophobic interaction between the proline's aliphatic cyclic structure and the 5-methyl group of the pyrimidine (5mC or T). As in wild-type Klf4 (E446), the proline at position 446 does not interact directly with either the 5mC N4 nitrogen or the thymine O4 oxygen. In contrast, the unmethylated cytosine's exocyclic N4 amino group (NH2) and its ring carbon C5 atom hydrogen bond directly with the aspartate carboxylate of the E446D variant. Both of these interactions would provide a preference for cytosine over thymine, and the latter one could explain the E446D preference for unmethylated cytosine. Finally, we evaluated the ability of these Klf4 mutants to regulate transcription of methylated and unmethylated promoters in a luciferase reporter assay.

  14. Increased MTHFR promoter methylation in mothers of Down syndrome individuals.

    Science.gov (United States)

    Coppedè, Fabio; Denaro, Maria; Tannorella, Pierpaola; Migliore, Lucia

    2016-05-01

    Despite that advanced maternal age at conception represents the major risk factor for the birth of a child with Down syndrome (DS), most of DS babies are born from women aging less than 35 years. Studies performed in peripheral lymphocytes of those women revealed several markers of global genome instability, including an increased frequency of micronuclei, shorter telomeres and impaired global DNA methylation. Furthermore, young mothers of DS individuals (MDS) are at increased risk to develop dementia later in life, suggesting that they might be "biologically older" than mothers of euploid babies of similar age. Mutations in folate pathway genes, and particularly in the methylenetetrahydrofolate reductase (MTHFR) one, have been often associated with maternal risk for a DS birth as well as with risk of dementia in the elderly. Recent studies pointed out that also changes in MTHFR methylation levels can contribute to human disease, but nothing is known about MTHFR methylation in MDS tissues. We investigated MTHFR promoter methylation in DNA extracted from perypheral lymphocytes of 40 MDS and 44 matched control women that coinceived their children before 35 years of age, observing a significantly increased MTHFR promoter methylation in the first group (33.3 ± 8.1% vs. 28.3 ± 5.8%; p=0.001). In addition, the frequency of micronucleated lymphocytes was available from the women included in the study, was higher in MDS than control mothers (16.1 ± 8.6‰ vs. 10.5 ± 4.3‰; p=0.0004), and correlated with MTHFR promoter methylation levels (r=0.33; p=0.006). Present data suggest that MTHFR epimutations are likely to contribute to the increased genomic instability observed in cells from MDS, and could play a role in the risk of birth of a child with DS as well as in the onset of age related diseases in those women. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. BathymetryB Hillshade [5m]--Monterey Canyon and Vicinity, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for 2-m and 5-m bathymetry and shaded-relief maps of Monterey Canyon and Vicinity, California. The raster data file is included in...

  16. BathymetryA [2m]--Monterey Canyon and Vicinity, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for 2-m and 5-m bathymetry and shaded-relief maps of Monterey Canyon and Vicinity, California. The raster data file is included in...

  17. BathymetryB [5m]--Monterey Canyon and Vicinity, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for 2-m and 5-m bathymetry and shaded-relief maps of Monterey Canyon and Vicinity, California. The raster data file is included in...

  18. BathymetryA Hillshade [2m]--Monterey Canyon and Vicinity, California

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This part of DS 781 presents data for 2-m and 5-m bathymetry and shaded-relief maps of Monterey Canyon and Vicinity, California. The raster data file is included in...

  19. Properties of Soils and Plants Uptake within the Vicinity of Selected ...

    African Journals Online (AJOL)

    Backyard farming is becoming popular among the auto mechanics near their workshops where spent engine oil and carcass of vehicles are continuously dumped in Nigeria. The properties of soil and maize plants sampled from the vicinity of selected auto mechanic workshops in Ile-Ife, Nigeria were investigated. The results ...

  20. Assessment of pollution trend of heavy metals in soils in the vicinity ...

    African Journals Online (AJOL)

    Topsoil and subsoil obtained in the vicinity of the Nigerian Gas Company were digested and analysed for some selected trace metals using atomic absorption spectrophotometer of model pye unicam SP 2900. The trace metals determined include nickel, copper, iron, barium, lead, cadmium and zinc respectively.

  1. Formation and sintering of Pt nanopartictes on vicinal rutile TiO2 surfaces

    DEFF Research Database (Denmark)

    Rieboldt, Felix; Helveg, S.; Bechstein, Ralf

    2014-01-01

    By means of scanning tunnelling microscopy (STM) the nucleation, growth and sintering of platinum nanoparticles (Pt NP's) was studied on vicinal and flat rutile titanium dioxide (TiO2) surfaces. Utilising physical vapour deposition, the nucleation of Pt NP's on TiO2 surfaces at room temperature (...

  2. [Analysis of optical emission spectra from ICP of Ar in the vicinity of plasma sheath].

    Science.gov (United States)

    Zhao, Wen-Feng; Chen, Jun-Fang; Meng, Ran

    2009-11-01

    In order to control the ion density and energy distribution in the vicinity of plasma sheath independently, the inductively coupled plasma and its glow discharge mechanism in the vicinity of plasma sheath were studied by means of optical emission spectroscopy (OES) under different RF power, different discharge and different substrate DC bias voltage. It was shown that the ion density is higher and the electron temperature is lower in the vicinity of inductively coupled plasma sheath according to the ionic line and atomic line. With changing the discharge pressure and RF power, the spectral characteristics analysis shows that the ion density in the vicinity of plasma sheath linearly increases with the RF power and rises with the pressure under the low pressure. The atomic spectral intensity of low excitation states increases rapidly. The atomic spectral intensity of high excitation states rises slowly and the intensity of ion spectrum increases not obviously. By applying the DC bias voltage to substrate, the intensity of emission spectroscopy was analyzed. The result shows that the intensity of spectra rises with the increase in positive bias voltage, while first reduces then increases with the increase in negative bias voltage, and is the weakest in the case of DC bias at -30 V. This shows that the fast ions and the electrons are the main source of energy for Ar ionization and excitation.

  3. Revised Hydrogeology for the Suprabasalt Aquifer System, 200-West Area and Vicinity, Hanford Site, Washington

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Bruce A.; Bjornstad, Bruce N.; Schalla, Ronald; Webber, William D.

    2002-05-14

    The primary objective of this study was to refine the conceptual groundwater flow model for the 200-West Area and vicinity. This is the second of two reports that combine to cover the 200 Area Plateau, an area that holds the largest inventory of radionuclide and chemical waste on the Hanford Site.

  4. Revised Hydrogeology for the Suprabasalt Aquifer System, 200-East Area and Vicinity, Hanford Site, Washington

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Bruce A.; Bjornstad, Bruce N.; Schalla, Ronald; Webber, William D.

    2000-04-20

    This study supports the Hanford Groundwater/Vadose integration project objectives to better understand the risk of groundwater contamination and potential risk to the public via groundwater flow paths. The primary objective of this study was to refine the conceptual groundwater flow model for the 200-East Area and vicinity.

  5. Surface-water quality, Oneida Reservation and vicinity, Wisconsin, 1997-98

    Science.gov (United States)

    Schmidt, Morgan A.; Scudder, Barbara C.; Richards, Kevin D.

    2000-01-01

    Streamwater samples were collected at 19 sites in the vicinity of the Oneida Tribe of Indians of Wisconsin Reservation. Samples were collected during 5 sampling periods in 1997-98. Field measurements were made and samples were analyzed for nutrients, suspended sediment, major ions, and pesticides.

  6. Parental smoking in the vicinity of children and tobacco control policies in the European region

    NARCIS (Netherlands)

    Kovess, V.; Pilowsky, D.J.; Boyd, A.; Pez, O.; Bitfoi, A.; Carta, M.G.; Eke, C.; Golitz, D.; Kuijpers, R.C.W.M.; Lesinskiene, S.; Mihova, Z.; Otten, R.; Susser, E.

    2013-01-01

    Objective: To ascertain patterns of parental smoking in the vicinity of children in Eastern and Western Europe and their relation to Tobacco Control Scale (TCS) scores. Methods: Data on parental smoking patterns were obtained from the School Child Mental Health Europe (SCMHE), a 2010

  7. 14 CFR 91.137 - Temporary flight restrictions in the vicinity of disaster/hazard areas.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 2 2010-01-01 2010-01-01 false Temporary flight restrictions in the vicinity of disaster/hazard areas. 91.137 Section 91.137 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) AIR TRAFFIC AND GENERAL OPERATING RULES GENERAL OPERATING AND FLIGHT RULES Flight Rules General §...

  8. Series Resistance Monitoring for Photovoltaic Modules in the Vicinity of MPP

    DEFF Research Database (Denmark)

    Sera, Dezso

    2010-01-01

    the time period with reduced power production. This paper focuses on the estimation of series resistance of flat silicone PV panels or arrays during operation, in the vicinity of their MPP. The method presented in this paper helps to detect failures by monitoring changes in the panel’s or array’s series...

  9. Establishment of background radiation dose rate in the vicinity of the ...

    African Journals Online (AJOL)

    The absorbed dose rate in air in the vicinity of the proposed Manyoni uranium mining project located in Singida region, Tanzania, was determined so as to establish the baseline data for background radiation dose rate data prior to commencement of uranium mining activities. Twenty stations in seven villages were selected ...

  10. 77 FR 71493 - Amendment of VOR Federal Airway V-8 in the Vicinity of Rifle, CO

    Science.gov (United States)

    2012-12-03

    ...This action amends VHF Omnidirectional Range (VOR) Federal Airway V-8 in the vicinity of Rifle, CO, to correct the description contained in part 71 to ensure it matches the information contained in the FAA's aeronautical database, matches the depiction on the associated charts, and to ensure the safety and efficiency of the National Airspace System (NAS).

  11. Parental smoking in the vicinity of children and tobacco control policies in the European region

    NARCIS (Netherlands)

    Kovess, V.; Pilowsky, D.J.; Boyd, A.; Pez, O.; Bitfoi, A.; Carta, M.G.; Eke, C.; Golitz, D.; Kuijpers, R.C.W.M.; Lesinskiene, S.; Mihova, Z.; Otten, R.; Susser, E.S.

    2013-01-01

    Objective: To ascertain patterns of parental smoking in the vicinity of children in Eastern and Western Europe and their relation to Tobacco Control Scale (TCS) scores. Methods: Data on parental smoking patterns were obtained from the School Child Mental Health Europe (SCMHE), a 2010 cross-sectional

  12. Methylation of Dietary Flavones Increases Their Metabolic Stability and Chemopreventive Effects

    Directory of Open Access Journals (Sweden)

    Thomas Walle

    2009-11-01

    Full Text Available Dietary flavones have promising chemoprotective properties, in particular with regard to cancer, but problems with low oral bioavailability and sometimes unacceptable toxicity have made their use as protective additives to normal diets questionable. However, methylation of free phenolic hydroxyl groups leads to derivatives not susceptible to glucuronic acid or sulfate conjugation, resulting in increased metabolic stability. Methylation also leads to greatly improved transport through biological membranes, such as in intestinal absorption, and much increased oral bioavailability. Recent studies also indicate that methylation results in derivatives with increasing potency to kill cancer cells. They also show high potency towards inhibition of hormone-regulating enzymes, e.g., aromatase, important in the causation of breast cancer. Methylation of the flavones may also result in derivatives with diminished toxic side-effects and improved aqueous solubility. In conclusion, it appears that methylation of dietary flavones as well as of other food products may produce derivatives with much improved health effects.

  13. Methylation effect on the ohmic resistance of a poly-GC DNA-like chain

    Energy Technology Data Exchange (ETDEWEB)

    Moura, F.A.B.F. de, E-mail: fidelis@fis.ufal.br [Instituto de Física, Universidade Federal de Alagoas, Maceió AL 57072-970 (Brazil); Lyra, M.L. [Instituto de Física, Universidade Federal de Alagoas, Maceió AL 57072-970 (Brazil); Almeida, M.L. de; Ourique, G.S.; Fulco, U.L.; Albuquerque, E.L. [Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN (Brazil)

    2016-10-14

    We determine, by using a tight-binding model Hamiltonian, the characteristic current–voltage (IxV) curves of a 5-methylated cytosine single strand poly-GC DNA-like finite segment, considering the methyl groups attached laterally to a random fraction of the cytosine basis. Striking, we found that the methylation significantly impacts the ohmic resistance (R) of the DNA-like segments, indicating that measurements of R can be used as a biosensor tool to probe the presence of anomalous methylation. - Highlights: • Ohmic resistance of finite segments of poly-CG DNA-like segments. • Possibility for the development of biosensor devices. • Methylation effect and electronic transport in DNA-like segments.

  14. ID4 methylation predicts high risk of leukemic transformation in patients with myelodysplastic syndrome.

    Science.gov (United States)

    Wang, Hong; Wang, Xiao-Qin; Xu, Xiao-Ping; Lin, Guo-Wei

    2010-05-01

    Epigenetic gene silencing due to promoter methylation is observed in human cancers like acute myeloid leukemia (AML). Little is known about aberrant methylation in myelodysplastic syndrome (MDS), a heterogeneous clonal stem cell disorder with a approximately 30% risk of transformation into secondary AML. Recent evidence demonstrated that ID4, a negative regulator of transcription, may act as a tumor-suppressor gene. To clarify the role of ID4 in MDS, we employed methylation-specific PCR (MSP) to examine the methylation status of ID4 in 144 adult de novo MDS patients. We found that ID4 methylation was present in 35.4% (n=51) of these MDS patients and methylaiton was correlated significantly with World Health Organization (WHO) subtypes and International Prognostic Scoring System (IPSS) risk groups. Patients with advanced stages of WHO subtypes (45.8% vs. 21.3%, P=0.002) and higher risk IPSS subgroups (45.7% vs. 26.0%, P=0.014) exhibited a significantly higher frequency of ID4 methylation. The median survival of patients with ID4 methylation was shorter than patients without ID4 methylation (12.2 months vs. 26.9 months, P=0.005). Multivariate analysis indicated that ID4 methylation status was the independent factor that impacted leukemia-free survival (LFS). Disease in patients with ID4 methylation progressed more rapidly than those without ID4 methylation (P=0.047, HR=2.11). Our results suggest that ID4 may be a therapeutic target in MDS. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

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

    2013-05-01

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

  16. [Faunal characteristics and distribution pattern of crustaceans in the vicinity of Pearl River estuary].

    Science.gov (United States)

    Huang, Zi-Rong; Sun, Dian-Rong; Chen, Zuo-Zhi; Zhang, Han-Hua; Wang, Xue-Hui; Wang, Yue-Zhong; Fang, Hong-Da; Dong, Yan-Hong

    2009-10-01

    Based on the data of bottom trawl surveys in the vicinity of Pearl River estuary in August (summer), October (autumn), December (winter) 2006, and April (spring) 2007, the faunal characteristics and distribution pattern of crustaceans were analyzed. A total of 54 species belonging to 25 genera, 17 families, and 2 orders were collected, including 22 species of shrimps, 22 species of crabs, and 10 species of squills. Most of the crustaceans were tropical-subtropical warm-water species, a few of them were eurythermal species, and no warm-water and cold-water species occurred. Euryhaline species were most abundant, followed by halophile species, and the low-salinity species were the least. Most of the crustacean species belonged to the fauna of Indian Ocean-western Pacific Ocean. The faunal assemblages were closer to those of the East China Sea, Philippine Sea, Indonesia Sea, and the Japan Sea, and estranger with those of the Yellow Sea, Bohai Sea, and Korea Sea. The dominant species were Metapenaeus joyner, Oratosquilla oratoria, Charybdis miles, Portunus sanguinolentus, Harpiosquilla harpax, Charybdis feriatus, Charybdis japonica, Oratosquilla nepa, Solenocera crassicornis, Portunus trituberculatus, and Calappa philargius. The crustaceans had the largest species number (33) in autumn and the least one (26) in spring, and the highest stock density at the water depth of < 40 m, especially at 10-20 m. The average stock density of the crustaceans was estimated to be 99.60 kg x km(-2), with the highest (198.93 kg x km(-2)) in summer and the lowest (42.35 kg x km(-2)) in spring. Of the 3 species groups, crabs had the highest stock density (41.81 kg x km(-2)), followed by shrimps (38.91 kg x km(-2)), and squills (18.88 kg x km(-2)). The stock densities of the 3 species groups showed an obvious seasonal variation. Shrimps had the highest stock density (120.32 kg x km(-2)) in summer and the lowest density (0.67 kg x km(-2)) in spring, while crabs and squills had the highest

  17. Potential usefulness of methyl gallate in the treatment of experimental colitis.

    Science.gov (United States)

    Anzoise, María Laura; Basso, Angeles Rodríguez; Del Mauro, Julieta Sofía; Carranza, Andrea; Ordieres, Graciela López; Gorzalczany, Susana

    2017-11-07

    Methyl gallate is a gallotannin widely distributed in nature. Previous studies have demonstrated its antioxidant, anti-inflammatory, antimicrobial and anti-tumor activities. In the present study, the activity of methyl gallate on experimental models of inflammatory bowel disease has been investigated. Experimental colitis was induced in Sprague-Dawley rats through the intracolonic instillation of an acetic acid solution (2 mL, 4% v/v). Methyl gallate (100 and 300 mg/kg, p.o.) and the reference drug mesalazine (100 mg/kg, p.o.) were tested. Methyl gallate induced a significant reduction in the colon weight/length ratio and macroscopic lesion score. Besides, the malondialdehyde content and the GSSG/GSH ratio were remarkably decreased. Furthermore, the administration of methyl gallate reduced the expression of COX 2 , IL-6, TNFα and the severity of microscopic tissue damage induced by acetic acid, while the mean goblet cell density was significantly higher in both the group treated with methyl gallate and the one treated with mesalazine, in comparison with untreated animals. The Na + K + ATPase pump activity was recovered in treated groups (control: 827.2 ± 59.6, colitis: 311.6 ± 54.8, methyl gallate 100 mg/kg: 642.2 ± 175.0, methyl gallate 300 mg/kg: 809.7 ± 100.6, mesalazine: 525.3 ± 81.7). Methyl gallate was also found to induce a significant reduction in the castor oil-induced intestinal motility in Swiss mice, decreasing the peristalsis by 74.5 and 58.82% at 100 and 300 mg/kg p.o., respectively. This compound also antagonized the jejunum contractions induced by Ach and CaCl 2 . This study demonstrates that methyl gallate exerts beneficial effects in a preclinical model of intestinal disorders.

  18. A Minimal DNA Methylation Signature in Oral Tongue Squamous Cell Carcinoma Links Altered Methylation with Tumor Attributes.

    Science.gov (United States)

    Krishnan, Neeraja M; Dhas, Kunal; Nair, Jayalakshmi; Palve, Vinayak; Bagwan, Jamir; Siddappa, Gangotri; Suresh, Amritha; Kekatpure, Vikram D; Kuriakose, Moni Abraham; Panda, Binay

    2016-09-01

    Oral tongue squamous cell carcinomas (OTSCC) are a homogenous group of aggressive tumors in the head and neck region that spread early to lymph nodes and have a higher incidence of regional failure. In addition, there is a rising incidence of oral tongue cancer in younger populations. Studies on functional DNA methylation changes linked with altered gene expression are critical for understanding the mechanisms underlying tumor development and metastasis. Such studies also provide important insight into biomarkers linked with viral infection, tumor metastasis, and patient survival in OTSCC. Therefore, we performed genome-wide methylation analysis of tumors (N = 52) and correlated altered methylation with differential gene expression. The minimal tumor-specific DNA 5-methylcytosine signature identified genes near 16 different differentially methylated regions, which were validated using genomic data from The Cancer Genome Atlas cohort. In our cohort, hypermethylation of MIR10B was significantly associated with the differential expression of its target genes NR4A3 and BCL2L11 (P = 0.0125 and P = 0.014, respectively), which was inversely correlated with disease-free survival (P = 9E-15 and P = 2E-15, respectively) in patients. Finally, differential methylation in FUT3, TRIM5, TSPAN7, MAP3K8, RPS6KA2, SLC9A9, and NPAS3 genes was found to be predictive of certain clinical and epidemiologic parameters. This study reveals a functional minimal methylation profile in oral tongue tumors with associated risk habits, clinical, and epidemiologic outcomes. In addition, NR4A3 downregulation and correlation with patient survival suggests a potential target for therapeutic intervention in oral tongue tumors. Data from the current study are deposited in the NCBI Geo database (accession number GSE75540). Mol Cancer Res; 14(9); 805-19. ©2016 AACR. ©2016 American Association for Cancer Research.

  19. Electron collisions with methyl-substituted ethylenes: Cross section measurements and calculations for 2-methyl-2-butene and 2,3-dimethyl-2-butene

    Science.gov (United States)

    Szmytkowski, Czesław; Stefanowska, Sylwia; Zawadzki, Mateusz; Ptasińska-Denga, ElŻbieta; MoŻejko, Paweł

    2015-08-01

    We report electron-scattering cross sections determined for 2-methyl-2-butene [(H3C)HC = C(CH3)2] and 2,3-dimethyl-2-butene [(H3C)2C = C(CH3)2] molecules. Absolute grand-total cross sections (TCSs) were measured for incident electron energies in the 0.5-300 eV range, using a linear electron-transmission technique. The experimental TCS energy dependences for the both targets appear to be very similar with respect to the shape. In each TCS curve, three features are discernible: the resonant-like structure located around 2.6-2.7 eV, the broad distinct enhancement peaking near 8.5 eV, and a weak hump in the vicinity of 24 eV. Theoretical integral elastic (ECS) and ionization (ICS) cross sections were computed up to 3 keV by means of the additivity rule (AR) approximation and the binary-encounter-Bethe method, respectively. Their sums, (ECS+ICS), are in a reasonable agreement with the respective measured TCSs. To examine the effect of methylation of hydrogen sides in the ethylene [H2C = CH2] molecule on the TCS, we compared the TCS energy curves for the sequence of methylated ethylenes: propene [H2C = CH(CH3)], 2-methylpropene [H2C = C(CH3)2], 2-methyl-2-butene [(H3C)HC = C(CH3)2], and 2,3-dimethyl-2-butene [(H3C)2C = C(CH3)2], measured in the same laboratory. Moreover, the isomeric effect is also discussed for the C5H10 and C6H12 compounds.

  20. 33 CFR 334.1120 - Pacific Ocean in the vicinity of Point Mugu, Calif.; naval small arms firing range.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Pacific Ocean in the vicinity of Point Mugu, Calif.; naval small arms firing range. 334.1120 Section 334.1120 Navigation and Navigable... REGULATIONS § 334.1120 Pacific Ocean in the vicinity of Point Mugu, Calif.; naval small arms firing range. (a...

  1. 33 CFR 334.620 - Straits of Florida and Florida Bay in vicinity of Key West, Fla.; operational training area...

    Science.gov (United States)

    2010-07-01

    ... Bay in vicinity of Key West, Fla.; operational training area, aerial gunnery range, and bombing and strafing target areas, Naval Air Station, Key West, Fla. 334.620 Section 334.620 Navigation and Navigable... REGULATIONS § 334.620 Straits of Florida and Florida Bay in vicinity of Key West, Fla.; operational training...

  2. Evolution of DNA Methylation across Insects.

    Science.gov (United States)

    Bewick, Adam J; Vogel, Kevin J; Moore, Allen J; Schmitz, Robert J

    2017-03-01

    DNA methylation contributes to gene and transcriptional regulation in eukaryotes, and therefore has been hypothesized to facilitate the evolution of plastic traits such as sociality in insects. However, DNA methylation is sparsely studied in insects. Therefore, we documented patterns of DNA methylation across a wide diversity of insects. We predicted that underlying enzymatic machinery is concordant with patterns of DNA methylation. Finally, given the suggestion that DNA methylation facilitated social evolution in Hymenoptera, we tested the hypothesis that the DNA methylation system will be associated with presence/absence of sociality among other insect orders. We found DNA methylation to be widespread, detected in all orders examined except Diptera (flies). Whole genome bisulfite sequencing showed that orders differed in levels of DNA methylation. Hymenopteran (ants, bees, wasps and sawflies) had some of the lowest levels, including several potential losses. Blattodea (cockroaches and termites) show all possible patterns, including a potential loss of DNA methylation in a eusocial species whereas solitary species had the highest levels. Species with DNA methylation do not always possess the typical enzymatic machinery. We identified a gene duplication event in the maintenance DNA methyltransferase 1 (DNMT1) that is shared by some Hymenoptera, and paralogs have experienced divergent, nonneutral evolution. This diversity and nonneutral evolution of underlying machinery suggests alternative DNA methylation pathways may exist. Phylogenetically corrected comparisons revealed no evidence that supports evolutionary association between sociality and DNA methylation. Future functional studies will be required to advance our understanding of DNA methylation in insects. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  3. X-ray investigations of sulfur-containing fungicides. IV. 4'-[[Benzoyl(4-chlorophenylhydrazono)methyl]sulfonyl]acetanilide and 4'-[[benzoyl(4-methoxyphenylhydrazono)methyl]sulfonyl]acetanilide.

    Science.gov (United States)

    Wolf, W M

    2001-09-01

    The conformations of the two approximately isomorphous structures 4'-[[benzoyl(4-chlorophenylhydrazono)methyl]sulfonyl]acetanilide, C(22)H(18)ClN(3)O(4)S, and 4'-[[benzoyl(4-methoxyphenylhydrazono)methyl]sulfonyl]acetanilide, C(23)H(21)N(3)O(5)S, are stabilized by resonance-assisted intramolecular hydrogen bonds linking the hydrazone moieties and sulfonyl groups. The stronger bond is observed in the former compound. The difference in electronic properties between the Cl atom and the methoxy group is too small to significantly alter the non-bonding interactions of the sulfonyl and beta-carbonyl groups.

  4. Changes in global DNA methylation intensity and DNMT1 transcription during the aging process of scallop Chlamys farreri

    Science.gov (United States)

    Lian, Shanshan; He, Yan; Li, Xue; Zhao, Bosong; Hou, Rui; Hu, Xiaoli; Zhang, Lingling; Bao, Zhenmin

    2015-08-01

    DNA methylation is an important epigenetic regulatory mechanism that influences genomic stability, gene activation, X-chromosome inactivation and other factors. A change in DNA methylation is usually associated with aging and cellular senescence. DNA methyltransferase 1 (DNMT1) is the most abundant DNA methyltransferase, and it plays an important role in maintaining the established methylation pattern during DNA replication in vertebrates. Although the effect of aging on DNA methylation has been well studied in vertebrates, little research has been conducted in invertebrates, especially in marine bivalves. In this study, we examined global DNA methylation levels in four groups of adult Zhikong scallop Chlamys farreri at different ages. The results showed that both the age and tissue type had a strong effect on the DNA methylation. In addition, a significant decrease in DNA methylation with aging (1-4 years) can be detected in mantle, kidney and hepatopancreas. We further measured the change in DNMT1 transcript abundance using quantitative reverse transcription PCR (qRT-PCR), which revealed that DNMT1 transcription significantly decreased with aging in mantle and hepatopancreas and strongly correlated with DNA methylation ( R = 0.72). Our data provided greater insight into the aging-related decline of DNA methylation, which could aid in gaining a better understanding of the relationship between DNA methylation and the aging process in bivalve mollusks.

  5. Detection of DNA methylation in eucaryotic cells.

    Science.gov (United States)

    Sulewska, Anetta; Niklinska, Wieslawa; Kozlowski, Miroslaw; Minarowski, Lukasz; Naumnik, Wojciech; Niklinski, Jacek; Dabrowska, Katarzyna; Chyczewski, Lech

    2007-01-01

    The methods of molecular biology allow for analyzing the methylation pattern in the whole genome and in particular genes. We differentiate methylated sequences from unmethylated ones by means of cutting the genomic template with methylation-sensitive restriction enzymes or by sodium bisulfite DNA modification. Chemical modification precedes most quantitative and qualitative PCR techniques: MS-PCR, MS-nested PCR, Real-Time PCR, QAMA, HeavyMethyl, MSHRM. Restriction enzymes, on the other hand, may be used together with PCR or hybridisation methods (Southern blot and microarrays). PCRs are conducted with primers specific for methylated and unmethylated sequences and sometimes, similarly to hybridisation techniques, with specifically labeled probes or dyes intercalating to double-stranded nucleic acids. The most advanced methylation detection techniques (MALDI-TOF MS and HPLC) significantly reduce the amount of biological material used for tests, but they require specialist equipment.

  6. Detection of DNA methylation in eucaryotic cells.

    Directory of Open Access Journals (Sweden)

    Lech Chyczewski

    2008-01-01

    Full Text Available The methods of molecular biology allow for analyzing the methylation pattern in the whole genome and in particular genes. We differentiate methylated sequences from unmethylated ones by means of cutting the genomic template with methylation-sensitive restriction enzymes or by sodium bisulfite DNA modification. Chemical modification precedes most quantitative and qualitative PCR techniques: MS-PCR, MS-nested PCR, Real-Time PCR, QAMA, HeavyMethyl, MSHRM. Restriction enzymes, on the other hand, may be used together with PCR or hybridisation methods (Southern blot and microarrays. PCRs are conducted with primers specific for methylated and unmethylated sequences and sometimes, similarly to hybridisation techniques, with specifically labeled probes or dyes intercalating to double-stranded nucleic acids. The most advanced methylation detection techniques (MALDI-TOF MS and HPLC significantly reduce the amount of biological material used for tests, but they require specialist equipment.

  7. Electrochemical reduction of imazamethabenz methyl on mercury and carbon electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Ruiz Montoya, Mercedes, E-mail: mmontoya@uhu.e [Departamento de Ingenieria Quimica, Quimica Fisica y Quimica Organica, Universidad de Huelva, Campus El Carmen, Facultad de Ciencias Experimentales, E-21071 Huelva (Spain); Pintado, Sara; Rodriguez Mellado, Jose Miguel [Departamento de Quimica Fisica y Termodinamica Aplicada, Universidad de Cordoba, Campus Universitario de Rabanales, edificio ' Marie Curie' , E-14014 Cordoba (Spain)

    2010-03-30

    This paper presents polarographic and voltammetric studies of the reduction of the herbicide imazamethabenz methyl (2/3-methyl-(4-isopropyl-4-methyl-5-oxo-2-imidazolin-2-yl)-p-toluate), on mercury and carbon electrodes. The electrochemical studies were performed in strongly acidic media (0.1-2.7 M H{sub 2}SO{sub 4}) as well as in the pH range of 1-12. The overall reduction process involves the uptake of two electrons. The results obtained in polarography show that there is the reduction of two species, related via an acid-base equilibrium, and having very close reduction potentials. The voltammetric results obtained with a glassy carbon electrode were very similar to those observed on mercury electrodes. The reducible group in the molecule is the imidazolinone ring. In strongly acidic media (pH < pK{sub a}), the reaction mechanism proposed is the reduction of the protonated herbicide by an electrochemical-chemical-electrochemical (ECE) process, being the r.d.s. the second electron transfer. At pH > pK{sub a} the neutral form of the herbicide is reduced and the second electron transfer becomes reversible or quasi-reversible. In basic media, the species reduced is the deprotonated imazamethabenz methyl and the r.d.s. is the second electron transfer.

  8. Aberrant gene promoter methylation in sputum from individuals exposed to smoky coal emissions

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Y.; Lan, Q.; Shen, M.; Jin, J.; Mumford, J.; Ren, D.X.; Keohavong, P. [University of Pittsburgh, Pittsburgh, PA (United States). Dept. of Environment and Occupational Health

    2008-07-15

    Recent studies suggested the potential for aberrant gene promoter methylation in sputum as a predictive marker for lung cancer. Here, the promoter methylation of p16, MGMT, RASSF1A and DAPK genes was investigated in sputum of individuals exposed to smoky coal emissions in Xuan Wei, China, where the lung cancer rate is more than 6 times the Chinese national average. Sputum DNA of 107 noncancer individuals and 58 lung cancer patients was screened for promoter methylation using methylation-specific PCR. Promoter methylation of the p16 gene was detected in about half (51.4% (551107)) of sputum DNA from noncancer individuals, a frequency higher than that observed for the RASSF1A (29.9%), MGMT (17.8%) and DAPK (15.9%) genes. Furthermore, the p16 gene was affected by promoter methylation at a frequency even higher among the lung cancer group, compared with the noncancer group (70.7% (41/58) versus 51.7% (55/107), p=0.017). Individuals exposed to smoky coal emissions in this region harbored frequent promoter methylation of these genes in their sputum and some of such alterations may be involved in lung tumor development.

  9. DNA methylation profile in chronic myelomonocytic leukemia associates with distinct clinical, biological and genetic features.

    Science.gov (United States)

    Palomo, Laura; Malinverni, Roberto; Cabezón, Marta; Xicoy, Blanca; Arnan, Montserrat; Coll, Rosa; Pomares, Helena; García, Olga; Fuster-Tormo, Francisco; Grau, Javier; Feliu, Evarist; Solé, Francesc; Buschbeck, Marcus; Zamora, Lurdes

    2017-11-21

    Chromosomal abnormalities are detected in 20-30% of patients with chronic myelomonocytic leukemia (CMML) and correlate with prognosis. On the mutation level, disruptive alterations are particularly frequent in chromatin regulatory genes. However, little is known about the consequential alterations in the epigenetic marking of the genome. Here, we report the analysis of genomic DNA methylation patterns of 64 CMML patients and 10 healthy controls, using a DNA methylation microarray focused on promoter regions. Differential methylation analysis between patients and controls allowed us to identify abnormalities in DNA methylation, including hypermethylation of specific genes and large genome regions with aberrant DNA methylation. Unsupervised hierarchical cluster analysis identified two main clusters that associated with the clinical, biological, and genetic features of patients. Group 1 was enriched in patients with adverse clinical and biological characteristics and poorer overall and progression-free survival. In addition, significant differences in DNA methylation were observed between patients with low risk and intermediate/high risk karyotypes and between TET2 mutant and wild type patients. Taken together, our results demonstrate that altered DNA methylation patterns reflect the CMML disease state and allow to identify patient groups with distinct clinical features.

  10. Ability of PITX2 methylation to predict survival in patients with prostate cancer.

    Science.gov (United States)

    Li, Jiu-Zhi; Zhang, Yu; Wen, Bin; Li, Ming; Wang, Yu-Jie

    2015-01-01

    The aim of this study was to explore whether candidate gene methylation can effectively predict death from prostate cancer. After reviewing the literature to identify likely candidate genes, we assembled a case-control cohort (in a 1:2 ratio) to explore the distribution of PITX2, WNT5a, SPARC, EPB41L3, and TPM4 methylation levels. The case group comprised 45 patients with a Gleason score ≤7 who had died as a result of prostate cancer, and the control group comprised 90 current prostate cancer patients or those who died of other causes. The methylation possibility of each of the candidate genes were maximized. Univariate conditional logistic was applied for data analysis and to evaluate prediction efficiency of gene methylation on prostate cancer. The results indicated that a raised level of PITX2 methylation increased the likelihood of death due to prostate cancer by 10% (odds ratio 1.56, 95% confidence interval 1.17-2.08; P=0.005). Methylation of SPARC was found to be able to distinguish between benign prostate hyperplasia and prostate cancer. Methylation of PITX2 is an effective biomarker to predict death from prostate cancer, particularly in patients with a low Gleason score.

  11. DNA methylation profiles of elderly individuals subjected to indentured childhood labor and trauma.

    Science.gov (United States)

    Marinova, Zoya; Maercker, Andreas; Küffer, Andreas; Robinson, Mark D; Wojdacz, Tomasz K; Walitza, Susanne; Grünblatt, Edna; Burri, Andrea

    2017-02-27

    Childhood trauma is associated with increased vulnerability to mental and somatic disorders later in life. Epigenetic modifications such as DNA methylation are one potential mechanism through which such long-lasting impairments/consequences can be explained. The aim of the present study was to investigate whether childhood trauma is associated with long-term DNA methylation alterations in old age. We assessed genome-wide DNA methylation profiles in a cohort of former indentured child laborers ("Verdingkinder") who suffered severe childhood adversities (N = 30; M age = 75.9 years), and compared them to control group with similar demographic characteristics (N = 15, M age = 72.8 years). DNA was isolated from epithelial buccal cells and hybridized to the Illumina Infinium 450 k DNA methylation array, which provides coverage of 485,000 methylation sites. After accounting for batch effects, age, gender and multiple testing, 71 differentially methylated CpG positions were identified between the two groups. They were annotated among others to genes involved in neuronal projections and neuronal development. Some of the identified genes with differential methylation (DLG associated protein 2, mechanistic target of rapamycin) have previously been associated with traumatic stress. The results indicate specific epigenetic alterations in elderly individuals who were subjected to childhood adversities. Psychiatric and somatic comorbidities as well as differences in buccal epithelial cells proportion may contribute to the observed epigenetic differences.

  12. DNA methylation profiling reveals the presence of population-specific signatures correlating with phenotypic characteristics.

    Science.gov (United States)

    Giri, Anil K; Bharadwaj, Soham; Banerjee, Priyanka; Chakraborty, Shraddha; Parekatt, Vaisak; Rajashekar, Donaka; Tomar, Abhishek; Ravindran, Aarthi; Basu, Analabha; Tandon, Nikhil; Bharadwaj, Dwaipayan

    2017-06-01

    Phenotypic characteristics are known to vary substantially among different ethnicities around the globe. These variations are mediated by number of stochastic events and cannot be attributed to genetic architecture alone. DNA methylation is a well-established mechanism that sculpts our epigenome influencing phenotypic variation including disease manifestation. Since DNA methylation is an important determinant for health issues of a population, it demands a thorough investigation of the natural differences in genome wide DNA methylation patterns across different ethnic groups. This study is based on comparative analyses of methylome from five different ethnicities with major focus on Indian subjects. The current study uses hierarchical clustering approaches, principal component analysis and locus specific differential methylation analysis on Illumina 450K methylation data to compare methylome of different ethnic subjects. Our data indicates that the variations in DNA methylation patterns of Indians are less among themselves compared to other global population. It empirically correlated with dietary, cultural and demographical divergences across different ethnic groups. Our work further suggests that Indians included in this study, despite their genetic similarity with the Caucasian population, are in close proximity with Japanese in terms of their methylation signatures.

  13. Methylation analysis of multiple genes in blood DNA of Alzheimer's disease and healthy individuals.

    Science.gov (United States)

    Tannorella, Pierpaola; Stoccoro, Andrea; Tognoni, Gloria; Petrozzi, Lucia; Salluzzo, Maria Grazia; Ragalmuto, Alda; Siciliano, Gabriele; Haslberger, Alexander; Bosco, Paolo; Bonuccelli, Ubaldo; Migliore, Lucia; Coppedè, Fabio

    2015-07-23

    We collected blood DNA from 120 late-onset Alzheimer's disease (AD) patients and 115 healthy matched controls and analysed the methylation levels of genes involved in amyloid-beta peptide production (PSEN1 and BACE1), in DNA methylation (DNMT1, DNMT3A and DNMT3B), and in one-carbon metabolism (MTHFR), searching for correlation with age and gender, with biomarkers of one-carbon metabolism (plasma homocysteine, and serum folate and vitamin B12 levels), and with disease status (being healthy or having AD). We also evaluated the contribution of the APOE ϵ4 allele, the major late-onset AD genetic risk factor, to the studied gene methylation levels. All the genes showed low mean methylation levels (DNA, no difference between groups, and no correlation with the studied biomarkers, except for MTHFR that showed methylation levels ranging from 5% to 75%, and correlation with circulating biomarkers of one-carbon metabolism. However, mean MTHFR methylation levels were similar between groups (31.1% in AD and 30.7% in controls, P=0.58). Overall, present data suggest that none of the studied regions is differently methylated in blood DNA between AD and control subjects. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  14. Brain-derived neurotrophic factor promoter methylation and cortical thickness in recurrent major depressive disorder.

    Science.gov (United States)

    Na, Kyoung-Sae; Won, Eunsoo; Kang, June; Chang, Hun Soo; Yoon, Ho-Kyoung; Tae, Woo Suk; Kim, Yong-Ku; Lee, Min-Soo; Joe, Sook-Haeng; Kim, Hyun; Ham, Byung-Joo

    2016-02-15

    Recent studies have reported that methylation of the brain-derived neurotrophic factor (BDNF) gene promoter is associated with major depressive disorder (MDD). This study aimed to investigate the association between cortical thickness and methylation of BDNF promoters as well as serum BDNF levels in MDD. The participants consisted of 65 patients with recurrent MDD and 65 age- and gender-matched healthy controls. Methylation of BDNF promoters and cortical thickness were compared between the groups. The right medial orbitofrontal, right lingual, right lateral occipital, left lateral orbitofrontal, left pars triangularis, and left lingual cortices were thinner in patients with MDD than in healthy controls. Among the MDD group, right pericalcarine, right medical orbitofrontal, right rostral middle frontal, right postcentral, right inferior temporal, right cuneus, right precuneus, left frontal pole, left superior frontal, left superior temporal, left rostral middle frontal and left lingual cortices had inverse correlations with methylation of BDNF promoters. Higher levels of BDNF promoter methylation may be closely associated with the reduced cortical thickness among patients with MDD. Serum BDNF levels were significantly lower in MDD, and showed an inverse relationship with BDNF methylation only in healthy controls. Particularly the prefrontal and occipital cortices seem to indicate key regions in which BDNF methylation has a significant effect on structure.

  15. Polymerization of Methyl Methacrylate Catalyzed by Co(II), Cu(II), and Zn(II) Complexes Bearing N-Methyl-N-((pyridin-2-yl)methyl) cyclohexanamine

    Energy Technology Data Exchange (ETDEWEB)

    Ahn, Seoung Hyun; Lee, Hyosun [Kyungpook National University, Daegu (Korea, Republic of); Shin, Jongwon [POSTECH, Pohang (Korea, Republic of); Nayab, Saira [Shaheed Benazir Bhutto University, Sheringal (Pakistan)

    2016-05-15

    We demonstrated the synthesis and characterization of Co(II), Cu(II), and Zn(II) complexes ligated to N-methyl-N-((pyridin-2-yl)methyl)cyclohexanamine. The complex [Co(nmpc)Cl{sub 2}] in the presence of MMAO showed the highest catalytic activity for MMA polymerization at 60 °C compared with its Zn(II) and Cu(II) analogs. The metal center showed an obvious influence on the catalytic activity, although this appeared to have no effect on the stereo-regularity of the resultant PMMA. X-ray diffraction analysis revealed that [Co(nmpc)Cl{sub 2}] and [Zn(nmpc)Cl{sub 2}] crystallized in the monoclinic system with space group P2{sub 1}/c and existed as monomeric and solvent-free complexes.

  16. Molecularly imprinted films of acrylonitrile/methyl methacrylate/acrylic acid terpolymers: influence of methyl methacrylate in the binding performance of L-ephedrine imprinted films.

    Science.gov (United States)

    Brisbane, Carrie; McCluskey, Adam; Bowyer, Michael; Holdsworth, Clovia I

    2013-05-07

    Molecularly imprinted polymeric films (MIPFs) highly selective to 1R,2S(-)ephedrine (L-ephedrine, EPD) were produced by phase inversion post-polymerization imprinting on poly(acrylonitrile-co-methyl methacrylate-co-acrylic acid) (PAMA) terpolymers. The inclusion of methyl methacrylate (MMA) to the polymer formulation resulted in enhanced EPD selectivity which appears to be dictated by polymer composition to achieve the necessary balance between polymer rigidity and porosity. Substitution of MMA with methyl acrylate, ethyl acrylate and n-butyl acrylate resulted in a loss of EPD selectivity and EPD entrapment within the polymer matrix not observed in PAMA MIPFs. MMA, by virtue of its methyl group, is able to provide the scaffolding and rigidity necessary for stability and preservation of imprinted cavities within the PAMA MIPF leading to high EPD selectivity.

  17. DNA Methylation Patterns in Crassostrea gigas

    OpenAIRE

    Olson, Claire; Roberts, Steven; Gavery, Mackenzie

    2013-01-01

    Poster presented at the NSA conference in Nashville in 2013.  This research uses the Pacific Oyster as a model organism to characterize the distribution and identify potential functions of DNA methylation.  We examined genome-wide methylation patterns to elucidate the mechanisms by which DNA methylation impacts transcriptional processes. ___________________________________________ This material is based upon work supported by the National Science Foundation under Grant Number 1158119. ...

  18. Hypoxic radiosensitization by the antimicrobial methyl paraben

    Energy Technology Data Exchange (ETDEWEB)

    Jacobs, G.P.; Sade, N.

    1984-08-01

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

  19. Influence of Group-III-metal and Ag adsorption on the Ge growth on Si(111) and its vicinal surface

    Energy Technology Data Exchange (ETDEWEB)

    Speckmann, Moritz

    2011-12-15

    In the framework of this thesis the surfactant-mediated heteroepitaxial growth of Ge on different Si surfaces has been investigated by means of low-energy electron microscopy, low-energy electron diffraction, spot-profile analysing low-energy electron diffraction, X-ray standing waves, grazing-incidence X-ray diffraction, x-ray photoemission electron microscopy, X-ray photoemission spectroscopy, scanning tunneling microscopy, scanning electron microscopy, transmission electron microscopy, and density functional theory calculations. As surfactants gallium, indium, and silver were used. The adsorption of Ga or In on the intrinsically faceted Si(112) surface leads to a smoothing of the surface and the formation of (N x 1) reconstructions, where a mixture of building blocks of different sizes is always present. For both adsorbates the overall periodicity on the surface is strongly dependent on the deposition temperature and the coverage. For the experimental conditions chosen here, the periodicities are in the range of 5.2{<=}N{<=}6.5 and 3.4{<=}N{<=}3.7 for Ga and In, respectively. The (N x 1) unit cells of Ga/Si(112) and In/Si(112) are found to consist of adsorbate atoms on terrace and step-edge sites, forming two atomic chains along the [110] direction. In the Ga-induced structures two Ga-vacancies per unit cell (one in the terrace and one in the step-edge site) are found and a continuous vacancy line on the surface is formed. In the In/Si(112) structure only one vacancy per unit cell in the step-edge site exists and, thus, a continuous adsorbate chain on the terrace sites is present. The adsorption of Ga or In on Si(112) strongly influences the subsequent Ge growth. Ge deposition on the Ga-terminated Si(112) surface leads to the formation of Ge nanowires, which are elongated along the Ga chains and reach lengths of up to 2000 nm for a growth temperature of 600 C. On In-covered Si(112), both small dash-like Ge islands and triangularly shaped islands are found, where the latter ones are terminated by (111), (013) and (103) side facets as well as a (112) top facet. Ga and In have a contrary impact on the Ge diffusion on the Si(112) surface. While Ga reduces the diffusion for Ge atoms, compared to the growth on the bare Si(112) surface, In increases the diffusion. For the first time Ag was employed as surfactant material for Ge growth on Si. On a completely ({radical}(3) x {radical}(3))-R 30 -Ag covered Si(111) surface a drastic increase of the diffusion length for Ge and, thus, the growth of huge Ge islands (sizes of several {mu}m) is observed. Their density is about three orders of magnitude lower as compared to the growth on the clean Si(111) surface. At a coverage of around 90 bilayers (layer thickness of around 28 nm) the islands are coalesced and a closed Ge film is formed. Ag deposition on both, Si(112) and Si(113), induces the formation of a regular array of nanometer-scale facets along the [110] direction, the sizes of which are dependent on the growth temperature and a maximum periodicity perpendicular to [110] of 55 nm is determined. On Si(112) the array consists of alternating (111) and (113) facets, whereas on Si(113) alternating (111) and (115) facets are found. Subsequently deposited Ge grows nicely along the direction of the facets. Thereby, Ge nanowires with lengths of up to 600 nm and aspect ratios of up to 10:1 are formed.

  20. Platinum and associated elements at the New Rambler mine and vicinity, Albany and Carbon Counties, Wyoming

    Science.gov (United States)

    Theobald, P.K.; Thompson, Charles Emmet

    1968-01-01

    Platinum-group metals in the Medicine Bow Mountains were first identified by W. C. Knight in 1901. In the Medicine Bow Mountains, these metals are commonly associated with copper, silver, or gold in shear zones that cut a series of mafic igneous and metamorphic rocks. At the New Rambler mine, where the initial discovery was made, about 50,000 tons of mine and mill waste contain an average of 0.3 percent copper, 7 ppm (parts per million) silver, 1 ppm platinum plus palladium, and 0.7 ppm gold. This material is believed to be from a low-grade envelope around the high-grade pod of complex ore that was mined selectively in the old workings. Soil samples in the vicinity of the New Rambler mine exhibit a wide range of content of several elements associated with the ore. Most of the variation can be attributed to contamination, from the mine workings. Even though soil samples identify a low-level copper anomaly that persists to the limit of the area sampled, soils do not offer a promising medium for tracing mineralization owing to the blanket of transported overburden. Stream sediments, if preconcentrated for analysis, do reveal anomalies not only in the contaminated stream below the New Rambler mine, but in adjacent drainage and on Dave Creek. Examination of a spectrum of elements in heavy-mineral concentrates from stream sediment may contribute to knowledge of the nature of the mineralization and of the basic geology of the environment. The sampling of bedrock exposures is not particularly fruitful because outcrops are sparse and the exposed rocks are the least altered and mineralized. Bedrock sampling does, however, provide information on the large size and provincial nature of the platinum-rich area. We feel that a properly integrated program of geological, geophysical, and geochemical exploration in the Medicine Bow Mountains and probably in the Sierra Madre to the west has a reasonable probability of successfully locating a complex ore body.

  1. Enantioselective Synthesis of Vicinal (R,R)-Diols by Saccharomyces cerevisiae Butanediol Dehydrogenase.

    Science.gov (United States)

    Calam, Eduard; González-Roca, Eva; Fernández, M Rosario; Dequin, Sylvie; Parés, Xavier; Virgili, Albert; Biosca, Josep A

    2016-01-04

    Butanediol dehydrogenase (Bdh1p) from Saccharomyces cerevisiae belongs to the superfamily of the medium-chain dehydrogenases and reductases and converts reversibly R-acetoin and S-acetoin to (2R,3R)-2,3-butanediol and meso-2,3-butanediol, respectively. It is specific for NAD(H) as a coenzyme, and it is the main enzyme involved in the last metabolic step leading to (2R,3R)-2,3-butanediol in yeast. In this study, we have used the activity of Bdh1p in different forms-purified enzyme, yeast extracts, permeabilized yeast cells, and as a fusion protein (with yeast formate dehydrogenase, Fdh1p)-to transform several vicinal diketones to the corresponding diols. We have also developed a new variant of the delitto perfetto methodology to place BDH1 under the control of the GAL1 promoter, resulting in a yeast strain that overexpresses butanediol dehydrogenase and formate dehydrogenase activities in the presence of galactose and regenerates NADH in the presence of formate. While the use of purified Bdh1p allows the synthesis of enantiopure (2R,3R)-2,3-butanediol, (2R,3R)-2,3-pentanediol, (2R,3R)-2,3-hexanediol, and (3R,4R)-3,4-hexanediol, the use of the engineered strain (as an extract or as permeabilized cells) yields mixtures of the diols. The production of pure diol stereoisomers has also been achieved by means of a chimeric fusion protein combining Fdh1p and Bdh1p. Finally, we have determined the selectivity of Bdh1p toward the oxidation/reduction of the hydroxyl/ketone groups from (2R,3R)-2,3-pentanediol/2,3-pentanedione and (2R,3R)-2,3-hexanediol/2,3-hexanedione. In conclusion, Bdh1p is an enzyme with biotechnological interest that can be used to synthesize chiral building blocks. A scheme of the favored pathway with the corresponding intermediates is proposed for the Bdh1p reaction. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  2. The Implications of DNA Methylation for Toxicology: Toward Toxicomethylomics, the Toxicology of DNA Methylation

    Science.gov (United States)

    Szyf, Moshe

    2011-01-01

    Identifying agents that have long-term deleterious impact on health but exhibit no immediate toxicity is of prime importance. It is well established that long-term toxicity of chemicals could be caused by their ability to generate changes in the DNA sequence through the process of mutagenesis. Several assays including the Ames test and its different modifications were developed to assess the mutagenic potential of chemicals (Ames, B. N., Durston, W. E., Yamasaki, E., and Lee, F. D. (1973a). Carcinogens are mutagens: a simple test system combining liver homogenates for activation and bacteria for detection. Proc. Natl. Acad. Sci. U.S.A. 70, 2281–2285; Ames, B. N., Lee, F. D., and Durston, W. E. (1973b). An improved bacterial test system for the detection and classification of mutagens and carcinogens. Proc. Natl. Acad. Sci. U.S.A. 70, 782–786). These tests have also been employed for assessing the carcinogenic potential of compounds. However, the DNA molecule contains within its chemical structure two layers of information. The DNA sequence that bears the ancestral genetic information and the pattern of distribution of covalently bound methyl groups on cytosines in DNA. DNA methylation patterns are generated by an innate program during gestation but are attuned to the environment in utero and throughout life including physical and social exposures. DNA function and health could be stably altered by exposure to environmental agents without changing the sequence, just by changing the state of DNA methylation. Our current screening tests do not detect agents that have long-range impact on the phenotype without altering the genotype. The realization that long-range damage could be caused without changing the DNA sequence has important implications on the way we assess the safety of chemicals, drugs, and food and broadens the scope of definition of toxic agents. PMID:21297083

  3. Tin-containing silicates: Alkali salts improve methyl lactate yield from sugars

    DEFF Research Database (Denmark)

    Tolborg, Søren; Sádaba, Irantzu; Osmundsen, Christian Mårup

    2015-01-01

    This study focuses on increasing the selectivity to methyl lactate from sugars using stannosilicates as heterogeneous catalyst. All group I ions are found to have a promoting effect on the resulting methyl lactate yield. Besides, the alkali ions can be added both during the preparation...... of the catalyst or directly to the solvent mixture to achieve the highest reported yield of methyl lactate (ca. 75%) from sucrose at 170 8C in methanol. The beneficial effect of adding alkali to the reaction media applies not only to highly defect-free Sn-Beta prepared through the fluoride route, but also...

  4. Methyl 2-(5-bromo-3-methylsulfinyl-1-benzofuran-2-ylacetate

    Directory of Open Access Journals (Sweden)

    Uk Lee

    2008-12-01

    Full Text Available The title compound, C12H11BrO4S, was synthesized by the oxidation of methyl 2-(5-bromo-3-methylsulfanyl-1-benzofuran-2-ylacetate with 3-chloroperoxybenzoic acid. The O atom and the methyl group of the methylsulfinyl substituent lie on opposite sides of the plane of the benzofuran ring system. The crystal structure is stabilized by C—H...π interactions, involving a methyl H atom and the benzene ring of a neighbouring molecule, and by weak intermolecular C—H...O hydrogen bonds.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-01-22

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

  6. Structure, bioactivity, and synthesis of methylated flavonoids.

    Science.gov (United States)

    Wen, Lingrong; Jiang, Yueming; Yang, Jiali; Zhao, Yupeng; Tian, Miaomiao; Yang, Bao

    2017-06-01

    Methylated flavonoids are an important type of natural flavonoid derivative with potentially multiple health benefits; among other things, they have improved bioavailability compared with flavonoid precursors. Flavonoids have been documented to have broad bioactivities, such as anticancer, immunomodulation, and antioxidant activities, that can be elevated, to a certain extent, by methylation. Understanding the structure, bioactivity, and bioavailability of methylated flavonoids, therefore, is an interesting topic with broad potential applications. Though methylated flavonoids are widely present in plants, their levels are usually low. Because developing efficient techniques to produce these chemicals would likely be beneficial, we provide an overview of their chemical and biological synthesis. © 2017 New York Academy of Sciences.

  7. Inheritance of allelic blueprints for methylation patterns.

    Science.gov (United States)

    Silva, A J; White, R

    1988-07-15

    We have developed a strategy to distinguish between the methylation patterns of homologous chromosomes in tissues, and to follow these patterns in human pedigrees. This genetic approach uncovered evidence of variation in the methylation of allelic sites on homologous chromosomes. This variation was tissue-specific and reproducible after transmission through the germ line, demonstrating that homologous chromosomes have distinct blueprints for the tissue-specific regulation of methylation. Furthermore, this approach can be used to study the relationship between parental imprinting and methylation in native mammalian loci.

  8. Inheritance of DNA methylation in Coprinus cinereus.

    Science.gov (United States)

    Zolan, M E; Pukkila, P J

    1986-01-01

    We examined the inheritance of 5-methylcytosine residues at a centromere-linked locus in the basidiomycete Coprinus cinereus. Although methylated and unmethylated tracts were inherited both mitotically and meiotically the lengths of these tracts were variable. This variation was not confined to any one phase of the life cycle of the organism, and it usually involved the simultaneous de novo methylation of at least four HpaII-MspI sites. We also found that the higher levels of methylation at this locus were transmitted through meiosis, regardless of the level of methylation of the homologous chromosome. Images PMID:3785146

  9. Druggability of methyl-lysine binding sites

    Science.gov (United States)

    Santiago, C.; Nguyen, K.; Schapira, M.

    2011-12-01

    Structural modules that specifically recognize—or read—methylated or acetylated lysine residues on histone peptides are important components of chromatin-mediated signaling and epigenetic regulation of gene expression. Deregulation of epigenetic mechanisms is associated with disease conditions, and antagonists of acetyl-lysine binding bromodomains are efficacious in animal models of cancer and inflammation, but little is known regarding the druggability of methyl-lysine binding modules. We conducted a systematic structural analysis of readers of methyl marks and derived a predictive druggability landscape of methyl-lysine binding modules. We show that these target classes are generally less druggable than bromodomains, but that some proteins stand as notable exceptions.

  10. Maternal micronutrients and brain global methylation patterns in the offspring.

    Science.gov (United States)

    Sable, Pratiksha; Randhir, Karuna; Kale, Anvita; Chavan-Gautam, Preeti; Joshi, Sadhana

    2015-01-01

    Studies have established the association of maternal nutrition and increased risk for non-communicable diseases. It has been suggested that this involves epigenetic modifications in the genome. However, the role of maternal micronutrients in the one-carbon cycle in influencing brain development of the offspring through methylation is unexplored. It is also unclear whether epigenomic marks established during early development can be reversed by a postnatal diet. The present study reports the effect of maternal micronutrients and omega-3 fatty acids on global DNA methylation patterns in the brain of the Wistar rat offspring at three timepoints (at birth, postnatal day 21, and 3 months of age). Pregnant rats were divided into control (n = 8) and five treatment groups (n = 16 dams in each group) at two levels of folic acid (normal and excess folate) in the presence and absence of vitamin B12 (NFBD, EFB, and EFBD). Omega-3 fatty acid supplementation was given to vitamin B12 deficient groups (NFBDO and EFBDO). Following delivery, eight dams from each group were shifted to control diet and remaining continued on the same treatment diet. Our results demonstrate that maternal micronutrient imbalance results in global hypomethylation in the offspring brain at birth. At adult age the cortex of the offspring displayed hypermethylation as compared with control, in spite of a postnatal control diet. In contrast, prenatal omega-3 fatty acid supplementation was able to normalize methylation at 3 months of age. Our findings provide clues for the role of omega-3 fatty acids in reversing methylation patterns thereby highlighting its contribution in neuroprotection and cognition.

  11. Chemically Methylated and Reduced Pectins: Preparation and Characterisation by 1H-NMR Spectroscopy, Enzymatic Degradation and Gelling Properties

    DEFF Research Database (Denmark)

    Rosenbohm, Christoph; Lundt, Inge; Christensen, T.M.I.E.

    2003-01-01

    The gelling properties of pectin are known to be closely related to the degree of methylation (DM) and the distribution of the ester groups. In order to investigate this dependency, a natural citrus pectin (DM=64%) has been methylated to pectins with higher DM’s or saponified to achieve pectins...

  12. Different diagnostic values of imaging parameters to predict pseudoprogression in glioblastoma subgroups stratified by MGMT promoter methylation

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Ra Gyoung [Catholic Kwandong University International St. Mary' s Hospital, Department of Radiology, Catholic Kwandong University College of Medicine, Incheon (Korea, Republic of); Kim, Ho Sung; Shim, Woo Hyun; Kim, Sang Joon [University of Ulsan College of Medicine, Asan Medical Center, Department of Radiology and Research Institute of Radiology, Seoul (Korea, Republic of); Paik, Wooyul [Dankook Unversity Hospital, Department of Radiology, Cheonan-si, Chungcheongnam-do (Korea, Republic of); Kim, Jeong Hoon [University of Ulsan College of Medicine, Asan Medical Center, Department of Neurosurgery, Seoul (Korea, Republic of)

    2017-01-15

    The aim of this study was to determine whether diffusion and perfusion imaging parameters demonstrate different diagnostic values for predicting pseudoprogression between glioblastoma subgroups stratified by O{sup 6}-mythylguanine-DNA methyltransferase (MGMT) promoter methylation status. We enrolled seventy-five glioblastoma patients that had presented with enlarged contrast-enhanced lesions on magnetic resonance imaging (MRI) one month after completing concurrent chemoradiotherapy and undergoing MGMT promoter methylation testing. The imaging parameters included 10 or 90 % histogram cutoffs of apparent diffusion coefficient (ADC10), normalized cerebral blood volume (nCBV90), and initial area under the time signal-intensity curve (IAUC90). The results of the areas under the receiver operating characteristic curve (AUCs) with cross-validation were compared between MGMT methylation and unmethylation groups. MR imaging parameters demonstrated a trend toward higher accuracy in the MGMT promoter methylation group than in the unmethylation group (cross-validated AUCs = 0.70-0.95 and 0.56-0.87, respectively). The combination of MGMT methylation status with imaging parameters improved the AUCs from 0.70 to 0.75-0.90 for both readers in comparison with MGMT methylation status alone. The probability of pseudoprogression was highest (95.7 %) when nCBV90 was below 4.02 in the MGMT promoter methylation group. MR imaging parameters could be stronger predictors of pseudoprogression in glioblastoma patients with the methylated MGMT promoter than in patients with the unmethylated MGMT promoter. (orig.)

  13. Leisure-time physical activity in the vicinity of Academias da Cidade Program in Belo Horizonte, Minas Gerais State, Brazil: the impact of a health promotion program on the community.

    Science.gov (United States)

    Fernandes, Amanda Paula; Andrade, Amanda Cristina de Souza; Ramos, Cynthia Graciane Carvalho; Friche, Amélia Augusta de Lima; Dias, Maria Angélica de Salles; Xavier, César Coelho; Proietti, Fernando Augusto; Caiaffa, Waleska Teixeira

    2015-11-01

    This study analyzed leisure-time physical activity among 1,621 adults who were non-users of the Academias da Cidade Program in Belo Horizonte, Minas Gerais State, Brazil, but who lived in the vicinity of a fitness center in operation (exposed Group I) or in the vicinity of two sites reserved for future installation of centers (control Groups II and III). The dependent variable was leisure-time physical activity, and linear distance from the households to the fitness centers was the exposure variable, categorized in radial buffers: leisure-time physical activity (OR = 1.16; 95%CI: 1.03-1.30), independently of socio-demographic factors; the same was not observed in the control groups (II and III). The findings suggests the program's potential for influencing physical activity in the population living closer to the fitness center and thus provide a strategic alternative for mitigating inequalities in leisure-time physical activity.

  14. Evaluation of Properties of Mineral Trioxide Aggregate with Methyl Cellulose as Liquid.

    Science.gov (United States)

    Dianat, Omid; Naseri, Mandana; Tabatabaei, Seyedeh Farnaz

    2017-01-01

    Mineral trioxide aggregate (MTA) is extensively used in endodontics. However, MTA is difficult to handle because of its granular consistency, low mechanical properties and initial looseness. The objective of this study was to assess the compressive strength (CS), diametral tensile strength (DTS), and pH of set MTA using methyl cellulose as liquid. White ProRoot MTA was used as the control group; modified MTA cement was prepared by mixing Portland cement, bismuth oxide and calcium sulfate (75%, 20% and 5%, respectively) as the experiment group. Methyl cellulose was used as hydrating liquid and compared with distilled water. The data were analyzed by two-way ANOVA. The pH values of modified MTA cement set using deionized water and methyl cellulose were slightly, but not significantly, different (P>0.05). The DTS and CS tests for modified MTA cement hydrated with methyl cellulose showed a significant difference at one day and one week (PMTA.

  15. [Methylcobalamin-dependent enzymatic methylation of DNA in a cell-free extract of Propionibacterium shermanii].

    Science.gov (United States)

    Antoshkina, N V; Vorob'eva, L I; Bur'ianov, Ia I

    1981-01-01

    The regulation of the functional activity of Propionibacterium shermanii cells by cobalamin is accompanied by an increase in the methylation of their DNA at the cytosine residue: the DNA from B12-deficient cells is undermethylated as compared with the DNA from control cells, i. e. cells synthesizing corrinoids. The results of in vitro experiments make it possible to correlate this phenomenon with the capability of DNA methylases from B12-deficient and control cells to function with different donors of methyl groups. Just as the enzymes methylating adenine and cytosine in B12-deficient cells, adenine DNA methylase from cells synthesizing corrinoids is active in vitro with S-adenosylmethionine. Cytosine DNA methylase from P. shermanii control cells is inactive with S-adenosylmethionine and transfers methyl groups only in the presence of cobalamins.

  16. Electric and magnetic field testing in vicinity of 110/x kV substations

    Directory of Open Access Journals (Sweden)

    Grbić Maja

    2016-01-01

    Full Text Available The levels of non-ionizing radiation (electric and magnetic fields at power frequency, which occur near 110/x kV substations are analyzed in this paper. The results of electric field strength and magnetic flux density measurements in the vicinity of three typical substations of the aforementioned voltage level are shown. With the purpose of estimating the exposure of the population to these fields, the obtained results were compared to the reference maximum levels set for increased sensitivity areas, which amount to 2 kV/m for electric field and 40 μT for magnetic flux density. The objective of the conducted analysis is to reach general conclusions on the levels of electric and magnetic fields, which may occur in the vicinity of the substations mentioned above, and evaluate their compliance with the national regulations on the population protection from non-ionizing radiation.

  17. DFT Study of the Molybdenum-Catalyzed Deoxydehydration of Vicinal Diols

    DEFF Research Database (Denmark)

    Lupp, Daniel; Christensen, Niels Johan; Dethlefsen, Johannes Rytter

    2015-01-01

    The mechanism of the molybdenum-catalyzed deoxydehydration (DODH) of vicinal diols has been investigated using density functional theory. The proposed catalytic cycle involves condensation of the diol with an MoVI oxo complex, oxidative cleavage of the diol resulting in an MoIV complex, and extru......The mechanism of the molybdenum-catalyzed deoxydehydration (DODH) of vicinal diols has been investigated using density functional theory. The proposed catalytic cycle involves condensation of the diol with an MoVI oxo complex, oxidative cleavage of the diol resulting in an MoIV complex......, and extrusion of the alkene. We have compared the proposed pathway with several alternatives, and the results have been corroborated by comparison with the molybdenum- catalyzed sulfoxide reduction recently published by Sanz et al. and with experimental observations for the DODH itself. Improved understanding...

  18. Temperature dependence of magnetic anisotropies in ultrathin Fe film on vicinal Si(111)

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yong-Sheng; He, Wei; Ye, Jun; Hu, Bo; Tang, Jin; Zhang, Xiang-Qun [State Key Laboratory of Magnetism and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Cheng, Zhao-Hua, E-mail: zhcheng@aphy.iphy.ac.cn [State Key Laboratory of Magnetism and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190 (China)

    2017-05-01

    The temperature dependence of magnetic anisotropy of ultrathin Fe film with different thickness epitaxially grown on vicinal Si(111) substrate has been quantitatively investigated using the anisotropic magnetoresistance(AMR) measurements. Due to the effect of the vicinal substrate, the magnetic anisotropy is the superposition of a four-fold, a two-fold and a weakly six-fold contribution. It is found that the temperature dependence of the first-order magnetocrystalline anisotropies coefficient follows power laws of the reduced magnetization m(T)(=M(T)/M(0)) being consistent with the Callen and Callen's theory. However the temperature dependence of uniaxial magnetic anisotropy (UMA) shows novel behavior that decreases roughly as a function of temperature with different power law for samples with different thickness. We also found that the six-fold magnetocrystalline anisotropy is almost invariable over a wide temperature range. Possible mechanisms leading to the different exponents are discussed.

  19. Impact of nucleation on step-meandering instabilities during step-flow growth on vicinal surfaces.

    Science.gov (United States)

    Beausoleil, A; Desjardins, P; Rochefort, A

    2014-03-01

    Step-meandering instabilities can manifest during step-flow growth on vicinal surfaces [Bales and Zangwill, Phys. Rev. B 41, 5500 (1990); Pierre-Louis, D'Orsogna, and Einstein, Phys. Rev. Lett. 82, 3661 (1999)]. A phase diagram based on the various growth regimes of a vicinal surface allows us to study the impact of nucleation on these meanders and to predict a meandering instability caused by the nucleation and the coalescence of both islands and steps. Using an accelerated kinetic Monte Carlo method, we find that the coalescence of islands with steps produces large protrusions and deep ripples and that the resulting meandering instability is reinforced by the growth of the islands at almost the same positions from one monolayer to the other. A coarsening phenomenon occurs for the instability wavelength until mounds appear, favored by a large Ehrlich-Schwoebel barrier. Such a meandering instability could be exploited for periodic self-assembly.

  20. A genome-wide methylation study on obesity Differential variability and differential methylation

    NARCIS (Netherlands)

    Xu, Xiaojing; Su, Shaoyong; Barnes, Vernon A.; De Miguel, Carmen; Pollock, Jennifer; Ownby, Dennis; Shi, Huidong; Zhu, Haidong; Snieder, Harold; Wang, Xiaoling

    2013-01-01

    Besides differential methylation, DNA methylation variation has recently been proposed and demonstrated to be a potential contributing factor to cancer risk. Here we aim to examine whether differential variability in methylation is also an important feature of obesity, a typical non-malignant common

  1. 21 CFR 177.2000 - Vinylidene chloride/methyl acrylate/methyl methacrylate polymers.

    Science.gov (United States)

    2010-04-01

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

  2. Fatty acid synthase methylation levels in adipose tissue: effects of an obesogenic diet and phenol compounds.

    Science.gov (United States)

    Gracia, Ana; Elcoroaristizabal, Xabier; Fernández-Quintela, Alfredo; Miranda, Jonatan; Bediaga, Naiara G; M de Pancorbo, Marian; Rimando, Agnes M; Portillo, María P

    2014-07-01

    DNA methylation is an epigenetic mechanism that can inhibit gene transcription. The aim of this study was to assess changes induced by an obesogenic diet in the methylation profile of genes involved in adipose tissue triacylglycerol metabolism, and to determine whether this methylation pattern can be altered by resveratrol and pterostilbene. Rats were divided into four groups. The control group was fed a commercial standard diet, and the other three groups were fed a commercial high-fat, high-sucrose diet (6 weeks): the high-fat, high-sucrose group, the resveratrol-treated group (RSV; 30 mg/kg/day), and the pterostilbene-treated group (PT; 30 mg/kg/day). Gene expression was measured by RT-PCR and gene methylation by pyrosequencing. The obesogenic diet induced a significant increase in adipose tissue weight. Resveratrol and pterostilbene partially prevented this effect. Methylation pattern of ppnla2 and pparg genes was similar among the experimental groups. In fasn, significant hypomethylation in -90-bp position and significant hypermethylation in -62-bp position were induced by obesogenic feeding. Only pterostilbene reversed the changes induced by the obesogenic diet in fasn methylation pattern. By contrast, the addition of resveratrol to the diet did not induce changes. Both phenolic compounds averted fasn up-regulation. These results demonstrate that the up-regulation of fasn gene induced by an obesogenic feeding, based on a high-fat, high-sucrose diet, is related to hypomethylation of this gene in position -90 bp. Under our experimental conditions, both molecules prevent fasn up-regulation, but this change in gene expression seems to be mediated by changes in methylation status only in the case of pterostilbene.

  3. Electric and magnetic field testing in vicinity of 110/x kV substations

    OpenAIRE

    Grbić Maja; Pavlović Aleksandar; Hrvić Dejan; Vulević Branislav

    2016-01-01

    The levels of non-ionizing radiation (electric and magnetic fields) at power frequency, which occur near 110/x kV substations are analyzed in this paper. The results of electric field strength and magnetic flux density measurements in the vicinity of three typical substations of the aforementioned voltage level are shown. With the purpose of estimating the exposure of the population to these fields, the obtained results were compared to the reference maximum levels set for increased sensitivi...

  4. Turbulent flow in a ribbed channel: Flow structures in the vicinity of a rib

    DEFF Research Database (Denmark)

    Wang, Lei; Salewski, Mirko; Sundén, Bengt

    2010-01-01

    PIV measurements are performed in a channel with periodic ribs on one wall. The emphasis of this study is to investigate the flow structures in the vicinity of a rib in terms of mean velocities, Reynolds stresses, probability density functions (PDF), and two-point correlations. The PDF distribution......-based visualization is applied to the separation bubble upstream of the rib. Salient critical points and limit cycles are extracted, which gives clues to the physical processes occurring in the flow....

  5. Flow- topography Interactions in the Vicinity of a Deep Ocean Island and a Ridge

    Science.gov (United States)

    2015-09-30

    moored platforms. 2 WORK COMPLETED Attend the FLEAT planning meeting in June 2015 at Scripps Institute of Oceanography. Preliminary deep -mooring...1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Flow-topography Interactions in the Vicinity of a Deep ...located north of Palau covers the submarine ridge, while the second mooring-line coveres deep slopes and the shallow bank just north of Palau (Figure 1

  6. STUDIES ON THE INITIATION MECHANISM OF ORGANIC PEROXIDE AND N-METHACRYLOYLOXYETHYL-N-METHYL ANILINE IN METHYL METHACRYLATE POLYMERIZATION

    Institute of Scientific and Technical Information of China (English)

    QIU Kunyuan; GUO Dajie; GUO Xinqiu; FENG Xinde

    1990-01-01

    The initiation mechanism of methyl methacrylate (MMA) polymerization by organic peroxide and polymerizable aromatic tertiary amine such as N-methacryloyloxyethyl-N-methyi aniline (MEMA) binary system has been studied. The kinetics of polymerization of MMA and the ESR spectra of organic peroxide/MEMA system were determined. Based on the ESR study and the end-group analysis by UV spectra of the polymer formed, the initiation mechanism is proposed.

  7. Direct observation of 2-(1-methoxycarbonylnaphthyl)methyl radical via photo-claisen type rearrangement

    Energy Technology Data Exchange (ETDEWEB)

    Yoshimi, Yasuharu; Mizuno, Kazuhiko; Maeda, Hajime [Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University, Sakai, Osaka (Japan); Ichinose, Nobuyuki; Tanaka, Tomoko; Kawanishi, Shun-ichi [Kansai Research Establishment, Japan Atomic Energy Research Institute, Neyagawa, Osaka (Japan)

    2001-03-01

    The photo-Claisen type rearrangement of 2-(1-methoxycarbonylnaphthyl)methyl phenyl ether derivatives 1a-f was investigated. The 2-(1-methoxycarbonylnaphthyl)methyl radical and its fluorescence by use of two colored laser flash photolysis (LFP) technique were directly observed as a reactive intermediate. The reactivity of the photorearrangement depended on the p-substituents on the phenoxy group. (author)

  8. DNA methylation patterns and gene expression associated with litter size in Berkshire pig placenta.

    Directory of Open Access Journals (Sweden)

    Jung Hye Hwang

    Full Text Available Increasing litter size is of great interest to the pig industry. DNA methylation is an important epigenetic modification that regulates gene expression, resulting in livestock phenotypes such as disease resistance, milk production, and reproduction. We classified Berkshire pigs into two groups according to litter size and estimated breeding value: smaller (SLG and larger (LLG litter size groups. Genome-wide DNA methylation and gene expression were analyzed using placenta genomic DNA and RNA to identify differentially methylated regions (DMRs and differentially expressed genes (DEGs associated with litter size. The methylation levels of CpG dinucleotides in different genomic regions were noticeably different between the groups, while global methylation pattern was similar, and excluding intergenic regions they were found the most frequently in gene body regions. Next, we analyzed RNA-Seq data to identify DEGs between the SLG and LLG groups. A total of 1591 DEGs were identified: 567 were downregulated and 1024 were upregulated in LLG compared to SLG. To identify genes that simultaneously exhibited changes in DNA methylation and mRNA expression, we integrated and analyzed the data from bisulfite-Seq and RNA-Seq. Nine DEGs positioned in DMRs were found. The expression of only three of these genes (PRKG2, CLCA4, and PCK1 was verified by RT-qPCR. Furthermore, we observed the same methylation patterns in blood samples as in the placental tissues by PCR-based methylation analysis. Together, these results provide useful data regarding potential epigenetic markers for selecting hyperprolific sows.

  9. Comprehensive analysis of genome-wide DNA methylation across human polycystic ovary syndrome ovary granulosa cell.

    Science.gov (United States)

    Xu, Jiawei; Bao, Xiao; Peng, Zhaofeng; Wang, Linlin; Du, Linqing; Niu, Wenbin; Sun, Yingpu

    2016-05-10

    Polycystic ovary syndrome (PCOS) affects approximately 7% of the reproductive-age women. A growing body of evidence indicated that epigenetic mechanisms contributed to the development of PCOS. The role of DNA modification in human PCOS ovary granulosa cell is still unknown in PCOS progression. Global DNA methylation and hydroxymethylation were detected between PCOS' and controls' granulosa cell. Genome-wide DNA methylation was profiled to investigate the putative function of DNA methylaiton. Selected genes expressions were analyzed between PCOS' and controls' granulosa cell. Our results showed that the granulosa cell global DNA methylation of PCOS patients was significant higher than the controls'. The global DNA hydroxymethylation showed low level and no statistical difference between PCOS and control. 6936 differentially methylated CpG sites were identified between control and PCOS-obesity. 12245 differential methylated CpG sites were detected between control and PCOS-nonobesity group. 5202 methylated CpG sites were significantly differential between PCOS-obesity and PCOS-nonobesity group. Our results showed that DNA methylation not hydroxymethylation altered genome-wide in PCOS granulosa cell. The different methylation genes were enriched in development protein, transcription factor activity, alternative splicing, sequence-specific DNA binding and embryonic morphogenesis. YWHAQ, NCF2, DHRS9 and SCNA were up-regulation in PCOS-obesity patients with no significance different between control and PCOS-nonobesity patients, which may be activated by lower DNA methylaiton. Global and genome-wide DNA methylation alteration may contribute to different genes expression and PCOS clinical pathology.

  10. Genome-wide DNA methylation profiling in cultured eutopic and ectopic endometrial stromal cells.

    Directory of Open Access Journals (Sweden)

    Yoshiaki Yamagata

    Full Text Available The objective of this study was to characterize the genome-wide DNA methylation profiles of isolated endometrial stromal cells obtained from eutopic endometria with (euESCa and without endometriosis (euESCb and ovarian endometrial cysts (choESC. Three samples were analyzed in each group. The infinium methylation array identified more hypermethylated and hypomethylated CpGs in choESC than in euESCa, and only a few genes were methylated differently in euESCa and euESCb. A functional analysis revealed that signal transduction, developmental processes, immunity, etc. were different in choESC and euESCa. A clustering analysis and a principal component analysis performed based on the methylation levels segregated choESC from euESC, while euESCa and euESCb were identical. A transcriptome analysis was then conducted and the results were compared with those of the DNA methylation analysis. Interestingly, the hierarchical clustering and principal component analyses showed that choESC were segregated from euESCa and euESCb in the DNA methylation analysis, while no segregation was recognized in the transcriptome analysis. The mRNA expression levels of the epigenetic modification enzymes, including DNA methyltransferases, obtained from the specimens were not significantly different between the groups. Some of the differentially methylated and/or expressed genes (NR5A1, STAR, STRA6 and HSD17B2, which are related with steroidogenesis, were validated by independent methods in a larger number of samples. Our findings indicate that different DNA methylation profiles exist in ectopic ESC, highlighting the benefits of genome wide DNA methylation analyses over transcriptome analyses in clarifying the development and characterization of endometriosis.

  11. Magnetostrictive hypersound generation by spiral magnets in the vicinity of magnetic field induced phase transition

    Energy Technology Data Exchange (ETDEWEB)

    Bychkov, Igor V. [Chelyabinsk State University, 129 Br. Kashirinykh Str., Chelyabinsk 454001 (Russian Federation); South Ural State University (National Research University), 76 Lenin Prospekt, Chelyabinsk 454080 (Russian Federation); Kuzmin, Dmitry A., E-mail: kuzminda@csu.ru [Chelyabinsk State University, 129 Br. Kashirinykh Str., Chelyabinsk 454001 (Russian Federation); South Ural State University (National Research University), 76 Lenin Prospekt, Chelyabinsk 454080 (Russian Federation); Kamantsev, Alexander P.; Koledov, Victor V.; Shavrov, Vladimir G. [Kotelnikov Institute of Radio-engineering and Electronics of RAS, Mokhovaya Street 11-7, Moscow 125009 (Russian Federation)

    2016-11-01

    In present work we have investigated magnetostrictive ultrasound generation by spiral magnets in the vicinity of magnetic field induced phase transition from spiral to collinear state. We found that such magnets may generate transverse sound waves with the wavelength equal to the spiral period. We have examined two types of spiral magnetic structures: with inhomogeneous exchange and Dzyaloshinskii–Moriya interactions. Frequency of the waves from exchange-caused spiral magnetic structure may reach some THz, while in case of Dzyaloshinskii–Moriya interaction-caused spiral it may reach some GHz. These waves will be emitted like a sound pulses. Amplitude of the waves is strictly depends on the phase transition speed. Some aspects of microwaves to hypersound transformation by spiral magnets in the vicinity of phase transition have been investigated as well. Results of the work may be interesting for investigation of phase transition kinetics as well, as for various hypersound applications. - Highlights: • Magnetostrictive ultrasound generation by spiral magnets at phase transition (PT) is studied. • Spiral magnets during PT may generate transverse sound with wavelength equal to spiral period. • Amplitude of the sound is strictly depends on the phase transition speed. • Microwave-to-sound transformation in the vicinity of PT is investigated as well.

  12. Targeted DNA methylation analysis by next-generation sequencing.

    Science.gov (United States)

    Masser, Dustin R; Stanford, David R; Freeman, Willard M

    2015-02-24

    The role of epigenetic processes in the control of gene expression has been known for a number of years. DNA methylation at cytosine residues is of particular interest for epigenetic studies as it has been demonstrated to be both a long lasting and a dynamic regulator of gene expression. Efforts to examine epigenetic changes in health and disease have been hindered by the lack of high-throughput, quantitatively accurate methods. With the advent and popularization of next-generation sequencing (NGS) technologies, these tools are now being applied to epigenomics in addition to existing genomic and transcriptomic methodologies. For epigenetic investigations of cytosine methylation where regions of interest, such as specific gene promoters or CpG islands, have been identified and there is a need to examine significant numbers of samples with high quantitative accuracy, we have developed a method called Bisulfite Amplicon Sequencing (BSAS). This method combines bisulfite conversion with targeted amplification of regions of interest, transposome-mediated library construction and benchtop NGS. BSAS offers a rapid and efficient method for analysis of up to 10 kb of targeted regions in up to 96 samples at a time that can be performed by most research groups with basic molecular biology skills. The results provide absolute quantitation of cytosine methylation with base specificity. BSAS can be applied to any genomic region from any DNA source. This method is useful for hypothesis testing studies of target regions of interest as well as confirmation of regions identified in genome-wide methylation analyses such as whole genome bisulfite sequencing, reduced representation bisulfite sequencing, and methylated DNA immunoprecipitation sequencing.

  13. Epigenetic regulation of motor neuron cell death through DNA methylation.

    Science.gov (United States)

    Chestnut, Barry A; Chang, Qing; Price, Ann; Lesuisse, Catherine; Wong, Margaret; Martin, Lee J

    2011-11-16

    DNA methylation is an epigenetic mechanism for gene silencing engaged by DNA methyltransferase (Dnmt)-catalyzed methyl group transfer to cytosine residues in gene-regulatory regions. It is unknown whether aberrant DNA methylation can cause neurodegeneration. We tested the hypothesis that Dnmts can mediate neuronal cell death. Enforced expression of Dnmt3a induced degeneration of cultured NSC34 cells. During apoptosis of NSC34 cells induced by camptothecin, levels of Dnmt1 and Dnmt3a increased fivefold and twofold, respectively, and 5-methylcytosine accumulated in nuclei. Truncation mutation of the Dnmt3a catalytic domain and Dnmt3a RNAi blocked apoptosis of cultured neurons. Inhibition of Dnmt catalytic activity with RG108 and procainamide protected cultured neurons from excessive DNA methylation and apoptosis. In vivo, Dnmt1 and Dnmt3a are expressed differentially during mouse brain and spinal cord maturation and in adulthood when Dnmt3a is abundant in synapses and mitochondria. Dnmt1 and Dnmt3a are expressed in motor neurons of adult mouse spinal cord, and, during their apoptosis induced by sciatic nerve avulsion, nuclear and cytoplasmic 5-methylcytosine immunoreactivity, Dnmt3a protein levels and Dnmt enzyme activity increased preapoptotically. Inhibition of Dnmts with RG108 blocked completely the increase in 5-methycytosine and the apoptosis of motor neurons in mice. In human amyotrophic lateral sclerosis (ALS), motor neurons showed changes in Dnmt1, Dnmt3a, and 5-methylcytosine similar to experimental models. Thus, motor neurons can engage epigenetic mechanisms to drive apoptosis, involving Dnmt upregulation and increased DNA methylation. These cellular mechanisms could be relevant to human ALS pathobiology and disease treatment.

  14. Laboratory study of methyl isocyanate ices under astrophysical conditions

    Science.gov (United States)

    Maté, B.; Molpeceres, G.; Timón, V.; Tanarro, I.; Escribano, R.; Guillemin, J. C.; Cernicharo, J.; Herrero, V. J.

    2017-10-01

    Methyl isocyanate has been recently detected in comet 67P/Churyumov-Gerasimenko (67P/CG) and in the interstellar medium. New physicochemical studies on this species are now necessary as tools for subsequent studies in astrophysics. In this work, infrared spectra of solid CH3NCO have been obtained at temperatures of relevance for astronomical environments. The spectra are dominated by a strong, characteristic multiplet feature at 2350-2250 cm-1, which can be attributed to the asymmetric stretching of the NCO group. A phase transition from amorphous to crystalline methyl isocyanate is observed at ˜90 K. The band strengths for the absorptions of CH3NCO in ice at 20 K have been measured. Deuterated methyl isocyanate is used to help with the spectral assignment. No X-ray structure has been reported for crystalline CH3NCO. Here we advance a tentative theoretical structure, based on density functional theory (DFT) calculations, derived taking the crystal of isocyanic acid as a starting point. A harmonic theoretical spectrum is then calculated for the proposed structure and compared with the experimental data. A mixed ice of H2O and CH3NCO was formed by simultaneous deposition of water and methyl isocyanate at 20 K. The absence of new spectral features indicates that methyl isocyanate and water do not react appreciably at 20 K, but form a stable mixture. The high CH3NCO/H2O ratio reported for comet 67P/CG, and the characteristic structure of the 2350-2250 cm-1 band, makes it a very good candidate for future astronomical searches.

  15. Different Levels of DNA Methylation Detected in Human Sperms after Morphological Selection Using High Magnification Microscopy

    Directory of Open Access Journals (Sweden)

    Nino Guy Cassuto

    2016-01-01

    Full Text Available Objective. To analyze DNA methylation levels between two groups of spermatozoa taken from the same sample, following morphological selection by high magnification (HM at 6100x microscopy. A prospective study was conducted and studied 876 spermatozoa from 10 randomly selected men. Sperm morphology was characterized at HM according to criteria previously established. High-scoring Score 6 and low-scoring Score 0 sperm were selected. Sperm DNA methylation level was assessed using an immunoassay method targeting 5-methylcytosine residues by fluorescence microscopy with imaging analysis system to detect DNA methylation in single spermatozoon. Results. In total, 448 S6 spermatozoa and 428 S0 spermatozoa were analyzed. A strong relationship was found between sperm DNA methylation levels and sperm morphology observed at HM. Sperm DNA methylation level in the S6 group was significantly lower compared with that in the S0 group (p<10-6, OR = 2.4; and p<0.001, as determined using the Wilcoxon test. Conclusion. Differences in DNA methylation levels are associated with sperm morphology variations as observed at HM, which allows spermatozoa with abnormal levels to be discarded and ultimately decrease birth defects, malformations, and epigenetic diseases that may be transmitted from sperm to offspring in ICSI.

  16. DNA Methylation and Hydroxymethylation Levels in Relation to Two Weight Loss Strategies: Energy-Restricted Diet or Bariatric Surgery.

    Science.gov (United States)

    Nicoletti, Carolina Ferreira; Nonino, Carla Barbosa; de Oliveira, Bruno Affonso Parenti; Pinhel, Marcela Augusta de Souza; Mansego, Maria Luisa; Milagro, Fermin Ignacio; Zulet, Maria Angeles; Martinez, José Alfredo

    2016-03-01

    Weight loss can be influenced by genetic factors and epigenetic mechanisms that participate in the regulation of body weight. This study aimed to investigate whether the weight loss induced by two different obesity treatments (energy restriction or bariatric surgery) may affect global DNA methylation (LINE-1) and hydroxymethylation profile, as well as the methylation patterns in inflammatory genes. This study encompassed women from three differents groups: 1. control group (n = 9), normal weight individuals; 2. energy restriction group (n = 22), obese patients following an energy-restricted Mediterranean-based dietary treatment (RESMENA); and 3. bariatric surgery group (n = 14), obese patients underwent a hypocaloric diet followed by bariatric surgery. Anthropometric measurements and 12-h fasting blood samples were collected before the interventions and after 6 months. Lipid and glucose biomarkers, global hydroxymethylation (by ELISA), LINE-1, SERPINE-1, and IL-6 (by MS-HRM) methylation levels were assessed in all participants. Baseline LINE-1 methylation was associated with serum glucose levels whereas baseline hydroxymethylation was associated with BMI, waist circumference, total cholesterol, and triglycerides. LINE-1 and SERPINE-1 methylation levels did not change after weight loss, whereas IL-6 methylation increased after energy restriction and decreased in the bariatric surgery group. An association between SERPINE-1 methylation and weight loss responses was found. Global DNA methylation and hydroxymethylation might be biomarkers for obesity and associated comorbidities. Depending on the obesity treatment (diet or surgery), the DNA methylation patterns behave differently. Baseline SERPINE-1 methylation may be a predictor of weight loss values after bariatric surgery.

  17. DNA Methylation Modulates Nociceptive Sensitization after Incision.

    Directory of Open Access Journals (Sweden)

    Yuan Sun

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

  18. Direct detection of methylation in genomic DNA

    NARCIS (Netherlands)

    Bart, A.; van Passel, M. W. J.; van Amsterdam, K.; van der Ende, A.

    2005-01-01

    The identification of methylated sites on bacterial genomic DNA would be a useful tool to study the major roles of DNA methylation in prokaryotes: distinction of self and nonself DNA, direction of post-replicative mismatch repair, control of DNA replication and cell cycle, and regulation of gene

  19. Adenine N6-methylation in diverse fungi

    NARCIS (Netherlands)

    Seidl, Michael F.

    2017-01-01

    A DNA modification - methylation of cytosines and adenines - has important roles in diverse processes such as regulation of gene expression and genome stability, yet until recently adenine methylation had been considered to be only a hallmark of prokaryotes. A new study identifies abundant

  20. Methylation sensitive amplified polymorphism (MSAP) reveals that ...

    African Journals Online (AJOL)

    ajl yemi

    2011-12-19

    Dec 19, 2011 ... regulation mechanism of DNA methylation, have not been fully understood. The ability of plants to differently regulate gene expression and protein function has been described as a key factor in plant resistance (Lo´pez-. Maury et al., 2008). In this regard, epigenetic mechanisms such as DNA methylation ...

  1. Methylation profiles of the BRCA1 promoter in hereditary and sporadic breast cancer among Han Chinese.

    Science.gov (United States)

    Pang, Da; Zhao, Yashuang; Xue, Weinan; Shan, Ming; Chen, Yanbo; Zhang, Youxue; Zhang, Guoqiang; Liu, Feng; Li, Dalin; Yang, Yanmei

    2012-09-01

    The development of breast cancer is a multistep process associated with complex changes in host gene expression patterns including inactivation of tumor suppressor genes and activation of oncogenes. Critically, hereditary predisposition plays a significant role in cancer susceptibility. However, mutation of the BRCA1 gene is found only in the minority of hereditary breast cancer, which indicates that there might be alternative, novel mechanisms contributing to inactivation of the BRCA1 gene. Studies have shown that aberrant methylation of genomic DNA plays an important role in carcinogenesis. The aim of this study was to investigate whether DNA methylation may be an alternative mechanism for the inactivation of BRCA1 as an epigenetic modification of the genome and whether hereditary breast cancer has a different BRCA1 methylation phenotype pattern than sporadic breast cancer. The pattern of CpG island methylation within the promoter region of BRCA1 was assessed by bisulfite sequencing DNA from peripheral blood cells of 72 patients with hereditary predisposition but without BRCA1 mutations and 30 sporadic breast cancer controls. The overall methylation level in patients with hereditary predisposition was significantly lower than that in the sporadic control group. However, patients with hereditary predisposition showed a significantly higher methylation susceptibility for the sites -518 when compared to controls. These results suggest that there might be different BRCA1 promoter methylation levels and patterns in sporadic and hereditary breast cancer in peripheral blood DNA. These findings may facilitate the early diagnosis of hereditary breast cancer.

  2. Characterization by NMR of ozonized methyl linoleate

    Energy Technology Data Exchange (ETDEWEB)

    Diaz, Maritza F. [National Center for Scientific Research, Havana (Cuba). Ozone Research Center. Dept. of Ozonized Substances]. E-mail: maritza.diaz@cnic.edu.cu; Gavin, Jose A. [University of the Laguna, Tenerife (Spain)

    2007-07-01

    In the present study ozonized methyl linoleate with peroxide index of 1,800 mmol-equiv kg{sup -1} was chemically characterized. Ozonation of methyl linoleate produced hydroperoxides, ozonides and aldehydes which were identified by {sup 1}H and {sup 13}C NMR two-dimensional. The standard methyl linoleate and ozonized methyl linoleate shown very similar {sup 1}H NMR spectra except for the signals at {delta} 9.7 and {delta} 9.6 that correspond to aldehydic hydrogen, {delta} 5.7 and {delta} 5.5 (olefinic signals from hydroperoxides) and {delta} 5.2 ppm (multiplet from ozonides methynic hydrogen). Other resonance assignments are based on the connectivities provided by the hydrogen scalar coupling constants. These results indicate that NMR spectroscopy can provide valuable information about the amount of formed oxygenated compounds in the ozonized methyl linoleate in order to use it to follow up ozone therapy and chemistry of ozonized vegetable oil. (author)

  3. Twin birth changes DNA methylation of subsequent siblings

    National Research Council Canada - National Science Library

    Shuai Li; Eunae Kim; Ee Ming Wong; Ji-Hoon Eric Joo; Tuong L Nguyen; Jennifer Stone; Yun-Mi Song; Louisa B Flander; Richard Saffery; Graham G Giles; Melissa C Southey; Joohon Sung; John L Hopper

    2017-01-01

    We asked if twin birth influences the DNA methylation of subsequent siblings. We measured whole blood methylation using the HumanMethylation450 array for siblings from two twin and family studies in Australia and Korea...

  4. DNA sequence explains seemingly disordered methylation levels in partially methylated domains of Mammalian genomes.

    Directory of Open Access Journals (Sweden)

    Dimos Gaidatzis

    2014-02-01

    Full Text Available 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% (R(2 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.

  5. Efficiency of methylated DNA immunoprecipitation bisulphite sequencing for whole-genome DNA methylation analysis.

    Science.gov (United States)

    Jeong, Hae Min; Lee, Sangseon; Chae, Heejoon; Kim, RyongNam; Kwon, Mi Jeong; Oh, Ensel; Choi, Yoon-La; Kim, Sun; Shin, Young Kee

    2016-08-01

    We compared four common methods for measuring DNA methylation levels and recommended the most efficient method in terms of cost and coverage. The DNA methylation status of liver and stomach tissues was profiled using four different methods, whole-genome bisulphite sequencing (WG-BS), targeted bisulphite sequencing (Targeted-BS), methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA immunoprecipitation bisulphite sequencing (MeDIP-BS). We calculated DNA methylation levels using each method and compared the results. MeDIP-BS yielded the most similar DNA methylation profile to WG-BS, with 20 times less data, suggesting remarkable cost savings and coverage efficiency compared with the other methods. MeDIP-BS is a practical cost-effective method for analyzing whole-genome DNA methylation that is highly accurate at base-pair resolution.

  6. Association of childhood chronic physical aggression with a DNA methylation signature in adult human T cells.

    Directory of Open Access Journals (Sweden)

    Nadine Provençal

    Full Text Available Chronic physical aggression (CPA is characterized by frequent use of physical aggression from early childhood to adolescence. Observed in approximately 5% of males, CPA is associated with early childhood adverse environments and long-term negative consequences. Alterations in DNA methylation, a covalent modification of DNA that regulates genome function, have been associated with early childhood adversity.To test the hypothesis that a trajectory of chronic physical aggression during childhood is associated with a distinct DNA methylation profile during adulthood.We analyzed genome-wide promoter DNA methylation profiles of T cells from two groups of adult males assessed annually for frequency of physical aggression between 6 and 15 years of age: a group with CPA and a control group. Methylation profiles covering the promoter regions of 20 000 genes and 400 microRNAs were generated using MeDIP followed by hybridization to microarrays.In total, 448 distinct gene promoters were differentially methylated in CPA. Functionally, many of these genes have previously been shown to play a role in aggression and were enriched in biological pathways affected by behavior. Their locations in the genome tended to form clusters spanning millions of bases in the genome.This study provides evidence of clustered and genome-wide variation in promoter DNA methylation in young adults that associates with a history of chronic physical aggression from 6 to 15 years of age. However, longitudinal studies of methylation during early childhood will be necessary to determine if and how this methylation variation in T cells DNA plays a role in early development of chronic physical aggression.

  7. Association of Childhood Chronic Physical Aggression with a DNA Methylation Signature in Adult Human T Cells

    Science.gov (United States)

    Guillemin, Claire; Vitaro, Frank; Côté, Sylvana M.; Hallett, Michael; Tremblay, Richard E.; Szyf, Moshe

    2014-01-01

    Background Chronic physical aggression (CPA) is characterized by frequent use of physical aggression from early childhood to adolescence. Observed in approximately 5% of males, CPA is associated with early childhood adverse environments and long-term negative consequences. Alterations in DNA methylation, a covalent modification of DNA that regulates genome function, have been associated with early childhood adversity. Aims To test the hypothesis that a trajectory of chronic physical aggression during childhood is associated with a distinct DNA methylation profile during adulthood. Methods We analyzed genome-wide promoter DNA methylation profiles of T cells from two groups of adult males assessed annually for frequency of physical aggression between 6 and 15 years of age: a group with CPA and a control group. Methylation profiles covering the promoter regions of 20 000 genes and 400 microRNAs were generated using MeDIP followed by hybridization to microarrays. Results In total, 448 distinct gene promoters were differentially methylated in CPA. Functionally, many of these genes have previously been shown to play a role in aggression and were enriched in biological pathways affected by behavior. Their locations in the genome tended to form clusters spanning millions of bases in the genome. Conclusions This study provides evidence of clustered and genome-wide variation in promoter DNA methylation in young adults that associates with a history of chronic physical aggression from 6 to 15 years of age. However, longitudinal studies of methylation during early childhood will be necessary to determine if and how this methylation variation in T cells DNA plays a role in early development of chronic physical aggression. PMID:24691403

  8. Gene Methylation Biomarkers in Sputum and Plasma as Predictors for Lung Cancer Recurrence.

    Science.gov (United States)

    Belinsky, Steven A; Leng, Shuguang; Wu, Guodong; Thomas, Cynthia L; Picchi, Maria A; Lee, Sandra J; Aisner, Seena; Ramalingam, Suresh; Khuri, Fadlo R; Karp, Daniel D

    2017-11-01

    Detection of methylated genes in exfoliated cells from the lungs of smokers provides an assessment of the extent of field cancerization, is a validated biomarker for predicting lung cancer, and provides some discrimination when interrogated in blood. The potential utility of this 8-gene methylation panel for predicting tumor recurrence has not been assessed. The Eastern Cooperative Oncology Group initiated a prevention trial (ECOG-ACRIN5597) that enrolled resected stage I non-small cell lung cancer patients who were randomized 2:1 to receive selenized yeast versus placebo for 4 years. We conducted a correlative biomarker study to assess prevalence for methylation of the 8-gene panel in longitudinally collected sputum and blood after tumor resection to determine whether selenium alters their methylation profile and whether this panel predicts local and/or distant recurrence. Patients (N = 1,561) were enrolled into the prevention trial; 565 participated in the biomarker study with 122 recurrences among that group. Assessing the association between recurrence and risk of gene methylation longitudinally for up to 48 months showed a 1.4-fold increase in OR for methylation in sputum in the placebo group independent of location (local or distant). Kaplan-Meier curves evaluating the association between number of methylated genes and time to recurrence showed no increased risk in sputum, while a significant HR of 1.5 was seen in plasma. Methylation detection in sputum and blood is associated with risk for recurrence. Cancer Prev Res; 10(11); 635-40. ©2017 AACR. ©2017 American Association for Cancer Research.

  9. Digital Geologic Map of Congaree National Park and Vicinity, South Carolina (NPS, GRD, GRI, CONG, CONG digital map)

    Data.gov (United States)

    National Park Service, Department of the Interior — The Digital Geologic Map of Congaree National Park and Vicinity, South Carolina is composed of GIS data layers complete with ArcMap 9.3 layer (.LYR) files, two...

  10. Digital Geologic Map of Bryce Canyon National Park and Vicinity, Utah (NPS, GRD, GRI, BRCA, BRCA digital map)

    Data.gov (United States)

    National Park Service, Department of the Interior — The Digital Geologic Map of Bryce Canyon National Park and Vicinity, Utah is composed of GIS data layers complete with ArcMap 9.3 layer (.LYR) files, two ancillary...

  11. Digital Geologic Map of San Juan Island National Historical Park and vicinity, Washington (NPS, GRD, GRE, SAJH, SAJH digital map)

    Data.gov (United States)

    National Park Service, Department of the Interior — The Digital Geologic Map of San Juan Island National Historical Park and vicinity, Washington is composed of GIS data layers complete with ArcMap 9.2 layer (.LYR)...

  12. Digital Geologic Map of the American Camp Unit and vicinity, Washington (NPS, GRD, GRE, SAJH, SJIS digital map)

    Data.gov (United States)

    National Park Service, Department of the Interior — The Digital Geologic Map of the American Camp Unit and vicinity, Washington is composed of GIS data layers complete with ArcMap 9.2 layer (.LYR) files, two ancillary...

  13. Digital Geologic Map of Palo Alto Battlefield National Historic Site and vicinity, Texas (NPS, GRD, GRE, PAAL, PAAL digital map)

    Data.gov (United States)

    National Park Service, Department of the Interior — The Digital Geologic Map of Palo Alto Battlefield National Historic Site and vicinity, Texas is composed of GIS data layers complete with ArcMap 9.2 layer (.LYR)...

  14. The Role of Cytosine Methylation on Charge Transport through a DNA Strand

    Energy Technology Data Exchange (ETDEWEB)

    Qi, Jianqing; Govind, Niranjan; Anantram, M.P.

    2015-09-04

    Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modifi-cation remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Using density functional theory and the Landauer-Buttiker method, we study the electronic properties and charge transport through an eight base-pair methylated DNA strand and its native counterpart. Specifically, we compare the results generated with the widely used B3LYP exchange-correlation (XC) functional and CAM-B3LYP based tuned range-separated hybrid density functional. We first analyze the effect of cytosine methylation on the tight-binding parameters of two DNA strands and then model the transmission of the electrons and conductance through the strands both with and without decoherence. We find that with both functionals, the main difference of the tight-binding parameters between the native DNA and the methylated DNA lies in the on-site energies of (methylated) cytosine bases. The intra- and interstrand hopping integrals between two nearest neighboring guanine base and (methylated) cytosine base also change with the addition of the methyl groups. Our calculations show that in the phase-coherent limit, the transmission of the methylated strand is close to the native strand when the energy is nearby the highest occupied molecular orbital (HOMO) level and larger than the native strand by 5 times in the bandgap. The trend in transmission also holds in the presence of the decoherence with both functionals. We also study the effect of contact coupling by choosing coupling strengths ranging from weak to strong coupling limit. Our results suggest that the effect of the two different functionals is to alter the on-site energies of the DNA bases at the HOMO level, while the transport properties don't depend much on the two

  15. Association of postmenopausal endogenous sex hormones with global methylation level of leukocyte DNA among Japanese women

    Directory of Open Access Journals (Sweden)

    Iwasaki Motoki

    2012-07-01

    Full Text Available Abstract Background Although global hypomethylation of leukocyte DNA has been associated with an increased risk of several sites of cancer, including breast cancer, determinants of global methylation level among healthy individuals remain largely unexplored. Here, we examined whether postmenopausal endogenous sex hormones were associated with the global methylation level of leukocyte DNA. Methods A cross-sectional study was conducted using the control group of a breast cancer case–control study in Nagano, Japan. Subjects were postmenopausal women aged 55 years or over who provided blood samples. We measured global methylation level of peripheral blood leukocyte DNA by luminometric methylation assay; estradiol, estrone, androstenedione, dehydroepiandrosterone sulfate, testosterone and free testosterone by radioimmunoassay; bioavailable estradiol by the ammonium sulfate precipitation method; and sex-hormone binding globulin by immunoradiometric assay. A linear trend of association between methylation and hormone levels was evaluated by regression coefficients in a multivariable liner regression model. A total of 185 women were included in the analyses. Results Mean global methylation level (standard deviation was 70.3% (3.1 and range was from 60.3% to 79.2%. Global methylation level decreased 0.27% per quartile category for estradiol and 0.39% per quartile category for estrone while it increased 0.41% per quartile category for bioavailable estradiol. However, we found no statistically significant association of any sex hormone level measured in the present study with global methylation level of leukocyte DNA. Conclusions Our findings suggest that endogenous sex hormones are not major determinants of the global methylation level of leukocyte DNA.

  16. Higher Alu methylation levels in catch-up growth in twenty-year-old offsprings.

    Directory of Open Access Journals (Sweden)

    Kittipan Rerkasem

    Full Text Available Alu elements and long interspersed element-1 (LINE-1 or L1 are two major human intersperse repetitive sequences. Lower Alu methylation, but not LINE-1, has been observed in blood cells of people in old age, and in menopausal women having lower bone mass and osteoporosis. Nevertheless, Alu methylation levels also vary among young individuals. Here, we explored phenotypes at birth that are associated with Alu methylation levels in young people. In 2010, 249 twenty-years-old volunteers whose mothers had participated in a study association between birth weight (BW and nutrition during pregnancy in 1990, were invited to take part in our present study. In this study, the LINE-1 and Alu methylation levels and patterns were measured in peripheral mononuclear cells and correlated with various nutritional parameters during intrauterine and postnatal period of offspring. This included the amount of maternal intake during pregnancy, the mother's weight gain during pregnancy, birth weight, birth length, and the rate of weight gain in the first year of life. Catch-up growth (CUG was defined when weight during the first year was >0.67 of the standard score, according to WHO data. No association with LINE-1 methylation was identified. The mean level of Alu methylation in the CUG group was significantly higher than those non-CUG (39.61% and 33.66 % respectively, P < 0.0001. The positive correlation between the history of CUG in the first year and higher Alu methylation indicates the role of Alu methylation, not only in aging cells, but also in the human growth process. Moreover, here is the first study that demonstrated the association between a phenotype during the newborn period and intersperse repetitive sequences methylation during young adulthood.

  17. Molecular structure of poly(methyl methacrylate) surface II: Effect of stereoregularity examined through all-atom molecular dynamics.

    Science.gov (United States)

    Jha, Kshitij C; Zhu, He; Dhinojwala, Ali; Tsige, Mesfin

    2014-11-04

    Utilizing all-atom molecular dynamics (MD), we have analyzed the effect of tacticity and temperature on the surface structure of poly(methyl methacrylate) (PMMA) at the polymer-vacuum interface. We quantify these effects primarily through orientation, measured as the tilt with respect to the surface normal, and the surface number densities of the α-methyl, ester-methyl, carbonyl, and backbone methylene groups. Molecular structure on the surface is a complex interplay between orientation and number densities and is challenging to capture through sum frequency generation (SFG) spectroscopy alone. Independent quantification of the number density and orientation of chemical groups through all-atom MD presents a comprehensive model of stereoregular PMMA on the surface. SFG analysis presented in part I of this joint publication measures the orientation of molecules that are in agreement with MD results. We observe the ester-methyl groups as preferentially oriented, irrespective of tacticity, followed by the α-methyl and carbonyl groups. SFG spectroscopy also points to ester-methyl being dominant on the surface. The backbone methylene groups show a very broad angular distribution, centered along the surface plane. The surface number density ratios of ester-methyl to α-methyl groups show syndiotactic PMMA having the lowest value. Isotactic PMMA has the highest ratios of ester- to α-methyl. These subtle trends in the relative angular orientation and number densities that influence the variation of surface structure with tacticity are highlighted in this article. A more planar conformation of the syndiotactic PMMA along the surface (x-y plane) can be visualized through the trajectories from all-atom MD. Results from conformation tensor calculations for chains with any of their segments contributing to the surface validate the visual observation.

  18. Methyl 4-methyl-2-oxo-3,4-dihydrodibenzo[b,d]furan-4a(2H-carboxylate

    Directory of Open Access Journals (Sweden)

    Yidong Jiang

    2017-03-01

    Full Text Available The title compound, C15H14O4, has structural similarities to the alkaloid galanthamine, used in the treatment of Alzheimer's disease. The structure consists of a fused three-ring system comprising benzene and cyclohexenone fused to a central furan ring. The furan ring exhibits an envelope conformation with the carboxylate-substituted C atom as the flap, deviating by 0.352 (3 Å from the mean plane of other four furan-ring atoms. The cyclohexenone ring also exhibits an envelope conformation, with the methyl-substituted C atom as the flap. The methyl and carboxylate groups are on opposite side of the plane of the other five atoms of the cyclohexenone ring. In the crystal, other than van der Waals contacts, there are weak intermolecular C—H...O interactions present linking the molecules to form a one-dimensional zigzag chain along the b-axis direction.

  19. Human biomonitoring of heavy metals in the vicinity of non-ferrous metal plants in Ath, Belgium

    Directory of Open Access Journals (Sweden)

    Sébastien Fierens

    2016-10-01

    Full Text Available Abstract Background A previous study revealed an environmental contamination by heavy metals in the vicinity of two non-ferrous metal plants in Ath, Belgium. The purpose of the current cross-sectional study was to estimate exposure of the population to heavy metals in the vicinity of the plants, in comparison with population living further away. Methods We did a random sampling in the general population of Ath in two areas: a central area, including the plants, and a peripheral area, presumably less exposed. We quantified cadmium, lead, nickel, chromium and cobalt in blood and/or urine of children and adults in three age groups: (i children aged 2.5 to 6 years (n = 98, (ii children aged 7 to 11 years (n = 74, and (iii adults aged 40 to 60 years (n = 106. We also studied subclinical health effects by quantifying retinol-binding protein and microalbuminuria, and by means of a Strengths and Difficulties Questionnaire. Results We obtained a participation rate of 24 %. Blood lead levels were significantly higher in young children living in the central area (18.2 μg/l ; 95 % CI: 15.9–20.9 compared to the peripheral area (14.8 μg/l ; 95 % CI: 12.6–17.4. We observed no other significant mean difference in metal concentrations between the two areas. In the whole population, blood lead levels were higher in men (31.7 μg/l ; 95 % CI: 27.9–36.1 than in women (21.4 μg/l ; 95 % CI: 18.1–25.3. Urine cadmium levels were 0.06 μg/g creatinine (95 % CI: 0.05–0.07, 0.21 μg/g creatinine (95 % CI: 0.17–0.27, and 0.25 μg/g creatinine (95 % CI: 0.20–0.30 for children, men, and women, respectively. Conclusions Despite higher blood lead levels in young children living close to the plants, observed metal concentrations remain in the range found in other similar biomonitoring studies in the general population and are below the levels of concern for public health.

  20. Vitamin B12 supplementation influences methylation of genes associated with Type 2 diabetes and its intermediate traits.

    Science.gov (United States)

    Yadav, Dilip K; Shrestha, Smeeta; Lillycrop, Karen A; Joglekar, Charu V; Pan, Hong; Holbrook, Joanna D; Fall, Caroline Hd; Yajnik, Chittaranjan S; Chandak, Giriraj R

    2018-01-01

    To investigate the effect of B12 and/or folic acid supplementation on genome-wide DNA methylation. We performed Infinium HumanMethylation450 BeadChip (Zymo Research, CA, USA) assay in children supplemented with B12 and/or folic acid (n = 12 in each group) and investigated the functional mechanism of selected differentially methylated loci. We noted significant methylation changes postsupplementation in B12 (589 differentially methylated CpGs and 2892 regions) and B12 + folic acid (169 differentially methylated CpGs and 3241 regions) groups. Type 2 diabetes-associated genes TCF7L2 and FTO; and a miRNA, miR21 were further investigated in another B12-supplementation cohort. We also demonstrate that methylation influences miR21 expression and FTO, TCF7L2, CREBBP/CBP and SIRT1 are direct targets of miR21-3p. B12 supplementation influences regulation of several metabolically important Type 2 diabetes-associated genes through methylation of miR21. Hence, our study provides novel epigenetic explanation for the association between disordered one carbon metabolism and risk of adiposity, insulin resistance and diabetes and has translational potential.

  1. Targeting DNA methylation with green tea catechins.

    Science.gov (United States)

    Yiannakopoulou, Eugenia C

    2015-01-01

    Aberrant epigenetic alterations in the genome such as DNA methylation play a significant role in cancer development. Green tea catechins have been reported to modulate epigenetic processes. This review aims to synthesize evidence on the modulation of DNA methylation by green tea catechins. Green tea catechins have been reported to reverse DNA methylation of tumor suppressor genes and increase transcription of these genes. Green tea catechins and especially epigallocatechin gallate modulate DNA methylation by attenuating the effect of DNA methyltransferase 1 (DNMT1). However, the exact mechanism of DNMT1 inhibition is not delineated. Suggested mechanisms include direct enzymatic inhibition, indirect enzymatic inhibition, reduced DNMT1 expression and translation. The possible effect of green tea catechins on other pathways of DNA methylation, i.e. methyl-CpG binding domain proteins, has not been investigated. Furthermore, the link between redox properties and epigenetic modulation by green tea catechins has not been defined either. Since green tea catechins are natural compounds with a rather acceptable safety profile, further research on their action as inhibitors of DNA methylation seems worthwhile. © 2015 S. Karger AG, Basel

  2. DNA Methylation Signatures of the Plant Chromomethyltransferases.

    Directory of Open Access Journals (Sweden)

    Quentin Gouil

    2016-12-01

    Full Text Available DNA methylation in plants is traditionally partitioned into CG, CHG and CHH contexts (with H any nucleotide but G. By investigating DNA methylation patterns in trinucleotide contexts in four angiosperm species, we show that such a representation hides spatial and functional partitioning of different methylation pathways and is incomplete. CG methylation (mCG is largely context-independent whereas, at CHG motifs, there is under-representation of mCCG in pericentric regions of A. thaliana and tomato and throughout the chromosomes of maize and rice. In A. thaliana the biased representation of mCCG in heterochromatin is related to specificities of H3K9 methyltransferase SUVH family members. At CHH motifs there is an over-representation of different variant forms of mCHH that, similarly to mCCG hypomethylation, is partitioned into the pericentric regions of the two dicots but dispersed in the monocot chromosomes. The over-represented mCHH motifs in A. thaliana associate with specific types of transposon including both class I and II elements. At mCHH the contextual bias is due to the involvement of various chromomethyltransferases whereas the context-independent CHH methylation in A. thaliana and tomato is mediated by the RNA-directed DNA methylation process that is most active in the gene-rich euchromatin. This analysis therefore reveals that the sequence context of the methylome of plant genomes is informative about the mechanisms associated with maintenance of methylation and the overlying chromatin structure.

  3. Relationship between nucleosome positioning and DNA methylation

    Science.gov (United States)

    Chodavarapu, Ramakrishna K.; Feng, Suhua; Bernatavichute, Yana V.; Chen, Pao-Yang; Stroud, Hume; Yu, Yanchun; Hetzel, Jonathan; Kuo, Frank; Kim, Jin; Cokus, Shawn J.; Casero, David; Bernal, Maria; Huijser, Peter; Clark, Amander T.; Krämer, Ute; Merchant, Sabeeha S.; Zhang, Xiaoyu; Jacobsen, Steven E.; Pellegrini, Matteo

    2010-01-01

    Nucleosomes compact and regulate access to DNA in the nucleus, and are composed of approximately 147 bases of DNA wrapped around a histone octamer1, 2. Here we report a genome-wide nucleosome positioning analysis of Arabidopsis thaliana utilizing massively parallel sequencing of mononucleosomes. By combining this data with profiles of DNA methylation at single base resolution, we identified ten base periodicities in the DNA methylation status of nucleosome-bound DNA and found that nucleosomal DNA was more highly methylated than flanking DNA. These results suggest that nucleosome positioning strongly influences DNA methylation patterning throughout the genome and that DNA methyltransferases preferentially target nucleosome-bound DNA. We also observed similar trends in human nucleosomal DNA suggesting that the relationships between nucleosomes and DNA methyltransferases are conserved. Finally, as has been observed in animals, nucleosomes were highly enriched on exons, and preferentially positioned at intron-exon and exon-intron boundaries. RNA Pol II was also enriched on exons relative to introns, consistent with the hypothesis that nucleosome positioning regulates Pol II processivity. DNA methylation is enriched on exons, consistent with the targeting of DNA methylation to nucleosomes, and suggesting a role for DNA methylation in exon definition. PMID:20512117

  4. [DNA sperm methylation in assisted reproductive techniques].

    Science.gov (United States)

    Benchaïb, M; Ajina, M; Braun, V; Niveleau, A; Guérin, J-F

    2006-09-01

    In the last few years, many tests were developed to study the fertilizing properties of the spermatozoa. However none of them was useful to obtain a prognostic factor. Indeed, the integrity of the spermatic DNA is also necessary to a successful fertilization for obtaining a pregnancy. DNA integrity could be evaluated by the measurement of the level of DNA methylation. Indeed, in the mammals, the methylation of the ADN is involved in diverse processes amongst them the regulation of the genome expression during the embryonic development. The objective of this study is to evaluate the impact of the level of methylation of the spermatic DNA in the success of in vitro fertilization (IVF), in terms of rate of fertilization, quality of the embryos and rate of pregnancy. The immunostaining of the 5-methylecytosine, then the quantification by image analysis or with flow cytometry, allowed an objective evaluation of the level of total methylation of spermatic DNA. Our data show that the level of DNA methylation influences neither the fertilization rate nor the embryos quality. On the other hand, the rate of pregnancy is decreased if the total level of DNA methylation is lower than a threshold value. The level of spermatic DNA methylation represents a new parameter of spermatic maturation.

  5. Determination of Total Tritium in Urine from Residents Living in the Vicinity of Nuclear Power Plants in Qinshan, China

    Directory of Open Access Journals (Sweden)

    Bao-Ming Shen

    2015-01-01

    Full Text Available To estimate the tritium doses of the residents living in the vicinity of a nuclear power plant, urine samples of 34 adults were collected from residents living near the Qinshan nuclear power plant. The tritium-in-urine (HTO plus OBT was measured by liquid scintillation counting. The doses of tritium-in-urine from participants living at 2, 10 and 22 km were in a range of 1.26–6.73 Bq/L, 1.31–3.09 Bq/L and 2.21–3.81 Bq/L, respectively, while the average activity concentrations of participants from the three groups were 3.53 ± 1.62, 2.09 ± 0.62 and 2.97 ± 0.78 Bq/L, respectively. The personal committed effective doses for males were 2.5 ± 1.7 nSv and for females they were 2.9 ± 1.3 nSv. These results indicate that tritium concentrations in urine samples from residents living at 2 km from a nuclear power plant are significantly higher than those at 10 km. It may be the downwind direction that caused a higher dose in participants living at 22 km. All the measured doses of tritium-in-urine are in a background level range.

  6. Hydrogeologic framework, groundwater movement, and water budget in the Puyallup River Watershed and vicinity, Pierce and King Counties, Washington

    Science.gov (United States)

    Welch, Wendy B.; Johnson, Kenneth H.; Savoca, Mark E.; Lane, Ron C.; Fasser, Elisabeth T.; Gendaszek, Andrew S.; Marshall, Cameron; Clothier, Burt G.; Knoedler, Eric N.

    2015-01-01

    This report presents information used to characterize the groundwater-flow system in the Puyallup River Watershed and vicinity, and includes descriptions of the geology and hydrogeologic framework; groundwater recharge and discharge; groundwater levels and flow directions; seasonal groundwater level fluctuations; interactions between aquifers and the surface-water system; and a water budget. The study area covers about 1,220 square miles in northern Pierce and southern King Counties, Washington; extends north to the Green River and Auburn Valley and southwest to the Puyallup River and adjacent uplands; and is bounded on the south and east by foothills of the Cascade Range and on the west by Puget Sound. The area is underlain by a northwest-thickening sequence of unconsolidated glacial and interglacial deposits, which overlie sedimentary and volcanic bedrock units that crop out in the foothills along the southern and eastern margin of the study area. Geologic units were grouped into 13 hydrogeologic units consisting of aquifers, confining units, and an underlying bedrock unit. A surficial hydrogeologic unit map was developed and used with well information from 1,012 drillers’ logs to construct 8 hydrogeologic sections, and unit extent and thickness maps.

  7. Determination of total tritium in urine from residents living in the vicinity of nuclear power plants in Qinshan, China.

    Science.gov (United States)

    Shen, Bao-Ming; Ji, Yan-Qin; Tian, Qing; Shao, Xiang-Zhang; Yin, Liang-Liang; Su, Xu

    2015-01-16

    To estimate the tritium doses of the residents living in the vicinity of a nuclear power plant, urine samples of 34 adults were collected from residents living near the Qinshan nuclear power plant. The tritium-in-urine (HTO plus OBT) was measured by liquid scintillation counting. The doses of tritium-in-urine from participants living at 2, 10 and 22 km were in a range of 1.26-6.73 Bq/L, 1.31-3.09 Bq/L and 2.21-3.81 Bq/L, respectively, while the average activity concentrations of participants from the three groups were 3.53 ± 1.62, 2.09 ± 0.62 and 2.97 ± 0.78 Bq/L, respectively. The personal committed effective doses for males were 2.5 ± 1.7 nSv and for females they were 2.9 ± 1.3 nSv. These results indicate that tritium concentrations in urine samples from residents living at 2 km from a nuclear power plant are significantly higher than those at 10 km. It may be the downwind direction that caused a higher dose in participants living at 22 km. All the measured doses of tritium-in-urine are in a background level range.

  8. The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status

    Science.gov (United States)

    Li, Dongming; Palanca, Ana Marie S; Won, So Youn; Gao, Lei; Feng, Ying; Vashisht, Ajay A; Liu, Li; Zhao, Yuanyuan; Liu, Xigang; Wu, Xiuyun; Li, Shaofang; Le, Brandon; Kim, Yun Ju; Yang, Guodong; Li, Shengben; Liu, Jinyuan; Wohlschlegel, James A; Guo, Hongwei; Mo, Beixin; Chen, Xuemei; Law, Julie A

    2017-01-01

    DNA methylation is associated with gene silencing in eukaryotic organisms. Although pathways controlling the establishment, maintenance and removal of DNA methylation are known, relatively little is understood about how DNA methylation influences gene expression. Here we identified a METHYL-CpG-BINDING DOMAIN 7 (MBD7) complex in Arabidopsis thaliana that suppresses the transcriptional silencing of two LUCIFERASE (LUC) reporters via a mechanism that is largely downstream of DNA methylation. Although mutations in components of the MBD7 complex resulted in modest increases in DNA methylation concomitant with decreased LUC expression, we found that these hyper-methylation and gene expression phenotypes can be genetically uncoupled. This finding, along with genome-wide profiling experiments showing minimal changes in DNA methylation upon disruption of the MBD7 complex, places the MBD7 complex amongst a small number of factors acting downstream of DNA methylation. This complex, however, is unique as it functions to suppress, rather than enforce, DNA methylation-mediated gene silencing. DOI: http://dx.doi.org/10.7554/eLife.19893.001 PMID:28452714

  9. DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure.

    Science.gov (United States)

    Gelfman, Sahar; Cohen, Noa; Yearim, Ahuvi; Ast, Gil

    2013-05-01

    DNA methylation is known to regulate transcription and was recently found to be involved in exon recognition via cotranscriptional splicing. We recently observed that exon-intron architectures can be grouped into two classes: one with higher GC content in exons compared to the flanking introns, and the other with similar GC content in exons and introns. The first group has higher nucleosome occupancy on exons than introns, whereas the second group exhibits weak nucleosome marking of exons, suggesting another type of epigenetic marker distinguishes exons from introns when GC content is similar. We find different and specific patterns of DNA methylation in each of the GC architectures; yet in both groups, DNA methylation clearly marks the exons. Exons of the leveled GC architecture exhibit a significantly stronger DNA methylation signal in relation to their flanking introns compared to exons of the differential GC architecture. This is accentuated by a reduction of the DNA methylation level in the intronic sequences in proximity to the splice sites and shows that different epigenetic modifications mark the location of exons already at the DNA level. Also, lower levels of methylated CpGs on alternative exons can successfully distinguish alternative exons from constitutive ones. Three positions at the splice sites show high CpG abundance and accompany elevated nucleosome occupancy in a leveled GC architecture. Overall, these results suggest that DNA methylation affects exon recognition and is influenced by the GC architecture of the exon and flanking introns.

  10. Methyl chloride via oxhydrochlorination of methane

    Energy Technology Data Exchange (ETDEWEB)

    Jarvis, R.F. Jr.

    1997-12-31

    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.

  11. Effects of methylation-sensitive enzymes on the enrichment of genic SNPs and the degree of genome complexity reduction in a two-enzyme genotyping-by-sequencing (GBS) approach: a case study in oil palm (Elaeis guineensis).

    Science.gov (United States)

    Pootakham, Wirulda; Sonthirod, Chutima; Naktang, Chaiwat; Jomchai, Nukoon; Sangsrakru, Duangjai; Tangphatsornruang, Sithichoke

    2016-01-01

    Advances in next generation sequencing have facilitated a large-scale single nucleotide polymorphism (SNP) discovery in many crop species. Genotyping-by-sequencing (GBS) approach couples next generation sequencing with genome complexity reduction techniques to simultaneously identify and genotype SNPs. Choice of enzymes used in GBS library preparation depends on several factors including the number of markers required, the desired level of multiplexing, and whether the enrichment of genic SNP is preferred. We evaluated various combinations of methylation-sensitive (AatII, PstI, MspI) and methylation-insensitive (SphI, MseI) enzymes for their effectiveness in genome complexity reduction and enrichment of genic SNPs. We discovered that the use of two methylation-sensitive enzymes effectively reduced genome complexity and did not require a size selection step. On the contrary, the genome coverage of libraries constructed with methylation-insensitive enzymes was quite high, and the additional size selection step may be required to increase the overall read depth. We also demonstrated the effectiveness of methylation-sensitive enzymes in enriching for SNPs located in genic regions. When two methylation-insensitive enzymes were used, only 16% of SNPs identified were located in genes and 18% in the vicinity (± 5 kb) of the genic regions, while most SNPs resided in the intergenic regions. In contrast, a remarkable degree of enrichment was observed when two methylation-sensitive enzymes were employed. Almost two thirds of the SNPs were located either inside (32-36%) or in the vicinity (28-31%) of the genic regions. These results provide useful information to help researchers choose appropriate GBS enzymes in oil palm and other crop species.

  12. [Association between serum aluminium level and methylation of amyloid precursor protein gene in workers engaged in aluminium electrolysis].

    Science.gov (United States)

    Yang, X J; Yuan, Y Z; Niu, Q

    2016-04-20

    To investigate the association between serum aluminium level and methylation of the promoter region of amyloid precursor protein (APP)gene in workers engaged in aluminium electrolysis. In 2012, 366 electrolysis workers in an aluminium factory were enrolled as exposure group (working years >10 and age >40 years)and divided into low-exposure group and high-exposure group based on the median serum aluminium level. Meanwhile, 102 workers in a cement plant not exposed to aluminium were enrolled as control group. Graphite furnace atomic absorption spectrometry was used to measure serum aluminium level, methylation specific PCR was used to measure the methylation rate of the promoter region of APP gene, and ELI-SA was used to measure the protein expression of APP in lymphocytes in peripheral blood. The exposure group had a significantly higher serum aluminium level than the control group (45.07 μg/L vs 30.51 μg/L, P0.05). The multivariate logistic regression analysis showed that with reference to the control group, low aluminium exposure (OR=1.86, 95% CI 1.67~3.52)and high aluminium exposure (OR=2.98, 95% CI 1.97~4.15)were risk factors for a reduced methylation rate of the promoter region of APP gene. Reduced methylation of the promoter region of APP gene may be associated with increased serum aluminium level, and downregulated methylation of the promoter region of APP gene may accelerate APP gene transcription.

  13. DNA Methylation and Temperature Stress in an Antarctic Polychaete, Spiophanes tcherniai

    Directory of Open Access Journals (Sweden)

    Adam G. Marsh

    2014-05-01

    Full Text Available Epigenetic modifications of DNA and histones are a primary mechanism by which gene expression activities may be modified in response to environmental stimuli. Here we characterize patterns of methyl-cytosine composition in the marine polychaete emph{Spiophanes tcherniai} from McMurdo Sound, Antarctica. We cultured adult worms at two temperatures, -1.5 C (ambient control and +4 C (warm treatment, for four weeks. We observed a rapid capacity for emph{S. tcherniai} organismal respiration rates and underlying catalytic rates of citrate synthase to acclimate at +4 C and return to control levels. We profiled changes in the methylation states of CpG sites in these treatments using an NGS strategy to computationally reconstruct and quantify methylation status across the genome. In our analysis we recovered 120,000 CpG sites in assembled contigs from both treatments. Of those, we were able to align 28,000 CpG sites in common between the two sample groups. In comparing these aligned sites between treatments, only 3,000 (11% evidenced a change in methylation state, but over 85% of changes involved a gain of a 5-methyl group on a CpG site (net increase in methyation. The ability to score CpG sites as partially methylated among gDNA copies in a sample opens up a new avenue for assessing DNA methylation responses to changing environments. By quantitatively distinguishing a ``mixed'' population of copies of one CpG site, we can begin to identify dynamic, non-binary, continuous-response reactions in DNA methylation intensity or density that previously may have been overlooked as noise.

  14. Concentration of NOX in the vicinity of the power plants Vojany EVO 1 and EVO 2

    Directory of Open Access Journals (Sweden)

    Ján Brehuv

    2006-12-01

    Full Text Available The paper presents a calculation of the maximal concentration of nitrogen oxides in the vicinity of point sources (main chimneys of power plants Vojany EVO1 and EVO2. The wind velocity u10,M (7, at which the concentration on a given place in the surrounding of the pollution source attains a maximal value, is calculated. The relation (8 for a calculation of the place with the maximal concentration for a given class of air stability (Table 1 and 2 and for a given wind velocity is derived. According to equation (3 and Table 3, a thermal capacity of EVO1 and EVO2 is calculated, considering a flat country in the vicinity of the sources (x3 = 0 in relation (1. Subsequently, it is also considered that the wind direction has the direction joining the source and the place of concentration calculation (x2 = 0. The calculations of concentration are performed for the 5th class of air stability. As to this class, favourable conditions for the pollutants dispersion are there. Thus, the maximum concentration is in a relatively small distance from the source with a sharp concentration maximum. As to other classes of the air stability (Table 1 and 2, the maximum concentration is located in larger distances from the source, i.e. about 10 km, as it is considered in Table 4 and 5. The theoretical calculation of NOX concentration in the vicinity of the sources, EVO1 and EVO2, shows (Table 4 and 5 that it does not exceed the allowable limit of 150 µg.m-3.

  15. Monitoring the ordering in biomolecular films on vicinal silicon surfaces by reflectance difference/anisotropy spectroscopy

    Science.gov (United States)

    Silaghi, Simona D.; Zahn, Dietrich R. T.

    2006-05-01

    DNA base molecules, adenine, thymine, guanine, and cytosine may be employed as charge transport molecules in biomolecular electronic devices. Their electronic properties are comparable with those of inorganic wide bandgap materials, e.g. GaN with the absorption onset in the near ultra-violet (UV) range. A recent field effect transistor study based on a modified DNA base revealed that the prototype bio-transistor gives rise to a better voltage gain compared to one based on carbon nanotubes (CNTs) [G. Mauricio, P. Visconti, V. Arima, S. D'Amico, A. Biasco, E. D'Amone, R. Cingolani, R. Rinaldi, Nanoletters 3 (2003) 479]. Here, in situ reflectance difference/anisotropy spectroscopy (RDS/RAS) is employed under ultra-high vacuum (UHV) conditions for monitoring the growth of DNA base molecules on vicinal hydrogen passivated Si(1 1 1) surfaces. Such vicinal substrates consisting of steps and terraces may serves as suitable templates for molecular ordering. Indeed, RDS/RAS measurements reveal information about molecular ordering of DNA bases induced by the density of steps on silicon surfaces. All four molecules, however, behave differently on the vicinal substrates. The first transition dipole moments corresponding to adenine and thymine molecules align mainly perpendicular to the step edge direction while for guanine and cytosine they align parallel to this direction, however, only in very thin layers. The RDS/RAS signal of the guanine and cytosine layers with thicknesses above 20 nm saturates due to a loss of ordering at higher coverages. Additionally, time-resolved RDS/RAS measurements at the silicon E 2 (4.25 eV) critical point (CP) demonstrate the sensitivity to the biomolecular/inorganic interface formation.

  16. Lie groups and algebraic groups

    Indian Academy of Sciences (India)

    identity. It is a remarkable fact that simple. Lie groups can be completely classified; they are the special linear groups, orthogonal groups and symplectic groups. Apart from these, the list is a finite one (the so-called exceptional groups). This is the Cartan–Killing classification, which nowadays, is described in terms of the.

  17. CCNA1 promoter methylation: a potential marker for grading Papanicolaou smear cervical squamous intraepithelial lesions.

    Science.gov (United States)

    Chujan, Suthipong; Kitkumthorn, Nakarin; Siriangkul, Sumalee; Mutirangura, Apiwat

    2014-01-01

    From our previous study, we established that cyclin A1 (CCNA1) promoter methylation is strongly correlated with multistep progression of HPV-associated cervical cancer, suggesting potential use as a diagnostic maker of disease. The purpose of the present study was to assess the prevalence of CCNA1 promoter methylation in residual cervical cells isolated from liquid-based cytology that underwent hrHPV DNA screening for cervical cancer, and then to evaluate this marker for diagnostic accuracy using parameters like sensitivity, specificity, predictive values and likelihood ratio. In this retrospective study, histopathology was used as the gold standard method with specimens separated into the following groups: negative (n=31), low- grade squamous intraepithelial lesions (LSIL, n=34) and high-grade squamous intraepithelial lesions or worse (HSIL+, n=32). The hrHPV was detected by Hybrid Capture 2 (HC2) and CCNA1 promoter methylation was examined by CCNA1 duplex methylation specific PCR. The results showed the frequencies of CCNA1 promoter methylation were 0%, 5.88% and 83.33%, while the percentages of hrHPV were 66.67%, 82.35% and 100% in the negative, LSIL and HSIL+ groups, respectively. Although hrHPV infection showed high frequency in all three groups, it could not differentiate between the different groups and grades of precancerous lesions. In contrast, CCNA1 promoter methylation clearly distinguished between negative/LSIL and HSIL+, with high levels of all statistic parameters. CCNA1 promoter methylation is a potential marker for distinguishing between histologic negative/LSIL and HSIL+using cervical cytology samples.

  18. Contribution to the knowledge of jumping spiders (Araneae: Salticidae from vicinity of Jagodina, Central Serbia

    Directory of Open Access Journals (Sweden)

    Stanković, B.

    2012-09-01

    Full Text Available During last 10 years, based on personal collectings, 21 species from 14 genera of Salticidae (Araneae are recorded from vicinity of Jagodina: Ballus chalybeius, Carrhotus xanthogramma, Evarcha arcuata, Evarcha falcata, Heliophanus auratus, Heliophanus cupreus, Heliophanus flavipes, Heliophanus kochii, Icius hamatus, Icius subinermis, Leptorchestes berolinensis, Macaroeris nidicolens, Marpissa muscosa, Marpissa nivoyi, Mendoza canestrinii, Pellenes tripunctatus, Phintella castriesiana, Phlegra fasciata, Pseudeuophrys erratica, Pseudeuophrys lanigera, Salticus scenicus. All those species are provided with habitat notes and global distribution. New records for the spider fauna of Serbia are Heliophanus kochii (Simon 1868, Icius subinermis (Simon, 1937, Marpissa nivoyi (Lucas, 1846 and Mendoza canestrinii (Ninni, 1868.

  19. Anisotropic Spin-Orbit Coupling and Magnetocrystalline Anisotropy in Vicinal Co Films

    Energy Technology Data Exchange (ETDEWEB)

    Dhesi, Sarnjeet S.; van der Laan, Gerrit; Dudzik, Esther; Shick, Alexander B.

    2001-08-06

    The anisotropy of the spin-orbit interaction, <<{lambda}{sub a}> , in vicinal Co films has been measured using x-ray magnetic linear dichroism (XMLD). A linear increase in <{lambda}{sub a}> with Co step density is found using a new sum rule and represents the first experimental confirmation that XMLD probes the magnetocrystalline anisotropy energy (MAE). X-ray magnetic circular dichroism is used to confirm that the XMLD arises from changes in the local step-edge electronic structure. The XMLD sum rule gives a larger MAE compared to macroscopic values and is discussed with respect to other local probes of the MAE.

  20. Investigation of the conductivity distribution in the vicinity of a cascade volcano

    Energy Technology Data Exchange (ETDEWEB)

    Mozley, E.C.

    1982-11-01

    Magnetotelluric and telluric data were acquired in the vicinity of Mount Hood Oregon as part of a multidisciplinary exploration program to evaluate the geothermal potential of this stratocone volcano. Eleven field components were acquired simultaneously over the frequency band of 50. to .001 hertz. These data consisted of one five component magnetotelluric base site, two sets of two component remote electric field measurements and one set of remote horizontal magnetic field measurements. The data were recorded digitally in the field and processed later using the remote electric and magnetic signals to obtain unbiased tensor impedance and geomagnetic transfer function (tipper) estimates.

  1. Current-phase relations in SIsFS junctions in the vicinity of 0-π transition

    Science.gov (United States)

    Bakurskiy, S. V.; Filippov, V. I.; Ruzhickiy, V. I.; Klenov, N. V.; Soloviev, I. I.; Kupriyanov, M. Yu.; Golubov, A. A.

    2017-03-01

    We consider the current-phase relation (CPR) in Josephson junctions with complex insulator-superconductor-ferromagnetic interlayers in the vicinity of the 0-π transition. We find a strong impact of the second harmonic on the CPR of the junctions. It is shown that the critical current can be kept constant in the region of 0-π transition, while the CPR transforms through multivalued hysteretic states depending on the relative values of tunnel transparency and magnetic thickness. Moreover, the CPR in the transition region has multiple branches with distinct ground states.

  2. Wave-induced nearshore flow patterns in the vicinity of Cochin harbour, India

    Digital Repository Service at National Institute of Oceanography (India)

    PrasannaKumar, S.; Vethamony, P.; Murty, C.S.

    , C. S. Murty Refraction function Wave length Wave period Wave orbital velocity 1 INTRODUCTION The dynamics of sediment movement in the littoral zone is governed primarily by wave-induced currents. Specific knowledge of these currents...) _\\] (2) The wave orbital velocities (Umax) at the lower boundary of the fluid Nearshore flow patterns in the vicinity of Cochin Harbour 115 75 ° &5' 7,6" 76~ 15' -- 10 ° i 15' 300 ec N I -10° :hin leltana ~ntnak~ ;Ranaz 30 Fig. 2. A typical...

  3. Relativistic theory for picosecond time transfer in the vicinity of Earth

    Science.gov (United States)

    Petit, G.; Wolf, P.

    1994-01-01

    The problem of light propagation is treated in a geocentric reference system with the goal of ensuring picosecond accuracy for time transfer techniques using electromagnetic signals in the vicinity of the Earth. We give an explicit formula for a one way time transfer, to be applied when the spatial coordinates of the time transfer stations are known in a geocentric reference system rotating with the Earth. This expression is extended, at the same accuracy level of one picosecond, to the special cases of two way and LASSO time transfers via geostationary satellites.

  4. Shell model calculation for Te and Sn isotopes in the vicinity of {sup 100}Sn

    Energy Technology Data Exchange (ETDEWEB)

    Yakhelef, A.; Bouldjedri, A. [Physics Department, Farhat abbas University, Setif (Algeria); Physics Department, Hadj Lakhdar University, Batna (Algeria)

    2012-06-27

    New Shell Model calculations for even-even isotopes {sup 104-108}Sn and {sup 106,108}Te, in the vicinity of {sup 100}Sn have been performed. The calculations have been carried out using the windows version of NuShell-MSU. The two body matrix elements TBMEs of the effective interaction between valence nucleons are obtained from the renormalized two body effective interaction based on G-matrix derived from the CD-bonn nucleon-nucleon potential. The single particle energies of the proton and neutron valence spaces orbitals are defined from the available spectra of lightest odd isotopes of Sb and Sn respectively.

  5. Chemistry of Nitroquinolones and Synthetic Application to Unnatural 1-Methyl-2-quinolone Derivatives

    Directory of Open Access Journals (Sweden)

    Nagatoshi Nishiwaki

    2010-07-01

    Full Text Available The 1-methyl-2-quinolone (MeQone framework is often found in alkaloids and recently attention was drawn to unnatural MeQone derivatives with the aim of finding new biologically active compounds, however, low reactivity of the MeQone framework prevents the syntheses of versatile derivatives. A nitro group is one of the useful activating groups for this framework that enables a concise chemical transformation. Among nitroquinolones, 1-methyl-3,6,8-trinitro-2-quinolone (TNQ exhibits unusual reactivity favoring region-selective cine-substitutions that afford 4-substituted 1-methyl-6,8-dinitro-2-quinolones upon treatment with nucleophilic reagents. Contrary to this, 1-methyl-3,6-dinitro-2-quinolone (3,6-DNQ does not undergo any reaction under the same conditions. The unusual reactivity of TNQ is caused by steric repulsion between the methyl group at the 1-position and the nitro group at the 8-position, which distorts the MeQone framework. As a result, the pyridone ring of TNQ loses aromaticity and acts rather as an activated nitroalkene. Indeed, the pyridone moiety of TNQ undergoes cycloaddition with electron-rich alkenes or dienes under mild conditions, whereby a new fused ring is constructed on the [c]-face of the MeQone. Consequently, TNQ can be used as a new scaffold leading to versatile unnatural MeQone derivatives.

  6. Choline nutrition programs brain development via DNA and histone methylation.

    Science.gov (United States)

    Blusztajn, Jan Krzysztof; Mellott, Tiffany J

    2012-06-01

    Choline is an essential nutrient for humans. Metabolically choline is used for the synthesis of membrane phospholipids (e.g. phosphatidylcholine), as a precursor of the neurotransmitter acetylcholine, and, following oxidation to betaine, choline functions as a methyl group donor in a pathway that produces S-adenosylmethionine. As a methyl donor choline influences DNA and histone methylation--two central epigenomic processes that regulate gene expression. Because the fetus and neonate have high demands for choline, its dietary intake during pregnancy and lactation is particularly important for normal development of the offspring. Studies in rodents have shown that high choline intake during gestation improves cognitive function in adulthood and prevents memory decline associated with old age. These behavioral changes are accompanied by electrophysiological, neuroanatomical, and neurochemical changes and by altered patterns of expression of multiple cortical and hippocampal genes including those encoding key proteins that contribute to the biochemical mechanisms of learning and memory. These actions of choline are observed long after the exposure to the nutrient ended (months) and correlate with fetal hepatic and cerebral cortical choline-evoked changes in global- and gene-specific DNA cytosine methylation and with dramatic changes of the methylation pattern of lysine residues 4, 9 and 27 of histone H3. Moreover, gestational choline modulates the expression of DNA (Dnmt1, Dnmt3a) and histone (G9a/Ehmt2/Kmt1c, Suv39h1/Kmt1a) methyltransferases. In addition to the central role of DNA and histone methylation in brain development, these processes are highly dynamic in adult brain, modulate the expression of genes critical for synaptic plasticity, and are involved in mechanisms of learning and memory. A recent study documented that in a cohort of normal elderly people, verbal and visual memory function correlated positively with the amount of dietary choline consumption

  7. Influence of N-methyl pyrrolidone on the activity of the pulp-dentine complex and bone

    OpenAIRE

    Gjoksi Bebeka

    2016-01-01

    AIM: To analyse the effect of systemic application of N methyl pyrrolidone (NMP) on the pulp dentine complex and on the jawbone of ovariectomized rats. METHOD: Female Sprague Dawley rats were randomly divided into a Sham operated group (Sham n = 6) and an oestrogen depletion by ovariectomy (OVX n = 12) group. In 6 of the ovariectomized animals N methyl pyrrolidone (NMP) in phosphate buffered saline (PBS) was administered systemically weekly by intraperitoneal injection (i.p.); the other 6 w...

  8. Iridium- and ruthenium-catalysed synthesis of 2,3-disubstituted indoles from anilines and vicinal diols

    DEFF Research Database (Denmark)

    Tursky, Matyas; Lorentz-Petersen, Linda Luise Reeh; Olsen, L. B.

    2010-01-01

    A straightforward and atom-economical method is described for the synthesis of 2,3-disubstituted indoles. Anilines and 1,2-diols are condensed under neat conditions with catalytic amounts of either [Cp*IrCl2](2)/MsOH or RuCl3 center dot xH(2)O/phosphine (phosphine = PPh3 or xantphos). The reaction...... does not require any stoichiometric additives and only produces water and dihydrogen as byproducts. Anilines containing methyl, methoxy, chloro and fluoro substituents can participate in the cyclocondensation. Meta-substituted anilines give good regioselectivity for 6-substituted indoles, while...... unsymmetrical diols afford excellent regioselectivity for the indole isomer with an aryl or large alkyl group in the 2-position. The mechanism for the cyclocondensation presumably involves initial formation of the alpha-hydroxyketone from the diol. The ketone subsequently reacts with aniline to generate...

  9. Photorejuvenation using topical 5-methyl aminolevulinate and red light.

    Science.gov (United States)

    Ruiz-Rodríguez, Ricardo; López, Laura; Candelas, Daniel; Pedraz, Javier

    2008-07-01

    Photodynamic therapy has been proved to be effective in skin rejuvenation. To evaluate clinical efficacy and side effects of photodynamic therapy using topical 5-methyl aminolevulinate and red light for photorejuvenation. A randomized, prospective, split-face comparison study of 10 white, adult patients with moderate photodamage, Fitzpatrick skin types 2 or 3, and no occurrence of actinic keratosis was performed. Three treatments using topical methyl aminolevulinate cream, applied for 1 hour on one half of the face and 3 hours on the other half before illumination with red light. A blinded investigator prior to treatment and 2 months after the third treatment evaluated each side of the subject's faces. A moderate improvement in fine lines, tactile roughness, and skin tightness was observed in most of the patients, mostly on the 3-hour time side. There were no changes in mottled pigmentation or telangiectasias. Side effects were observed in all subjects (erythema, edema, scaling) mainly in the 3-hour incubation time side. The small number of patients and the lack of placebo group. Methyl aminolevulinic-photodynamic therapy with red light can improve fine lines, tactile roughness and skin tightness in patients with moderate photoaging and no occurrence of actinic keratosis.

  10. MethylQuant: A Tool for Sensitive Validation of Enzyme-Mediated Protein Methylation Sites from Heavy-Methyl SILAC Data.

    Science.gov (United States)

    Tay, Aidan P; Geoghegan, Vincent; Yagoub, Daniel; Wilkins, Marc R; Hart-Smith, Gene

    2018-01-05

    The study of post-translational methylation is hampered by the fact that large-scale LC-MS/MS experiments produce high methylpeptide false discovery rates (FDRs). The use of heavy-methyl stable isotope labeling by amino acids in cell culture (heavy-methyl SILAC) can drastically reduce these FDRs; however, this approach is limited by a lack of heavy-methyl SILAC compatible software. To fill this gap, we recently developed MethylQuant. Here, using an updated version of MethylQuant, we demonstrate its methylpeptide validation and quantification capabilities and provide guidelines for its best use. Using reference heavy-methyl SILAC data sets, we show that MethylQuant predicts with statistical significance the true or false positive status of methylpeptides in samples of varying complexity, degree of methylpeptide enrichment, and heavy to light mixing ratios. We introduce methylpeptide confidence indicators, MethylQuant Confidence and MethylQuant Score, and demonstrate their strong performance in complex samples characterized by a lack of methylpeptide enrichment. For these challenging data sets, MethylQuant identifies 882 of 1165 true positive methylpeptide spectrum matches (i.e., >75% sensitivity) at high specificity (<2% FDR) and achieves near-perfect specificity at 41% sensitivity. We also demonstrate that MethylQuant produces high accuracy relative quantification data that are tolerant of interference from coeluting peptide ions. Together MethylQuant's capabilities provide a path toward routine, accurate characterizations of the methylproteome using heavy-methyl SILAC.

  11. Surface treatment with methyl formate-methyl acetate increased the shear bond strength between reline resins and denture base resin.

    Science.gov (United States)

    Osathananda, Rachanee; Wiwatwarrapan, Chairat

    2016-06-01

    Chemical surface treatment increases the shear bond strength (SBS) between hard reline resins (HRRs) and denture base resin. To evaluate the effect of methyl formate-methyl acetate (MF-MA), when used as a surface treatment agent, on the SBS between denture base resin and different HRRs. One hundred and twenty specimens of heat-polymerised acrylic resin denture base (Meliodent(®) ) were divided into 12 groups. These groups comprised denture base relined with three self-polymerised HRRs [Unifast trad(®) (UT), Tokuyama(®) RebaseII Fast (TR), Ufi gel hard(®) (UG)], and treated with their respective Bonding Agent (BA) or by MF:MA solutions at ratios of 35:65, 25:75, and 15:85 for 15 s. The SBS was measured using a Universal Testing Machine. The data were analysed using two-way anova and post hoc Tukey's analysis at p < 0.05. The highest SBS was in the UT treated with MF:MA at a ratio of 25:75 group, followed by UT treated with MF:MA at ratios of 15:85, 35:65, UT treated with BA, and all UG treated with MF:MA groups. The SBS of the UT treated with MF:MA at a ratio of 25:75 group was significantly higher than those of the groups treated with BA. The SBS of the UG treated with MF:MA groups was significantly higher than control. The TR groups treated with BA or MF:MA groups showed no significant difference in SBS. Surface treatment with MF-MA significantly enhanced the SBS of denture base resin and UT and UG compared to that of the groups treated with BA. © 2014 John Wiley & Sons A/S and The Gerodontology Association. Published by John Wiley & Sons Ltd.

  12. Incorporating DNA Methylation Dynamics Into Epigenetic Codes

    Science.gov (United States)

    Szulwach, Keith E.; Jin, Peng

    2014-01-01

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

  13. Modeling spatiotemporal dynamics of DNA methylation

    DEFF Research Database (Denmark)

    Lövkvist, Cecilia Elisabet

    Epigenetics explains how cells with identical genetic material can have different gene expression patterns and thereby varying phenotypes. By the definition used in this thesis, a “mark” is considered to be epigenetic, if it affects gene expression, is stable over time, and is inherited upon cell...... division. The patterns of epigentic marks depend on enzymes that ensure their maintenance and introduction. Using theoretical models, this thesis proposes new mechanisms for how enzymes operate to maintain patterns of epigenetic marks. Through analysis of experimental data this work gives new insight...... into how epigenetic marks are distributed in the human genome. In the first part of the thesis, we investigate DNA methylation and maintenance of methylation patterns throughout cell division. We argue that collaborative models, those where the methylation of CpG sites depends on the methylation status...

  14. Group X

    Energy Technology Data Exchange (ETDEWEB)

    Fields, Susannah

    2007-08-16

    This project is currently under contract for research through the Department of Homeland Security until 2011. The group I was responsible for studying has to remain confidential so as not to affect the current project. All dates, reference links and authors, and other distinguishing characteristics of the original group have been removed from this report. All references to the name of this group or the individual splinter groups has been changed to 'Group X'. I have been collecting texts from a variety of sources intended for the use of recruiting and radicalizing members for Group X splinter groups for the purpose of researching the motivation and intent of leaders of those groups and their influence over the likelihood of group radicalization. This work included visiting many Group X websites to find information on splinter group leaders and finding their statements to new and old members. This proved difficult because the splinter groups of Group X are united in beliefs, but differ in public opinion. They are eager to tear each other down, prove their superiority, and yet remain anonymous. After a few weeks of intense searching, a list of eight recruiting texts and eight radicalizing texts from a variety of Group X leaders were compiled.

  15. Microbial Methylation of Metalloids: Arsenic, Antimony, and Bismuth

    Science.gov (United States)

    Bentley, Ronald; Chasteen, Thomas G.

    2002-01-01

    A significant 19th century public health problem was that the inhabitants of many houses containing wallpaper decorated with green arsenical pigments experienced illness and death. The problem was caused by certain fungi that grew in the presence of inorganic arsenic to form a toxic, garlic-odored gas. The garlic odor was actually put to use in a very delicate microbiological test for arsenic. In 1933, the gas was shown to be trimethylarsine. It was not until 1971 that arsenic methylation by bacteria was demonstrated. Further research in biomethylation has been facilitated by the development of delicate techniques for the determination of arsenic species. As described in this review, many microorganisms (bacteria, fungi, and yeasts) and animals are now known to biomethylate arsenic, forming both volatile (e.g., methylarsines) and nonvolatile (e.g., methylarsonic acid and dimethylarsinic acid) compounds. The enzymatic mechanisms for this biomethylation are discussed. The microbial conversion of sodium arsenate to trimethylarsine proceeds by alternate reduction and methylation steps, with S-adenosylmethionine as the usual methyl donor. Thiols have important roles in the reductions. In anaerobic bacteria, methylcobalamin may be the donor. The other metalloid elements of the periodic table group 15, antimony and bismuth, also undergo biomethylation to some extent. Trimethylstibine formation by microorganisms is now well established, but this process apparently does not occur in animals. Formation of trimethylbismuth by microorganisms has been reported in a few cases. Microbial methylation plays important roles in the biogeochemical cycling of these metalloid elements and possibly in their detoxification. The wheel has come full circle, and public health considerations are again important. PMID:12040126

  16. Solubilities of carbon dioxide and oxygen in the ionic liquids methyl trioctyl ammonium bis(trifluoromethylsulfonyl)imide, 1-butyl-3-methyl imidazolium bis(trifluoromethylsulfonyl)imide, and 1-butyl-3-methyl imidazolium methyl sulfate.

    Science.gov (United States)

    Bahadur, Indra; Osman, Khalid; Coquelet, Christophe; Naidoo, Paramespri; Ramjugernath, Deresh

    2015-01-29

    Ionic liquids (ILs) are being considered as solvents for gas absorption processes as they have the potential, in general, for improved efficiency of gas separations, as well as lower capital and operating costs compared to current commercial processes. In this study the solvent properties of ILs are investigated for use in the absorption of carbon dioxide (CO2) and oxygen (O2). The absorption of these gases in ILs was measured in the temperature range 303.15-333.15 K and at pressures up to 1.5 MPa by gravimetric analysis. The ILs used were methyl trioctyl ammonium bis (trifluoromethylsulfonyl) imide ([MOA][Tf2N]), 1-butyl-3-methyl imidazolium bis (trifluoromethylsulfonyl) imide ([BMIM][Tf2N]), and 1-butyl-3-methyl imidazolium methyl sulfate ([BMIM][MeSO4]). The measurement technique employed in this study is fast and accurate, and requires small quantities of solvent. The results indicated that absorption of both gases increased with a decrease in operating temperature and an increase in pressure. [MOA][Tf2N] had the highest CO2 and O2 solubility. [BMIM][Tf2N] was determined to have the highest selectivity for CO2 absorption. [BMIM][MeSO4] achieved the lowest CO2 absorption with a moderate O2 absorption, revealing this IL to be the least desirable for CO2 and O2 absorption. Calculation of Henry's law constants for all systems confirmed the deductions made from absorption data analysis. Calculation of enthalpy and entropy of absorption for each system revealed CO2 absorption in [MOA][Tf2N] to be the least sensitive to temperature increases. The absorption data was modeled using the generic Redlich-Kwong cubic equation of state (RK-EOS) coupled with a group contribution method.

  17. Association between global leukocyte DNA methylation and cardiovascular risk in postmenopausal women.

    Science.gov (United States)

    Ramos, Ramon Bossardi; Fabris, Vitor; Lecke, Sheila Bunecker; Maturana, Maria Augusta; Spritzer, Poli Mara

    2016-10-10

    Genetic studies to date have not provided satisfactory evidence regarding risk polymorphisms for cardiovascular disease (CVD). Conversely, epigenetic mechanisms, including DNA methylation, seem to influence the risk of CVD and related conditions. Because postmenopausal women experience an increase in CVD, we set out to determine whether global DNA methylation was associated with cardiovascular risk in this population. In this cross sectional study carried out in a university hospital, 90 postmenopausal women without prior CVD diagnosis (55.5 ± 4.9 years, 5.8 [3.0-10.0] years since menopause) were enrolled. DNA was extracted from peripheral leukocytes and global DNA methylation levels were obtained with an ELISA kit. Cardiovascular risk was estimated by the Framingham General Cardiovascular Risk Score (10-year risk) (FRS). Clinical and laboratory variables were assessed. Patients were stratified into two CVD risk groups: low (FRS: <10 %, n = 69) and intermediate/high risk (FRS ≥10 %, n = 21). Age, time since menopause, blood pressure, total cholesterol, and LDL-c levels were higher in FRS ≥10 % group vs. FRS <10 % group. BMI, triglycerides, HDL-c, HOMA-IR, glucose and hsC-reactive protein levels were similar in the two groups. Global DNA methylation (% 5mC) in the overall sample was 26.5 % (23.6-36.9). The FRS ≥10 % group presented lower global methylation levels compared with the FRS <10 % group: 23.9 % (20.6-29.1) vs. 28.8 % (24.3-39.6), p = 0.02. This analysis remained significant even after adjustment for time since menopause (p = 0.02). Our results indicate that lower global DNA methylation is associated with higher cardiovascular risk in postmenopausal women.

  18. [The role of promoter CpG islands methylation of leptin gene in osteoarthritis].

    Science.gov (United States)

    Niu, Su-ping; Huang, Ci-bo; Zhao, Li-ke; Cheng, Yong-jing; Yang, Tuo

    2011-01-01

    To investigate the effects of 5-Aza-CdR (methylation transferase inhibitor)on the expression levels of leptin gene in chondrocytes and methylation states of leptin promoter region between osteoarthritis (OA) group and control. The chondrocytes in osteoarthritis group were treated with 5-Aza-CdR with different doses and time-points, and the expression level of leptin was detected by real-time polymerase chain reaction for picking up the optimum dose and time-point. Next, the chondrocytes in 5 osteoarthritis patients and 5 control patients (amputation due to severe trauma) were treated with 5-Aza-CdR. Lastly, leptin mRNA expression levels in the four groups osteoarthritis and control chondrocytes treated with/without 5-Aza-CdR were measured by real-time PCR and the methylation state of promoter region (-280 - +79) was detected by epitope quantitative DNA methylation analysis. (1) After treating the chondrocytes in OA groups with 10 µmol/L 5-Aza-CdR for 72 h, the mRNA expression levels of leptin were increased significantly. (2) The mRNA expression levels of leptin were significantly different among the four groups (P osteoarthritis groups treated with 5-Aza-CdR showed a marked induction of leptin mRNA expression. (3) Analysis of quantitative methylation data using an unsupervised hierarchical clustering algorithm, showed that methylation patterns of leptin promoter was different between control and osteoarthritis chondrocyte treated with/without 5-Aza-CdR. Demethylation of leptin promoter might up-regulate leptin gene expression level and it might contribute to osteoarthritis.

  19. LINE-1 Methylation Patterns as a Predictor of Postmolar Gestational Trophoblastic Neoplasia

    Directory of Open Access Journals (Sweden)

    Ruangsak Lertkhachonsuk

    2015-01-01

    Full Text Available Objective. To study the potential of long interspersed element-1 (LINE-1 methylation change in the prediction of postmolar gestational trophoblastic neoplasia (GTN. Methods. The LINE-1 methylation pattern from first trimester placenta, hydatidiform mole, and malignant trophoblast specimens were compared. Then, hydatidiform mole patients from 11999 to 2010 were classified into the following 2 groups: a remission group and a group that developed postmolar GTN. Specimens were prepared for a methylation study. The methylation levels and percentages of LINE-1 loci were evaluated for their sensitivity, specificity, and accuracy for the prediction of postmolar GTN. Results. First, 12 placentas, 38 moles, and 19 malignant trophoblast specimens were compared. The hydatidiform mole group had the highest LINE-1 methylation level (p = 0.003 and the uCuC of LINE-1 increased in the malignant trophoblast group (p ≤ 0.001. One hundred forty-five hydatidiform mole patients were classified as 103 remission and 42 postmolar GTN patients. The %mCuC and %uCmC of LINE-1 showed the lowest p value for distinguishing between the two groups (p < 0.001. The combination of the pretreatment β-hCG level (≥100,000 mIU/mL with the %mCuC and %uCmC, sensitivity, specificity, PPV, NPV, and accuracy modified the levels to 60.0%, 92.2%, 77.4%, 83.8%, and 82.3%, respectively. Conclusions. A reduction in the partial methylation of LINE-1 occurs early before the clinical appearance of malignant transformation. The %mCuC and %uCmC of LINE-1s may be promising markers for monitoring hydatidiform moles before progression to GTN.

  20. Computational Modeling Approach in Probing the Effects of Cytosine Methylation on the Transcription Factor Binding to DNA.

    Science.gov (United States)

    Tenayuca, John; Cousins, Kimberley; Yang, Shumei; Zhang, Lubo

    2017-01-01

    Cytosine methylation at CpG dinucleotides is a chief mechanism in epigenetic modification of gene expression patterns. Previous studies demonstrated that increased CpG methylation of Sp1 sites at -268 and -346 of protein kinase C ε promoter repressed the gene expression. The present study investigated the impact of CpG methylation on the Sp1 binding via molecular modeling and electrophoretic mobility shift assay. Each of the Sp1 sites contain two CpGs. Methylation of either CpG lowered the binding affinity of Sp1, whereas methylation of both CpGs produced a greater decrease in the binding affinity. Computation of van der Waals (VDW) energy of Sp1 in complex with the Sp1 sites demonstrated increased VDW values from one to two sites of CpG methylation. Molecular modeling indicated that single CpG methylation caused underwinding of the DNA fragment, with the phosphate groups at C1, C4 and C5 reoriented from their original positions. Methylation of both CpGs pinched the minor groove and increased the helical twist concomitant with a shallow, hydrophobic major groove. Additionally, double methylation eliminated hydrogen bonds on recognition helix residues located at positions -1 and 1, which were essential for interaction with O6/N7 of G-bases. Bonding from linker residues Arg565, Lys595 and Lys596 were also reduced. Methylation of single or both CpGs significantly affected hydrogen bonding from all three Sp1 DNA binding domains, demonstrating that the consequences of cytosine modification extend beyond the neighboring nucleotides. The results indicate that cytosine methylation causes subtle structural alterations in Sp1 binding sites consequently resulting in inhibition of side chain interactions critical for specific base recognition and reduction of the binding affinity of Sp1. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  1. Heterochromatin Dynamics during the Differentiation Process Revealed by the DNA Methylation Reporter Mouse, MethylRO

    Directory of Open Access Journals (Sweden)

    Jun Ueda

    2014-06-01

    Full Text Available In mammals, DNA is methylated at CpG sites, which play pivotal roles in gene silencing and chromatin organization. Furthermore, DNA methylation undergoes dynamic changes during development, differentiation, and in pathological processes. The conventional methods represent snapshots; therefore, the dynamics of this marker within living organisms remains unclear. To track this dynamics, we made a knockin mouse that expresses a red fluorescent protein (RFP-fused methyl-CpG-binding domain (MBD protein from the ROSA26 locus ubiquitously; we named it MethylRO (methylation probe in ROSA26 locus. Using this mouse, we performed RFP-mediated methylated DNA immunoprecipitation sequencing (MeDIP-seq, whole-body section analysis, and live-cell imaging. We discovered that mobility and pattern of heterochromatin as well as DNA methylation signal intensity inside the nuclei can be markers for cellular differentiation status. Thus, the MethylRO mouse represents a powerful bioresource and technique for DNA methylation dynamics studies in developmental biology, stem cell biology, as well as in disease states.

  2. Pulsed-laser deposition of vicinal and c-axis oriented high temperature superconducting thin films

    CERN Document Server

    Rössler, R

    2000-01-01

    respect to the temperature, oxygen pressure and laser fluence. (Re,Hg)Ba sub 2 Ca sub ( n-1)Cu sub n O sub x films are synthesized on (001) and vicinal SrTiO sub 3 substrates in a two step process employing pulsed-laser deposition of Hg-free precursor films and Hg-vapour annealing in a sealed quartz tube. The sealed quartz tube technique is described in detail and the thermodynamics and the phase formation are discussed. The influence of the Hg-vapour pressure and the annealing temperature on the film properties are investigated. The influence of Hg-vapour annealing on Bi sub 2 Sr sub 2 CaCu sub 2 O sub x films is described. YBa sub 2 Cu sub 3 O sub x films with thicknesses 20 to 480 nm are deposited on vicinal SrTiO sub 3 substrates (10 degrees tilt angle). Variation of the resistivities and changes in the film morphology depending on film thickness are described. The influence of post-annealing treatments on the film properties is discussed. Pulsed-laser deposition (PLD) of high temperature superconducting ...

  3. Chemistry of spring and well waters on Kilauea Volcano, Hawaii, and vicinity

    Energy Technology Data Exchange (ETDEWEB)

    Janik, C.J.; Nathenson, M.; Scholl, M.A.

    1994-12-31

    Published and new data for chemical and isotopic samples from wells and springs on Kilauea Volcano and vicinity are presented. These data are used to understand processes that determine the chemistry of dilute meteoric water, mixtures with sea water, and thermal water. Data for well and spring samples of non-thermal water indicate that mixing with sea water and dissolution of rock from weathering are the major processes that determine the composition of dissolved constituents in water. Data from coastal springs demonstrate that there is a large thermal system south of the lower east rift of Kilauea. Samples of thermal water from shallow wells in the lower east rift and vicinity have rather variable chemistry indicating that a number of processes operate in the near surface. Water sampled from the available deep wells is different in composition from the shallow thermal water, indicating that generally there is not a significant component of deep water in the shallow wells. Data for samples from available deep wells show significant gradients in chemistry and steam content of the reservoir fluid. These gradients are interpreted to indicate that the reservoir tapped by the existing wells is an evolving vapor-dominated system.

  4. Mapping human vulnerability to chemical accidents in the vicinity of chemical industry parks.

    Science.gov (United States)

    Li, Fengying; Bi, Jun; Huang, Lei; Qu, Changsheng; Yang, Jie; Bu, Quanmin

    2010-07-15

    China is suffering from severe pollution accidents which may have catastrophic impacts on the local population and environment. Some questions are unclear to local governments and industry operators like "who are vulnerable to the chemical risks?" and "what is the magnitude of vulnerability?". This paper concentrates on exploring the concepts of human vulnerability and the methodology of analyzing human vulnerability to chemical accidents in the vicinity of chemical industry parks. A conceptual model of human vulnerability to chemical accidents is developed, revealing the roots of human vulnerability and emphasizing its role in risk management. A geographical information system (GIS)-based methodology for mapping vulnerability is proposed and applied to the Nanjing Chemical Industry Park in China. By combining physical vulnerability and social vulnerability spatially, the total vulnerability is revealed to better respond to accidents. It is proposed to improve traffic lines and allocation of medical services, and include vulnerability assessment in land-use planning to reduce future risks. In other words, it seems feasible and effective to reveal physical, social and total vulnerability of residents in the vicinity of chemical risk sources. 2010 Elsevier B.V. All rights reserved.

  5. Neutron diffraction analysis of residual strain/stress distribution in the vicinity of high strength welds

    Directory of Open Access Journals (Sweden)

    Hamák I.

    2010-06-01

    Full Text Available Residual stresses resulting from non homogeneous heat distribution during welding process belong to most significant factor influencing behavior of welded structures. These stresses are responsible for defect occurrence during welding and they are also responsible for crack initiation and propagation at the either static or dynamic load. The significant effect of weld metal chemical composition as well as the effect of fatigue load and local plastic deformation on residual stress distribution and fatigue life have been recognized for high strength steels welds. The changes in residual stress distribution have then positive effect on cold cracking behavior and also on fatigue properties of the welds [1-3]. Several experimental methods, both destructive and non-destructive, such as hole drilling method, X-ray diffraction, neutron diffraction and others, have been used to examine residual stress distribution in all three significant orientations in the vicinity of the welds. The present contribution summarizes the results of neutron diffraction measurements of residual stress distribution in the vicinity of single-pass high-strength-steel welds having different chemical composition as well as the influence of fatigue load and local plastic deformation. It has been observed that the chemical composition of the weld metal has a significant influence on the stress distribution around the weld. Similarly, by aplying both cyclic load or pre-stress load on the specimens, stress relaxation was observed even in the region of approximately 40 mm far from the weld toe.

  6. Local temperature measurement in the vicinity of electromagnetically heated magnetite and gold nanoparticles

    Science.gov (United States)

    Gupta, Amit; Kane, Ravi S.; Borca-Tasciuc, Diana-Andra

    2010-09-01

    This paper describes a new technique employing fluorescent quantum dots as temperature probes for measuring the temperature rise in the proximity of nanoparticles heated by a radio frequency (rf) electromagnetic field. The remote heating of nanoparticles by an rf field is a promising approach to control biological transformations at the molecular level. In principle, the heat dissipated by each nanoparticle might produce a temperature increase in its proximity, facilitating a change in the molecules directly attached to it but not in the others. Although this method has been demonstrated to provide control over biological transformations, the proposed mechanism involves producing and maintaining large temperature differences across small distances, in the range of several degrees Celsius across tens of nanometers. Existing theories for heat generation and transfer in rf heated nanoparticle systems cannot account for these gradients. To better understand the limitations of local heating, the temperature in the vicinity of rf heated nanoparticles was measured. Dilute aqueous suspensions of gold and magnetite nanoparticles were remotely heated by an rf field between 600-800 kHz. Two systems were investigated: a control sample consisting of quantum dots mixed with nanoparticles and a solution of quantum dots covalently linked to nanoparticles. The temperature of the fluorescent probes represents the average temperature in the former and the local temperature in the later. For the experimental conditions employed in this study, the measured temperature rise in the vicinity of rf heated nanoparticles were similar to the average or "bulk" temperature, in agreement with theoretical predictions.

  7. Tracking an electronic wave packet in the vicinity of a conical intersection

    Science.gov (United States)

    Qi, Da-Long; Duan, Hong-Guang; Sun, Zhen-Rong; Miller, R. J. Dwayne; Thorwart, Michael

    2017-08-01

    This work treats the impact of vibrational coherence on the quantum efficiency of a dissipative electronic wave packet in the vicinity of a conical intersection by monitoring the time-dependent wave packet projection onto the tuning and the coupling mode. The vibrational coherence of the wave packet is tuned by varying the strength of the dissipative vibrational coupling of the tuning and the coupling modes to their thermal baths. We observe that the most coherent wave packet yields a quantum efficiency of 93%, but with a large transfer time constant. The quantum yield is dramatically decreased to 50% for a strongly damped incoherent wave packet, but the associated transfer time of the strongly localized wave packet is short. In addition, we find for the strongly damped wave packet that the transfer occurs via tunneling of the wave packet between the potential energy surfaces before the seam of the conical intersection is reached and a direct passage takes over. Our results provide direct evidence that vibrational coherence of the electronic wave packet is a decisive factor which determines the dynamical behavior of a wave packet in the vicinity of the conical intersection.

  8. Nanoscale patterning, macroscopic reconstruction, and enhanced surface stress by organic adsorption on vicinal surfaces

    Science.gov (United States)

    Pollinger, Florian; Schmitt, Stefan; Sander, Dirk; Tian, Zhen; Kirschner, Jürgen; Vrdoljak, Pavo; Stadler, Christoph; Maier, Florian; Marchetto, Helder; Schmidt, Thomas; Schöll, Achim; Umbach, Eberhard

    2017-01-01

    Self-organization is a promising method within the framework of bottom-up architectures to generate nanostructures in an efficient way. The present work demonstrates that self-organization on the length scale of a few to several tens of nanometers can be achieved by a proper combination of a large (organic) molecule and a vicinal metal surface if the local bonding of the molecule on steps is significantly stronger than that on low-index surfaces. In this case thermal annealing may lead to large mass transport of the subjacent substrate atoms such that nanometer-wide and micrometer-long molecular stripes or other patterns are being formed on high-index planes. The formation of these patterns can be controlled by the initial surface orientation and adsorbate coverage. The patterns arrange self-organized in regular arrays by repulsive mechanical interactions over long distances accompanied by a significant enhancement of surface stress. We demonstrate this effect using the planar organic molecule PTCDA as adsorbate and Ag(10 8 7) and Ag(775) surfaces as substrate. The patterns are directly observed by STM, the formation of vicinal surfaces is monitored by high-resolution electron diffraction, the microscopic surface morphology changes are followed by spectro-microscopy, and the macroscopic changes of surface stress are measured by a cantilever bending method. The in situ combination of these complementary techniques provides compelling evidence for elastic interaction and a significant stress contribution to long-range order and nanopattern formation.

  9. Scanning Tunneling Microscopy Study of a Vicinal Anatase TiO2 Surface

    Science.gov (United States)

    Li, Shao-Chun; Dulub, Olga; Diebold, Ulrike

    2009-03-01

    Titanium dioxide finds versatile applications in various technical fields including gas sensing, coatings, pigments, heterogeneous catalysis, photocatalytic degradation of pollutants, and solar cells. TiO2 is found in three main crystallographic phases: rutile, anatase and brookite. Rutile is the thermodynamically most stable form and is considered a model system for basic research. However, anatase TiO2 is often considered to be catalytically more active than rutile for reasons not yet completely understood. In this work, using scanning tunneling microscopy (STM) and low energy electron diffraction (LEED), the structure of the anatase TiO2(5 14) surface, ˜10 vicinal to the -- lowest energy -- (101) plane, has been studied. The surface was found to facet into a structure composed of ridges with a uniform width of 5 lattice units. Based on atomically-resolved STM and electron counting rules, it is proposed that the sides of the ridges are parallel to (1 10) and (112) planes. These sides might be reconstructed to stabilize the microfaceted structure. Vapor-deposited gold shows pronounced clustering between the ridges, indicating a one-dimensional template effect of the vicinal surface, which supports denser and more uniformly sized Au clusters, as compared to the flat (101) surface.

  10. Localization of the electromagnetic field in the vicinity of gold nanoparticles: Surface modification of different substrates

    Energy Technology Data Exchange (ETDEWEB)

    Atanasov, Petar A. [Institute of Electronics, Bulgarian Academy of Sciences, Tzarigradsko Shousse 72, Sofia 1784 (Bulgaria)], E-mail: paatanas@ie.bas.bg; Nedyalkov, Nikolay N. [Department of Electronics and Electrical Engineering, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522 (Japan); Institute of Electronics, Bulgarian Academy of Sciences, Tzarigradsko Shousse 72, Sofia 1784 (Bulgaria); Sakai, Tetsuo; Obara, Minoru [Department of Electronics and Electrical Engineering, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522 (Japan)

    2007-12-15

    Theoretical predictions and experimental results for nanosized modification of metal (Au), semiconductor (Si), or dielectric (soda lime glass) substrates using near-electromagnetic field enhancement in the vicinity of gold nanoparticles are presented. The near field properties for the system consisting of an isolated gold nanoparticle or nanoparticle aggregate deposited on the substrates, which is irradiated by electromagnetic wave, are investigated using Finite Difference Time Domain Simulation technique. The influence of the substrate material on the near field distribution characteristics is predicted. The results reveal that the field on the substrate surface is enhanced in the three investigated cases, but its spatial distribution and magnitude depend on the substrate material. In the case of the metal and semiconductor substrate the enhanced near field is strongly localized in the vicinity of the contact point with the particle, in an area with diameter smaller than the particle's one. The intensity of the enhanced field on the glass is more than an order of magnitude lower than the case of using silicon substrate. The properties of the near field on the substrate surface also depend on the particle arrangement. For a two-dimensional gold nanoparticle array, when the particles are closely arrayed, the intensity of the enhanced field on the substrate surface is minimal. With the increase of the interparticle distance the near field intensity increases. The validity of the obtained theoretical results is confirmed experimentally.

  11. Mechanisms of Hg(II) uptake and methylation in methylating bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Morel, Francois M. M. [Princeton Univ., NJ (United States). Geosciences

    2016-10-14

    The goal of this project was to understand the critical factors which control the availability and transport of Hg(II) into cells, a first step in the production of the neurotoxin, methylmercury. Specifically, this research focused on understanding the mechanism of bacterial mercury uptake and how mercury speciation affects the specificity and kinetics of mercury transport. Our research has shown that Hg(II) uptake in three different iron and sulfate-reducing proteobacteria occurs by the following mechanism (1) : Hg(II) uptake is an active transport process requiring energy, (2) it is dependent upon the structure of the Hg binding ligand, and (3) it is mediated by a heavy metal transporter such as one which transports the essential metal, Zn(II). In order to determine whether this mechanism extends to more diverse phylogenetic groups, we have begun examining Hg(II) uptake and bioavailability in two representative Hg methylating strains within the Firmicutes. These organisms have remarkably different membrane structures distinct from the Proteobacteria. Our results show low uptake rates in these two species of Firmicutes relative to the previously characterized Proteobacteria. This may explain the low methylation rates and yields observed in these organisms. Most surprisingly, however, these organisms appear to take up Hg(II) passively, as the addition of a protonophore failed to reduce Hg(II) uptake in these organisms. This is quite different to what has been observed previously for the Proteobacteria and suggests a different mechanism for Hg(II) uptake in the Firmicutes. We are continuing to understand and describe Hg(II) uptake in these organisms. A manuscript is expected to be submitted on this research in June 2016.

  12. Group Flow and Group Genius

    Science.gov (United States)

    Sawyer, Keith

    2015-01-01

    Keith Sawyer views the spontaneous collaboration of group creativity and improvisation actions as "group flow," which organizations can use to function at optimum levels. Sawyer establishes ideal conditions for group flow: group goals, close listening, complete concentration, being in control, blending egos, equal participation, knowing…

  13. cap alpha. -deuterium and carbon-13 isotope effects for methyl transfer catalyzed by catechol O-methyltransferase. S/sub N/2-like transition state

    Energy Technology Data Exchange (ETDEWEB)

    Hegazi, M.F.; Borchardt, R.T.; Schowen, R.L.

    1979-07-18

    The rate at near saturation of methylation of 3,4-dihydroxyacetophenone by S-adenosyl-L-methionine, catalyzed by rat-liver catechol O-methyltransferase at pH 7.58 and 37.00 +- 0.05/sup 0/C, is increased by deuteration of the methyl group (V/sub CH/sub 3///V/sub CD/sub 3// = 0.83 +- 0.05) and decreased by introduction of /sup 13/C to the methyl group (V/sub 12//V/sub 13/ = 1.09 +- 0.05). This shows the rate-determining step to be transfer of the methyl group, with an S/sub N/2-like transition state in which the methyl is located symmetrically and tightly between leaving group and nucleophile.

  14. Chronic methyl mercury poisoning may trigger endemic pemphigus foliaceus "fogo selvagem".

    Science.gov (United States)

    Robledo, Mary Ann

    2012-01-01

    In endemic pemphigus foliaceus (EPF) or "fogo selvagem" the epidemiological evidence shows that all the described outbreaks occur on the banks of rivers where there is mercury contamination from alluvium gold mining and deforestation. Pathophysiological evidence shows a similarity to pemphigus induced by sulphydryl (SH-) drugs that act by denaturing cadherins at the desmosomal level, which are the pemphigus antigens. The sulfhydryl radical (SH-) call also thiol or mercaptans from the SH-drugs, act at the level of SH-groups of cystein as would the methyl mercury from the contaminated animals and fish in the diet of humans from endemic areas of pemphigus foliaceus. The methyl mercury would join the SH-groups from the cysteines amino acids from cadherin proteins in the skin. The autoimmune disease would only be triggered in genetically susceptible individuals with human leukocyte antigen HLA-DRB 1 haplotypes, just as Brown-Norway (BN) rats which are susceptible to develop Th2-dependent autoimmunity induced by metals. Immunological evidence from all the seroepidemiological studies could also be explained by binding mechanism of the methyl mercury to the SH-groups from the cysteines in the desmosomal cadherins proteins. The conclusion is that chronic methyl mercury poisoning is the most likely trigger of endemic pemphigus foliaceus "fogo selvagem". To reduce the contamination of methyl mercury in the animals of the polluted rivers is pertinent to the design of campaigns and education programs with the population. Implement reforestation and biological control measures like phytoremediation technologies using decontaminant plants to decrease the methylation, and the process of biomagnifications of the methyl mercury in the Latin-America EPF foci. Copyright © 2011 Elsevier Ltd. All rights reserved.

  15. Differentially Methylated Epiloci Generated from Numerous Genotypes of Contrasting Tolerances Are Associated with Osmotic-Tolerance in Rice Seedlings.

    Science.gov (United States)

    Xia, Hui; Huang, Weixia; Xiong, Jie; Yan, Shuaigang; Tao, Tao; Li, Jiajia; Wu, Jinhong; Luo, Lijun

    2017-01-01

    DNA methylation plays an essential role in plant responses to environmental stress. Since drought develops into a rising problem in rice cultivation, investigations on genome-wide DNA methylation in responses to drought stress and in-depth explorations of its association with drought-tolerance are required. For this study, 68 rice accessions were used for an evaluation of their osmotic-tolerance related to 20% PEG6000 simulated physiological traits. The tolerant group revealed significantly higher levels of total antioxidant capacity and higher contents of H2O2 in both normal and osmotic-stressed treatments, as well as higher survival ratios. We furthermore investigated the DNA methylation status in normal, osmotic-stressed, and re-watering treatments via the methylation-sensitive amplification polymorphism (MSAP). The averaged similarity between two rice accessions from tolerant and susceptible groups was approximately 50%, similar with that between two accessions within the tolerant/susceptible group. However, the proportion of overall tolerance-associated epiloci was only 5.2% of total epiloci. The drought-tolerant accessions revealed lower DNA methylation levels in the stressed condition and more de-methylation events when they encountered osmotic stress, compared to the susceptible group. During the recovery process, the drought-tolerant accessions possessed more re-methylation events. Fourteen differentially methylated epiloci (DME) were, respectively, generated in normal, osmotic-stressed, and re-watering treatments. Approximately, 35.7% DME were determined as tolerance-associated epiloci. Additionally, rice accessions with lower methylation degrees on DME in the stressed conditions had a higher survival ratio compared to these with higher methylation degrees. This result is consistent with the lower DNA methylation levels of tolerant accessions observed in the stressed treatment. Methylation degrees on a differentially methylated epilocus may further

  16. DNA Methylation, Nuclear Organization, and Cancer.

    Science.gov (United States)

    Madakashira, Bhavani P; Sadler, Kirsten C

    2017-01-01

    The dramatic re-organization of the cancer cell nucleus creates telltale morphological features critical for pathological staging of tumors. In addition, the changes to the mutational and epigenetic landscape in cancer cells alter the structure and stability of the genome and directly contribute to malignancy. DNA methylation is one of the best studied epigenetic changes in cancer, as nearly every type of cancer studied shows a loss of DNA methylation spread across most of the genome. This global hypomethylation is accompanied by hypermethylation at distinct loci, and much of the work on DNA methylation in cancer has focused on how local changes contribute to gene expression. However, the emerging picture is that the changes to DNA methylation in cancer cells has little direct effect on gene expression but instead impacts the organization of the genome in the nucleus. Several recent studies that take a broad view of the cancer epigenome find that the most profound changes to the cancer methylome are spread across large segments of the genome, and that the focal changes are reflective of a whole reorganization of epigenome. Hallmarks of nuclear reorganization in cancer are found in the long regions of chromatin marked by histone methylation (LOCKs) and nuclear lamina interactions (LADs). In this review, we focus on a novel perspective that DNA methylation changes in cancer impact the global structure of heterochromatin, LADs and LOCKs, and how these global changes, in turn, contribute to gene expression changes and genomic stability.

  17. DNA Methylation, Nuclear Organization, and Cancer

    Directory of Open Access Journals (Sweden)

    Bhavani P. Madakashira

    2017-06-01

    Full Text Available The dramatic re-organization of the cancer cell nucleus creates telltale morphological features critical for pathological staging of tumors. In addition, the changes to the mutational and epigenetic landscape in cancer cells alter the structure and stability of the genome and directly contribute to malignancy. DNA methylation is one of the best studied epigenetic changes in cancer, as nearly every type of cancer studied shows a loss of DNA methylation spread across most of the genome. This global hypomethylation is accompanied by hypermethylation at distinct loci, and much of the work on DNA methylation in cancer has focused on how local changes contribute to gene expression. However, the emerging picture is that the changes to DNA methylation in cancer cells has little direct effect on gene expression but instead impacts the organization of the genome in the nucleus. Several recent studies that take a broad view of the cancer epigenome find that the most profound changes to the cancer methylome are spread across large segments of the genome, and that the focal changes are reflective of a whole reorganization of epigenome. Hallmarks of nuclear reorganization in cancer are found in the long regions of chromatin marked by histone methylation (LOCKs and nuclear lamina interactions (LADs. In this review, we focus on a novel perspective that DNA methylation changes in cancer impact the global structure of heterochromatin, LADs and LOCKs, and how these global changes, in turn, contribute to gene expression changes and genomic stability.

  18. DNA Methylation Biomarkers: Cancer and Beyond

    Science.gov (United States)

    Mikeska, Thomas; Craig, Jeffrey M.

    2014-01-01

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

  19. Global DNA methylation in neonatal sepsis.

    Science.gov (United States)

    Dhas, Benet Bosco; Antony, Hiasindh Ashmi; Bhat, Vishnu; Newton, Banupriya; Parija, Subhash Chandra

    2015-04-01

    To find out whether gDNA methylation can be used as a diagnostic/prognostic method for neonatal sepsis. The study was conducted in the neonatal division of a tertiary care referral hospital. Fifty one newborns as cases and thirty seven newborns as controls were enrolled in the study. Using 5-mC DNA ELISA method, the percentage of genomic DNA methylated in these newborns was established. Highly significant difference in percentage of gDNA methylated was found between the cases and controls (Cases: 2.4 ± 0.39; 2.07 ± 0.35; P sepsis (clinical, probable and culture positive) and without sepsis. Although the global DNA methylation was not a highly sensitive diagnostic method, this study reveals that DNA methylation might play a vital role in neonatal sepsis susceptibility. Identification of the specific differentially methylated genes might serve as a promising future diagnostic/prognostic marker for neonatal sepsis.

  20. DNA Methylation Biomarkers: Cancer and Beyond

    Directory of Open Access Journals (Sweden)

    Thomas Mikeska

    2014-09-01

    Full Text Available 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.

  1. The methylproteome and the intracellular methylation network.

    Science.gov (United States)

    Erce, Melissa A; Pang, Chi N I; Hart-Smith, Gene; Wilkins, Marc R

    2012-02-01

    Since its discovery more than 50 years ago, post-translational modification (PTM) of proteins via methylation has grown in prominence, its involvement having been recognised in a number of central processes in the cell. Of these, the best characterised is its role in the epigenetic code. However, there is increasing evidence that its role extends far beyond this and we propose that it is a key regulator in interactome dynamics. In this review, we focus on the role of methylation in regulating protein-protein interactions and illustrate, by providing a broad-scale summary of our current knowledge of methylation and its impact on systems biology, how this can ultimately affect interactome dynamics. We describe the variety of analytical techniques available for the study of the methylproteome, comment on their advantages and limitations, and consider how these tools can help elucidate how methylation regulates the dynamics of the interactome. The insights gained from methyltransferase-substrate networks will be summarised and the ability of protein methylation to facilitate or block protein-protein interactions as well as their interplay with other post-translational modifications, in particular phosphorylation, is highlighted. Finally, the importance of methylation in pathology-associated protein interaction networks will be discussed using examples involving human diseases and the p53 protein. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Frequency of micronuclei among persons resident in the vicinity of a mineral sand processing factory in Pulmoddai, Sri Lanka.

    Science.gov (United States)

    Warnakulasuriya, Tania; Williams, Senani; Dabarera, Mangala; Rodrigo, Kusum; Weerakkody, Thiwanka; Wickremasinghe, Rajitha

    2017-10-17

    Lanka Mineral Sands Ltd (LMS), a government-owned company, has been mining mineral sands including monazite which contains thorium (Th) at Pulmoddai, Sri Lanka since 1957. Th emits alpha particles on decay and gamma rays are emitted by the daughter products. The cytokinesis-blocked micronucleus (MN) assay is popular for large scale radiation exposure studies as it is an easy, fast and reliable method of biodosimetry. The objective of the study was to determine the frequency of micronuclei among persons residing in the vicinity of LMS. A cross-sectional study was conducted from November 2012 to September 2016 among persons 35-45 years of age to evaluate the frequency of micronuclei in peripheral blood lymphocytes. Fifty-three employees of LMS factory, 25 residents within 5 km from LMS, 25 residents 20-25 km from LMS and 29 residents from >50 km away from LMS were included in the study. The highest median frequency of micronuclei per 1000 binucleated (BN) cells was in the group residing within 5 km from LMS with a median (IQ range) of 0.67 (0.17-2.17). The median (IQ range) of MN frequency of employees of LMS, residents 20-25 km from LMS and residents >50 km from LMS were 0.66 (0.16-1.16), 0.33 (0.00-0.67) and 0.33 (0.33-0.67), respectively. There was no significant difference in the MN frequency between employees of LMS and the group residing within 5 km from LMS. Being a resident of Pulmoddai and being exposed to X-rays were significant predictors of MN frequency. Persons residing within 5 km from LMS had a higher risk of MN formation irrespective of being employed at LMS. © The Author 2017. Published by Oxford University Press on behalf of the UK Environmental Mutagen Society. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  3. Multi-dimensional histone methylations for coordinated regulation of gene expression under hypoxia.

    Science.gov (United States)

    Lee, Seongyeol; Lee, Jieon; Chae, Sehyun; Moon, Yunwon; Lee, Ho-Youl; Park, Bongju; Yang, Eun Gyeong; Hwang, Daehee; Park, Hyunsung

    2017-11-16

    Hypoxia increases both active and repressive histone methylation levels via decreased activity of histone demethylases. However, how such increases coordinately regulate induction or repression of hypoxia-responsive genes is largely unknown. Here, we profiled active and repressive histone tri-methylations (H3K4me3, H3K9me3, and H3K27me3) and analyzed gene expression profiles in human adipocyte-derived stem cells under hypoxia. We identified differentially expressed genes (DEGs) and differentially methylated genes (DMGs) by hypoxia and clustered the DEGs and DMGs into four major groups. We found that each group of DEGs was predominantly associated with alterations in only one type among the three histone tri-methylations. Moreover, the four groups of DEGs were associated with different TFs and localization patterns of their predominant types of H3K4me3, H3K9me3 and H3K27me3. Our results suggest that the association of altered gene expression with prominent single-type histone tri-methylations characterized by different localization patterns and with different sets of TFs contributes to regulation of particular sets of genes, which can serve as a model for coordinated epigenetic regulation of gene expression under hypoxia. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. GSTP1 Methylation and Protein Expression in Prostate Cancer: Diagnostic Implications

    Directory of Open Access Journals (Sweden)

    Filippo Martignano

    2016-01-01

    Full Text Available GSTP1 belongs to the GSTs family, a group of enzymes involved in detoxification of exogenous substances and it also plays an important role in cell cycle regulation. Its dysregulation correlates with a large variety of tumors, in particular with prostate cancer. We investigated GSTP1 methylation status with methylation specific PCR (MS-PCR in prostate cancer (PCa and in benign tissue of 56 prostatectomies. We also performed immunohistochemistry (IHC so as to correlate gene methylation with gene silencing. GSTP1 appears methylated in PCa and not in healthy tissue; IHC confirmed that methylation leads to protein underexpression (p<0.001. GSTP1 is highly expressed in basal cell layer and luminal cells in benign glands while in prostatic intraepithelial neoplasia (PIN it stains only basal cell layer, whereas PCa glands are completely negative. We demonstrated that methylation leads to underexpression of GSTP1. The progressive loss of GSTP1 expression from healthy glands to PIN and to PCa glands underlines its involvement in early carcinogenesis.

  5. DDMGD: the database of text-mined associations between genes methylated in diseases from different species.

    Science.gov (United States)

    Bin Raies, Arwa; Mansour, Hicham; Incitti, Roberto; Bajic, Vladimir B

    2015-01-01

    Gathering information about associations between methylated genes and diseases is important for diseases diagnosis and treatment decisions. Recent advancements in epigenetics research allow for large-scale discoveries of associations of genes methylated in diseases in different species. Searching manually for such information is not easy, as it is scattered across a large number of electronic publications and repositories. Therefore, we developed DDMGD database (http://www.cbrc.kaust.edu.sa/ddmgd/) to provide a comprehensive repository of information related to genes methylated in diseases that can be found through text mining. DDMGD's scope is not limited to a particular group of genes, diseases or species. Using the text mining system DEMGD we developed earlier and additional post-processing, we extracted associations of genes methylated in different diseases from PubMed Central articles and PubMed abstracts. The accuracy of extracted associations is 82% as estimated on 2500 hand-curated entries. DDMGD provides a user-friendly interface facilitating retrieval of these associations ranked according to confidence scores. Submission of new associations to DDMGD is provided. A comparison analysis of DDMGD with several other databases focused on genes methylated in diseases shows that DDMGD is comprehensive and includes most of the recent information on genes methylated in diseases. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. A novel method for identification and quantification of consistently differentially methylated regions.

    Directory of Open Access Journals (Sweden)

    Ching-Lin Hsiao

    Full Text Available Advances in biotechnology have resulted in large-scale studies of DNA methylation. A differentially methylated region (DMR is a genomic region with multiple adjacent CpG sites that exhibit different methylation statuses among multiple samples. Many so-called "supervised" methods have been established to identify DMRs between two or more comparison groups. Methods for the identification of DMRs without reference to phenotypic information are, however, less well studied. An alternative "unsupervised" approach was proposed, in which DMRs in studied samples were identified with consideration of nature dependence structure of methylation measurements between neighboring probes from tiling arrays. Through simulation study, we investigated effects of dependencies between neighboring probes on determining DMRs where a lot of spurious signals would be produced if the methylation data were analyzed independently of the probe. In contrast, our newly proposed method could successfully correct for this effect with a well-controlled false positive rate and a comparable sensitivity. By applying to two real datasets, we demonstrated that our method could provide a global picture of methylation variation in studied samples. R source codes to implement the proposed method were freely available at http://www.csjfann.ibms.sinica.edu.tw/eag/programlist/ICDMR/ICDMR.html.

  7. The concerted impact of domestication and transposon insertions on methylation patterns between dogs and gray wolves

    Science.gov (United States)

    Koch, Ilana Janowitz; Clark, Michelle M.; Thompson, Michael J.; Deere-Machemer, Kerry A.; Wang, Jun; Duarte, Lionel; Gnanadesikan, Gitanjali E.; McCoy, Eskender L.; Rubbi, Liudmilla; Stahler, Daniel R.; Pellegrini, Matteo; Ostrander, Elaine A.; Wayne, Robert K.; Sinsheimer, Janet S.; vonHoldt, Bridgett M.

    2015-01-01

    The process of domestication can exert intense trait-targeted selection on genes and regulatory regions. Specifically, rapid shifts in the structure and sequence of genomic regulatory elements could provide an explanation for the extensive, and sometimes extreme, variation in phenotypic traits observed in domesticated species. Here, we explored methylation differences from >24,000 cytosines distributed across the genomes of the domesticated dog (Canis familiaris) and the gray wolf (C. lupus). PCA and model-based cluster analyses identified two primary groups, domestic versus wild canids. A scan for significantly differentially methylated sites (DMSs) revealed species-specific patterns at 68 sites after correcting for cell heterogeneity, with weak yet significant hyper-methylation typical of purebred dogs when compared to wolves (59% and 58%, pdogs. The majority (>66%) of differentially methylated regions contained or were associated with repetitive elements, indicative of a genotype-mediated trend. However, DMSs were also often linked to functionally relevant genes (e.g. neurotransmitters). Finally, we utilized known genealogical relationships among Yellowstone wolves to survey transmission stability of methylation marks, from which we found a substantial fraction that demonstrated high heritability (both H2 and h2>0.99). These analyses provide a unique epigenetic insight into the molecular consequences of recent selection and radiation of our most ancient domesticated companion, the dog. These findings suggest selection has acted on methylation patterns, providing a new genomic perspective on phenotypic diversification in domesticated species. PMID:27112634

  8. DDMGD: the database of text-mined associations between genes methylated in diseases from different species

    KAUST Repository

    Raies, A. B.

    2014-11-14

    Gathering information about associations between methylated genes and diseases is important for diseases diagnosis and treatment decisions. Recent advancements in epigenetics research allow for large-scale discoveries of associations of genes methylated in diseases in different species. Searching manually for such information is not easy, as it is scattered across a large number of electronic publications and repositories. Therefore, we developed DDMGD database (http://www.cbrc.kaust.edu.sa/ddmgd/) to provide a comprehensive repository of information related to genes methylated in diseases that can be found through text mining. DDMGD\\'s scope is not limited to a particular group of genes, diseases or species. Using the text mining system DEMGD we developed earlier and additional post-processing, we extracted associations of genes methylated in different diseases from PubMed Central articles and PubMed abstracts. The accuracy of extracted associations is 82% as estimated on 2500 hand-curated entries. DDMGD provides a user-friendly interface facilitating retrieval of these associations ranked according to confidence scores. Submission of new associations to DDMGD is provided. A comparison analysis of DDMGD with several other databases focused on genes methylated in diseases shows that DDMGD is comprehensive and includes most of the recent information on genes methylated in diseases.

  9. DNA Methylation Levels of Melanoma Risk Genes Are Associated with Clinical Characteristics of Melanoma Patients

    Directory of Open Access Journals (Sweden)

    Érica S. S. de Araújo

    2015-01-01

    Full Text Available In melanoma development, oncogenic process is mediated by genetic and epigenetic mutations, and few studies have so far explored the role of DNA methylation either as predisposition factor or biomarker. We tested patient samples for germline CDKN2A methylation status and found no evidence of inactivation by promoter hypermethylation. We have also investigated the association of clinical characteristics of samples with the DNA methylation pattern of twelve genes relevant for melanomagenesis. Five genes (BAP1, MGMT, MITF, PALB2, and POT1 presented statistical association between blood DNA methylation levels and either CDKN2A-mutation status, number of lesions, or Breslow thickness. In tumors, five genes (KIT, MGMT, MITF, TERT, and TNF exhibited methylation levels significantly different between tumor groups including acral compared to nonacral melanomas and matched primary lesions and metastases. Our data pinpoint that the methylation level of eight melanoma-associated genes could potentially represent markers for this disease both in peripheral blood and in tumor samples.

  10. De novo DNMTs and DNA methylation: novel insights into disease pathogenesis and therapy from epigenomics.

    Science.gov (United States)

    Leppert, Sylwia; Matarazzo, Maria R

    2014-01-01

    DNA methylation plays an important role in epigenetics signaling, having an impact on gene regulation, chromatin structure and development. Within the family of de novo DNA methyltransferases two active enzymes, DNMT3A and DNMT3B, are responsible for the establishment of the proper cytosine methylation profile during development. Defects in DNMT3s function correlate with pathogenesis and progression of monogenic diseases and cancers. Among monogenic diseases, Immunodeficiency, Centromeric instability and Facial anomalies (ICF) syndrome is the only Mendelian disorder associated with DNMT3B mutations and DNA methylation defects of satellite and non-satellite regions. Similar CpG hypomethylation of the repetitive elements and gene-specific hypermethylation are observed in many types of cancer. DNA hyper-methylation sites provide targets for the epigenetic therapy. Generally, we can distinguish two groups of epi-drugs affecting DNMTs activity, i) nucleoside inhibitors, covalently trapping the enzymes, and bringing higher cytotoxic effect and (ii) nonnucleoside inhibitors, which block their active sites, showing less side-effects. Moreover, combining drugs targeting chromatin and those targeting DNA methylation enhances the efficacy of the therapy and gives more chances of patient recovery. However, development of more specific and effective epigenetic therapies requires more complete understanding of epigenomic landscapes. Here, we give an overview of the recent findings in the epigenomics field, focusing on those related to DNA methylation defects in disease pathogenesis and therapy.

  11. DNA methylation at stress-related genes is associated with exposure to early life institutionalization.

    Science.gov (United States)

    Non, Amy L; Hollister, Brittany M; Humphreys, Kathryn L; Childebayeva, Ainash; Esteves, Kyle; Zeanah, Charles H; Fox, Nathan A; Nelson, Charles A; Drury, Stacy S

    2016-09-01

    Differences in DNA methylation have been associated with early life adversity, suggesting that alterations in methylation function as one pathway through which adverse early environments are biologically embedded. This study examined associations between exposure to institutional care, quantified as the proportion of time in institutional care at specified follow-up assessment ages, and DNA methylation status in two stress-related genes: FKBP5 and SLC6A4. We analyzed data from the Bucharest Early Intervention Project, which is a prospective study in which children reared in institutional settings were randomly assigned (mean age 22 months) to either newly created foster care or care as usual (to remain in their current placement) and prospectively followed. A group of children from the same geographic area, with no history of institutionalized caregiving, were also recruited. DNA methylation status was determined in DNA extracted from buccal epithelial cells of children at age 12. An inverse association was identified such that more time spent in institutional care was associated with lower DNA methylation at specific CpG sites within both genes. These results suggest a lasting impact of early severe social deprivation on methylation patterns in these genes, and contribute to a growing literature linking early adversity and epigenetic variation in children. Am J Phys Anthropol 161:84-93, 2016.. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  12. Modulation of age- and cancer-associated DNA methylation change in the healthy colon by aspirin and lifestyle.

    Science.gov (United States)

    Noreen, Faiza; Röösli, Martin; Gaj, Pawel; Pietrzak, Jakub; Weis, Stefan; Urfer, Patric; Regula, Jaroslaw; Schär, Primo; Truninger, Kaspar

    2014-07-01

    Aberrant DNA methylation in gene promoters is associated with aging and cancer, but the circumstances determining methylation change are unknown. We investigated the impact of lifestyle modulators of colorectal cancer (CRC) risk on the stability of gene promoter methylation in the colonic mucosa. We measured genome-wide promoter CpG methylation in normal colon biopsies (n = 1092) from a female screening cohort, investigated the interaction of lifestyle factors with age-dependent increase in methylation with log-linear multivariable regression, and related their modifying effect to hypermethylation in CRC. All statistical tests were two-sided. Of 20025 promoter-associated CpGs analyzed, 1713 showed statistically significant age-dependent methylation gains. Fewer CpGs acquired methylation in users of aspirin (≥ 2 years) and hormonal replacement therapy (HRT age ≥ 50 years) compared with nonusers (43 vs 1355; 1 vs1377, respectively), whereas more CpGs were affected in smokers (≥ 20 years) and individuals with a body mass index (BMI) of 25 kg/m(2) and greater compared with control groups (180 vs 39; 554 vs 144, respectively). Fifty percent of the CpGs showing age-dependent methylation were found hypermethylated in CRC (odds ratio [OR] = 20; 95% confidence interval [CI] = 18 to 23; P cancer-related genes, whereas smoking (P colonic epithelium and thereby impacts the evolution of cancer methylomes. © The Author 2014. Published by Oxford University Press.

  13. Antihyperglycemic activity and antidiabetic effect of methyl caffeate isolated from Solanum torvum Swartz. fruit in streptozotocin induced diabetic rats.

    Science.gov (United States)

    Gandhi, Gopalsamy Rajiv; Ignacimuthu, Savarimuthu; Paulraj, Michael Gabriel; Sasikumar, Ponnusamy

    2011-11-30

    Natural remedies from medicinal plants are considered to be effective and safe alternatives to treat diabetes mellitus. Solanum torvum Swartz. fruit is widely used in the traditional system of medicine to treat diabetes. In the present study methyl caffeate, isolated from S. torvum fruit, was screened for its efficacy in controlling diabetes in animal models. Antihyperglycemic effect of methyl caffeate was studied in normal glucose-fed rats. The effects of oral administration of methyl caffeate (10, 20 and 40 mg/kg) for 28 days on body weight, fasting blood glucose, plasma insulin, hemoglobin, glycated hemoglobin, total protein, hepatic glycogen and carbohydrate metabolism enzymes in streptozotocin induced diabetic rats were investigated. Histological observations in the pancreas and GLUT4 expression in skeletal muscles were also studied. Methyl caffeate at 40 mg/kg significantly prevented the increase in blood glucose level after glucose administration at 60 min in comparison to the hyperglycemic control group. In streptozotocin induced diabetic rats, methyl caffeate produced significant reduction in blood glucose and increased body weight. The levels and/or activities of other biochemical parameters were near normal due to treatment with methyl caffeate. Methyl caffeate treated diabetic rats showed upregulation of GLUT4 and regeneration of β-cells in the pancreas. These results substantiated that methyl caffeate possessed hypoglycemic effect, and it could be developed into a potent oral antidiabetic drug. Copyright © 2011 Elsevier B.V. All rights reserved.

  14. Alteration in methylation pattern of GATA-4 promoter region in vitamin A-deficient offspring's heart.

    Science.gov (United States)

    Feng, Yi; Zhao, Ling-Zi; Hong, Li; Shan, Chuan; Shi, Wen; Cai, Wei

    2013-07-01

    Epigenetics might explain correlations between lifestyle and risk of disease. Maternal diet has been shown to dynamically alter epigenetic regulation, including affecting DNA methylation status. This study was designed to test the hypothesis that GATA-4 gene methylation would lead to congenital heart defects in vitamin A-deficient offspring. Ten weaning female rats (VAN group) were fed with a diet which contents 4 IU vitamin A/g diet, while 20 rats (VAD group) were maintained on a diet without vitamin A. After 10 weeks of feeding, all the female rats were mated with normal male rats. The VAN group and a portion of VAD group rats were still given the same diet as before mating, while the rest of the rats from the VAD group (VADS group) were transferred to a diet with enough added vitamin A (10 IU/g diet) for the pregnancy cycle. The embryo hearts were dissected out at embryonic day 13.5 (E13.5) for observation of cardiac development, GATA-4 gene methylation status and the expression of DNA methyltransferases (DNMTs). Embryos from vitamin A-deficient group exhibited a high incidence of cardiac defects. High methylation was present in the CpG loci of GATA-4 gene with a low expression of GATA-4 mRNA from vitamin A-deficient group embryos. Moreover, up-regulation of DNMT1 and down-regulation of DNMT3a and DNMT3b expression were found in this group embryo. These findings show that aberrant methylation is one of key mechanisms to heart defects in vitamin A-deficient offspring. DNMTs play a critical role in this process. Copyright © 2013 Elsevier Inc. All rights reserved.

  15. DNA methylation markers for oral pre-cancer progression: A critical review.

    Science.gov (United States)

    Shridhar, Krithiga; Walia, Gagandeep Kaur; Aggarwal, Aastha; Gulati, Smriti; Geetha, A V; Prabhakaran, Dorairaj; Dhillon, Preet K; Rajaraman, Preetha

    2016-02-01

    Although oral cancers are generally preceded by a well-established pre-cancerous stage, there is a lack of well-defined clinical and morphological criteria to detect and signal progression from pre-cancer to malignant tumours. We conducted a critical review to summarize the evidence regarding aberrant DNA methylation patterns as a potential diagnostic biomarker predicting progression. We identified all relevant human studies published in English prior to 30th April 2015 that examined DNA methylation (%) in oral pre-cancer by searching PubMed, Web-of-Science and Embase databases using combined key-searches. Twenty-one studies (18-cross-sectional; 3-longitudinal) were eligible for inclusion in the review, with sample sizes ranging from 4 to 156 affected cases. Eligible studies examined promoter region hyper-methylation of tumour suppressor genes in pathways including cell-cycle-control (n=15), DNA-repair (n=7), cell-cycle-signalling (n=4) and apoptosis (n=3). Hyper-methylated loci reported in three or more studies included p16, p14, MGMT and DAPK. Two longitudinal studies reported greater p16 hyper-methylation in pre-cancerous lesions transformed to malignancy compared to lesions that regressed (57-63.6% versus 8-32.1%; pmethylation patterns reported three novel hyper-methylated loci (TRHDE; ZNF454; KCNAB3). The majority of reviewed studies were small, cross-sectional studies with poorly defined control groups and lacking validation. Whilst limitations in sample size and study design preclude definitive conclusions, current evidence suggests a potential utility of DNA methylation patterns as a diagnostic biomarker for oral pre-cancer progression. Robust studies such as large epigenome-wide methylation explorations of oral pre-cancer with longitudinal tracking are needed to validate the currently reported signals and identify new risk-loci and the biological pathways of disease progression. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  16. TLR4 Methylation Moderates the Relationship Between Alcohol Use Severity and Gray Matter Loss.

    Science.gov (United States)

    Karoly, Hollis C; Thayer, Rachel E; Hagerty, Sarah L; Hutchison, Kent E

    2017-09-01

    Alcohol use disorders (AUDs) are associated with decreased gray matter, and neuroinflammation is one mechanism through which alcohol may confer such damage, given that heavy alcohol use may promote neural damage via activation of toll-like receptor 4 (TLR4)-mediated inflammatory signaling cascades. We previously demonstrated that TLR4 is differentially methylated in AUD compared with control subjects, and the present study aims to extend this work by examining whether TLR4 methylation moderates the relationship between alcohol use and gray matter. We examined TLR4 methylation and gray matter thickness in a large sample (N = 707; 441 males) of adults (ages 18-56) reporting a range of AUD severity (mean Alcohol Use Disorders Identification Test score = 13.18; SD = 8.02). We used a series of ordinary least squares multiple regression equations to regress gray matter in four bilateral brain regions (precuneus, lateral orbitofrontal, inferior parietal, and superior temporal) on alcohol use, TLR4 methylation, and their interaction, controlling for demographic, psychological, and other substance use variables. After we corrected for multiple tests, a significant Alcohol × TLR4 Methylation interaction emerged in the equations modeling left precuneus and right inferior parietal gray matter. Follow-up analyses examining the nature of these interactions demonstrated a significant negative association between alcohol and precuneus and inferior parietal gray matter in individuals with low TLR4 methylation, but no relationship between alcohol and gray matter in the high methylation group. These findings suggest that TLR4 methylation may be protective against the damage conferred by alcohol on precuneus and inferior parietal gray matter, thereby implicating TLR4 for further investigation as a possible AUD treatment target.

  17. Distinct DNA methylation patterns of cognitive impairment and trisomy 21 in Down syndrome.

    Science.gov (United States)

    Jones, Meaghan J; Farré, Pau; McEwen, Lisa M; Macisaac, Julia L; Watt, Kim; Neumann, Sarah M; Emberly, Eldon; Cynader, Max S; Virji-Babul, Naznin; Kobor, Michael S

    2013-12-27

    The presence of an extra whole or part of chromosome 21 in people with Down syndrome (DS) is associated with multiple neurological changes, including pathological aging that often meets the criteria for Alzheimer's Disease (AD). In addition, trisomies have been shown to disrupt normal epigenetic marks across the genome, perhaps in response to changes in gene dosage. We hypothesized that trisomy 21 would result in global epigenetic changes across all participants, and that DS patients with cognitive impairment would show an additional epigenetic signature. We therefore examined whole-genome DNA methylation in buccal epithelial cells of 10 adults with DS and 10 controls to determine whether patterns of DNA methylation were correlated with DS and/or cognitive impairment. In addition we examined DNA methylation at the APP gene itself, to see whether there were changes in DNA methylation in this population. Using the Illumina Infinium 450 K Human Methylation Array, we examined more than 485,000 CpG sites distributed across the genome in buccal epithelial cells. We found 3300 CpGs to be differentially methylated between the groups, including 495 CpGs that overlap with clusters of differentially methylated probes. In addition, we found 5 probes that were correlated with cognitive function including two probes in the TSC2 gene that has previously been associated with Alzheimer's disease pathology. We found no enrichment on chromosome 21 in either case, and targeted analysis of the APP gene revealed weak evidence for epigenetic impacts related to the AD phenotype. Overall, our results indicated that both Trisomy 21 and cognitive impairment were associated with distinct patterns of DNA methylation.

  18. Rapid response to changing environments during biological invasions: DNA methylation perspectives.

    Science.gov (United States)

    Huang, Xuena; Li, Shiguo; Ni, Ping; Gao, Yangchun; Jiang, Bei; Zhou, Zunchun; Zhan, Aibin

    2017-12-01

    Dissecting complex interactions between species and their environments has long been a research hot spot in the fields of ecology and evolutionary biology. The well-recognized Darwinian evolution has well-explained long-term adaptation scenarios; however, "rapid" processes of biological responses to environmental changes remain largely unexplored, particularly molecular mechanisms such as DNA methylation that have recently been proposed to play crucial roles in rapid environmental adaptation. Invasive species, which have capacities to successfully survive rapidly changing environments during biological invasions, provide great opportunities to study molecular mechanisms of rapid environmental adaptation. Here, we used the methylation-sensitive amplified polymorphism (MSAP) technique in an invasive model ascidian, Ciona savignyi, to investigate how species interact with rapidly changing environments at the whole-genome level. We detected quite rapid DNA methylation response: significant changes of DNA methylation frequency and epigenetic differentiation between treatment and control groups occurred only after 1 hr of high-temperature exposure or after 3 hr of low-salinity challenge. In addition, we detected time-dependent hemimethylation changes and increased intragroup epigenetic divergence induced by environmental stresses. Interestingly, we found evidence of DNA methylation resilience, as most stress-induced DNA methylation variation maintained shortly (~48 hr) and quickly returned back to the control levels. Our findings clearly showed that invasive species could rapidly respond to acute environmental changes through DNA methylation modifications, and rapid environmental changes left significant epigenetic signatures at the whole-genome level. All these results provide fundamental background to deeply investigate the contribution of DNA methylation mechanisms to rapid contemporary environmental adaptation. © 2017 John Wiley & Sons Ltd.

  19. Obesity-induced sperm DNA methylation changes at satellite repeats are reprogrammed in rat offspring

    Directory of Open Access Journals (Sweden)

    Neil A Youngson

    2016-01-01

    Full Text Available There is now strong evidence that the paternal contribution to offspring phenotype at fertilisation is more than just DNA. However, the identity and mechanisms of this nongenetic inheritance are poorly understood. One of the more important questions in this research area is: do changes in sperm DNA methylation have phenotypic consequences for offspring? We have previously reported that offspring of obese male rats have altered glucose metabolism compared with controls and that this effect was inherited through nongenetic means. Here, we describe investigations into sperm DNA methylation in a new cohort using the same protocol. Male rats on a high-fat diet were 30% heavier than control-fed males at the time of mating (16-19 weeks old, n = 14/14. A small (0.25% increase in total 5-methyl-2Ͳ-deoxycytidine was detected in obese rat spermatozoa by liquid chromatography tandem mass spectrometry. Examination of the repetitive fraction of the genome with methyl-CpG binding domain protein-enriched genome sequencing (MBD-Seq and pyrosequencing revealed that retrotransposon DNA methylation states in spermatozoa were not affected by obesity, but methylation at satellite repeats throughout the genome was increased. However, examination of muscle, liver, and spermatozoa from male 27-week-old offspring from obese and control fathers (both groups from n = 8 fathers revealed that normal DNA methylation levels were restored during offspring de